Miracle-dz/UniFAR-FTUs huggingface dataset:
Population structure and genetic variation of fragmented mountain birch forests in Iceland

Abstract Betula pubescens Ehrh. (mountain birch) is the only forest-forming tree in Iceland. Since human settlement (874 AD), the continuous 25,000 to 30,000 km2 forest has shrunk to 1.200 km2 of fragmented patches, making it a good object to study population genetic consequences of habitat fragmentation and disturbance. Further, genetic studies have also shown that hybridization between the tetraploid (2n = 56) B. pubescens and the diploid (2n = 28) Betula nana L. (dwarf birch) occurs among Iceland’s natural populations. This study assessed the genetic variation within and among 11 birch forests remaining across Iceland. Genotype-by-sequencing methodology provided a total of 24,585 single nucleotide polymorphisms (SNP´s), with a minor allele frequency >5% for genetic analyses. The analysis showed similar diversity within forests, suggesting that fragmentation and hybridization have had a limited effect on the genetic variation within sites. A clear genetic divergence is found among forests from the different regions of Iceland that may reflect historical isolation; the differentiation between forests increased with geographic distances reflecting isolation by distance. Information on the distribution of genetic variation of birch in Iceland is essential for its conservation and to establish genotype–phenotype associations to predict responses to new environmental conditions imposed by climate change and novel biotic/abiotic stressors.
Hierarchical star cluster assembly in globally collapsing molecular clouds

We discuss the mechanism of cluster formation in a numerical simulation of a molecular cloud (MC) undergoing global hierarchical collapse (GHC). The global nature of the collapse implies that the SFR increases over time. The hierarchical nature of the collapse consists of small-scale collapses within larger-scale ones. The large-scale collapses culminate a few Myr later than the small-scale ones and consist of filamentary flows that accrete onto massive central clumps. The small-scale collapses form clumps that are embedded in the filaments and falling onto the large-scale collapse centers. The stars formed in the early, small-scale collapses share the infall motion of their parent clumps. Thus, the filaments feed both gaseous and stellar material to the massive central clump. This leads to the presence of a few older stars in a region where new protostars are forming, and also to a self-similar structure, in which each unit is composed of smaller-scale sub-units that approach each other and may merge. Because the older stars formed in the filaments share the infall motion of the gas onto the central clump, they tend to have larger velocities and to be distributed over larger areas than the younger stars formed in the central clump. Finally, interpreting the IMF at face-value as a probability distribution implies that massive stars only form once the {\it local} SFR is large enough to sample the IMF up to high masses. In combination with the increase of the SFR, this implies that massive stars tend to appear late in the evolution of the MC, and only in the central massive clumps. We discuss the correspondence of these features with observed properties of young stellar clusters, finding very good qualitative agreement, thus providing support to the scenario of global, hierarchical collapse of MCs, while explaining the origin of the observed cluster structure.
Long‐term variations and potency of neutralizing antibodies against Omicron subvariants after CoronaVac‐inactivated booster: A 7‐month follow‐up study

The long‐term protective efficacy of neutralizing antibodies (Nabs) against Omicron subvariants after inactivated booster vaccines remains elusive. During the follow‐up study, 54 healthy volunteers aged 20–31 years received inactivated CoronaVac booster vaccinations and were monitored for 221 days. The dynamic efficacy and durability of Nab against Omicron subvariants BA.1, BA.2, BA.2. 12.2, and BA4/5 were assessed using a pseudotyped virus neutralization assay at up to nine time points post immunization. The antibody response against Omicron subvariants was substantially weaker than D614G, with BA.4/5 being the least responsive. The geometric mean titer (GMT) of Nab against Omicron subvariants BA.1, BA.2, BA.2. 12.1, and BA.4/5 was 2.2‐, 1.7‐, 1.8‐, and 2.2‐fold lower than that against D614G (ps < 0.0001). The gap in Nab response between Omicron subvariants was pronounced during the 2 weeks–2 months following booster vaccination (ps < 0.05). Seven months post booster, the antibody potency against D614G was maintained at 100% (50% for Nab titers ≥ 100 50% inhibitory dilution [EC50]), whereas at 77.3% for BA.1, 90.9% for BA.2, 86.4% for BA.2. 12.1, and 86.4% for BA.4/5 (almost 20% for Nab titers ≥ 100 EC50). Despite the inevitable immune escape, Omicron subvariants maintained sustained and measurable antibody potency post‐booster vaccination during long‐term monitoring, which could help optimize immunization strategies.
Drinking and swimming around waterways: The role of alcohol, sensation-seeking, peer influence and risk in young people

