Miracle-dz/UniFAR-FTUs huggingface dataset:
Signatures of Delocalization in the Fermionic 1D Hubbard Model with Box Disorder: Comparative Study with DMRG and R-DMFT

We investigate the 1D Anderson-Hubbard model at half filling with box-disorder. The ground state phase diagram is obtained by means of real-space dynamical mean-field theory (R-DMFT) and the density matrix renormalization group (DMRG). We find Mott insulating and Anderson localized regimes as well as a strong indication of a delocalized phase for intermediate interaction and disorder strength within accessible system sizes. These phases are characterized and distinguished by qualitatively different scaling behavior of the local density of states, the energy gap in the excitation spectrum and the inverse participation number.
ON THE INTRINSIC DIVERSITY OF TYPE II-PLATEAU SUPERNOVAE

Hydrogen-rich Type II-Plateau supernovae (SNe) exhibit correlations between the plateau luminosity L pl ? > , the nickel mass M Ni ? > , the explosion energy E exp ? > , and the ejecta mass M ej ? > . Using our global, self-consistent, multi-band model of nearby well-observed SNe, we find that the covariances of these quantities are strong and that the confidence ellipsoids are oriented in the direction of the correlations, which reduces their significance. By proper treatment of the covariance matrix of the model, we discover a significant intrinsic width to the correlations between L pl ? > , E exp ? > and M Ni ? > , where the uncertainties due to the distance and the extinction dominate. For fixed E exp ? > , the spread in M Ni ? > is about 0.25 dex, which we attribute to the differences in the progenitor internal structure. We argue that the effects of incomplete γ-ray trapping are not important in our sample. Similarly, the physics of the Type II-Plateau SN light curves leads to inherently degenerate estimates of E exp ? > and M ej ? > , which makes their observed correlation weak. Ignoring the covariances of SN parameters or the intrinsic width of the correlations causes significant biases in the slopes of the fitted relations. Our results imply that Type II-Plateau SN explosions are not described by a single physical parameter or a simple one-dimensional trajectory through the parameter space, but instead reflect the diversity of the core and surface properties of their progenitors. We discuss the implications for the physics of the explosion mechanism and possible future observational constraints.
From Whitney Forms to Metamaterials: a Rigorous Homogenization Theory

A rigorous homogenization theory of metamaterials -- artificial periodic structures judiciously designed to control the propagation of electromagnetic waves -- is developed. All coarse-grained fields are unambiguously defined and effective parameters are then derived without any heuristic assumptions. The theory is an amalgamation of two concepts: Smith & Pendry's physical insight into field averaging and the mathematical framework of Whitney-Nedelec-Bossavit-Kotiuga interpolation. All coarse-grained fields are defined via Whitney forms and satisfy Maxwell's equations exactly. The new approach is illustrated with several analytical and numerical examples and agrees well with the established results (e.g. the Maxwell-Garnett formula and the zero cell-size limit) within the range of applicability of the latter. The sources of approximation error and the respective suitable error indicators are clearly identified, along with systematic routes for improving the accuracy further. The proposed approach should be applicable in areas beyond metamaterials and electromagnetic waves -- e.g. in acoustics and elasticity.
Production of dark matter axions from collapse of string-wall systems

We analyze the spectrum of axions radiated from collapse of domain walls, which have received less attention in the literature. The evolution of topological defects related to the axion models is investigated by performing field-theoretic lattice simulations. We simulate the whole process of evolution of the defects, including the formation of global strings, the formation of domain walls and the annihilation of the defects due to the tension of walls. The spectrum of radiated axions has a peak at the low frequency, which implies that axions produced by the collapse of domain walls are not highly relativistic. We revisit the relic abundance of cold dark matter axions and find that the contribution from the decay of defects can be comparable with the contribution from strings. This result leads to a more severe upper bound on the axion decay constant.
THE ACS LCID PROJECT. II. FAINT VARIABLE STARS IN THE ISOLATED DWARF IRREGULAR GALAXY IC 1613

