Miracle-dz/UniFAR-FTUs huggingface dataset:
Li-SegPNet: Encoder-Decoder Mode Lightweight Segmentation Network for Colorectal Polyps Analysis

Objective: One of the fundamental and crucial tasks for the automated diagnosis of colorectal cancer is the segmentation of the acute gastrointestinal lesions, most commonly colorectal polyps. Therefore, in this work, we present a novel lightweight encoder-decoder mode of architecture with the attention mechanism to address this challenging task. Methods: The proposed Li-SegPNet architecture harnesses cross-dimensional interaction in feature maps with novel encoder block with modified triplet attention. We have used atrous spatial pyramid pooling to handle the problem of segmenting objects at multiple scales. We also address the semantic gap between the encoder and decoder through a modified skip connection using attention gating. Results: We applied our model to colonoscopy still images and trained and validated it on two publicly available datasets, Kvasir-SEG and CVC-ClinicDB. We achieve mean Intersection-Over-Union (mIoU) and dice scores of 0.88, 0.9058 and 0.8969, 0.9372 on Kvasir-SEG and CVC-ClinicDB, respectively. We analyze the generalizability of Li-SegPNet by testing it on two independent previously unseen datasets, Hyper-Kvasir and EndoTect 2020, and establish the model efficiency in cross-dataset evaluation. We employ multi-scale testing to examine the model performance on different sizes of polyps. Li-SegPNet performs best on medium-sized polyps with a mIoU and dice score of 0.9086 and 0.9137, respectively on the Kvasir-SEG dataset and 0.9425, 0.9434 of mIoU and dice score, respectively on CVC-ClinicDB. Conclusion: The experimental results convey that we establish a new benchmark on these four datasets for the segmentation of polyps. Significance: The proposed model can be used as a new benchmark model for polyps segmentation. Lesser parameters in comparison to other models give the edge in the applicability of the proposed Li-SegPNet model in real-time clinical analysis.
COORDINATED X-RAY AND OPTICAL OBSERVATIONS OF STAR–PLANET INTERACTION IN HD 17156

The large number of close-in Jupiter-size exoplanets prompts the question whether star–planet interaction (SPI) effects can be detected. We focused our attention on the system HD 17156, having a Jupiter-mass planet in a very eccentric orbit. Here we present results of the XMM-Newton observations and of a five month coordinated optical campaign with the HARPS-N spectrograph. We observed HD 17156 with XMM-Newton when the planet was approaching the apoastron and then at the following periastron passage, quasi-simultaneously with HARPS-N. We obtained a clear ( ≈ 5.5 &sgr; ? > ) X-ray detection only at the periastron visit, accompanied by a significant increase of the R HK ′ ? > chromospheric index. We discuss two possible scenarios for the activity enhancement: magnetic reconnection and flaring or accretion onto the star of material tidally stripped from the planet. In any case, this is possibly the first evidence of a magnetic SPI effect caught in action.
Precision estimates of relative and absolute cerebral blood flow in Alzheimer’s disease and cognitively normal individuals

Alzheimer’s disease is characterized by regional reductions in cerebral blood flow (CBF). Although the gold standard for measuring CBF is [15O]H2O PET, proxies of relative CBF, derived from the early distribution phase of amyloid and tau tracers, have gained attention. The present study assessed precision of [15O]H2O derived relative and absolute CBF, and compared precision of these measures with that of (relative) CBF proxies. Dynamic [15O]H2O, [18F]florbetapir and [18F]flortaucipir PET test-retest (TrT) datasets with eleven, nine and fourteen subjects, respectively, were included. Analyses were performed using an arterial input model and/or a simplified reference tissue model, depending on the data available. Relative CBF values (i.e. K1/K1′ and/or R1) were obtained using cerebellar cortex as reference tissue and TrT repeatability (i.e. precision) was calculated and compared between tracers, parameters and clinical groups. Relative CBF had significantly better TrT repeatability than absolute CBF derived from [15O]H2O (r = −0.53), while best TrT repeatability was observed for [18F]florbetapir and [18F]flortaucipir R1 (r = −0.23, r = −0.33). Furthermore, only R1 showed, better TrT repeatability for cognitively normal individuals. High precision of CBF proxies could be due to a compensatory effect of the extraction fraction, although changes in extraction fraction could also bias these proxies, but not the gold standard.
Descending pathways from the superior colliculus mediating autonomic and respiratory effects associated with orienting behaviour

