Miracle-dz/UniFAR-FTUs huggingface dataset:
Wigner Distribution Function: Relation to Short-Term Spectral Estimation, Smoothing, and Performance in Noise.

Abstract : The properties and behavior of the Wigner Distribution Function (WDF) are investigated both analytically and by means of a number of simple informative examples. The lack of local temporal averaging when obtaining the instantaneous correlation function, and the lack of weighting the longer delay values when transforming to the instantaneous spectrum, are shown to be the causes of the deleterious interference effects that are inherent to the WDF. The equivalence of short-term spectral estimation to the smoothed WDF offers an attractive alternative with guaranteed positive distribution values and no interference effects. The performance of a processor which estimates the WDF of a signal waveform in the presence of additive noise is investigated in terms of the output mean, bias, and variance. Dependence on filtering the input and time-weighting is allowed and included in the analysis. Numerical application to a particular example is carried out. Keywords: Wigner distribution function; Short term spectral estimation; Smoothing; Noise performance; Linear frequency; Modulation; Interference effects; Gaussian amplitude modulation; Marginals; Moments; Spread of distribution; Positive distributions; Ambiguity function.
Lipid and protein content profiling of isolated native autophagic vesicles

Autophagy is responsible for clearance of an extensive portfolio of cargoes, which are sequestered into vesicles, called autophagosomes, and are delivered to lysosomes for degradation. The pathway is highly dynamic and responsive to several stress conditions. However, the phospholipid composition and protein contents of human autophagosomes under changing autophagy rates are elusive so far. Here, we introduce an antibody‐based FACS‐mediated approach for the isolation of native autophagic vesicles and ensured the quality of the preparations. Employing quantitative lipidomics, we analyze phospholipids present within human autophagic vesicles purified upon basal autophagy, starvation, and proteasome inhibition. Importantly, besides phosphoglycerides, we identify sphingomyelin within autophagic vesicles and show that the phospholipid composition is unaffected by the different conditions. Employing quantitative proteomics, we obtain cargo profiles of autophagic vesicles isolated upon the different treatment paradigms. Interestingly, starvation shows only subtle effects, while proteasome inhibition results in the enhanced presence of ubiquitin–proteasome pathway factors within autophagic vesicles. Thus, here we present a powerful method for the isolation of native autophagic vesicles, which enabled profound phospholipid and cargo analyses.
Quantum estimation of the Schwarzschild spacetime parameters of the Earth

We propose a quantum experiment to measure with high precision the Schwarzschild spacetime parameters of the Earth. The scheme can also be applied to measure distances by taking into account the curvature of the Earth’s spacetime. As a wave packet of (entangled) light is sent from the Earth to a satellite it is redshifted and deformed due to the curvature of spacetime. Measurements after the propagation enable the estimation of the spacetime parameters. We compare our results with the state of the art, which involves classical measurement methods, and discuss what developments are required in space-based quantum experiments to improve on the current measurement of the Schwarzschild radius of the Earth.
Identification of central amygdala and trigeminal motor nucleus connectivity in humans: An ultra‐high field diffusion MRI study

The neuroanatomical circuitry of jaw muscles has been mostly explored in non‐human animals. A recent rodent study revealed a novel circuit from the central amygdala (CeA) to the trigeminal motor nucleus (5M), which controls biting attacks. This circuit has yet to be delineated in humans. Ultra‐high diffusion‐weighted imaging data from the Human Connectome Project (HCP) allow in vivo delineation of circuits identified in other species—for example, the CeA–5M pathway—in humans. We hypothesized that the CeA–5M circuit could be resolved in humans at both 7 and 3 T. We performed probabilistic tractography between the CeA and 5M in 30 healthy young adults from the HCP database. As a negative control, we performed tractography between the basolateral amygdala (BLAT) and 5M, as CeA is the only amygdalar nucleus with extensive projections to the brainstem. Connectivity strength was operationalized as the number of streamlines between each region of interest. Connectivity strength between CeA–5M and BLAT–5M within each hemisphere was compared, and CeA–5M circuit had significantly stronger connectivity than the BLAT–5M circuit, bilaterally at both 7 T (all p < .001) and 3 T (all p < .001). This study is the first to delineate the CeA–5M circuit in humans.
Maternal exposure of rats to sodium saccharin during gestation and lactation on male offspring

