Miracle-dz/UniFAR-FTUs huggingface dataset:
X-ray exploration of the outskirts of the nearby Centaurus cluster using Suzaku and Chandra

We present Suzaku observations of the Centaurus cluster out to 0.95r200, taken along a strip to the north west. We have also used congruent Chandra observations of the outskirts to resolve point sources down to a threshold flux around 7 times lower than that achievable with just Suzaku data, considerably reducing the systematic uncertainties in the cosmic X-ray background emission in the outskirts. We find that the temperature decreases by a factor of 2 from the peak temperature to the outskirts. The entropy profile demonstrates a central excess (within 0.5r200) over the baseline entropy profile predicted by simulations of purely gravitational hierarchical structure formation. In the outskirts the entropy profile is in reasonable agreement with the baseline entropy profile from Voit et al., but lies slightly below it. We find that the pressure profile agrees with the universal pressure profile of Arnaud et al. but lies slightly above it in the outskirts. The excess pressure and decrement in entropy in the outskirts appear to be the result of an excess in the measured gas density, possible due to gas clumping biasing the density measurements high. The gas mass fraction rises and reaches the mean cosmic baryon fraction at the largest radius studied. The clumping corrected gas mass fraction agrees with the expected hot gas fraction and with the simulations of Young et al. We further the analysis of Walker et al. which studied the shapes of the entropy profiles of the clusters so far explored in the outskirts with Suzaku. When scaled by the self similar entropy the Suzaku entropy profiles demonstrate a central excess over the baseline entropy profile, and are consistent with it at around r500 . However outside r500 the entropy profiles tend to lie below the baseline entropy profile.
Exploring the Higgs sector of a most natural NMSSM

The Next to Minimal Supersymmetric Standard Model (NMSSM) with a Higgs-singlet coupling {\lambda} close to unity, moderate tan {\beta} and stop masses below 1 TeV minimizes the fine tuning of the electroweak scale, making possible that the lightest new particles, except perhaps for the LSP, be part of the extended Higgs system. We show how the measurements of the couplings of the 126 GeV Higgs boson constrain the region of the physical parameters of a generic NMSSM most relevant to this context. In the same region of parameter space we determine the cross section for the production of a heavier CP-even scalar together with its total width and its most relevant branching ratios. For comparison we show the same analysis for the MSSM. We also comment on how a coupling {\lambda} ~ 1 can be compatible with gauge coupling unification.
Cultural heritage image classification using transfer learning for feature extraction: a comparison

Image classification in the domain of cultural heritage becomes extremely important with the development of digitisation practices. This study aims to analyze how classification performance on the small dataset representing cultural heritage changes depending on the feature extraction method. The dataset comprised of 150 images belonging to three classes: (i) archaeological sites, (ii) frescoes, and (iii) monasteries. Five transfer learning architectures were used to extract the features from images, while classification was per-formed using four traditional machine learning algorithms, mainly Random forest, Naïve Bayes, Decision tree, and Multilayer perceptron classifier. The results suggest that Random forest and Multilayer perceptron are the most suitable algorithms for classification of cultural heritage images, especially when used in combination with the DenseNet121 pre-trained architecture. Naïve Bayes also performed well, with a maximum accuracy of 100% obtained when features are extracted using EfficientNetB0. However, the Decision tree algorithm reached only moderate performance.
Dynamics of Mitochondrial NAD+ Import Reveal Preference for Oxidized Ligand and Substrate Led Transport