The ability to discriminate competing external stimuli and initiate contextually appropriate behaviours is a key brain function. Neurons in the deep superior colliculus (dSC) integrate multisensory inputs and activate descending projections to premotor pathways responsible for orienting, attention and defence, behaviours which involve adjustments to respiratory and cardiovascular parameters. However, the neural pathways that subserve the physiological components of orienting are poorly understood. We report that orienting responses to optogenetic dSC stimulation are accompanied by short‐latency autonomic, respiratory and electroencephalographic effects in awake rats, closely mimicking those evoked by naturalistic alerting stimuli. Physiological responses were not accompanied by detectable aversion or fear, and persisted under urethane anaesthesia, indicating independence from emotional stress. Anterograde and trans‐synaptic viral tracing identified a monosynaptic pathway that links the dSC to spinally projecting neurons in the medullary gigantocellular reticular nucleus (GiA), a key hub for the coordination of orienting and locomotor behaviours. In urethane‐anaesthetized animals, sympathoexcitatory and cardiovascular, but not respiratory, responses to dSC stimulation were replicated by optogenetic stimulation of the dSC–GiA terminals, suggesting a likely role for this pathway in mediating the autonomic components of dSC‐mediated responses. Similarly, extracellular recordings from putative GiA sympathetic premotor neurons confirmed short‐latency excitatory inputs from the dSC. This pathway represents a likely substrate for autonomic components of orienting responses that are mediated by dSC neurons and suggests a mechanism through which physiological and motor components of orienting behaviours may be integrated without the involvement of higher centres that mediate affective components of defensive responses.
Inertial blob-hole symmetry breaking in magnetised plasma filaments

Symmetry breaking between the propagation velocities of magnetised plasma filaments with large positive (blob) and negative (hole) amplitudes, as implied by a dimensional analysis scaling, is studied with global (‘full-n’) non-Boussinesq gyrofluid computations, which include finite inertia effects through nonlinear polarisation. Interchange blobs on a flat density background have higher inertia and propagate more slowly than holes. In the presence of a large enough density gradient, the effect is reversed: blobs accelerate down the gradient and holes are slowed in their propagation up the gradient. Drift wave blobs spread their initial vorticity rapidly into a fully developed turbulent state, whereas primary holes can remain coherent for many eddy turnover times. The results bear implications for plasma edge zonal flow evolution and tokamak scrape-off-layer transport.
Stabilization of the tetragonal structure in (Ba 1 -x Sr x ) CuSi 2 O 6

We present a structural analysis of the substituted system (Ba$_{1-x}$Sr$_{x}$)CuSi$_{2}$O$_{6}$, which reveals a stable tetragonal crystal structure down to 1.5 K. We explore the structural details with lowtemperature neutron and synchrotron powder diffraction, room-temperature and cryogenic highresolution NMR, as well as magnetic- and specific-heat measurements and verify that a structural phase transition into the orthorhombic structure which occurs in the parent compound BaCuSi2O6, is absent for the x = 0.1 sample. Furthermore, synchrotron powder-diffraction patterns show a reduction of the unit cell for x = 0.1 and magnetic measurements prove that the Cu-dimers are preserved, yet with a slightly reduced intradimer coupling Jintra. Pulse-field magnetization measurements reveal the emergence of a field-induced ordered state, tantamount to Bose-Einsteincondensation (BEC) of triplons, within the tetragonal crystal structure of $I\,4_{1}/acd$. This material offers the opportunity to study the critical properties of triplon condensation in a simple crystal structure.
Prediction of postoperative atrial fibrillation with postoperative epicardial electrograms

Abstract Objectives. New-onset postoperative atrial fibrillation (POAF) is a common complication after cardiac surgery. The arrhythmia often entails a longer hospital stay, greater risk of other complications, and higher mortality both short- and long-term. An investigation of the use of early atrial electrograms in predicting POAF in cardiac surgery was performed. Design. In this prospective observational study, a total of 99 consecutive adult patients undergoing coronary artery bypass grafting, valve surgery or both were included. On the first postoperative morning, standard 12-lead electrograms (ECG), unipolar atrial electrograms (aEG), and vital values were recorded. The outcome was new-onset POAF within one month postoperatively. Results. Three multivariable prediction models for POAF were formed using measurements derived from the ECG, aEG, and patient characteristics. Age, body mass index, and two unipolar electrogram measurements quantifying local activation time and fractionation were strongly associated with the outcome POAF. The performance of the POAF prediction models was assessed through receiver operating curve characteristics with cross-validation, and discrimination using the leave-one-out-method to internally validate the models. The cross-validated area under the receiver operating characteristic curve (AUC) was improved in a prediction model using atrial-derived electrogram variables (AUC 0.796, 95% CI 0.698–0.894), compared with previous ECG and clinical models (AUC 0.716, 95% CI 0.606–0.826 and AUC 0.718, 95% CI 0.613–0.822, respectively). Conclusions. This study found that easily obtainable measurements from atrial electrograms may be helpful in identifying patients at risk of POAF in cardiac surgery.
MEASURING GALAXY STAR FORMATION RATES FROM INTEGRATED PHOTOMETRY: INSIGHTS FROM COLOR–MAGNITUDE DIAGRAMS OF RESOLVED STARS

