julilili42/papers huggingface dataset:
Differences in childhood stress between Neanderthals and early modern humans as reflected by dental enamel growth disruptions
2024-01-08

<title>Abstract</title> Neanderthals’ lives historically portrayed as highly stressful, shaped by constant pressures to survive in harsh ecological conditions, thus potentially contributing to their extinction. Recent work has challenged this interpretation, leaving the issue of stress among Paleolithic populations highly contested and warranting in-depth examination. Here, we analyze the frequency of dental enamel hypoplasia, a physiological stress induced pathology, in the largest sample of Neanderthal and Upper Paleolithic dentitions investigated to date. To track potential species-specific patterns in the ontogenetic distribution of childhood stress, we present the first comprehensive Bayesian modelling of the likelihood of occurrence of individual and matched enamel growth disruptions throughout ontogeny. Our findings support similar overall stress levels in both groups but reveal species-specific patterns in its ontogenetic distribution. While Neanderthal children faced increasing stress starting with the weaning process and culminating in intensity post-weaning, physiological stress in Upper Paleolithic children was found to be limited to the period of weaning and substantially dropping right after its completion. These results might, at least in part, reflect differences in childcare or other behavioral strategies between the two taxa, including those that were advantageous for modern humans’ long-term survival.
Role of the repeat expansion size in predicting age of onset and severity in RFC1 disease
2024-01-09

Abstract RFC1 disease, caused by biallelic repeat expansion in RFC1, is clinically heterogeneous in terms of age of onset, disease progression and phenotype. We investigated the role of the repeat size in influencing clinical variables in RFC1 disease. We also assessed the presence and role of meiotic and somatic instability of the repeat. In this study, we identified 553 patients carrying biallelic RFC1 expansions and measured the repeat expansion size in 392 cases. Pearson’s coefficient was calculated to assess the correlation between the repeat size and age at disease onset. A Cox model with robust cluster standard errors was adopted to describe the effect of repeat size on age at disease onset, on age at onset of each individual symptoms, and on disease progression. A quasi-Poisson regression model was used to analyse the relationship between phenotype and repeat size. We performed multivariate linear regression to assess the association of the repeat size with the degree of cerebellar atrophy. Meiotic stability was assessed by Southern blotting on first-degree relatives of 27 probands. Finally, somatic instability was investigated by optical genome mapping on cerebellar and frontal cortex and unaffected peripheral tissue from four post-mortem cases. A larger repeat size of both smaller and larger allele was associated with an earlier age at neurological onset [smaller allele hazard ratio (HR) = 2.06, P &amp;lt; 0.001; larger allele HR = 1.53, P &amp;lt; 0.001] and with a higher hazard of developing disabling symptoms, such as dysarthria or dysphagia (smaller allele HR = 3.40, P &amp;lt; 0.001; larger allele HR = 1.71, P = 0.002) or loss of independent walking (smaller allele HR = 2.78, P &amp;lt; 0.001; larger allele HR = 1.60; P &amp;lt; 0.001) earlier in disease course. Patients with more complex phenotypes carried larger expansions [smaller allele: complex neuropathy rate ratio (RR) = 1.30, P = 0.003; cerebellar ataxia, neuropathy and vestibular areflexia syndrome (CANVAS) RR = 1.34, P &amp;lt; 0.001; larger allele: complex neuropathy RR = 1.33, P = 0.008; CANVAS RR = 1.31, P = 0.009]. Furthermore, larger repeat expansions in the smaller allele were associated with more pronounced cerebellar vermis atrophy (lobules I–V β = −1.06, P &amp;lt; 0.001; lobules VI–VII β = −0.34, P = 0.005). The repeat did not show significant instability during vertical transmission and across different tissues and brain regions. RFC1 repeat size, particularly of the smaller allele, is one of the determinants of variability in RFC1 disease and represents a key prognostic factor to predict disease onset, phenotype and severity. Assessing the repeat size is warranted as part of the diagnostic test for RFC1 expansion.
The history, systematics, and nomenclature of Thalattosuchia (Archosauria: Crocodylomorpha)
2024-01-09

