Miracle-dz/UniFAR-FTUs huggingface dataset:
An Evolved 5′ Untranslated Region of Alfalfa Mosaic Virus Allows the RNA Transport of Movement-Defective Variants

The results obtained in the present work could challenge the view of the role of the virus particle in the systemic transport of plant viruses. In this sense, we show that two different MPs are competent to systemically transport the AMV genome without the requirement of the virus particles, as reported for viruses lacking a CP (e.g., Umbravirus). ABSTRACT Although the coat protein (CP) has a relevant role in the long-distance movement of alfalfa mosaic virus (AMV) and brome mosaic virus (BMV), its precise function is not fully understood. Previous results showed that a specific interaction between the C termini of the movement protein (MP) and the cognate CP is required for systemic transport. Thus, we have performed a compensatory evolution experiment using an AMV RNA3 derivative defective in long-distance transport that carries a BMV MP lacking the C-terminal 48 residues and unable to interact with the AMV CP. After several passages, five independent evolution lineages were able to move long distance. The analysis of the viral RNA of these lineages showed the presence of three different modifications located exclusively at the 5′ untranslated region (5′ UTR). The three evolved 5′ UTR variants accumulated comparable levels of viral RNA and CP but reduced the accumulation of virus particles and the affinity between the 5′ UTR and the AMV CP. In addition, the evolved 5′ UTR increased cell-to-cell transport for both the AMV RNA3 carrying the BMV MP and that carrying the AMV MP. Finally, the evolved 5′ UTRs allowed the systemic transport of an AMV RNA3 carrying a CP mutant defective in virus particles and increased the systemic transport of several AMV RNA3 derivatives carrying different viral MPs associated with the 30K superfamily. Altogether, our findings indicate that virus particles are not required for the systemic transport of AMV but also that BMV MP is competent for the short- and long-distance transport without the interaction with the CP. IMPORTANCE The results obtained in the present work could challenge the view of the role of the virus particle in the systemic transport of plant viruses. In this sense, we show that two different MPs are competent to systemically transport the AMV genome without the requirement of the virus particles, as reported for viruses lacking a CP (e.g., Umbravirus). The incapability of the viral MP to interact with the CP triggered virus variants that evolved to reduce the formation of virus particles, probably to increase the accessibility of the MP to the viral progeny. Our results point to the idea that virus particles would not be necessary for the viral systemic transport but would be necessary for vector virus transmission. This idea is reinforced by the observation that heterologous MPs also increased the systemic transport of the AMV constructs that have reduced encapsidation capabilities.
Practical Training Approaches for Discordant Atopic Dermatitis Severity Datasets: Merging Methods With Soft-Label and Train-Set Pruning

Objective assessment of atopic dermatitis (AD) is essential for choosing proper management strategies. This study investigated the performance of convolutional neural networks (CNN) models in grading the severity of AD. Five board-certified dermatologists independently evaluated the severity of 9,192 AD images. The severity of AD was evaluated based on an Investigator's Global Assessment (IGA) and six signs of AD. For CNN training, we applied three distinct approaches: 1) ensemble vs. integration 2) hard-label vs. soft-label and 3) train-set pruning. For the IGA prediction, the two best models were chosen based on the macro-averaged AUROC and F-1 score. The ensemble–soft-label–pruning model was chosen based on AUROC 0.943, 0.927 for the internal and external validation set respectively, and integration–soft-label–whole dataset model was chosen based on the F1-score 0.750, 0.721 for the internal and external validation set respectively. CNN models trained by multi-evaluator dataset outperformed the models by an individual evaluator dataset, and they performed better to the dataset in which the assessment of dermatologists was concordant. In conclusion, CNN models for AD could be improved by labeled dataset from multiple evaluators, merging methods with soft-label and train-set pruning.
Mixed order parameter symmetries in cuprate superconductors