Abstract We investigated the effects of fetal programming in Sprague–Dawley rats through the maternal consumption of sodium saccharin on the testicular structure and function in male offspring. Feed intake and efficiency, organ and fat weight, quantification and expression of androgen receptor (AR), and proliferating cell nuclear antigen (PCNA) proteins, sperm count, and hormone levels were determined. Consumption alterations were found in the final weeks of the experiment. Decreases in AR and PCNA expression and quantification, tubular diameter, and luminal volume, and increases in epithelial and interstitial relative volumes were observed. Lower sperm count and transit, and lower estradiol concentration were also found. Sodium saccharin consumption by dams programmed male offspring by affecting the hypothalamic–pituitary–gonad axis with alterations in the Sertoli cell population, in spermatogonia proliferation, the expression and quantification of AR, and in sperm count. We hypothesized that these changes may be due to an estradiol reduction that caused the loosening of adhesion junctions of the blood–testis barrier, causing cell losses during spermatogenesis, also reflected by a decrease in tubular diameter with an increase in epithelial volume and consequent decrease in luminal volume. We conclude that maternal sodium saccharin consumption during pregnancy and lactation programmed alterations in the reproductive parameters of male offspring, thus influencing spermatogenesis. Summary Sentence Maternal consumption of sodium saccharin during gestation and lactation reduced the population of seminiferous epithelium cells and plasma estradiol and affected reproductive capacity in male offspring. Graphical Abstract
Protoporphyrin IX delayed fluorescence imaging: a modality for hypoxia-based surgical guidance

Abstract. Significance Hypoxia imaging for surgical guidance has never been possible, yet it is well known that most tumors have microregional chronic and/or cycling hypoxia present as well as chaotic blood flow. The ability to image oxygen partial pressure (pO2) is therefore a unique control of tissue metabolism and can be used in a range of disease applications to understand the complex biochemistry of oxygen supply and consumption. Aim Delayed fluorescence (DF) from the endogenous molecule protoporphyrin IX (PpIX) has been shown to be a truly unique reporter of the local oxygen partial pressure in tissue. PpIX is endogenously synthesized by mitochondria in most tissues, and the particular property of DF emission is directly related to low microenvironmental oxygen concentration. Here, it is shown that PpIX has a unique emission in hypoxic tumor tissue regions, which is measured as a DF signal in the red to near-infrared spectrum. Approach A time-gated imaging system was used for PpIX DF for wide field direct mapping of pO2 changes. Acquiring both prompt and DF in a rapid sequential cycle allowed for imaging oxygenation in a way that was insensitive to the PpIX concentration. By choosing adequate parameters, the video rate acquisition of pO2 images could be achieved, providing real-time tissue metabolic information. Results In this report, we show the first demonstration of imaging hypoxia signals from PpIX in a pancreatic cancer model, exhibiting >5X contrast relative to surrounding normal oxygenated tissues. Additionally, tissue palpation amplifies the signal and provides intuitive temporal contrast based upon neoangiogenic blood flow differences. Conclusions PpIX DF provides a mechanism for tumor contrast that could easily be translated to human use as an intrinsic contrast mechanism for oncologic surgical guidance.
Identification of potential crucial genes and mechanisms associated with metastasis of medulloblastoma based on gene expression profile