We present the results of a new search for variable stars in the Local Group (LG) isolated dwarf galaxy IC 1613, based on 24 orbits of F475W and F814W photometry from the Advanced Camera for Surveys (ACS) on board the Hubble Space Telescope. We detected 259 candidate variables in this field, of which only 13 (all of them bright Cepheids) were previously known. Out of the confirmed variables, we found 90 RR Lyrae stars, 49 classical Cepheids (including 36 new discoveries), and 38 eclipsing binary stars for which we could determine a period. The RR Lyrae include 61 fundamental (RRab) and 24 first-overtone (FO, RRc) pulsators, and five pulsating in both modes simultaneously (RRd). As for the majority of LG dwarfs, the mean periods of the RRab and RRc (0.611 and 0.334 days, respectively) as well as the fraction of overtone pulsators (fc = 0.28) place this galaxy in the intermediate regime between the Oosterhoff types. From their position on the period–luminosity diagram and light-curve morphology, we can unambiguously classify 25 and 14 Cepheids as fundamental and FO mode pulsators, respectively. Another two are clearly second-overtone Cepheids, the first ones to be discovered beyond the Magellanic Clouds. Among the remaining candidate variables, five were classified as δ-Scuti and five as long-period variables. Most of the others are located on the main sequence, the majority of them likely eclipsing binary systems, although some present variations similar to pulsating stars. We estimate the distance to IC 1613 using various methods based on the photometric and pulsational properties of the Cepheids and RR Lyrae stars. The values we find are in very good agreement with each other and with previous estimates based on independent methods. When corrected to a common reddening of E(B − V) = 0.025 and true Large Magellanic Cloud (LMC) distance modulus of (m−M)LMC,0 = 18.515 ± 0.085, we find that all the distance determinations from the literature converge to a common value of (m−M)0 = 24.400 ± 0.014 (statistical) or 760 kpc. The parallel WFPC2 field, which lies within three core radii, was also searched for variable stars. We discovered nine RR Lyrae stars (four RRab, four RRc, and one RRd) and two Cepheids, even though the lower signal-to-noise ratio of the observations did not allow us to measure their periods as accurately as for the variables in the ACS field of view. We provide their coordinates and approximate properties for completeness.
Neurophysiological basis of hemodynamic responses in the developing human brain before the time of normal birth

Neurovascular coupling that links neural activity to localized increases in blood flow is essential both for brain function and to prevent tissue injury. In the healthy human brain, this underlies an association between the duration of EEG microstates, which represent coordinated and metastable activation of neuronal ensembles, and increases in hemodynamic activity. However, in early human life it is not clear whether neurovascular coupling is functional as the underlying physiological mechanisms may be too immature to effectively support it. Here, we combined MRI compatible robotics with simultaneous EEG and fMRI data acquisition in 13 preterm infants to assess whether the relationship between neural activity and hemodynamic responses is present in this critical period of early life. Passive sensorimotor stimulation elicited both a distinct sequence of four EEG microstates and a significant rise in the blood oxygen level dependent (BOLD) fMRI signal in the left primary sensorimotor cortex. Furthermore, EEG microstate duration was significantly related to BOLD response amplitude. These results suggest that effective neurovascular coupling is present in the human brain even before the normal time of birth and reveal a complex relationship between EEG and fMRI signals underpinned by patterns of activity across distinct neural ensembles.
The trans-zeatin-type side-chain modification of cytokinins controls rice growth