The recent observation of an inflection point in the temperature dependence of the in-plane magnetic field dependence (λab) is investigated within a two-band model with coupled order parameters of different symmetries. While the dominant order parameter has d-wave symmetry, the smaller one is of s-wave symmetry. Superconductivity is robust in the d-wave channel and induced via interband interactions in the s-wave subsystem.
Spectral evolution of weak bursts from SGR 1806-20 observed with INTEGRAL

We report on bursts from the Soft Gamma-Ray Repeater SGR 1806-20 detected with INTEGRAL in October 2003, during a period of moderate activity of the source. The spectral and temporal properties of 21 short bursts are consistent with those found in previous observations, even if these bursts are among the faintest observed in the 15-200 keV range from this source. During some of the bursts a clear spectral evolution is visible. The data also show, for the first time, evidence for a hardness-intensity anti-correlation within SGR 1806-20 bursts.
The Problem of Purity in Moral Psychology

Academic Abstract The idea of “purity” transformed moral psychology. Here, we provide the first systematic review of this concept. Although often discussed as one construct, we reveal ~9 understandings of purity, ranging from respecting God to not eating gross things. This striking heterogeneity arises because purity—unlike other moral constructs—is not understood by what it is but what it isn’t: obvious interpersonal harm. This poses many problems for moral psychology and explains why purity lacks convergent and divergent validity and why purity is confounded with politics, religion, weirdness, and perceived harm. Because purity is not a coherent construct, it cannot be a distinct basis of moral judgment or specially tied to disgust. Rather than a specific moral domain, purity is best understood as a loose set of themes in moral rhetoric. These themes are scaffolded on cultural understandings of harm—the broad, pluralistic harm outlined by the Theory of Dyadic Morality. Public Abstract People are fascinated by morality—how do people make moral judgments and why do liberals and conservatives seem to frequently disagree? “Purity” is one moral concept often discussed when talking about morality—it has been suggested to capture moral differences across politics and to demonstrate the evolutionary roots of morality, especially the role of disgust in moral judgment. However, despite the many books and articles that mention purity, there is no systematic analysis of purity. Here, we review all existing academic articles focused on purity in morality. We find that purity is an especially messy concept that lacks scientific validity. Because it is so poorly defined and inconsistently measured, it should not be invoked to explain our moral minds or political differences.
The clinical yield of bronchoscopy in the management of cystic fibrosis: A retrospective multicenter study

Pulmonary disease is the leading cause of morbidity and mortality in people with cystic fibrosis (pwCF). Several studies have shown no benefit for bronchoscopy and bronchoalveolar lavage (BAL) over sputum to obtain microbiological cultures, hence the role of bronchoscopy in pwCF is unclear.
Relationship between early neural responses to syntactic and acoustic irregularities in music

Humans can detect various anomalies in a sound sequence without attending to each dimension explicitly. Event‐related potentials (ERPs) have been used to examine the processes of auditory deviance detection. Previous research has shown that music‐syntactic anomalies elicit early right anterior negativity (ERAN), whereas more general acoustic irregularities elicit mismatch negativity (MMN). Although these ERP components occur in a similar latency range with a similar scalp topography, the relationship between the detection processes they reflect remains unclear. This study compared these components by manipulating music‐syntactic (chord progression) and acoustic (intensity) irregularities orthogonally in two experiments. Non‐musicians (Experiment 1: N = 39; Experiment 2: N = 24) were asked to listen to chord sequences, each consisting of 5 four‐voice chords, as they watched a silent video clip. Standard, harmonic‐deviant, intensity‐deviant and double‐deviant chords occurred at the final position in each sequence. Deviant stimuli were presented infrequently (p = .10) in Experiment 1 and equiprobably (p = .25) in Experiment 2. Regardless of deviance probability, both harmonic and intensity deviants elicited similar negativities, which were indistinguishable in terms of latency or scalp distribution. When the two deviant types occurred simultaneously, the negativity increased in an additive manner; that is, the amplitude of the double‐deviant ERP was as large as the sum of the single‐deviant ERPs. These findings suggest that the detection of music‐syntactic and acoustic irregularities works independently, based on different regularity representations.
Tissue response curve‐shape analysis of dynamic glucose‐enhanced and dynamic contrast‐enhanced magnetic resonance imaging in patients with brain tumor