We use empirical star formation histories (SFHs), measured from Hubble-Space-Telescope-based resolved star color–magnitude diagrams, as input into population synthesis codes to model the broadband spectral energy distributions (SEDs) of 50 nearby dwarf galaxies (6.5 < log M*/M☉ < 8.5, with metallicities ∼10% solar). In the presence of realistic SFHs, we compare the modeled and observed SEDs from the ultraviolet (UV) through near-infrared and assess the reliability of widely used UV-based star formation rate (SFR) indicators. In the FUV through i bands, we find that the observed and modeled SEDs are in excellent agreement. In the Spitzer 3.6 μm and 4.5 μm bands, we find that modeled SEDs systematically overpredict observed luminosities by up to ∼0.2 dex, depending on treatment of the TP-AGB stars in the synthesis models. We assess the reliability of UV luminosity as a SFR indicator, in light of independently constrained SFHs. We find that fluctuations in the SFHs alone can cause factor of ∼2 variations in the UV luminosities relative to the assumption of a constant SFH over the past 100 Myr. These variations are not strongly correlated with UV-optical colors, implying that correcting UV-based SFRs for the effects of realistic SFHs is difficult using only the broadband SED. Additionally, for this diverse sample of galaxies, we find that stars older than 100 Myr can contribute from <5%–100% of the present day UV luminosity, highlighting the challenges in defining a characteristic star formation timescale associated with UV emission. We do find a relationship between UV emission timescale and broadband UV-optical color, though it is different than predictions based on exponentially declining SFH models. Our findings have significant implications for the comparison of UV-based SFRs across low-metallicity populations with diverse SFHs.
Human oncogenic viruses: an overview of protein biomarkers in viral cancers and their potential use in clinics

ABSTRACT Introduction Although the idea that carcinogenesis might be caused by viruses was first voiced about 100 years ago, today’s data disappointingly show that we have not made much progress in preventing and/or treating viral cancers in a century. According to recent studies, infections are responsible for approximately 13% of cancer development in the world. Today, it is accepted and proven by many authorities that Epstein-Barr virus (EBV), Hepatitis B virus (HBV), Hepatitis C virus (HCV), Human Herpesvirus 8 (HHV8), Human T-cell Lymphotropic virus 1 (HTLV1) and highly oncogenic Human Papillomaviruses (HPVs) cause or/and contribute to cancer development in humans. Areas covered Considering the insufficient prevention and/or treatment strategies for viral cancers, in this review we present the current knowledge on protein biomarkers of oncogenic viruses. In addition, we aimed to decipher their potential for clinical use by evaluating whether the proposed biomarkers are expressed in body fluids, are druggable, and act as tumor suppressors or oncoproteins. Expert opinion Consequently, we believe that this review will shed light on researchers and provide a guide to find remarkable solutions for the prevention and/or treatment of viral cancers.
Viscoelastic multicomponent fluids in confined flow-focusing devices

The effects of elasticity on the break-up of liquid threads in microfluidic cross-junctions is investigated using numerical simulations based on the “lattice Boltzmann models” (LBM). Working at small Capillary numbers, we investigate the effects of non-Newtonian phases in the transition from droplet formation at the cross-junction (DCJ) and droplet formation downstream of the cross-junction (DC) (Liu & Zhang, Phys. Fluids. 23, 082101 (2011)). Viscoelasticity is found to influence the break-up point of the threads, which moves closer to the cross-junction and stabilizes. This is attributed to an increase of the polymer feedback stress forming in the corner flows, where the side channels of the device meet the main channel.
Cohort profile: the ECHO prenatal and early childhood pathways to health consortium (ECHO-PATHWAYS)

Purpose Exposures early in life, beginning in utero, have long-term impacts on mental and physical health. The ECHO prenatal and early childhood pathways to health consortium (ECHO-PATHWAYS) was established to examine the independent and combined impact of pregnancy and childhood chemical exposures and psychosocial stressors on child neurodevelopment and airway health, as well as the placental mechanisms underlying these associations. Participants The ECHO-PATHWAYS consortium harmonises extant data from 2684 mother–child dyads in three pregnancy cohort studies (CANDLE [Conditions Affecting Neurocognitive Development and Learning in Early Childhood], TIDES [The Infant Development and Environment Study] and GAPPS [Global Alliance to Prevent Prematurity and Stillbirth]) and collects prospective data under a unified protocol. Study participants are socioeconomically diverse and include a large proportion of Black families (38% Black and 51% White), often under-represented in research. Children are currently 5–15 years old. New data collection includes multimodal assessments of primary outcomes (airway health and neurodevelopment) and exposures (air pollution, phthalates and psychosocial stress) as well as rich covariate characterisation. ECHO-PATHWAYS is compiling extant and new biospecimens in a central biorepository and generating the largest placental transcriptomics data set to date (N=1083). Findings to date Early analyses demonstrate adverse associations of prenatal exposure to air pollution, phthalates and maternal stress with early childhood airway outcomes and neurodevelopment. Placental transcriptomics work suggests that phthalate exposure alters placental gene expression, pointing to mechanistic pathways for the developmental toxicity of phthalates. We also observe associations between prenatal maternal stress and placental corticotropin releasing hormone, a marker of hormonal activation during pregnancy relevant for child health. Other publications describe novel methods for examining exposure mixtures and the development of a national spatiotemporal model of ambient outdoor air pollution. Future plans The first wave of data from the unified protocol (child age 8–9) is nearly complete. Future work will leverage these data to examine the combined impact of early life social and chemical exposures on middle childhood health outcomes and underlying placental mechanisms.
Molecular determinants of tetrahydrocannabinol binding to the glycine receptor