The role of individual and sociocultural factors contributing to drowning risk for young adults is complex and poorly understood. This study examined the relationship between behaviour in and around waterways and: 1) alcohol consumption; 2) resistance to peer influence; 3) sensation-seeking; 4) perception of risk among people aged 15–24 in Western Australia. A cross-sectional online survey was conducted at three time-points with a convenience sample. Predictor variables included: Alcohol Use Disorder Identification Test Consumption (AUDIT_C); Resistance to Peer Influence; Brief Sensation Seeking scale; Benthin’s Perception of risk. Pearson chi-squared tests determined the association between demographic and predictor variables. Logistic regression explored influence of potential predictor variables on behaviour in and around water. The final sample (n = 730) participants, consisted of females (n = 537, 74.5%), metropolitan dwelling (n = 616, 84.4%), and attended university (n = 410, 56.9%). Significant associations were found for those who swum after drinking alcohol compared with those that had not by age, gender, education. For every 1-unit increase in AUDIT-C participants were 60% more likely to swim after drinking (OR 95% CI 1.60 1.44–1.78). Participants who considered an adverse event serious were 15% less likely to have swum after drinking alcohol (OR 0.85 95% CI 0.73–0.99). The complex relationship between social participation in activities in and around waterways, higher drowning rates, propensity for risk, and the meaning young adults attach to risk locations and practices present unique challenges for drowning prevention research. Findings should be used to improve the awareness and education components of future youth water safety strategies in high-income settings.
Influence of Lime and Phosphorus Application Rates on Growth of Maize in an Acid Soil

The interactive effects of lime and phosphorus on maize growth in an acid soil were investigated in a greenhouse experiment. A completely randomized design with 12 treatments consisting of four lime levels, 0, 2, 10, and 20 t ha−1, in a factorial combination with three phosphorus rates, 0, 30, and 100 kg ha−1, was used. Maize was grown in pots for six weeks and its heights and dry matter yield were determined and soils were analyzed for available P and exchangeable acidity. Liming significantly reduced the exchangeable acidity in the soils. The effect of lime on available P was not significant but available P increased with increasing P rates. There was a significant effect of lime, P, and P by lime interactions on plant heights and dry matter. Without lime application, dry matter increased with increasing P rates but, with lime, dry mattes increased from 0 to 30 kg P ha−1 but declined from 30 to 100 kg P ha−1. The highest dry matter yield (13.8 g pot−1) was obtained with a combined 2 t ha−1 of lime with 30 kg P ha−1 suggesting that lime application at low rates combined with moderate amounts of P would be appropriate in this soil.
mcr-1 colistin resistance gene sharing between Escherichia coli from cohabiting dogs and humans, Lisbon, Portugal, 2018 to 2020