Dynamic glucose‐enhanced (DGE) MRI is used to study the signal intensity time course (tissue response curve) after D‐glucose injection. D‐glucose has potential as a biodegradable alternative or complement to gadolinium‐based contrast agents, with DGE being comparable with dynamic contrast‐enhanced (DCE) MRI. However, the tissue uptake kinetics as well as the detection methods of DGE differ from DCE MRI, and it is relevant to compare these techniques in terms of spatiotemporal enhancement patterns. This study aims to develop a DGE analysis method based on tissue response curve shapes, and to investigate whether DGE MRI provides similar or complementary information to DCE MRI. Eleven patients with suspected gliomas were studied. Tissue response curves were measured for DGE and DCE MRI at 7 T and the area under the curve (AUC) was assessed. Seven types of response curve shapes were postulated and subsequently identified by deep learning to create color‐coded “curve maps” showing the spatial distribution of different curve types. DGE AUC values were significantly higher in lesions than in normal tissue (p < 0.007). Furthermore, the distribution of curve types differed between lesions and normal tissue for both DGE and DCE. The DGE and DCE response curves in a 6‐min postinjection time interval were classified as the same curve type in 20% of the lesion voxels, which increased to 29% when a 12‐min DGE time interval was considered. While both DGE and DCE tissue response curve‐shape analysis enabled differentiation of lesions from normal brain tissue in humans, their enhancements were neither temporally identical nor confined entirely to the same regions. Curve maps can provide accessible and intuitive information about the shape of DGE response curves, which is expected to be useful in the continued work towards the interpretation of DGE uptake curves in terms of D‐glucose delivery, transport, and metabolism.
THE PANCHROMATIC STARBURST IRREGULAR DWARF SURVEY (STARBIRDS): OBSERVATIONS AND DATA ARCHIVE

Understanding star formation in resolved low mass systems requires the integration of information obtained from observations at different wavelengths. We have combined new and archival multi-wavelength observations on a set of 20 nearby starburst and post-starburst dwarf galaxies to create a data archive of calibrated, homogeneously reduced images. Named the panchromatic “STARBurst IRregular Dwarf Survey” archive, the data are publicly accessible through the Mikulski Archive for Space Telescopes. This first release of the archive includes images from the Galaxy Evolution Explorer Telescope (GALEX), the Hubble Space Telescope (HST), and the Spitzer Space Telescope (Spitzer) Multiband Imaging Photometer instrument. The data sets include flux calibrated, background subtracted images, that are registered to the same world coordinate system. Additionally, a set of images are available that are all cropped to match the HST field of view. The GALEX and Spitzer images are available with foreground and background contamination masked. Larger GALEX images extending to 4 times the optical extent of the galaxies are also available. Finally, HST images convolved with a 5″ point spread function and rebinned to the larger pixel scale of the GALEX and Spitzer 24 μm images are provided. Future additions are planned that will include data at other wavelengths such as Spitzer IRAC, ground-based Hα, Chandra X-ray, and Green Bank Telescope H i imaging.
C-reactive protein to albumin ratio predicts for severity of coronary artery disease and ischemia.

