Miracle-dz/UniFAR-FTUs huggingface dataset:
From Genomics to Integrative Taxonomy? The Case Study of Pocillopora Corals

With the advent of genomics, sequencing thousands of loci from hundreds of individuals now appears feasible at reasonable costs, allowing complex phylogenies to be resolved. This is particularly relevant for cnidarians, for which insufficient data due to the small number of currently available markers, coupled with difficulties in inferring gene trees and morphological incongruences, encrypts species boundaries, thereby blurring the study and conservation of these organisms. Yet, can genomics alone be used to delimit species in an integrative taxonomic context? Here, focusing on the coral genus Pocillopora, which plays key roles in Indo-Pacific reef ecosystems but has challenged taxonomists for decades, we explored and discussed the usefulness of multiple criteria (genetics, morphology, biogeography and symbiosis ecology) to delimit species of this genus. Phylogenetic inferences, clustering approaches and species delimitation methods based on genome-wide single-nucleotide polymorphisms (SNPs) were first used to resolve Pocillopora phylogeny and propose genomic species hypotheses from 356 colonies sampled across the Indo-Pacific (western Indian Ocean, tropical southwestern Pacific and south-east Polynesia). These species hypotheses were then compared to previous genetic evidences, as well as to evidences based on morphology, biogeography and symbiosis. Genomics allowed to delimit 21 species hypotheses where only seven are currently recognised based on current taxonomy. Moreover, 13 species were strongly supported by all approaches, either confirming their currently recognised species status, or supporting the presence of new species that need to be formally described. Some of the other genomic species hypotheses were supported by biogeographic or symbiosis evidences, but additional investigations are needed to state on their species status. Altogether, our results support (1) the obsolescence of macromorphology (i.e., overall colony and branches shape) but the relevance of micromorphology (i.e., corallite structures) to refine Pocillopora species limits, (2) the need to identify molecularly species prior to their study, as morphology can blur species identification on the field, (3) the relevance of the mtORF (coupled with other markers in some cases) as a diagnostic marker of most species, and (4) the need for a taxonomical revision in the Pocillopora genus. These results give new insights into the usefulness of multiple criteria for resolving Pocillopora species limits and will ultimately provide helpful insights for the conservation of the species from this scleractinian genus. [biogeography; cryptic species delimitation; Indo-Pacific; microsatellites; morphology; phylogenetics; single-nucleotide polymorphism (SNP); Symbiodiniaceae]
Development of serum substitute medium for bone tissue engineering

In tissue engineering, cells are grown often on scaffolds and subjected to chemical/mechanical stimuli. Most such cultures still use fetal bovine serum (FBS) despite its known disadvantages including ethical concerns, safety issues, and variability in composition, which greatly influences the experimental outcomes. To overcome the disadvantages of using FBS, chemically defined serum substitute medium needs to be developed. Development of such medium depends on cell type and application - which makes it impossible to define one universal serum substitute medium for all cells in any application. Here, we developed a serum substitute medium for bone tissue engineering (BTE) in a step-by-step process. Essential components were added to the medium while human bone marrow mesenchymal stromal cells (hBMSCs, osteoblast progenitor cells) were cultured in two-dimensional (2D) and three-dimensional (3D) substrates. In a 3-week culture, the developed serum substitute medium worked equally well as FBS containing medium in term of cell attachment to the substrate, cell survival, osteoblast differentiation, and deposition of extracellular matrix. In the next step, the use of serum substitute medium was evaluated when culturing cells under mechanical loading in the form of shear stress. The outcomes showed that the application of shear stress is essential to improve extracellular matrix formation while using serum substitute medium. The developed serum substitute medium could pave the way in replacing FBS for BTE studies eliminating the use of controversial FBS and providing a better-defined chemical environment for BTE studies. Graphical abstract
Oscillations and aperiodic activity: Evidence for dynamic changes in both during memory encoding