ABSTRACT Objectives Medulloblastoma is the most common malignant brain tumor in childhood. Although metastasis constitutes one of the poorest prognostic indicators in this disease, the mechanisms that drive metastasis have received less attention. The aim of our study is to provide valid biological information for the metastasis mechanism of medulloblastoma. Methods Gene expression profile of GSE468 was downloaded from GEO database and was analyzed using limma R package. Function and enrichment analyses of DEGs were performed based on PANTHER database. PPI network construction, hub gene selection and module analysis were conducted in Cytoscape software. Results Nine upregulated genes and 34 downregulated genes were selected as DEGs. The upregulated genes were mainly enriched in molecular function and cell component, which mainly included protein binding and nucleus respectively. A total of 120 enriched GO terms and 40 KEGG pathways were identified. The main enriched GO terms were the biological process such as apoptosis and MAPK activity. Besides, the enriched KEGG pathways also included MAPK signaling pathway. A PPI network was obtained, and JUN was identified as a hub gene. Also, we firstly investigated the role and regulatory mechanism of JUN in the metastasis of medulloblastoma. Conclusions Through the bioinformatics analysis of the gene microarray in GEO, we found some crucial genes and pathways associated with the metastasis of medulloblastoma.
Particle Correlations in Bose-Einstein Condensates

The impact of interparticle correlations on the behavior of Bose-Einstein Condensates (BECs) is discussed using two approaches. In the first approach, the wavefunction of a BEC is encoded in the $N$-particle sector of an extended "catalytic state". Going to a time-dependent interaction picture, we can organize the effective Hamiltonian by powers of ${N}^{-1/2}$. Requiring the terms of order ${N}^{1/2}$ to vanish, we get the Gross-Pitaevskii Equation. Going to the next order, $N^0$, we obtain the number-conserving Bogoliubov approximation. Our approach allows one to stay in the Schr\"{o}dinger picture and to apply many techniques from quantum optics. Moreover, it is easier to track different orders in the Hamiltonian and to generalize to the multi-component case. In the second approach, I consider a state of $N =l\times n$ bosons that is derived by symmetrizing the $n$-fold tensor product of an arbitrary $l$-boson state. Particularly, we are interested in the pure state case for $l=2$, which we call the Pair-Correlated State (PCS). I show that PCS reproduces the number-conserving Bogoliubov approximation; moreover, it also works in the strong interaction regime where the Bogoliubov approximation fails. For the two-site Bose-Hubbard model, I find numerically that the error (measured by the trace distance of the two-particle reduced density matrices) of PCS is less than two percent over the entire parameter space, thus making PCS a bridge between the superfluid and Mott insulating phases. Amazingly, the error of PCS does not increase, in the time-dependent case, as the system evolves for longer times. I derive both time-dependent and -independent equations for the ground state and the time evolution of the PCS ansatz. The time complexity of simulating PCS does not depend on $N$ and is linear in the number of orbitals in use.
Loss of ribonuclease DIS3 hampers genome integrity in myeloma by disrupting DNA:RNA hybrid metabolism

The ribonuclease DIS3 is one of the most frequently mutated genes in the hematological cancer multiple myeloma, yet the basis of its tumor suppressor function in this disease remains unclear. Herein, exploiting the TCGA dataset, we found that DIS3 plays a prominent role in the DNA damage response. DIS3 inactivation causes genomic instability by increasing mutational load, and a pervasive accumulation of DNA:RNA hybrids that induces genomic DNA double‐strand breaks (DSBs). DNA:RNA hybrid accumulation also prevents binding of the homologous recombination (HR) machinery to double‐strand breaks, hampering DSB repair. DIS3‐inactivated cells become sensitive to PARP inhibitors, suggestive of a defect in homologous recombination repair. Accordingly, multiple myeloma patient cells mutated for DIS3 harbor an increased mutational burden and a pervasive overexpression of pro‐inflammatory interferon, correlating with the accumulation of DNA:RNA hybrids. We propose DIS3 loss in myeloma to be a driving force for tumorigenesis via DNA:RNA hybrid‐dependent enhanced genome instability and increased mutational rate. At the same time, DIS3 loss represents a liability that might be therapeutically exploited in patients whose cancer cells harbor DIS3 mutations.
Perinatal Morphine Exposure Leads to Sex-Dependent Executive Function Deficits and Microglial Changes in Mice