OBJECTIVE Myocardial perfusion scintigraphy (MPS) has prognostic importance in demonstrating myocardial ischemia, and the Syntax score (SS) in coronary angiography has prognostic importance in demonstrating the extent of coronary artery disease (CAD). C-reactive protein (CRP) and albumin are prognostic markers for both atherosclerosis and inflammation. In this study, we aimed at investigating the relationship of CRP/albumin ratio (CAR) with the severity of myocardial ischemia and SS in patients with stable CAD. PATIENTS AND METHODS We retrospectively evaluated 355 patients between January 2018 and January 2020. Patients were divided into normal, mild-moderate, and severe ischemia groups according to MPS. SS was classified as low risk (< 32) and high risk (≥ 32) groups. The association between CAR, SS, and MPS findings were analyzed. RESULTS The median CAR level was higher in the high-risk group compared to the low-risk group (20.7 vs. 13.8, p < 0.05), and higher in the low-risk group compared to the normal group (13.8 vs. 7.4, p < 0.05). The increase in CAR level was associated with increased ischemia severity (p < 0.001). Increased CAR level was found to be an independent predictor of both high-risk and severe ischemia (OR = 1.04, p = 0.006; OR = 1.05, p = 0.001, respectively). The cut-off value of CAR > 10.2 was a common point in predicting both low-risk and mild-moderate ischemia (AUC: 0.736, p < 0.001; AUC: 0.741, p < 0.001, respectively). CONCLUSIONS High CAR level was an independent predictor of both the severity of ischemia and the extent of CAD. Therefore, CAR can be a potential screening tool in patients with suspected CAD and in risk stratification.
Radiative properties of multicarrier bound excitons in GaAs

Excitons in semiconductors can have multiple lifetimes due to spin dependent oscillator strengths and interference between different recombination pathways. In addition, strain and symmetry effects can further modify lifetimes via the removal of degeneracies. We present a convenient formalism for predicting the optical properties of ${k=0}$ excitons with an arbitrary number of charge carriers in different symmetry environments. Using this formalism, we predict three distinct lifetimes for the neutral acceptor bound exciton in GaAs, and confirm this prediction through polarization dependent and time-resolved photoluminescence experiments. We find the acceptor bound-exciton lifetimes to be ${T_o (1,3,3/4)}$ where ${T_o = (0.61 \pm 0.12) \text{ns}}$. Furthermore, we provide an estimate of the intra-level and inter-level exciton spin-relaxation rates.
High serum AMH inhibits pathological growth of the low biomass endometrial microbiome.

OBJECTIVE Although host microbiome play a role in both hormonal status and fertility, this issue has not yet been clarified. Since the endometrium is a sterile tissue, it is accepted that microbiota does not grow under normal conditions. The aim of the study was to reveal the characteristics of endometrial microbiota according to serum AMH levels in women with implantation failure. PATIENTS AND METHODS Forty-five women aged 20-30 years with two or more implantation failures were included in the study. They were divided into 3 groups according to their serum AMH values: Group 1 -AMH <1.3 ng/ml; Group 2 - AMH between 1.3-2.6 ng/ml; Group 3 - AMH >2.6 ng/ml. Twenty-two healthy fertile women who were the same age as the infertile group and applied for cervical smear screening were accepted as the control group. Following the embryo transfer, the tip of the catheter was inserted into the transport medium under sterile conditions. Sowing was carried out by touching the tips of the catheter to the blood agar medium. After the evaluation of the petri dishes at the end of 48 hours of incubation, colonies were stained with Gram stain. Microorganisms in the colonies were identified with the Vitek-2 device according to their gram-staining characteristics and their antibiograms were made. RESULTS A negative correlation was detected between low AMH values and the microbiome detection rates in endometrial cultures. In patients with low serum AMH levels, the chance of endometrial microbiota growth was higher in the endometrial culture medium. The most common bacteria were found to be MSSA, MRKNS and lactobacillus. Clinical pregnancy rates were found to be significantly higher in the group with high AMH levels. As AMH levels increased, positive flora detection rates decreased, while clinical pregnancy rates increased. CONCLUSIONS Low serum AMH level increases the rate of positive endometrial microbiome in culture and decreases clinical pregnancy rates.
Emergent transport in a many-body open system driven by interacting quantum baths

We analyze an open many-body system that is strongly coupled at its boundaries to interacting quantum baths. We show that the two-body interactions inside the baths induce emergent phenomena in the spin transport. The system and baths are modeled as independent spin chains resulting in a global nonhomogeneous XXZ model. The evolution of the system-bath state is simulated using matrix-product-states methods. We present two phase transitions induced by bath interactions. For weak bath interactions we observe ballistic and insulating phases. However, for strong bath interactions a diffusive phase emerges with a distinct power-law decay of the time-dependent spin current Q alpha t(-alpha). Furthermore, we investigate long-lasting current oscillations arising from the non-Markovian dynamics in the homogeneous case and find a sharp change in their frequency scaling coinciding with the triple point of the phase diagram.
SkiNet: A deep learning framework for skin lesion diagnosis with uncertainty estimation and explainability