SLC25A51 is a member of the mitochondrial carrier family (MCF) but lacks key residues that have been attributed to the mechanism of other nucleotide MCF transporters. Thus, how SLC25A51 transports NAD+ across the inner mitochondrial membrane remains unclear. To elucidate its mechanism, we used Molecular Dynamic simulations to study reconstituted SLC25A51 homology models in lipid bilayers. We observed spontaneous binding of cardiolipin phospholipids to three distinct sites on the exterior of SLC25A51’s central pore and found that mutation of these sites impaired transporter activity. We also observed that stable formation of the required matrix gate was controlled by a single salt bridge. Using simulation data and in-cell activity assays we identified binding sites in SLC25A51 for NAD+ and showed that its binding was guided by an electrostatic interaction between NAD+ and a negatively charged patch in the pore. In turn, interaction of NAD+ with interior residue E132 guided the ligand to dynamically engage and weaken the salt bridge gate, representing a ligand-induced initiation of transport. Significance NAD+ is an intermediary metabolite whose multiple functions are entwined with respiration, catabolism, and stress responses in cells. Previous sensor measurements had indicated that its continuous biosynthesis was required to sustain mitochondrial matrix levels in respiring cells, and SLC25A51 was identified as the required importer of NAD+ across the inner mitochondrial membrane. However, SLC25A51 has little homology to other nucleotide carriers at its substrate binding site. By combining modeling approaches and experimental assays, this work provides mechanistic insight into how human SLC25A51 recognizes its ligand, how the transporter can be regulated by its lipid environment, and an observation of ligand-induced gate opening. This represents the first description of the ligand binding site for an NAD+ mitochondrial carrier.
VERY LONG BASELINE ARRAY ASTROMETRIC OBSERVATIONS OF THE CASSINI SPACECRAFT AT SATURN

The planetary ephemeris is an essential tool for interplanetary spacecraft navigation, studies of solar system dynamics (including, for example, barycenter corrections for pulsar timing ephemerides), the prediction of occultations, and tests of general relativity. We are carrying out a series of astrometric very long baseline interferometry observations of the Cassini spacecraft currently in orbit around Saturn, using the Very Long Baseline Array (VLBA). These observations provide positions for the center of mass of Saturn in the International Celestial Reference Frame (ICRF) with accuracies ∼0.3 mas (1.5 nrad) or about 2 km at the average distance of Saturn. This paper reports results from eight observing epochs between 2006 October and 2009 April. These data are combined with two VLBA observations by other investigators in 2004 and a Cassini-based gravitational deflection measurement by Fomalont et al. in 2009 to constrain a new ephemeris (DE 422). The DE 422 post-fit residuals for Saturn with respect to the VLBA data are generally 0.2 mas, but additional observations are needed to improve the positions of all of our phase reference sources to this level. Over time we expect to be able to improve the accuracy of all three coordinates in the Saturn ephemeris (latitude, longitude, and range) by a factor of at least three. This will represent a significant improvement not just in the Saturn ephemeris but also in the link between the inner and outer solar system ephemerides and in the link to the inertial ICRF.
Using SNOMED CT as a Semantic Model for Controlled Natural Language Guided Capture of Clinical Data

Capturing clinical data in written textual form is by far the most popular and accepted method in health care. The workshop paper presents the author’s preliminary results from creating a controlled natural language based on the SNOMED Clinical Terminology. This language can be used as a user interface that allows bidirectional translation between lexical expressions in a natural language and SNOMED post-coordinated expressions. E.g., natural language can be used for capturing machine-readable SNOMED data. Also, in the opposite direction, captured SNOMED CT terms can be displayed as a sentence in a natural language, shown perhaps with different wordings or linguistic styles based on the presentation context. This controlled language is shown to be useful for reporting clinical situations, which has long been placed in the gray area known as the boundary problem between information and terminology models. The paper concludes that clinical situations can be recorded within the terminology model if an appropriate user interface is used. The paper’s contribution is to propose and evaluate a methodology that can be used for recording clinical data in a formal, machine-readable form and validate the data correctness already during data capture at the point of care.
Obsessive–compulsive disorder (OCD) is associated with increased engagement of frontal brain regions across multiple event-related potentials