Abstract Children exposed prenatally to opioids are at an increased risk for behavioral problems and executive function deficits. The prefrontal cortex (PFC) and amygdala (AMG) regulate executive function and social behavior and are sensitive to opioids prenatally. Opioids can bind to toll-like receptor 4 (TLR4) to activate microglia, which may be developmentally important for synaptic pruning. Therefore, we tested the effects of perinatal morphine exposure on executive function and social behavior in male and female mouse offspring, along with microglial-related and synaptic-related outcomes. Dams were injected once daily subcutaneously with saline (n = 8) or morphine (MO; 10 mg/kg; n = 12) throughout pregestation, gestation, and lactation until offspring were weaned on postnatal day 21 (P21). Male MO offspring had impairments in attention and accuracy in the five-choice serial reaction time task, while female MO offspring were less affected. Targeted gene expression analysis at P21 in the PFC identified alterations in microglial-related and TLR4-related genes, while immunohistochemical analysis in adult brains indicated decreased microglial Iba1 and phagocytic CD68 proteins in the PFC and AMG in males, but females had an increase. Further, both male and female MO offspring had increased social preference. Overall, these data demonstrate male vulnerability to executive function deficits in response to perinatal opioid exposure and evidence for disruptions in neuron–microglial signaling.
Simulation of optical interstellar scintillation

Aims. Stars twinkle because their light propagates through the atmosphere. The same phenomenon is expected on a longer time scale when the light of remote stars crosses an interstellar turbulent molecular cloud, but it has never been observed at optical wavelengths. The aim of the study described in this paper is to fully simulate the scintillation process, starting from the molecular cloud description as a fractal object, ending with the simulations of fluctuating stellar light curves. Methods. Fast Fourier transforms are first used to simulate fractal clouds. Then, the illumination pattern resulting from the crossing of background star light through these refractive clouds is calculated from a Fresnel integral that also uses fast Fourier transform techniques. Regularisation procedure and computing limitations are discussed, along with the effect of spatial and temporal coherency (source size and wavelength passband). Results. We quantify the expected modulation index of stellar light curves as a function of the turbulence strength – characterised by the diffraction radius Rdiff – and the projected source size, introduce the timing aspects, and establish connections between the light curve observables and the refractive cloud. We extend our discussion to clouds with different structure functions from Kolmogorovtype turbulence. Conclusions. Our study confirms that current telescopes of ∼4 m with fast-readout, wide-field detectors have the capability of discovering the first interstellar optical scintillation effects. We also show that this effect should be unambiguously distinguished from any other type of variability through the observation of desynchronised light curves, simultaneously measured by two distant telescopes.
Determinants of Length of Stay after Neonatal Cardiac Surgery Using Path Analysis

After neonatal cardiac surgery, families, and the health care team strive for exclusive oral feedings before hospital discharge. With the hypothesis that exclusive oral feedings would reduce the length of stay (LOS), a multidimensional path analysis was used to examine a cross-section of 280 neonates from 2009 to 2013. Buttigieg, Abela, and Pace’s theoretical framework of structural and process-related determinants of LOS was modeled with hypothesis-driven correlation and directionality. The recursive path model had a good global and local fit with outcome variances of 26% for exclusive oral feeding and LOS. In the full cohort and model groups (single and biventricular), when controlling for covariances: sepsis, birth distance, necrotizing enterocolitis, genetic differences, specialty consults, the age at which neonatal cardiac surgery occurred (β = .23, p ≤ .001) and the duration of postoperative intubation (β = .47, p ≤ .001) more significantly influenced the LOS than intermediate mediation of exclusive oral feedings at discharge.
Retrospective serological and molecular survey of myxoma or antigenically related virus in the Iberian hare, Lepus granatensis