Skin cancer is considered to be the most common human malignancy. Around 5 million new cases of skin cancer are recorded in the United States annually. Early identification and evaluation of skin lesions are of great clinical significance, but the disproportionate dermatologist-patient ratio poses a significant problem in most developing nations. Therefore a novel deep architecture, named as SkiNet, is proposed to provide faster screening solution and assistance to newly trained physicians in the process of clinical diagnosis of skin cancer. The main motive behind SkiNet’s design and development is to provide a white box solution, addressing a critical problem of trust and interpretability which is crucial for the wider adoption of Computer-aided diagnosis systems by medical practitioners. The proposed SkiNet is a two-stage pipeline wherein the lesion segmentation is followed by the lesion classification. Monte Carlo dropout and test time augmentation techniques have been employed in the proposed method to estimate epistemic and aleatoric uncertainty. A novel segmentation model named Bayesian MultiResUNet is used to estimate the uncertainty on the predicted segmentation map. Saliency-based methods like XRAI, Grad-CAM and Guided Backprop are explored to provide post-hoc explanations of the deep learning models. The ISIC-2018 dataset is used to perform the experimentation and ablation studies. The results establish the robustness of the proposed model on the traditional benchmarks while addressing the black-box nature of such models to alleviate the skepticism of medical practitioners by incorporating transparency and confidence to the model’s prediction.
Cell‐surface contacts determine volume and mechanical properties of human embryonic kidney 293 T cells

Alterations in the organization of the cytoskeleton precede the escape of adherent cells from the framework of cell–cell and cell‐matrix interactions into suspension. With cytoskeletal dynamics being linked to cell mechanical properties, many studies elucidated this relationship under either native adherent or suspended conditions. In contrast, tethered cells that mimic the transition between both states have not been the focus of recent research. Using human embryonic kidney 293 T cells we investigated all three conditions in the light of alterations in cellular shape, volume, as well as mechanical properties and relate these findings to the level, structure, and intracellular localization of filamentous actin (F‐actin). For cells adhered to a substrate, our data shows that seeding density affects cell size but does not alter their elastic properties. Removing surface contacts leads to cell stiffening that is accompanied by changes in cell shape, and a reduction in cellular volume but no alterations in F‐actin density. Instead, we observe changes in the organization of F‐actin indicated by the appearance of blebs in the semi‐adherent state. In summary, our work reveals an interplay between molecular and mechanical alterations when cells detach from a surface that is mainly dominated by cell morphology.
Ground-state properties of artificial bosonic atoms, Bose interaction blockade, and the single-atom pipette

We analyze the ground-state properties of an artificial atom made out of repulsive bosons attracted to a center for the case that all the interactions are short ranged. Such bosonic atoms could be created by optically trapping ultracold particles of alkali-metal vapors; we present the theory describing how their properties depend on experimentally adjustable strength of 'nuclear' attraction and interparticle repulsion. The binding ability of the short-range potential increases with space dimensionality, only a limited number of particles can be bound in one dimension, while in two and three dimensions the number of bound bosons can be chosen at will. Particularly in three dimensions we find an unusual effect of enhanced resonant binding: for not very strong interparticle repulsion the equilibrium number of bosons bound to a nuclear potential having a sufficiently shallow single-particle state increases without bound as the nuclear potential becomes less attractive. As a consequence of the competing nuclear attraction enhanced by the Bose statistics and interparticle repulsions, the dependence of the ground-state energy of the atom on the number of particles has a minimum whose position is experimentally tunable. This implies a staircase dependence of the equilibrium number of bound bosons on external parameters which maymore » be used to create a single-atom pipette--an arrangement which allows the transport of atoms into and out of a reservoir, one at a time. « less