Electrical recordings of human brain activity via electroencephalography (EEG) show prominent, rhythmic voltage fluctuations. These periodic oscillations have been linked to nearly every cognitive and perceptual process, as well numerous disease states. Recent methodological and theoretical advances, however, have given rise to evidence for a functional role for non-oscillatory, aperiodic neural activity. Physiologically, this aperiodic activity has been linked to the relative contributions of neuronal excitatory and inhibitory signaling. Most importantly, however, traditional data analysis methods often conflate oscillations and aperiodic activity, masking the potentially separate roles these processes play in perception, cognition, and disease. Here we present a reanalysis of intracranial human EEG recordings from Fellner et al., 2019, using new methods for separately parameterizing oscillations and aperiodic activity in a time-resolved manner. We find that human memory encoding is not related to just oscillations or aperiodic activity, but rather that both processes are rapidly co-modulated during memory encoding. These results provide strong evidence for event-related dynamics of aperiodic and oscillatory activity in human memory, paving the way for future investigations into the unique functional roles of these two independent, but linked, processes in human cognition.
THE PROPER MOTION OF PALOMAR 5

Palomar 5 (Pal 5) is a faint halo globular cluster associated with narrow tidal tails. It is a useful system to understand the process of tidal dissolution, as well as to constrain the potential of the Milky Way. A well-determined orbit for Pal 5 would enable detailed study of these open questions. We present here the first CCD-based proper motion measurement of Pal 5 obtained using SDSS as a first epoch and new Large Binocular Telescope/Large Binocular Camera (LBC) images as a second, giving a baseline of 15 years. We perform relative astrometry, using SDSS as a distortion-free reference, and images of the cluster and also of the Pal 5 stream for the derivation of the distortion correction for LBC. The reference frame is made up of background galaxies. We correct for differential chromatic refraction using relations obtained from SDSS colors as well as from flux-calibrated spectra, finding that the correction relations for stars and for galaxies are different. We obtain μα = −2.296 ± 0.186 mas yr−1 and μδ = −2.257 ± 0.181 mas yr−1 for the proper motion of Pal 5. We use this motion, and the publicly available code galpy, to model the disruption of Pal 5 in different Milky Way models consisting of a bulge, a disk, and a spherical dark matter halo. Our fits to the observed stream properties (streak and radial velocity gradient) result in a preference for a relatively large Pal 5 distance of around 24 kpc. A slightly larger absolute proper motion than what we measure also results in better matches but the best solutions need a change in distance. We find that a spherical Milky Way model, with V0 = 220 km s−1 and V20 kpc, i.e., approximately at the apocenter of Pal 5, of 218 km s−1, can match the data well, at least for our choice of disk and bulge parametrization.
Relationship between the CMB, Sunyaev-Zel’dovich cluster counts, and local Hubble parameter measurements in a simple void model

The discrepancy between the amplitudes of matter fluctuations inferred from Sunyaev-Zel'dovich (SZ) cluster number counts, the primary temperature, and the polarization anisotropies of the cosmic microwave background (CMB) measured by the Planck satellite can be reconciled if the local universe is embedded in an under-dense region as shown by Lee, 2014. Here using a simple void model assuming the open Friedmann-Robertson-Walker geometry and a Markov Chain Monte Carlo technique, we investigate how deep the local under-dense region needs to be to resolve this discrepancy. Such local void, if exists, predicts the local Hubble parameter value that is different from the global Hubble constant. We derive the posterior distribution of the local Hubble parameter from a joint fitting of the Planck CMB data and SZ cluster number counts assuming the simple void model. We show that the predicted local Hubble parameter value of $H_{\rm loc}=70.1\pm0.34~{\rm km\,s^{-1}Mpc^{-1}}$ is in better agreement with direct local Hubble parameter measurements, indicating that the local void model may provide a consistent solution to the cluster number counts and Hubble parameter discrepancies.
Spectroscopy of snake states using a graphene Hall bar

An approach to observe snake states in a graphene Hall bar containing a pn-junction is proposed. The magnetic field dependence of the bend resistance in a ballistic graphene Hall bar structure containing a tilted pn-junction oscillates as a function of applied magnetic field. We show that each oscillation is due to a specific snake state that moves along the pn-interface. Furthermore, depending on the value of the magnetic field and applied potential, we can control the lead in which the electrons will end up and hence control the response of the system.
Effects of Steady-State Plasma Exposure on Tungsten Surface Cracking due to Elm-Like Pulsed Plasma Bombardment