Abstract The 2018 outbreak of myxomatosis in the Iberian hare (Lepus granatensis) has been hypothesized to originate from a species jump of the rabbit‐associated myxoma virus (MYXV), after natural recombination with an unknown poxvirus. Iberian hares were long considered resistant to myxomatosis as no prior outbreaks were reported. To provide insights into the emergence of this recombinant virus (ha‐MYXV), we investigated serum samples from 451 Iberian hares collected over two time periods almost two decades apart, 1994–1999 and 2017–2019 for the presence of antibodies and MYXV‐DNA. First, we screened all serum samples using a rabbit commercial indirect ELISA (iELISA) and then tested a subset of these samples in parallel using indirect immunofluorescence test (IFT), competitive ELISA (cELISA) and qPCR targeting M000.5L/R gene conserved in MYXV and ha‐MYXV. The cut‐off of iELISA relative index 10 = 6.1 was selected from a semiparametric finite mixture analysis aiming to minimize the probability of false positive results. Overall, MYXV related‐antibodies were detected in 57 hares (12.6%) including 38 apparently healthy hares (n = 10, sampled in 1994–1999, none MYXV‐DNA positive, and n = 28 sampled in 2017–2019 of which four were also ha‐MYXV‐DNA positive) and 19 found‐dead and ha‐MYXV‐DNA‐positive sampled in 2018–2019. Interestingly, four seronegative hares sampled in 1997 were MYXV‐DNA positive by qPCR, the result being confirmed by sequencing of three of them. For the Iberian hares hunted or live trapped (both apparently health), seroprevalence was significantly higher in 2017–2019 (13.0%, CI95% 9.2–18.2%) than in 1994–1999 (5.4%, CI95% 3.0–9.6%) (p = .009). Within the second period, seroprevalence was significantly higher in 2019 compared to 2017 (24.7 vs 1.7% considering all the sample, p = .007), and lower during the winter than the autumn (p < .001). While our molecular and serological results show that Iberian hares have been in contact with MYXV or an antigenically similar virus at least since 1996, they also show an increase in seroprevalence in 2018–2019. The remote contact with MYXV may have occurred with strains that circulated in rabbits, or with unnoticed strains already circulating in Iberian hare populations. This work strongly suggests the infection of Iberian hares with MYXV or an antigenically related virus, at least 20 years before the severe virus outbreaks were registered in 2018.
Diagnostic signature and immune characteristic of aging-related genes from placentas in Preeclampsia

ABSTRACT Introduction Preeclampsia (PE) is a serious pregnancy syndrome. Advanced maternal age (≥ 35 years old) is one of the major risk factors of PE and placental aging is considered to be related to this disease. However, the mechanisms underlying these phenomena remain obscured. Methods Gene expression profiles of PE and non-PE placental samples were curated from the GSE75010 dataset. A diagnostic model was constructed and immune characteristics of PE subtypes were estimated. Results A total of 58 aging-related genes, which may be associated with PE, were identified. Among them, LEP and FLT1 may be key aging-related genes. Based on 5 top genes (PIK3CB, FLT1, LEP, PIK3R1, CSNK1E), a diagnostic nomogram for PE was built (AUC = 0.872 in the GSE75010 dataset). Three molecular subtypes were clustered, which had different immune and angiogenesis characteristics. Conclusion The present study suggests the potential implications of aging-related genes in diagnosing PE. Diverse immune characteristics may be involved in the placental aging of PE.
Heisenberg spin bus as a robust transmission line for quantum-state transfer

We study quantum-state transfer (QST) through a strongly coupled antiferromagnetic spin chain (acting as a spin bus), between weakly coupled external qubits. By treating the weak coupling as a perturbation, we find that QST is enabled specifically by the second-order terms in the perturbative expansion. We show that QST is robust against disorder in the couplings, either within the bus or to the external qubits. We find that the protocol works when the qubits are attached to any node on an even-size bus or to the antiferromagnetic nodes on an odd-size bus. The optimal time for QST is found to depend nonmonotonically on qubit separation.