Abstract The use of more than one nomenclatural code is becoming increasingly common in some biological sub-disciplines. To minimize nomenclatural instability, we have decided to establish a higher level systematization for Thalattosuchia under both the International Code of Phylogenetic Nomenclature (‘PhyloCode’) and the International Code of Zoological Nomenclature (‘Zoological Code’). We undertook a series of phylogenetic analyses with an expanded dataset to examine the origins of Thalattosuchia within Crocodylomorpha, and determined the clade’s diagnostic characters. Based on these analyses, we provide updated diagnoses for Thalattosuchia and its subclades under both the PhyloCode and Zoological Code. We also introduce two new nomina that are regulated under the PhyloCode (Neothalattosuchia and Euthalattosuchia), and the nomen Dakosaurina, which is registered under both nomenclatural codes. Moreover, we introduce PhyloCode-compliant phylogenetic definitions for Thalattosuchia and its subclades. As we cannot reliably discriminate between the positional hypotheses for Thalattosuchia within Crocodylomorpha, the clades’ origins are as much of a mystery today as they were over a century ago. However, we hope that using the same diagnostic characters to define the same clades, with the same nomina, under both nomenclatural codes will be an example to others to follow.
Deep learning‐accelerated image reconstruction in MRI of the orbit to shorten acquisition time and enhance image quality
2024-01-09

Abstract Background and Purpose This study explores the use of deep learning (DL) techniques in MRI of the orbit to enhance imaging. Standard protocols, although detailed, have lengthy acquisition times. We investigate DL‐based methods for T2‐weighted and T1‐weighted, fat‐saturated, contrast‐enhanced turbo spin echo (TSE) sequences, aiming to improve image quality, reduce acquisition time, minimize artifacts, and enhance diagnostic confidence in orbital imaging. Methods In a 3‐Tesla MRI study of 50 patients evaluating orbital diseases from March to July 2023, conventional (TSE S ) and DL TSE sequences (TSE DL ) were used. Two neuroradiologists independently assessed the image datasets for image quality, diagnostic confidence, noise levels, artifacts, and image sharpness using a randomized and blinded 4‐point Likert scale. Results TSE DL significantly reduced image noise and artifacts, enhanced image sharpness, and decreased scan time, outperforming TSE S ( p &lt; .05). TSE DL showed superior overall image quality and diagnostic confidence, with relevant findings effectively detected in both DL‐based and conventional images. In 94% of cases, readers preferred accelerated imaging. Conclusion The study proved that using DL for MRI image reconstruction in orbital scans significantly cut acquisition time by 69%. This approach also enhanced image quality, reduced image noise, sharpened images, and boosted diagnostic confidence.
Aminopyrimidine Derivatives as Multiflavivirus Antiviral Compounds Identified from a Consensus Virtual Screening Approach
2024-01-09

Around three billion people are at risk of infection by the dengue virus (DENV) and potentially other flaviviruses. Worldwide outbreaks of DENV, Zika virus (ZIKV), and yellow fever virus (YFV), the lack of antiviral drugs, and limitations on vaccine usage emphasize the need for novel antiviral research. Here, we propose a consensus virtual screening approach to discover potential protease inhibitors (NS3<sup>pro</sup>) against different flavivirus. We employed an <i>in silico</i> combination of a hologram quantitative structure-activity relationship (HQSAR) model and molecular docking on characterized binding sites followed by molecular dynamics (MD) simulations, which filtered a data set of 7.6 million compounds to 2,775 hits. Lastly, docking and MD simulations selected six final potential NS3<sup>pro</sup> inhibitors with stable interactions along the simulations. Five compounds had their antiviral activity confirmed against ZIKV, YFV, DENV-2, and DENV-3 (ranging from 4.21 ± 0.14 to 37.51 ± 0.8 μM), displaying aggregator characteristics for enzymatic inhibition against ZIKV NS3<sup>pro</sup> (ranging from 28 ± 7 to 70 ± 7 μM). Taken together, the compounds identified in this approach may contribute to the design of promising candidates to treat different flavivirus infections.
Ultra-processed foods consumption, depression, and the risk of diabetes complications in the CARTaGENE project: a prospective cohort study in Quebec, Canada
2024-01-09

