Miracle-dz/UniFAR-FTUs huggingface dataset:
Coherence factors beyond the BCS result

The dynamics of BCS (Bardeen-Cooper-Schrieffer) superconductors is fairly well understood due to the availability of a mean-field solution for the pairing Hamiltonian, a solution which gives the quantum state of a superconductor as a state of almost-free fermions interacting only with a condensate. As a result, transition probabilities may be computed, and expressed in terms of matrix elements of electron creation and annihilation operators between approximate eigenstates. These matrix elements are also called ``coherence factors. '' Mean-field theory is however not sufficient to describe all eigenstates of a superconductor, a deficiency which is hardly important in (or very close to) equilibrium, but one that becomes relevant in certain out-of-equilibrium situations. We report here on a computation of matrix elements (coherence factors) for the pairing Hamiltonian between any ``two-arc'' eigenstates in the thermodynamic limit.
LOCAL SIMULATIONS OF THE MAGNETOROTATIONAL INSTABILITY IN CORE-COLLAPSE SUPERNOVAE

Bearing in mind the application of core-collapse supernovae, we study the nonlinear properties of the magnetorotational instability (MRI) by means of three-dimensional simulations in the framework of a local shearing box approximation. By systematically changing the shear rates that symbolize the degree of differential rotation in nascent proto-neutron stars (PNSs), we derive a scaling relation between the turbulent stress sustained by the MRI and the shear-vorticity ratio. Our parametric survey shows a power-law scaling between the turbulent stress (〈〈wtot〉〉) and the shear-vorticity ratio (gq) as 〈〈wtot〉〉∝gδq with an index of δ ∼ 0.5. The MRI-amplified magnetic energy has a similar scaling relative to the turbulent stress, while the Maxwell stress has a slightly smaller power-law index (∼0.36). By modeling the effect of viscous heating rates from MRI turbulence, we show that the stronger magnetic fields, or the larger shear rates initially imposed, lead to higher dissipation rates. For a rapidly rotating PNS with a spin period in milliseconds and with strong magnetic fields of 1015 G, the energy dissipation rate is estimated to exceed 1051 erg s−1. Our results suggest that the conventional magnetohydrodynamic (MHD) mechanism of core-collapse supernovae is likely to be affected by MRI-driven turbulence, which we speculate, on the one hand, could harm the MHD-driven explosions due to the dissipation of the shear rotational energy at the PNS surface; or, on the other hand, its energy deposition might be potentially favorable for the working of the neutrino-heating mechanism.
Indirect Imaging of Cataclysmic Variable Stars

Cataclysmic variable stars (CVs) are compact binaries consisting of a white dwarf, a late main-sequence star and an accretion structure. Due to their distance, their apparent sizes are too small to allow direct imaging. Their short orbital periods of 1 to 10 hours allow the usage of indirect imaging or mapping methods which base on different observing angles to the observed object.I developed, analyzed, and applied three new mapping methods for CVs. The first two of these basically do a forward synthesis of light curves of magnetic systems. The third method uses spectra of either accretion disk or magnetic systems. These synthetic data are modified until the light curves or spectra fit to the observed data. The fitting algorithm uses an evolution strategy for the optimization process.My eclipse mapping method for magnitic CVs is applied to UV data of UZ For taken with the Hubble Space Telescope. I extend the eclipse mapping method to use data taken over a full binary star orbit. This approach is applied to optical data of another magnetic CV system, HU Aqr. For the third mapping method add spectral resolution as a second dimension to the dataset. I apply the spectral fitting method, which I dubbed "orbital mapping", to two non-magnetic CVs: With data of the newly discovered HS0455+83, an SW Sex system, I try to substantiate the stream overflow model of this subtype of CVs. The SU UMa System V436 Cen is analyzed for the radial intensity gradient in the accretion disk and absorption signatures which cannot be explained by a simple disk model.A short description of the CVcat project - a database on CVs - is given in the appendix.
Complete Genome Sequence of the Uropathogenic Methicillin-Resistant Staphylococcus aureus Strain MRSA-1369