Background Obsessive-Compulsive Disorder (OCD) is a psychiatric condition leading to significant distress and poor quality of life. Successful treatment of OCD is restricted by the limited knowledge about its pathophysiology. This study aimed to investigate the pathophysiology of OCD using electroencephalographic (EEG) event related potentials (ERP), elicited from multiple tasks to characterise disorder-related differences in underlying brain activity across multiple neural processes. Methods ERP data were obtained from 25 OCD patients and 27 age- and sex-matched healthy controls (HC) by recording EEG during Flanker and Go/Nogo tasks. Error-related negativity (ERN) was elicited by the Flanker task, while N200 and P300 were generated using the Go/Nogo task. Primary comparisons of the neural response amplitudes and the topographical distribution of neural activity were conducted using scalp field differences across all time points and electrodes. Results Compared to HC, the OCD group showed altered ERP distributions. Contrasting with the previous literature on ERN and N200 topographies in OCD where fronto-central negative voltages were reported, we detected positive voltages. Additionally, the P300 was found to be less negative in the frontal regions. None of these ERP findings were associated with OCD symptom severity. Conclusions These results indicate that individuals with OCD show altered frontal neural activity across multiple executive function related processes, supporting the frontal dysfunction theory of OCD. Furthermore, due to the lack of association between altered ERPs and OCD symptom severity, they may be considered potential candidate endophenotypes for OCD.
Hydrodynamic and anthropogenic disturbances co-shape microbiota rhythmicity and community assembly within intertidal groundwater-surface water continuum

Tidal hydrodynamics drive the groundwater-seawater exchange and shifts in microbiota structure in the coastal zone. However, how the coastal water microbiota structure and assembly patterns respond to periodic tidal fluctuations and anthropogenic disturbance remain unexplored in the intertidal groundwater-surface water (GW-SW) continuum, although it affects biogeochemical cycles and coastal water quality therein. Here, through hourly time-series sampling in the saltmarsh tidal creek, rhythmic patterns of microbiota structure in response to daily and monthly tidal fluctuations in intertidal surface water are disentangled for the first time. The similarity in archaeal community structures between groundwater and ebb-tide surface water (R2=0.06, p=0.2) demonstrated archaeal transport through groundwater discharge, whereas multi-source transport mechanisms led to unique bacterial biota in ebb-tide water. Homogeneous selection (58.6%-69.3%) dominated microbiota assembly in the natural intertidal GW-SW continuum and the presence of 157 rhythmic ASVs identified at ebb tide and 141 at flood tide could be attributed to different environmental selection between groundwater and seawater. For intertidal groundwater in the tidal creek affected by anthropogenically contaminated riverine inputs, higher microbial diversity and shift in community structure were primarily controlled by increased co-contribution of dispersal limitation and drift (jointly 57.8%) and enhanced microbial interactions. Overall, this study fills the knowledge gaps in the tide-driven water microbial dynamics in coastal transition zone and the response of intertidal groundwater microbiota to anthropogenic pollution of overlying waters. It also highlights the potential of microbiome analysis in enhancing coastal water quality monitoring and identifying anthropogenic pollution sources (e.g., aquaculture pathogenic Vibrio) through the detection of rhythmic microbial variances associated with intertidal groundwater discharge and seawater intrusion.
Emission lines in early-type galaxies: active nuclei or stars?

We selected 27 244 nearby, red, giant early-type galaxies (RGEs) from the Sloan Digital Sky Survey (SDSS). In a large fraction (53%) of their spectra the [O III]λ5007 emission line is detected, with an equivalent width (EW) distribution strongly clustered around ~0.75 A. The vast majority of those RGEs for which it is possible to derive emission line ratios (amounting to about half of the sample) show values characteristic of LINERs. The close connection between emission lines and stellar continuum points to stellar processes as the most likely source of the bulk of the ionizing photons in RGEs, rather than active nuclei. In particular, the observed EW and optical line ratios are consistent with the predictions of models in which the photoionization comes from hot evolved stars. Shocks driven by supernovae or stellar ejecta might also contribute to the ionization budget. A minority, ~4%, of the galaxies show emission lines with an equivalent width that is a factor of ≳2 greater than the sample median. Only among them are Seyfert-like spectra found. Furthermore, 40% of this subgroup have a radio counterpart, compared to ~6% of the rest of the sample. These characteristics argue in favor of an AGN origin for their emission lines. Emission lines diagnostic diagrams do not reveal a distinction between the AGN subset and the other members of the sample, and consequently they are not a useful tool for establishing the dominant source of the ionizing photons, which is better predicted by the EW of the emission lines.
Noise reduction strategies in metagenomic chromosome confirmation capture to link antibiotic resistance genes to microbial hosts