Cytokinins (CKs), a class of phytohormones with vital roles in growth and development, occur naturally with various side-chain structures, including N6-(Δ2-isopentenyl)adenine-, cis-zeatin- and trans-zeatin (tZ)-types. Recent studies in a model dicot plant Arabidopsis demonstrated that tZ-type CKs are biosynthesized via cytochrome P450 monooxygenase (P450) CYP735A, and have a specific function in shoot growth promotion. Although the function of some of these CKs has been demonstrated in a few dicotyledonous plant species, the significance of these variations and their biosynthetic mechanism and function in monocots and in plants with distinctive side-chain profiles than Arabidopsis, such as Oryza sativa (rice), remain elusive. In this study, we characterized CYP735A3 and CYP735A4 to investigate the role of tZ-type CKs in rice. Complementation test of the Arabidopsis CYP735A-deficient mutant and CK profiling of loss-of-function rice mutant, cyp735a3 cyp735a4, demonstrated that CYP735A3 and CYP735A4 encode P450s required for tZ-type side-chain modification in rice. CYP735As are expressed in both roots and shoots. The cyp735a3 cyp735a4 mutants exhibited growth retardation concomitant with reduction in CK activity in both roots and shoots, indicating that tZ-type CKs function in growth promotion of both organs. Expression analysis revealed that tZ-type CK biosynthesis is negatively regulated by auxin, abscisic acid, and cytokinin and positively by dual nitrogen nutrient signals, namely glutamine-related and nitrate-specific signals. These results suggest that the physiological role of tZ-type CKs in rice is different from that in Arabidopsis and they control growth of both roots and shoots in response to internal and environmental cues in rice.
Cell cycle dynamics and window of MUTE action during the terminal division of stomata and ramification of its loss-of-function on the cell cycle of an uncommitted precursor

Plants develop in the absence of cell migration. As such, cell division and differentiation need to be coordinated for functional tissue formation. Cellular valves on the plant epidermis, stomata, are generated through a stereotypical sequence of cell division and differentiation events. In Arabidopsis, three master-regulatory transcription factors, SPEECHLESS (SPCH), MUTE, and FAMA sequentially drive initiation, proliferation, and differentiation of stomata. Among them, MUTE switches the cell cycle mode from proliferative asymmetric division to terminal symmetric division and orchestrates the execution of the single symmetric division event. However, it remains unclear to what extent MUTE regulates the expression of cell cycle genes through the symmetric division and whether MUTE accumulation itself is gated by the cell cycle. Here, we show that MUTE directly upregulates the expression of cell cycle components throughout the terminal cell cycle phases of a stomatal precursor, not only the core cell cycle engines but also checkpoint regulators. Time-lapse live imaging using the multi-color cell cycle indicator PlaCCI revealed that MUTE accumulates up to the early G2 phase, whereas its successor and direct target, FAMA, accumulates at late G2 through terminal mitosis. In the absence of MUTE, meristemoids fail to differentiate, and their G1 phase elongates as they reiterate asymmetric divisions. Combined, our work provides the framework of cell cycle and master regulatory transcription factors to coordinate a single symmetric cell division, and suggests a mechanism for the eventual cell cycle arrest of an uncommitted stem-cell-like precursor at the G1 phase.
High-resolution profiling of neoantigen-specific T cell receptor activation signatures links moderate stimulation patterns to resilience and sustained tumor control

Neoantigen-specific T cell receptors (neoTCRs) promise a safe, highly personalized therapeutic approach in anti-tumor immunotherapy. Substantial progress has been made regarding their identification whereas detailed functional assessment of single TCR characteristics impacting therapeutic efficacy is lacking. We previously identified and functionally characterized neoTCRs specific for neoepitopes derived from KIF2C and SYTL4 demonstrating differences in functional avidity in a patient with metastatic melanoma. In this work, we now combined single-cell TCR- and RNA-sequencing using stimulated peripheral blood derived CD8+ T cells of this patient and thereby identified two new neoTCRs recognizing the previously identified mutated epitope KIF2CP13L. Analyzing patient-derived neoTCR expressing T cells, we detected distinct activation patterns as a measure for substantial heterogeneity within oligoclonal T cell responses towards neoantigens upon specific ex vivo-restimulation. Moreover, neoTCR-transgenic T cells from healthy donors were employed for detailed in vitro and in vivo fine-characterization focusing on TCR-intrinsic functional patterns. Most importantly, in a xenogeneic mouse model experimentally simulating rechallenge of tumor infiltrating lymphocytes (TILs) after adoptive T cell transfer, we found that T cells expressing neoTCRs with a moderate activation profile provide a stable and more sustained anti-tumor response upon repeated in vivo tumor challenge as compared to neoTCRs with a stronger, burst-like reactivity. These insights have significant implications for engineering TCR-transgenic T cells for therapeutic purposes. One Sentence Summary Combining TCR specificity linked single-cell transcriptomics with in vitro and in vivo characterization of transgenic T cells helps to decipher functional potential and persistence of neoantigen-specific T cell receptors (TCRs) for TCR-transgenic T cell-based adoptive cellular anti-tumor immunotherapy.
Allosteric regulation and crystallographic fragment screening of SARS-CoV-2 NSP15 endoribonuclease