Background The emergence of colistin resistance is a One Health antimicrobial resistance challenge worldwide. The close contact between companion animals and humans creates opportunities for transmission and dissemination of colistin-resistant bacteria. Aim To detect potential animal reservoirs of colistin-resistant Escherichia coli and investigate the possible sharing of these bacteria between dogs, cats and their cohabiting humans in the community in Lisbon, Portugal. Methods A prospective longitudinal study was performed from 2018 to 2020. Faecal samples from dogs and cats either healthy or diagnosed with a skin and soft tissue or urinary tract infection, and their cohabiting humans were screened for the presence of colistin-resistant E. coli. All isolates were tested by broth microdilution against colistin and 12 other antimicrobials. Colistin-resistant isolates were screened for 30 resistance genes, including plasmid-mediated colistin resistance genes (mcr-1 to mcr-9), and typed by multilocus sequence typing. Genetic relatedness between animal and human isolates was analysed by whole genome sequencing. Results Colistin-resistant E. coli strains harbouring the mcr-1 gene were recovered from faecal samples of companion animals (8/102; 7.8%) and humans (4/125; 3.2%). No difference between control and infection group was detected. Indistinguishable multidrug-resistant E. coli ST744 strains harbouring the mcr-1 gene were found in humans and their dogs in two households. Conclusions The identification of identical E. coli strains containing the plasmid-mediated mcr-1 gene in companion animals and humans in daily close contact is of concern. These results demonstrate the importance of the animal–human unit as possible disseminators of clinically important resistance genes in the community setting.
Galaxy and Quasar Fueling Caught in the Act from the Intragroup to the Interstellar Medium

We report the discovery of six spatially extended (10–100 kpc) line-emitting nebulae in the z ≈ 0.57 galaxy group hosting PKS 0405−123, one of the most luminous quasars at z < 1. The discovery is enabled by the Multi Unit Spectroscopic Explorer and provides tantalizing evidence connecting large-scale gas streams with nuclear activity on scales of <10 proper kpc (pkpc). One of the nebulae exhibits a narrow, filamentary morphology extending over 50 pkpc toward the quasar with narrow internal velocity dispersion (50 ) and is not associated with any detected galaxies, consistent with a cool intragroup medium filament. Two of the nebulae are 10 pkpc north and south of the quasar with tidal-arm–like morphologies. These two nebulae, along with a continuum-emitting arm extending 60 pkpc from the quasar, are signatures of interactions that are expected to redistribute angular momentum in the host interstellar medium (ISM) to facilitate star formation and quasar fueling in the nucleus. The three remaining nebulae are among the largest and most luminous [O iii] emitting “blobs” known (1400–2400 pkpc2) and correspond both kinematically and morphologically to interacting galaxy pairs in the quasar host group, consistent with arising from stripped ISM rather than large-scale quasar outflows. The presence of these large- and small-scale nebulae in the vicinity of a luminous quasar bears significantly on the effect of large-scale environment on galaxy and black hole fueling, providing a natural explanation for the previously known correlation between quasar luminosity and cool circumgalactic medium.
The effective temperature in the quenching of coarsening systems to and to below TC

We overview the general scaling behaviour of the effective temperature in quenches of simple non-disordered systems, such as ferromagnets, to and to below TC. Emphasis is on the behaviour as the dimensionality is varied. Consequences for the shape of the asymptotic parametric representation are derived. In particular, this is always trivial in critical quenches with TC>0. We clarify that the quench to TC = 0 at the lower critical dimensionality dL, cannot be regarded as a critical quench. Implications for the behaviour of the exponent a of the ageing response function in quenches to below TC are developed.
Electronic structure of the BaTi 2 As 2 O parent compound of the titanium-based oxypnictide superconductor

The electronic structure of ${\text{BaTi}}_{2}$${\text{As}}_{2}O$, a parent compound of the newly discovered titanium-based oxypnictide superconductors, is studied by angle-resolved photoemission spectroscopy and first-principles calculation. The experimental electronic structure shows a multiorbital nature and three-dimensional character, which is consistent with the calculated results. An anomalous temperature-dependent spectral weight redistribution and broad line shape indicate the incoherent nature of the spectral function. At the density-wave-like transition temperature around 200 K, a partial gap opens at the Fermi patches. These findings suggest that ${\text{BaTi}}_{2}$${\text{As}}_{2}O$ is likely a charge density wave material in the strong-interaction regime.
Bioscaffold developed with decellularized human amniotic membrane seeded with mesenchymal stromal cells: assessment of efficacy and safety profiles in a second-degree burn preclinical model