The gut microbiota is a reservoir for antimicrobial resistance genes (ARGs). With current sequencing methods, it is difficult to assign ARGs to their microbial hosts, particularly if these ARGs are located on plasmids. Metagenomic chromosome conformation capture approaches (meta3C and Hi-C), have recently been developed to link bacterial genes to phylogenetic markers, thus potentially allowing the assignment of ARGs to their hosts on a microbiome-wide scale. Here, we generated a meta3C dataset of a human stool sample and used previously published meta3C and Hi-C datasets to investigate bacterial hosts of ARGs in the human gut microbiome. Sequence reads mapping to repetitive elements were found to cause problematic noise in, and may importantly skew interpretation of, meta3C and Hi-C data. We provide a strategy to improve the signal-to-noise ratio by discarding reads that map to repetitive elements and to the end of contigs. We also show the importance of using spike-in controls to quantify whether the cross-linking step in meta3C and Hi-C protocols has been successful. After filtering for spurious links, 87 ARGs were linked to their bacterial hosts across all datasets, including 27 ARGs in the meta3C dataset we generated. We show that commensal gut bacteria are an important reservoir for ARGs, with genes encoding for aminoglycoside and tetracycline resistance being widespread in anaerobic commensals of the human gut.
Complex third-party effects in the Dictyostelium-Paraburkholderia symbiosis: prey bacteria that are eaten, carried, or left behind

Symbiotic interactions may change depending on the abundance of third parties like predators, prey, or pathogens. Third-party interactions with prey bacteria are central to the symbiosis between Dictyostelium discoideum social amoeba hosts and Paraburkholderia facultative bacterial symbionts. Symbiosis with inedible Paraburkholderia allows host D. discoideum to carry prey bacteria through the dispersal stage where host amoebae aggregate and develop into fruiting bodies that disperse spores. Carrying prey bacteria benefits hosts when prey bacteria are scarce but harms hosts when prey bacteria are plentiful. Symbiont-carrying hosts leave some bacteria behind; this could explain the harm to hosts if left-behind bacteria include uneaten prey bacteria. Thus, understanding both benefits and costs in this symbiosis requires measuring how many prey bacteria are eaten, carried, and left behind by infected hosts. We found that Paraburkholderia infection makes hosts leave behind both symbionts and prey bacteria. However, the number of prey bacteria left uneaten was small and did not explain why infected hosts produced fewer spores than uninfected hosts. Turning to the bacteria that are carried, we found that hosts carry more prey bacteria after developing in prey- poor environments than in prey-rich ones. This suggests that carriage is actively modified to ensure hosts have prey in the harshest conditions. Our results show that multifaceted interactions with third parties shape the evolution of symbioses in complex ways.
Structural transitions in TCTP tumor protein upon Mcl-1 binding

Summary Translationally Controlled Tumour Protein (TCTP) is a pro-survival factor in tumor cells. TCTP inhibits the mitochondrial apoptosis pathway by potentiating the anti-apoptotic Bcl-2 family members Mcl-1 and Bcl-xL. Specifically, TCTP binds Bcl-xL and inhibits the Bax-dependent Bcl-xL-induced cytochrome c release and TCTP reduces Mcl-1 turnover by inhibiting its ubiquitinylation, thus resulting in decreased Mcl-1 mediated apoptosis. TCTP owns a BH3-like motif forming a β-strand buried in the globular domain of the protein. The crystal structure of TCTP BH3-like peptide in complex with Bcl-xL highlighted the α-helical conformation of TCTP BH3-like motif, suggesting major changes in TCTP structure upon complex formation. However, the structural impact of the interaction on the full-length TCTP and the structural description of TCTP/Mcl-1 interaction are still lacking. Here using biophysical/biochemical methods (NMR, SAXS, circular dichroism, limited proteolysis), we provide an in-depth description of the TCTP/Mcl-1 complex. We demonstrate that full length TCTP binds to the BH3 binding groove of Mcl-1 via its BH3-like motif which interconverts between different binding modes at the micro- to milli-second timescale. As a consequence of the engagement of the BH3-like motif in the interface, the TCTP globular domain is destabilized into a molten-globule state. We also establish that the residue D16 in TCTP BH3-like motif is crucial for the stability and dynamics of the intermolecular interface. As a conclusion, we reveal here in details the structural plasticity of TCTP and discuss its implications for TCTP biology and for future anticancer drug design strategies aiming at targeting TCTP complexes. Contact Ewen Lescop, ewen.lescop@cnrs.fr. Supplementary Information Supplementary figures, tables and files.
Frequency-dependent attenuation and elasticity in unconsolidated earth materials: Effect of damping