Abstract Sequential exposures of W surfaces to steady-state and pulsed (∼0.5 ms) plasmas have been performed in a linear divertor plasma simulator and a magnetized coaxial plasma gun to investigate effects of D blisters, nano-sized He bubbles, and He-induced W fuzz on surface cracking by pulsed plasma loads. Surface cracks appeared on samples containing D blisters or He bubbles following 10 shots at ∼0.5 MJ/m2 per shot, while a mirror-polished sample with no pre-plasma exposure did not exhibit cracks after similar transient exposures. Note that the cracking is limited to the edge region for a sample with D blisters. This means that the energy density threshold for surface cracking is lowered by the existence of D blisters and, especially, He bubbles. On the other hand, it is found that fuzzy surfaces possess a good resistance to surface cracking, although arcing is prone to occur.
Lemaitres Limit

Georges Lemaitre gave a theoretical proof for his 1927 doctoral thesis in astronomy that the maximum spherical radius of our Universe can be computed from first principles to be 14.2 billion light-years (Lemaitre 1927a). That estimate, which is known as Lemaitres limit, is surprisingly close to current estimates of the Universes age. Such coincidence, to within 3%, between the predicted size and observed age of the Universe is more significant today because of the resurrection in the late 1990s of the cosmological constant (also known as vacuum or dark energy). The most precise Hubble constant to date, H = 69.32 km/s/Mpc based on the full nine-years of Wilkinson Microwave Anisotropy Probe measurements, is within 1% of the value predicted based on Lemaitres Limit, H = 68.7 km/s/Mpc. If Lemaitres Limit is resurrected, it will revolutionize cosmology.
Postoperative anion gap associates with short- and long-term mortality after cardiac surgery: A large-scale cohort study

Objective To investigate whether postoperative anion gap (AG) is associated with short- and long-term mortality in patients following cardiac surgery. Materials and methods We conducted a retrospective cohort study of adults who underwent cardiac surgery from the Medical Information Mart for Intensive Care - III database. The generalized additive model (GAM), logistic regression, and Cox regression were performed to assess the correlations between AG levels and in-hospital, 90-day, and 4-year mortality. Linear regression was used to evaluate the associations between AG and length of stay (LOS). Results Totally, 6,410 subjects were enrolled in this study and classified into tertiles based on the initial AG levels. The GAM indicated a positive association between initial AG and in-hospital mortality after adjusting for potential confounders. Multivariate logistic analysis revealed that the risk of in-hospital mortality was higher among patients in tertile 2 (OR 2.05, 95% CI 1.11–3.76, P = 0.021) and tertile 3 (OR 4.51, 95% CI 2.57–7.91, P < 0.001) compared with those in tertile 1. For 90-day and 4-year mortality, multivariate Cox regression found similar associations between AG tertiles and mortality. The LOS in ICU and hospital also increased as AG tertiles increased. The E-value indicated robustness to unmeasured confounders. Conclusion This study found a positive association between postoperative AG levels and short- and long-term mortality among patients after cardiac surgery. This relationship warrants further research.
Star formation and environment in clusters up to z~2.2