Therapies to deep burn injuries remain a global challenge. Human amniotic membrane (hAM) is a biomaterial that has been increasingly explored by the field of regenerative medicine. A decellularized hAM (DhAM) can be used as scaffold for mesenchymal stromal cells (MSCs) to grow without the loss of their stemness potential, allowing its application as cell therapy for wound healing. In this work, we associated DhAM with adipose-derived MSCs (DhAM + AD-MSCs), as a therapy strategy for second-degree burns in a preclinical model. Animals with induced second-degree burns were divided into four groups: control, which consists of a non-adherent gauze; a synthetic commercial dressing as the positive control (Control+); DhAM; and DhAM plus rat AD-MSCs (DhAM + AD-MSCs), followed by detailed and long term analysis (5 weeks). The macroscopical analysis showed the healing improvement in the wound area after the DhAM + AD-MSC treatment. Histological analysis also showed no alteration in the animal organs and a regular epithelial progression in comparison to the control. This observation was also confirmed by the analysis of suprabasal layers in the neoepidermis with CK10, showing a stratified and differentiated epithelium, when compared to Control and Control+. A strong CD73 (ecto-5′-nucleotidase) labeling was observed in the first 2 weeks postburn in dermis and epidermis. The expression in dermis was stronger in the second week in the middle of the wound, when comparing the Control+ with DhAM + AD-MSCs (p = 0.0238). In the epidermis the expression of CD73 was increased in all regions when compared to the control. This data suggests the involvement of this protein on wound healing. A low CD11b labeling was observed in DhAM + AD-MSCs treatment group mainly in the last treatment week, in comparison to Control and Control+ (p < 0.0001), which indicates a reduction in the inflammatory process. MSCs through CD73 can release high concentrations of adenosine, an immunosuppressive molecule, suggesting that this could be the mechanism by which the inflammation was better modulated in the DhAM + AD-MSCs group. The results obtained with this preclinical model confirm the effectiveness and safety of this low-cost and highly available dressing for future clinical application as a therapy for burn treatments.
Alignstein: Optimal transport for improved LC-MS retention time alignment

Abstract Background Reproducibility of liquid chromatography separation is limited by retention time drift. As a result, measured signals lack correspondence over replicates of the liquid chromatography–mass spectrometry (LC-MS) experiments. Correction of these errors is named retention time alignment and needs to be performed before further quantitative analysis. Despite the availability of numerous alignment algorithms, their accuracy is limited (e.g., for retention time drift that swaps analytes’ elution order). Results We present the Alignstein, an algorithm for LC-MS retention time alignment. It correctly finds correspondence even for swapped signals. To achieve this, we implemented the generalization of the Wasserstein distance to compare multidimensional features without any reduction of the information or dimension of the analyzed data. Moreover, Alignstein by design requires neither a reference sample nor prior signal identification. We validate the algorithm on publicly available benchmark datasets obtaining competitive results. Finally, we show that it can detect the information contained in the tandem mass spectrum by the spatial properties of chromatograms. Conclusions We show that the use of optimal transport effectively overcomes the limitations of existing algorithms for statistical analysis of mass spectrometry datasets. The algorithm’s source code is available at https://github.com/grzsko/Alignstein.
Physics of a clumpy lensed galaxy at z = 1.6