MRSA-1369 is a uropathogenic methicillin-resistant Staphylococcus aureus (MRSA) strain. Here, we present the complete genome sequence of MRSA-1369, which consists of one chromosome (2.87 Mb) and two plasmids (16.68 kb and 3.13 kb). This will serve as a reference genome for future Staphylococcus aureus pathogenesis and multiomic studies. ABSTRACT MRSA-1369 is a uropathogenic methicillin-resistant Staphylococcus aureus (MRSA) strain. Here, we present the complete genome sequence of MRSA-1369, which consists of one chromosome (2.87 Mb) and two plasmids (16.68 kb and 3.13 kb). This will serve as a reference genome for future Staphylococcus aureus pathogenesis and multiomic studies.
Endovascular Aorto-Iliac Reconstruction vs. Aortobifemoral Bypass as First Choice for a Durable Revascularization for Aorto-Iliac Occlusive Disease

Introduction Aortoiliac occlusive disease (AIOD) is defined as atherosclerotic obstruction of the distal abdominal aorta and iliac arteries. Multiple options exist for management of AIOD including endovascular aortoiliac reconstruction and aortobifemoral bypass. As new technologies are developed, the best approach to manage this condition is evolving. Methods We performed a literature review to assess the current state of endovascular aortoiliac reconstruction and aortobifemoral bypass as options for revascularization of aortoiliac occlusive disease. Conclusion Endovascular aortoiliac reconstruction and aortobifemoral bypass are both feasible and clinically effective options for management of aortoiliac occlusive disease. No randomized controlled trial has been performed to show one option to be more effective than the other. Recent literature demonstrates comparable long-term patency, limb salvage and survival among endovascular approaches to the treatment of AIOD with quicker recovery, lower costs and improved quality of life when compared to open aortobifemoral bypass (ABF) surgery. Selection of procedure should be tailored to the individual patient in order to develop an effective long-term successful strategy for management of aortoiliac occlusive disease. Further study is warranted to define durability of these endovascular approaches as well as patient specific characteristics that influence outcomes.
In2O3 nanowires as chemical sensors

We present an approach to use individual In2O3 nanowire transistors as chemical sensors working at room temperature. Upon exposure to a small amount of NO2 or NH3, the nanowire transistors showed a decrease in conductance up to six or five orders of magnitude and also substantial shifts in the threshold gate voltage. These devices exhibited significantly improved chemical sensing performance compared to existing solid-state sensors in many aspects, such as the sensitivity, the selectivity, the response time, and the lowest detectable concentrations. Furthermore, the recovery time of our devices can be shortened to just 30 s by illuminating the devices with UV light in vacuum.
Savanna vegetation increase triggers freshwater community shifts

Tropical savannas are globally extensive and ecologically invaluable ecosystems. As most ecosystems however, they are subject to serious anthropogenic stress. Defaunation, and especially the loss of large mammals, is pervasive in tropical savannas and known to trigger wide‐ranging ecological effects, from vegetation changes to the loss of ecosystem function. Despite what is currently known about the terrestrial consequences of defaunation, and the potential cross‐ecosystem influence of large mammals, virtually no research has investigated associated effects on small adjacent water bodies. This research gap persists because (1) tropical savannas have been historically neglected, (2) the ecological value of small water bodies (e.g. ponds) is only recently being recognized, and (3) empirical baseline data are often lacking. In this paper, we compared a rare pre‐change dataset with newly collected data on 213 freshwater assemblages, to investigate community structure and composition before and after a major defaunation event. Our research focused on a diverse species assemblage of amphibian larvae (i.e. tadpoles) in temporary savanna ponds. We found that pond vegetation cover increased from 16.0% to 45.6% post‐defaunation, that is, a near three‐fold increase. Such habitat changes seemed to have benefitted those species that use vegetation during reproduction (e.g. the leaf‐folding Afrixalus spp.), while others have declined. Interestingly, we found a strong correlation between tadpole community shifts and other freshwater organisms, which indicates that habitat changes have affected a wide variety of aquatic organisms. Given that organisms inhabiting temporary aquatic habitats often have complex life histories with terrestrial adult life stages, we propose that the terrestrial effects of defaunation have indirectly led to distinct aquatic communities, in addition to direct habitat effects. These results shed new light on the potential role of large‐bodied mammals in shaping adjacent ecosystems, and raise important questions concerning the functioning of temporary aquatic systems in the Anthropocene.
Mapping hippocampal glutamate in mesial temporal lobe epilepsy with glutamate weighted CEST (GluCEST) imaging