The dependence of galaxy star formation activity on environment - especially in clusters - at high redshift is still poorly understood, as illustrated by the still limited number of z>1.4 clusters on the one hand, and by the still debated star formation-density relation at high redshift on the other hand. The zphot~2.2 JKCS041 cluster allows to probe such environmental dependence of star formation activity at an unprecedented combination of redshifts and environments. Its study permits to enlarge the knowledge of high redshift clusters and to put strong leverage on observational constraints for galaxy evolution models. We analyze deep u\astg'r'i'z'JHKs images from the CFHTLS/WIRDS surveys, which cover JKCS041 cluster field. We first estimate photometric redshifts based on multi-wavelength photometry. We then lead a careful analysis to test the presence of a Butcher-Oemler effect. We work on galaxies within 2\timesr200 and with masses >1.34\times10^11 Msun, and use two comparison clusters at z=0 and z=1 of similar mass. We estimate the radial profiles of the fraction of blue galaxies, taking into account the star aging with decreasing redshift. After confirming the high redshift nature of JKCS041, we find no evidence for a Butcher-Oemler effect between z~2.2 and z~0 for galaxies more massive than 1.34\times10^11 Msun. In the cluster center, a change greater than \Deltafblue/\Deltaz=0.16 between z~0 and z~2.2 would be easily detected. We also find that JKCS041 shows a consistent and systematic increase of the fraction of star-forming galaxies with cluster-centric distance, hence with decreasing density, for both a M>1.34\times10^11 Msun selected sample and a lower mass sample. In particular, very few (less than 15%) star-forming galaxies are found within r200/2 among high mass (M>1.34\times10^11 Msun) galaxies. Our results show that the present-day star formation-density relation is already in place at z~2.2.
Pion Transverse Momentum Spectrum, Elliptic Flow, and Interferometry in the Granular Source Model for RHIC and LHC Heavy Ion Collisions

We systematically investigate the pion transverse momentum spectrum, elliptic flow, and Hanbury-Brown-Twiss (HBT) interferometry in the granular source model for the heavy ion collisions of Au-Au at GeV and Pb-Pb at TeV with different centralities. The granular source model can well reproduce the experimental results of the heavy ion collisions at the Relativistic Heavy Ion Collider (RHIC) and the Large Hadron Collider (LHC). We examine the parameters involved in the granular source model. The experimental data of the momentum spectrum, elliptic flow, and HBT radii for the two collision energies and different centralities impose very strict constraints on the model parameters. They exhibit certain regularities for collision centrality and energy. The space-time structure and expansion velocities of the granular sources for the heavy ion collisions at the RHIC and LHC energies with different centralities are investigated.
Energy-length scaling of critical phase fluctuations in the cuprate pseudogap phase

The quantum origin of the cuprate pseudogap and its relationship to symmetry-breaking orders is a central conundrum of unconventional superconductors. The difficulty is deeply rooted in modeling simultaneous organizations in multiple degrees of freedom (including spin, momentum, and real space) generated by strong electron-electron correlations. Beyond early theories focusing on the description in spin and momentum space, recent studies turn to examine the spatial organization and intertwining mechanism of multiple orders. In this review, we summarize some progress in understanding the spatial organization of critical fluctuations and highlight the recent discovery of a universal energy-length scaling. This scaling quantitatively explains the nontrivial magnitude and doping dependence of the pseudogap energy and critical temperature and their relations to charge and superconducting ordering. We close with a prospect of the spatial organization mechanism of intertwined orders and its possible composite energy scaling.
The Cosmic Chemical Evolution as seen by the Brightest Events in the Universe

Abstract Gamma-ray bursts (GRBs) are the brightest events in the universe. They have been used in the last five years to study the cosmic chemical evolution, from the local universe to the first stars. The sample size is still relatively small when compared to field galaxy surveys. However, GRBs show a universe that is surprising. At z > 2, the cold interstellar medium in galaxies is chemically evolved, with a mean metallicity of about 1/10 solar. At lower redshift (z < 1), metallicities of the ionized gas are relatively low, on average 1/6 solar. Not only is there no evidence of redshift evolution in the interval 0 < z < 6.3, but also the dispersion in the ~30 objects is large. This suggests that the metallicity of host galaxies is not the physical quantity triggering GRB events. From the investigation of other galaxy parameters, it emerges that active star-formation might be a stronger requirement to produce a GRB. Several recent striking results strongly support the idea that GRB studies open a new view on our understanding of galaxy formation and evolution, back to the very primordial universe at z ~ 8.
A modified deep residual network for short-term load forecasting