Introduction This study aimed to assess the association between depression, ultra-processed food consumption (UPFs), and the risk of developing diabetes-specific complications in adults with type 2 diabetes (T2D). Methods Baseline data came from the CARTaGENE study, a health survey of adults (40–69 years) in Quebec, Canada. The incidence of T2D complications was examined in N= 683 participants with T2D without complications at baseline by linking survey data with administrative health data. Food and drink consumption was assessed using the Canadian Diet History Questionnaire and categorized by NOVA classification. Participants were categorized into tertiles of UPFs consumption. Depression was defined as having elevated depressive symptoms based on the Patient Health Questionnaire-9 or the use of antidepressant medications. Cox regression models were used to estimate the associations between UPFs, depression, and T2D complications. Results In total, 105 individuals developed diabetes-related complications over a 7-year period. Participants with high depressive symptoms and high UPFs consumption had the highest risk for diabetes complications (adjusted hazard ratio (aHR) 2.07, 95% CI: 0.91 – 4.70), compared to participants with low depressive symptoms and low UPFs consumption. Higher risks for diabetes complications were observed when high depressive symptoms and antidepressant use were combined with high UPFs consumption (aHR 2.59, 95% CI: 1.32 – 5.06). Conclusion This study indicates that those with co-occurring depression and high UPFs consumption have a greater risk of diabetes complications. Early management and monitoring of both risk factors might be essential to prevent diabetes complications.
Single versus Combination Treatment in Tinnitus: An International, Multicentre, Parallel-arm, Superiority, Randomised Controlled Trial
2024-01-09

Abstract Tinnitus is associated with a variety of aetiologies, phenotypes, and underlying pathophysiological mechanisms, and available treatments have limited efficacy. A combination of treatments, addressing various aspects of tinnitus, might provide a viable and superior treatment strategy. In this international multicentre, parallel-arm, superiority, randomised controlled trial, patients with chronic subjective tinnitus were recruited from five clinical sites across the EU as part of the interdisciplinary collaborative UNITI project. Patients were randomly assigned using a web-based system, stratified by their hearing and distress level, to single or combination treatment of 12 weeks. Cognitive-behavioural therapy, hearing aids, structured counselling, and sound therapy were administered either alone or as a combination of two treatments resulting in ten treatment arms. The primary outcome was the difference in the change from baseline to week 12 in the total score of the Tinnitus Handicap Inventory (THI) between single and combination treatments in the intention-to-treat population. All statistical analysis were performed blinded to treatment allocation. 674 patients of both sexes aged between 18 and 80 years were screened for eligibility. 461 participants (190 females) with chronic subjective tinnitus and at least mild tinnitus handicap were enrolled, 230 of which were randomly assigned to single and 231 to combination treatment. Least-squares mean changes from baseline to week 12 were -11.7 for single treatment (95% confidence interval [CI], -14.4 to -9.0) and -14.9 for combination treatments (95% CI, -17.7 to -12.1), with a statistically significant group difference ( p =0.034). Cognitive-behavioural therapy and hearing aids alone had large effect sizes, which could not be further increased by combination treatment. No serious adverse events occurred. In this trial involving patients with chronic tinnitus, all treatment arms showed improvement in THI scores from baseline to week 12. Combination treatments showed a stronger clinical effect than single treatment, however, no clear synergistic effect was observed when combining treatments. We observed rather a compensatory effect, where a more effective treatment offsets the clinical effects of a less effective treatment. ClinicalTrials.gov Identifier: NCT04663828 .
Efficient Energy Transfer and Singlet Fission in Co‐Deposited Thin Films of Pentacene and Anthradithiophene
2024-01-09