Temporal lobe epilepsy (TLE) is one of the most common subtypes of focal epilepsy, with mesial temporal sclerosis (MTS) being a common radiological and histopathological finding. Accurate identification of MTS during presurgical evaluation confers an increased chance of good surgical outcome. Here we propose the use of glutamate‐weighted chemical exchange saturation transfer (GluCEST) magnetic resonance imaging (MRI) at 7 Tesla for mapping hippocampal glutamate distribution in epilepsy, allowing to differentiate lesional from non‐lesional mesial TLE. We demonstrate that a directional asymmetry index, which quantifies the relative difference between GluCEST contrast in hippocampi ipsilateral and contralateral to the seizure onset zone, can differentiate between sclerotic and non‐sclerotic hippocampi, even in instances where traditional presurgical MRI assessments did not provide evidence of sclerosis. Overall, our results suggest that hippocampal glutamate mapping through GluCEST imaging is a valuable addition to the presurgical epilepsy evaluation toolbox.
Hospital Variation of Spironolactone Use in Patients Hospitalized for Heart Failure in China—The China PEACE Retrospective Heart Failure Study

Background Although aldosterone antagonists improve outcomes in select individuals with heart failure and reduced ejection fraction, studies in the United States have raised concerns about underuse and overuse. Variations in the prescription of aldosterone antagonist in China are unknown. Methods and Results In the multicenter, hospital‐based, retrospective China PEACE (China Patient‐Centered Evaluative Assessment of Cardiac Events) study, we identified a nationally representative cohort of admissions for heart failure in a nationally representative sample of Chinese hospitals in 2015. Patients were classified into 1 of 3 groups according to their eligibility for spironolactone—“ideal” (left ventricular ejection fraction <40% and without contraindications), “contraindicated” (a documented contraindication, irrespective of left ventricular ejection fraction), and “uncertain‐benefit” (all others). We measured hospital variation of spironolactone prescriptions at discharge in the “ideal” and “contraindicated” group and calculated the median odds ratio (MOR), a measure of institution‐level variation for 2 individuals with similar characteristics discharged at 2 randomly selected hospitals. Hospital characteristics associated with spironolactone use were identified using multivariable linear regression model. Among 1222 ideal patients from 97 hospitals, the median rate of spironolactone prescription was 78.6% (interquartile range [IQR], 42.8%–89.6% [range, 0%–100%], MOR, 3.4 [95% CI, 2.7–4.0]) at discharge. Among 900 contraindicated patients from 83 hospitals, the median rate of spironolactone prescription was 30.0% (IQR, 9.1%–50.0% [range, 0%–100%], MOR, 3.1 [95% CI, 2.4–3.9]) at discharge. Hospitals with independent departments of cardiology and located in Eastern China were associated with a 38.0% (95% CI, 18.7–57.3; P<0.001) and a 14.6% (95% CI, 2.3%–26.9%; P=0.020) higher rate of spironolactone use for ideal patients. Conclusions In this national study of hospitals in China, the use of spironolactone among ideal patients and the inappropriate use of spironolactone among patients with contraindications was substantial, with rates that varied markedly by institution. Registration URL: https://www.clinicaltrials. gov. Unique identifier: NCT02877914.
Cervimycin-Resistant Staphylococcus aureus Strains Display Vancomycin-Intermediate Resistant Phenotypes