SARS-CoV-2 is the causative agent of COVID-19. The highly conserved viral NSP15 endoribonuclease, NendoU, is a key enzyme involved in viral immune evasion, and a promising target for the development of new classes of antivirals. Yet, the broad variety of recognition sequences, complex assembly and kinetics, and lack of structural complexes hampers the development of new competitive or allosteric inhibitors for this target. Here, we performed enzymatic characterization of NendoU in its monomeric and hexameric form, showing that hexamers are allosteric enzymes with a positive cooperative index of 2. By using cryo-EM at distinct pH’s combined with X-ray crystallography and structural analysis, we demonstrate the potential for NendoU to shift between open and closed states, and assembly in larger supramolecular entities, which might serve as a mechanism of self-regulation. Further, we report results from a large fragment screening campaign against NendoU, revealing multiple new allosteric sites for the development of inhibitors.
Sequencing of monkeypox virus from infected patients reveals viral genomes with APOBEC3‐like editing, gene inactivation, and bacterial agents of skin superinfection

A large outbreak of Monkeypox virus (MPXV) infections has arisen in May 2022 in nonendemic countries. Here, we performed DNA metagenomics using next‐generation sequencing with Illumina or Nanopore technologies for clinical samples from MPXV‐infected patients diagnosed between June and July 2022. Classification of the MPXV genomes and determination of their mutational patterns were performed using Nextclade. Twenty‐five samples from 25 patients were studied. A MPXV genome was obtained for 18 patients, essentially from skin lesions and rectal swabbing. All 18 genomes were classified in clade IIb, lineage B.1, and we identified four B.1 sublineages (B.1.1, B.1.10, B.1.12, B.1.14). We detected a high number of mutations (range, 64−73) relatively to a 2018 Nigerian genome (genome GenBank Accession no. NC_063383.1), which were harbored by a large part of a set of 3184 MPXV genomes of lineage B.1 recovered from GenBank and Nextstrain; and we detected 35 mutations relatively to genome ON563414.3 (a B.1 lineage reference genome). Nonsynonymous mutations occurred in genes encoding central proteins, among which transcription factors and core and envelope proteins, and included two mutations that would truncate a RNA polymerase subunit and a phospholipase d‐like protein, suggesting an alternative start codon and gene inactivation, respectively. A large majority (94%) of nucleotide substitutions were G > A or C > U, suggesting the action of human APOBEC3 enzymes. Finally, >1000 reads were identified as from Staphylococcus aureus and Streptococcus pyogenes for 3 and 6 samples, respectively. These findings warrant a close genomic monitoring of MPXV to get a better picture of the genetic micro‐evolution and mutational patterns of this virus, and a close clinical monitoring of skin bacterial superinfection in monkeypox patients.
The population-level impact of Enterococcus faecalis genetics on intestinal colonisation and extraintestinal infection