Abstract Co‐deposited molecular heterostructures with statistical intermixing of the constituents are attractive candidates to tune the optical and the transport properties, as well as the ability to promote photophysical processes like singlet fission. In order to comprehend and control the singlet fission mechanism in these systems, it is of utmost interest to study the underlying excited state dynamics. In this work, thin films of anthradithiophene blended with the efficient singlet fission material pentacene are investigated by means of time‐resolved and temperature‐dependent photoluminescence spectroscopy with a time resolution of a few picoseconds. The analysis of the photoluminescence dynamics points toward efficient funneling of excitons from anthradithiophene via isolated pentacene molecules to agglomerates of pentacene, where eventually singlet fission occurs. The efficient and largely temperature‐independent quenching of the luminescence in anthradithiophene is attributed to a favorable cascade‐like alignment of the energy levels, and it is hypothesized that Förster resonance energy transfer is the main driving mechanism for exciton transport to pentacene agglomerates. The system investigated here can serve as a blueprint for the design of other molecular heterostructures with spatially separated light harvesting and singlet fission regions.
Discussing trust and resilience: The need for a healthy dose of distrust
2024-01-09

Abstract How are trust and reslience related? There is a lack of conceptual discussions. This paper analyzes trust and resilience with respect to the system of critical infrastructures and engineers working on critical infrastructure resilience. The results are three findings based on the assumption that resilience and trust are mechanisms to cope with complexity and uncertainty inherent to modern societies and critical infrastructures. First, they are no functional alternatives. Trust is an everyday process where favorable expectations help to act “as if” uncertainty was successfully resolved. Resilience helps to cope in “what if” cases when disaster strikes. Second, resembling the risk perception paradox, too much trust in critical infrastructures might lead to complacency, decreasing individual coping capacities and subsequently resilience. People need a healthy dose of distrust—distrust being a functional alternative to trust and not its opposite—to be aware that a disruption might happen and prepare for it. Third, notwithstanding the difficulties of uncertainty communication, engineers need to communicate limits to knowledge resulting from complexity transparently. This might decrease trust in specific solutions, but could sustain overall system trust, because it helps to adjust favorable expectations.
Muon Veto of the LEGEND Experiment
2024-01-09

The arge nriched ermanium xperiment for eutrinoless ecay (LEGEND) is an experiment searching for neutrinoless decay of the Ge isotope. LEGEND-1000, with 1000 kg of Ge mass, is designed to reach half-life sensitivity of years. To be sensitive to such a half life, a number of measures are required to reduce background events. \\nFor the current experimental phase LEGEND-200, a Water-Cherenkov-Veto system actively reduces background from radioactive isotopes and cosmic radiation like muons. It uses photomultiplier tubes (PMTs) as light sensors in a water-tank covered with a reflective foil to increase the light yield inside the water volume. \\nThis muon veto has been stably taking data since March 2023. Regular calibration of the PMTs ensures measurements of up to 100 photoelectrons per PMT. A first look on the data of the muon veto shows a stable total muon rate of mHz over two months. A small area of the muon veto directly below the cryostat, called the ''Pillbox'', can increase the detection efficiency of muons in the experiment through determining coincidences between the muon veto and the liquid argon (LAr) instrumentation or High Purity Germanium (HPGe) detectors. It has been demonstrated that of the muon veto PMTs can detect of the coincident muon events. \\nConsidering these results, plans for the improved LEGEND-1000 muon veto are presented, including an optimised PMT distribution.
Polarized High-frequency Wave Propagation Beyond the Nonlinear Schrödinger Approximation
2024-01-09

.This paper studies highly oscillatory solutions to a class of systems of semilinear hyperbolic equations with a small parameter, in a setting that includes Klein–Gordon equations and the Maxwell–Lorentz system. The interest here is in solutions that are polarized in the sense that up to a small error, the oscillations in the solution depend on only one of the frequencies that satisfy the dispersion relation with a given wave vector appearing in the initial wave packet. The construction and analysis of such polarized solutions is done using modulated Fourier expansions. This approach includes higher harmonics and yields approximations to polarized solutions that are of arbitrary order in the small parameter, going well beyond the known first-order approximation via a nonlinear Schrödinger equation. The given construction of polarized solutions is explicit, uses in addition a linear Schrödinger equation for each further order of approximation, and is accessible to direct numerical approximation.Keywordssemilinear high-frequency wave propagationmodulated Fourier expansionsnonlinear polarizationerror analysisMSC codes35A3535B0535B4035L6035Q60
Renormalization of a Standard Model extension with a Dark Abelian Sector and predictions for the W-boson mass
2024-01-09