Observations have shown that massive star-forming clumps are present in the internal structure of high-redshift galaxies. One way to study these clumps in detail with a higher spatial resolution is by exploiting the power of strong gravitational lensing which stretches images on the sky. In this work, we present an analysis of the clumpy galaxy A68-HLS115 at z = 1.5858, located behind the cluster Abell 68, but strongly lensed by a cluster galaxy member. Resolved observations with SINFONI/VLT in the near-infrared (NIR) show Hα, Hβ, [NII], and [OIII] emission lines. Combined with images covering the B band to the far-infrared (FIR) and CO(2–1) observations, this makes this galaxy one of the only sources for which such multi-band observations are available and for which it is possible to study the properties of resolved star-forming clumps and to perform a detailed analysis of the integrated properties, kinematics, and metallicity. We obtain a stability of υrot/σ0 = 2.73 by modeling the kinematics, which means that the galaxy is dominated by rotation, but this ratio also indicates that the disk is marginally stable. We find a high intrinsic velocity dispersion of 80 ± 10 km s−1 that could be explained by the high gas fraction of fgas = 0.75 ± 0.15 observed in this galaxy. This high fgas and the observed sSFR of 3.12 Gyr−1 suggest that the disk turbulence and instabilities are mostly regulated by incoming gas (available gas reservoir for star formation). The direct measure of the Toomre stability criterion of Qcrit = 0.70 could also indicate the presence of a quasi-stable thick disk. Finally, we identify three clumps in the Hα map which have similar velocity dispersions, metallicities, and seem to be embedded in the rotating disk. These three clumps contribute together to ∼40% on the SFRHα of the galaxy and show a star formation rate density about ∼100 times higher than HII regions in the local Universe.
Short-Period Variable Stars in the M31 Halo

We report the findings of a new search for RR Lyrae stars in an M31 halo field located 40′ from the nucleus of the galaxy along the minor axis. We detected 37 variable stars, of which 24 are classified as RR Lyrae and the others are ambiguous. Estimating a completeness fraction of ∼24%, we calculate that there are approximately 100 RR Lyrae stars in the field, which is consistent with what is expected from deep Hubble Space Telescope (HST) color-magnitude diagrams. We calculate a mean magnitude of ⟨g⟩ = 25.15 ± 0.03, which we interpret to mean that the mean metallicity of RR Lyrae stars is significantly lower than that of the M31 halo as a whole. The presence of ancient, metal-poor stars opens the possibility that initially the M31 halo appeared much like the Milky Way halo.
Water Use Efficiency of Soybean under Different Tillage and Irrigation Methods

FIELD study was carried out during two growing seasons of 2012/2013 and 2013/2014 at the Water Requirements Research Station, Water Management Research Institute, Kafer El-Sheikh Governorate to compare two irrigation methods, surge (SI) and alternate (AI) with traditional furrow irrigation method (FI) in relation to two tillage systems, conventional (CT) and no-tillage (NT) on water use efficiency and crop yield production of soybean. In both seasons, the lowest amount of irrigation water was applied with AI treatments, whereas, the highest amount of irrigation water was applied with FI treatments. The irrigation water amounts were saved by using AI and SI methods. The AI and SI saved about 29.0 % and 15.0 % of water applied in comparison with FI under CT and NT systems. Irrigation water productivity (IWP) and crop water use efficiency (CWUE) were higher when applying AI compared to SI and FI under both tillage systems. Surge irrigation had the potential to improve irrigation application efficiency (AE) followed by AI compared to FI. The highest seed yield and yield attributes were obtained with FI followed by SI and AI in both seasons, respectively. Significant differences in seed yield, yield attributes and plant growth characteristics were found only between FI and AI under CT and NT. The SI surpasses the AI in obtaining higher seed yield, yield attributes without any significant reduction of soybean yield. These results suggesting that an extra irrigation water amount may be saved without any significant loss in yield of soybean when applying SI method under both tillage systems. The results also showed the effect of CT on reducing applied water and increasing irrigation water productivity and crop water consumptive use compared to NT. However, no significant difference between the two tillage systems in yield and yield attributes was found. Values of ETc should be adjusted according to the used irrigation and tillage methods. The crop water stress index (CWSI) has proven to be a good indicator for monitoring and quantifying water stress of soybean with different irrigation methods and tillage systems.