Staphylococcus aureus is a frequent cause of infections in both the community and hospital setting. Resistance development of S. aureus to various antibiotics is a severe problem for the treatment of this pathogen worldwide. ABSTRACT Resistance to antibiotics is an increasing problem and necessitates novel antibacterial therapies. The polyketide antibiotics cervimycin A to D are natural products of Streptomyces tendae HKI 0179 with promising activity against multidrug-resistant staphylococci and vancomycin-resistant enterococci. To initiate mode of action studies, we selected cervimycin C- and D-resistant (CmR) Staphylococcus aureus strains. Genome sequencing of CmR mutants revealed amino acid exchanges in the essential histidine kinase WalK, the Clp protease proteolytic subunit ClpP or the Clp ATPase ClpC, and the heat shock protein DnaK. Interestingly, all characterized CmR mutants harbored a combination of mutations in walK and clpP or clpC. In vitro and in vivo analyses showed that the mutations in the Clp proteins abolished ClpP or ClpC activity, and the deletion of clpP rendered S. aureus but not all Bacillus subtilis strains cervimycin-resistant. The essential gene walK was the second mutational hotspot in the CmR S. aureus strains, which decreased WalK activity in vitro and generated a vancomycin-intermediate resistant phenotype, with a thickened cell wall, a lower growth rate, and reduced cell lysis. Transcriptomic and proteomic analyses revealed massive alterations in the CmR strains compared to the parent strain S. aureus SG511, with major shifts in the heat shock regulon, the metal ion homeostasis, and the carbohydrate metabolism. Taken together, mutations in the heat shock genes clpP, clpC, and dnaK, and the walK kinase gene in CmR mutants induced a vancomycin-intermediate resistant phenotype in S. aureus, suggesting cell wall metabolism or the Clp protease system as primary target of cervimycin. IMPORTANCE Staphylococcus aureus is a frequent cause of infections in both the community and hospital setting. Resistance development of S. aureus to various antibiotics is a severe problem for the treatment of this pathogen worldwide. New powerful antimicrobial agents against Gram-positives are needed, since antibiotics like vancomycin fail to cure vancomycin-intermediate resistant S. aureus (VISA) and vancomycin-resistant enterococci (VRE) infections. One candidate substance with promising activity against these organisms is cervimycin, which is an antibiotic complex with a yet unknown mode of action. In our study, we provide first insights into the mode of action of cervimycins. By characterizing cervimycin-resistant S. aureus strains, we revealed the Clp system and the essential kinase WalK as mutational hotspots for cervimycin resistance in S. aureus. It further emerged that cervimycin-resistant S. aureus strains show a VISA phenotype, indicating a role of cervimycin in perturbing the bacterial cell envelope.
A high-quality genome assembly of Lactarius hatsudake strain JH5

Abstract Lactarius hatsudake is a species of Lactarius commonly found in pine forests, is edible with a delicious and nutritious fruiting body, and exhibits medicinal properties. It is an ideal natural multifunctional food with bioactive components including fungal polysaccharides, crude fiber, unsaturated fatty acids, nucleic acid derivatives, various amino acids, and vitamins. However, biological and genomic analyses of this mycorrhizal mushroom are sparse, thereby hindering large-scale cultivation. Previously, we isolated and screened L. hatsudake JH5 strains and have applied our garnered knowledge to the large-scale cultivation of mycorrhizal seedlings. In this study, we produced a high-quality genome assembly of L. hatsudake JH5 by combining Illumina paired-end and PacBio single molecule real-time sequencing, resulting in PacBio single molecule real-time reads of 7.67 Gb and Illumina Pair-End reads of 1,560 Mb. Based on the distribution of k-mer frequencies, the genome size of this strain was estimated to be 63.84 Mb (1.14% heterozygosity). Based on de novo genome assembly, the final genome size was determined to be 76.7 Mb, with scaffold N50 of 223.2 kb and N90 of 54.5 kb, and a GC content of 54.38%. BUSCO assessment showed that genome completeness was 89.0%. The N50 length of the JH5 genome was 43.6% longer than that of the previously published L. hatsudake MG20 genome. This high-quality L. hatsudake genome assembly will facilitate research on the functional genome, molecular breeding, yield enhancement, and sustainability of L. hatsudake cultivation.
Ultrasound Imaging With a Flexible Probe Based on Element Array Geometry Estimation Using Deep Neural Network