The electrical load has a prominent position and a very important role in the day-to-day operations of the entire power system. Due to this, many researchers proposed various models for forecasting load. However, these models are having issues with over-fitting and the capability of generalization. In this paper, by adopting state-of-the-art of deep learning, a modified deep residual network (deep-ResNet) is proposed to improve the precision of short-term load forecasting and overcome the above issues. In addition, the concept of statistical correlational analysis is used to identify the appropriate input features extraction ability and generalization capability in order to progress the accuracy of the model. Two utility (ISO-NE and IESO-Canada) datasets are considered for evaluating the proposed model performance. Finally, the prediction results obtained from the proposed model are promising as well as accurate when compared with the other existing models in the literature.
Genetic polymorphisms of toll-like receptors in leprosy patients from southern Brazil

Leprosy is a chronic disease and also a global health issue, with a high number of new cases per year. Toll-like receptors can respond to mycobacterial molecules in the early stage of infection. As important components of the innate immune response, alterations in genes coding for these receptors may contribute to susceptibility/protection against diseases. In this context, we used a case-control study model (183 leprosy cases vs. 185 controls) to investigate whether leprosy patients and the control group, in southern Brazil, have different frequencies in TLR1 (TLR1 G>T; rs5743618), TLR2 (TLR2 T>C, rs1816702 and rs4696483), and TLR4 (TLR4 A>G, rs1927911) polymorphisms. Analysis of the TLR1 1805G>T polymorphism presented the G/G genotype more frequently in the control group. TLR2 T>C rs1816702 and TLR2 T>C rs4696483, the T/T and C/T genotype, respectively, were more frequent in the control group than in leprosy patients, suggesting protection from leprosy when the T allele is present (rs4696483). Haplotype analyses between TLR1 (rs5743618) and TLR2 (rs1816702 and rs4696483) polymorphisms suggest risk for the presence of the TCC haplotype and protection in the presence of the TCT haplotype. This study suggests that polymorphisms in TLR1 and TLR2 are factors that may contribute to development/resistance of leprosy.
“RETIRED” PLANET HOSTS: NOT SO MASSIVE, MAYBE JUST PORTLY AFTER LUNCH

Studies of the planet abundance as a function of stellar mass have suggested a strong increase in the frequency of planet occurrence around stars more massive than 1.5 M☉, and that such stars are deficit in short-period planets. These planet searches have relied on giant stars for a sample of high mass stars, which are hostile to precision Doppler measurements due to rotation and activity while on the main sequence. This Letter considers the observed vsin i and observationally inferred mass for exoplanet hosting giants with the vsin i of distribution of field stars, which show discrepancies that can be explained by erroneous mass determinations of some exoplanet host stars. By comparison with an expected mass distribution constructed from integrating isochrones, it is shown that the exoplanet hosts are inconsistent with a population of massive stars. These stars are more likely to have originated from a main-sequence population of late F/early G dwarfs with mass 1.0–1.2 M☉, only slightly more massive than the typical FGK dwarfs with Doppler detected planets. The deficit of short-period planets is most likely explained by tidal capture. The planet abundance difference requires either a steeper increase in planet frequency with mass than previously thought or a high rate of false positives due to signals of stellar origin. The measurement of photospheric carbon isotope ratios is suggested as a method to discriminate whether this sample of giant stars is significantly more massive than the population of FGK dwarfs with Doppler detected planets.
Mechanisms of venetoclax resistance and solutions

The BCL-2 inhibitor venetoclax is currently approved for treatment of hematologic diseases and is widely used either as monotherapy or in combination strategies. It has produced promising results in the treatment of refractory or relapsed (R/R) and aged malignant hematologic diseases. However, with clinical use, resistance to venetoclax has emerged. We review the mechanism of reduced dependence on BCL-2 mediated by the upregulation of antiapoptotic proteins other than BCL-2, such as MCL-1 and BCL-XL, which is the primary mechanism of venetoclax resistance, and find that this mechanism is achieved through different pathways in different hematologic diseases. Additionally, this paper also summarizes the current investigations of the mechanisms of venetoclax resistance in terms of altered cellular metabolism, changes in the mitochondrial structure, altered or modified BCL-2 binding domains, and some other aspects; this article also reviews relevant strategies to address these resistance mechanisms.