Enterococcus faecalis is a commensal pathogenic bacterium commonly found in the human gastrointestinal tract and a cause of opportunistic infections typically associated with multidrug resistance. The E. faecalis genetic changes associated with pathogenicity and extraintestinal infection, particularly through gut-to-bloodstream translocation, are poorly understood. Here, we investigate the E. faecalis genetic signatures associated with intestinal colonisation and extraintestinal infection and infection of hospitalised and non-hospitalised individuals using heritability estimation and a genome-wide association study (GWAS). We analysed 750 whole-genome sequences of faecal and bloodstream E. faecalis isolates from hospitalised patients and non-hospitalised individuals, respectively, predominantly in Europe. We found that E. faecalis infection of individuals depending on their hospitalisation status and extraintestinal infection are heritable traits and that ∼24% and ∼34% of their variation is explained by the considered genetic effects, respectively. Further, a GWAS using linear mixed models did not pinpoint any clear enrichment of individual genetic changes in isolates from different isolation sites and individuals with varying hospitalisation statuses, suggesting that these traits are highly polygenic. Altogether, our findings indicate that E. faecalis infection and extraintestinal infection are influenced by variation in genetic, host, and environmental factors, and ultimately the opportunistic pathogenic lifestyle of this versatile host generalist bacterium. Author summary Enterococcus faecalis is a commensal host generalist bacterium that also causes life-threatening invasive hospital- and community-associated infections usually associated with multidrug resistance globally. Although E. faecalis typically cause opportunistic infections associated with antibiotic use, immunocompromised immune status, and other factors; it also possesses an arsenal of virulence factors crucial for its pathogenicity. Despite this, the relative contribution of these virulence factors and other genetic changes on the pathogenicity of E. faecalis strains remain poorly understood. Here, we investigated whether specific genomic changes in the genomics of E. faecalis isolates influence its pathogenicity – infection of hospitalised and non-hospitalised individuals and the propensity to cause extraintestinal infection and intestinal colonisation, are poorly understood, partly due to the limited availability of well-sampled E. faecalis population genomic datasets. Our findings indicate that E. faecalis genetics partially influence infection of hospitalised and non-hospitalised individuals, and the propensity to cause extraintestinal infection compared to intestinal colonisation, possibly due to gut-to-bloodstream translocation, highlighting the potential substantial role of host and environmental factors, including the gut microbiota, on the opportunistic pathogenic lifestyle of this bacterium.
Mathematical and Negative Information Are Similarly Processed: Pupil Dilation as an Indicator

Background: Emotional perception of math-related information can affect an individual’s attitude and professional choices, especially in the area of science, technology, engineering, and math (STEM) professions. Method: The study compared the processing of math-related words, words with negative emotional valence, and words with neutral valence, using the physiological measure of pupil dilation on a random sample of 30 adults. Pupil responses were examined during a lexical decision task (LDT). We sought to show that exposure to math-related stimuli would cause arousal of the sympathetic system leading to an increase in pupil dilation, similar to that caused by exposure to negative stimuli. Results: pupillary responses were sensitive to words with emotional valence; exposure to math-related words led to increased pupil dilation compared to neutral words; exposure to words with negative valence led to increased pupil dilation compared to neutral words; exposure to math-related words and words with negative valence led to similar pupil dilation. The study concludes math-related textual stimuli lead to increased pupil dilation, similar to negative affective valence textual stimuli. Conclusion: These findings create new possibilities for studying the cognitive and emotional effort required to process math-related information using pupillary response, with implications for researchers, educators, and leaders in the field.
Hearing Aid Use Time Is Causally Influenced by Psychological Parameters in Mildly Distressed Patients with Chronic Tinnitus and Mild-to-Moderate Hearing Loss

Background: Hearing aids (HAs) can improve tinnitus-related distress (TRD) and speech-comprehension (SC) in silence or at 55 dB noise-interference (SC_55 dB) in patients with chronic tinnitus and mild-to-moderate hearing loss. However, the role of HA use time in relation to psychological, audiological, or self-reported tinnitus characteristics is under-investigated. Methods: We examine 177 gender-stratified patients before (t1) and after an intervention comprising binaural DSLchild algorithm-based HA fitting and auditory training (t2) and at a 70-day follow up [t3]. HA use time was retrospectively retrieved (at t2) for the pre-post- and (at t3) post-follow up periods. General linear models investigated HA use time in relation to (1) general audiological, (2) tinnitus-related audiological, (3) tinnitus-related self-report, and (4) distress-related self-report indices before and after treatment, where applicable. Receiver operator characteristic analyses identified optimal HA use time for hereby-mediated treatment changes. Results: At t1 and t2, psychological, but not audiological indices causally influenced prospective HA use time—except for SC_55 dB at t1, which, however, correlated with patients’ anxiety, depressivity, and psychological distress levels. Correlations did not differ between patient subgroups defined by categorical tinnitus-related audiological or self-report indices. HA use time partly mediated treatment-related improvement in TRD, but not SC. Optimal use amounted to 9.5–10.5 h/day. Conclusions: An awareness of psychological influences may help clinicians facilitate HA use and, thereby, TRD improvement with hearing amplification.