Conventionally, ultrasound (US) diagnosis is performed using hand-held rigid probes. Such devices are difficult to be used for long-term monitoring because they need to be continuously pressed against the body to remove the air between the probe and body. Flexible probes, which can deform and effectively adhere to the body, are a promising technology for long-term monitoring applications. However, owing to the flexible element array geometry, the reconstructed image becomes blurred and distorted. In this study, we propose a flexible probe U.S. imaging method based on element array geometry estimation from radio frequency (RF) data using a deep neural network (DNN). The input and output of the DNN are the RF data and parameters that determine the element array geometry, respectively. The DNN was first trained from scratch with simulation data and then fine-tuned with in vivo data. The DNN performance was evaluated according to the element position mean absolute error (MAE) and the reconstructed image quality. The reconstructed image quality was evaluated with peak-signal-to-noise ratio (PSNR) and mean structural similarity (MSSIM). In the test conducted with simulation data, the average element position MAE was 0.86 mm, and the average reconstructed image PSNR and MSSIM were 20.6 and 0.791, respectively. In the test conducted with in vivo data, the average element position MAE was 1.11 mm, and the average reconstructed image PSNR and MSSIM were 19.4 and 0.798, respectively. The average estimation time was 0.045 s. These results demonstrate the feasibility of the proposed method for long-term real-time monitoring using flexible probes.
Predictors of Discussing Lung Cancer Screening with a Health Care Provider Among Current and Former Smokers in HINTS: A Secondary Data Analysis

Introduction Lung cancer screening is greatly underutilized among those who may benefit from early detection. Methods We analysed data from a subsample (n = 929) of the 2020 Health Information National Trends Survey. We tested multivariable logistic regression models of associations of cancer worry, information insufficiency, and perceived information gathering capacity with reports of having discussed lung cancer screening with a health care provider. Results Among former smokers, no factors were associated significantly with lung cancer screening information seeking. However, for current smokers, extreme cancer worry was positively and significantly associated with having discussed lung cancer screening with a health care provider (OR: 12.95; 95% CI: 2.11, 79.39). Conclusion To increase uptake of lung cancer screening, public health campaigns and healthcare providers will face the dual challenge of increasing perceived need for screening among former smokers while directing current smokers with high levels of worry to see the benefits of early detection.
Theory of noise suppression in Λ -type quantum memories by means of a cavity

Quantum memories, capable of storing single photons or other quantum states of light, to be retrieved on demand, offer a route to large-scale quantum information processing with light. A promising class of memories is based on far-off-resonant Raman absorption in ensembles of Λ-type atoms. However, at room temperature these systems exhibit unwanted four-wave mixing, which is prohibitive for applications at the single-photon level. Here, we show how this noise can be suppressed by placing the storage medium inside a moderate-finesse optical cavity, thereby removing the main roadblock hindering this approach to quantum memory.
Facilitating early parent-infant emotional connection improves cortical networks in preterm infants

Exposure to environmental adversities during early brain development, such as preterm birth, can affect early brain organization. Here, we studied whether development of cortical activity networks in preterm infants may be improved by a multimodal environmental enrichment via bedside facilitation of mother-infant emotional connection. We examined functional cortico-cortical connectivity at term age using high-density electroencephalography recordings in infants participating in a randomized controlled trial of Family Nurture Intervention (FNI). Our results identify several large-scale, frequency-specific network effects of FNI, most extensively in the alpha frequency in fronto-central cortical regions. The connectivity strength in this network was correlated to later neurocognitive performance, and it was comparable to healthy term-born infants rather than the infants receiving standard care. These findings suggest that preterm neurodevelopmental care can be improved by a biologically driven environmental enrichment, such as early facilitation of direct human connection. Description Bedside facilitation of human emotional contact improves development of preterm cortical activity. Promoting human connection Early brain development in preterm births occurs while babies are in neonatal intensive care unit. Exposure to this unnatural environment can affect brain network organization. Here, Yrjola et al. tested whether bedside facilitation of mother-infant connection in preterm babies could affect brain network organization and cognitive performance later in life. Engagement of mothers and their preterm infants in intimate sensory interactions affected cortical network activity at multiple frequencies, prevented some of the abnormalities seen in preterm infants, and improved cognitive performance later during childhood. The results suggest that promoting human connection can have beneficial effects on brain development in preterm babies.