ABSTRACTWe used the discrete element method (DEM) to understand the underlying attenuation mechanism in granular media, with special applicability to the measurements of the so-called effective mass developed earlier. We considered that the particles interacted via Hertz-Mindlin elastic contact forces and that the damping was describable as a force proportional to the velocity difference of contacting grains. We determined the behavior of the complex-valued normal-mode frequencies using (1) DEM, (2) direct diagonalization of the relevant matrix, and (3) a numerical search for the zeros of the relevant determinant. All three methods were in strong agreement with each other. The real and the imaginary parts of each normal-mode frequency characterized the elastic and the dissipative properties, respectively, of the granular medium. We found that as the interparticle damping ξ increased, the normal modes exhibited nearly circular trajectories in the complex frequency plane, and that for a given value of ξ, th.
Emergent Friedmann dynamics with a quantum bounce from quantum gravity condensates

We study the effective cosmological dynamics, emerging as the hydrodynamics of simple condensate states, of a group field theory (GFT) model for quantum gravity coupled to a massless scalar field and reduced to its isotropic sector. The quantum equations of motion for these GFT condensate states are given in relational terms with respect to the scalar field, from which effective dynamics for spatially flat, homogeneous and isotropic space–times can be extracted. The result is a generalisation of the Friedmann equations, including quantum gravity modifications, in a specific regime of the theory corresponding to a Gross–Pitaevskii approximation where interactions are subdominant. The classical Friedmann equations of general relativity are recovered in a suitable semi-classical limit for some range of parameters of the microscopic dynamics. An important result is that the quantum geometries associated with these GFT condensate states are non-singular: a bounce generically occurs in the Planck regime. For some choices of condensate states, these modified Friedmann equations are very similar to those of loop quantum cosmology.
LARGE-SCALE STAR-FORMATION-DRIVEN OUTFLOWS AT 1 < z < 2 IN THE 3D-HST SURVEY

We present evidence of large-scale outflows from three low-mass (log(M*/M☉) ∼ 9.75) star-forming (SFR > 4 M☉ yr−1) galaxies observed at z = 1.24, z = 1.35, and z = 1.75 in the 3D-HST Survey. Each of these galaxies is located within a projected physical distance of 60 kpc around the sight line to the quasar SDSS J123622.93+621526.6, which exhibits well-separated strong (Wλ2796r ≳ 0.8 Å) Mg ii absorption systems matching precisely to the redshifts of the three galaxies. We derive the star formation surface densities from the Hα emission in the WFC3 G141 grism observations for the galaxies and find that in each case the star formation surface density well exceeds 0.1 M☉ yr−1 kpc−2, the typical threshold for starburst galaxies in the local universe. From a small but complete parallel census of the 0.65 < z < 2.6 galaxies with H140 ≲ 24 proximate to the quasar sight line, we detect Mg ii absorption associated with galaxies extending to physical distances of 130 kpc. We determine that the Wr > 0.8 Å Mg ii covering fraction of star-forming galaxies at 1 < z < 2 may be as large as unity on scales extending to at least 60 kpc, providing early constraints on the typical extent of starburst-driven winds around galaxies at this redshift. Our observations additionally suggest that the azimuthal distribution of Wr > 0.4 Å Mg ii absorbing gas around star-forming galaxies may evolve from z ∼ 2 to the present, consistent with recent observations of an increasing collimation of star-formation-driven outflows with time from z ∼ 3.