A bstract The described Dark Abelian Sector Model (DASM) extends the Standard Model (SM) by a “dark” sector containing a spontaneously broken U(1) d gauge group. Keeping this dark sector quite generic we only add one additional Higgs boson, one Dirac fermion, and right-handed SM-like neutrinos to the SM. Using the only two singlet operators of the SM with dimension less than 4 (the U(1) Y field-strength tensor and the SM Higgs mass operator |Φ| 2 ) as well as the right-handed neutrino fields we open up three portals to the dark sector. Dark sectors, such as the one of the DASM, that introduce an additional Higgs boson H as well as an additional Z′ gauge boson can have a large influence on the predictions for electroweak precision observables and even accommodate possible dark matter candidates. We consider one of the two Higgs bosons to be the known 125 GeV Higgs boson and parameterize the extension of the scalar sector by the mass of the second Higgs boson, the Higgs mixing angle, and a Higgs self-coupling. We do not assume any mass hierarchy in the gauge sector and use the mass of the additional Z′ boson and a corresponding gauge-boson mixing angle to parameterize the extension of the gauge sector. The fermion sector is parameterized by the mass of the additional fermion and a fermion mixing angle. We describe an on-shell as well as an <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mover> <mml:mi>MS</mml:mi> <mml:mo> ̄</mml:mo> </mml:mover> </mml:math> renormalization scheme for the DASM sectors and give explicit results for the renormalization constants at the 1-loop level, and, thus, prepare the ground for full NLO predictions for collider observables in the DASM. As a first example, we provide the DASM prediction for the W-boson mass derived from muon decay.
Interplay of As (im)mobilisation processes in groundwater: Learning from hydrochemical investigations
2024-01-09

Millions of people worldwide are exposed to arsenic (As) contaminated groundwater. Despite decades of research and evidence of As mobilisation in anoxic aquifers being caused by reductive dissolution of iron minerals, the mechanisms behind the local scale variability of dissolved As remains unclear. Therefore, the trans-disciplinary AdvectAs project investigates the environmental behaviour and spatial heterogeneity of dissolved As in groundwater in the Red River delta, Vietnam. Here we present the results from hydrochemical and water isotope investigations. In particular, we will show how the large As variability (0.1–510 mg/L) is related to consecutive As (im)mobilisation steps, depending on site hydrology, geology and the interplay of Fe, Mn, S and organic matter cycles. Such complexity of (im)mobilisation processes can be simplified in 5 major hydro(geo) chemical zones, providing a conceptual tool with potential for application at other sites in Asia affected by geogenic As contamination of groundwater.
The possible influence of third-order shim coils on gradient–magnet interactions: an inter-field and inter-site study
2024-01-10

Abstract Objective To assess the possible influence of third-order shim coils on the behavior of the gradient field and in gradient–magnet interactions at 7 T and above. Materials and methods Gradient impulse response function measurements were performed at 5 sites spanning field strengths from 7 to 11.7 T, all of them sharing the same exact whole-body gradient coil design. Mechanical fixation and boundary conditions of the gradient coil were altered in several ways at one site to study the impact of mechanical coupling with the magnet on the field perturbations. Vibrations, power deposition in the He bath, and field dynamics were characterized at 11.7 T with the third-order shim coils connected and disconnected inside the Faraday cage. Results For the same whole-body gradient coil design, all measurements differed greatly based on the third-order shim coil configuration (connected or not). Vibrations and gradient transfer function peaks could be affected by a factor of 2 or more, depending on the resonances. Disconnecting the third-order shim coils at 11.7 T also suppressed almost completely power deposition peaks at some frequencies. Discussion Third-order shim coil configurations can have major impact in gradient–magnet interactions with consequences on potential hardware damage, magnet heating, and image quality going beyond EPI acquisitions.