The recognition of Cannabis as a source of new compounds suitable for medical use has attracted strong interest from the scientific community in its research, and substantial progress has accumulated regarding cannabinoids' activity; however, a thorough description of their molecular mechanisms of action remains a task to complete. Highlighting their complex pharmacology, the list of cannabinoids' interactors has vastly expanded beyond the canonical cannabinoid receptors. Among those, we have focused our study on the glycine receptor (GlyR), an ion channel involved in the modulation of nervous system responses, including, to our interest, sensitivity to peripheral pain. Here, we report the use of computational methods to investigate possible binding modes between the GlyR and Δ9‐tetrahydrocannabinol (THC). After obtaining a first pose for the THC binding from a biased molecular docking simulation and subsequently evaluating it by molecular dynamic simulations, we found a dynamic system with an identifiable representative binding mode characterized by the specific interaction with two transmembrane residues (Phe293 and Ser296). Complementarily, we assessed the role of membrane cholesterol in this interaction and positively established its relevance for THC binding to GlyR. Lastly, the use of restrained molecular dynamics simulations allowed us to refine the description of the binding mode and of the cholesterol effect. Altogether, our findings contribute to the current knowledge about the GlyR‐THC mode of binding and propose a new starting point for future research on how cannabinoids in general, and THC in particular, modulate pain perception in view of its possible clinical applications.
A study of microtubule dipole lattices

of a dissertation at the University of Miami. Dissertation supervised by Professor Joshua L. Cohn and Professor Neil F. Johnson. No. of pages in text. (117) Microtubules are cytoskeletal protein polymers orchestrating a host of important cellular functions including, but not limited to, cell support, cell division, cell motility and cell transport. In this thesis, we construct a toy-model of the microtubule lattice composed of vector Ising spins representing tubulin molecules, the building block of microtubules. Nearest-neighbor and next-to-nearest neighbor interactions are considered within an anisotropic dielectric medium. As a consequence of the helical topology, we observe that certain spin orientations render the lattice frustrated with nearest neighbor ferroelectric and next-to-nearest neighbor antiferroelectric bonds. Under these conditions, the lattice displays the remarkable property of stabilizing certain spin patterns that are robust to thermal fluctuations. We model this behavior in the framework of a generalized Ising model known as the J1 J2 model and theoretically determine the set of stable patterns. Employing Monte-Carlo methods, we demonstrate the stability of such patterns in the microtubule lattice at human physiological temperatures. This suggests a novel biological mechanism for storing information in living organisms, whereby the tubulin spin (dipole moment) states become information bits and information gets stored in microtubules in a way that is robust to thermal fluctuations. I dedicate this thesis to my father. May his soul rest in peace.
LaGAT: link-aware graph attention network for drug–drug interaction prediction

Abstract Motivation Drug–drug interaction (DDI) prediction is a challenging problem in pharmacology and clinical applications. With the increasing availability of large biomedical databases, large-scale biological knowledge graphs containing drug information have been widely used for DDI prediction. However, large knowledge graphs inevitably suffer from data noise problems, which limit the performance and interpretability of models based on the knowledge graph. Recent studies attempt to improve models by introducing inductive bias through an attention mechanism. However, they all only depend on the topology of entity nodes independently to generate fixed attention pathways, without considering the semantic diversity of entity nodes in different drug pair links. This makes it difficult for models to select more meaningful nodes to overcome data quality limitations and make more interpretable predictions. Results To address this issue, we propose a Link-aware Graph Attention method for DDI prediction, called LaGAT, which is able to generate different attention pathways for drug entities based on different drug pair links. For a drug pair link, the LaGAT uses the embedding representation of one of the drugs as a query vector to calculate the attention weights, thereby selecting the appropriate topological neighbor nodes to obtain the semantic information of the other drug. We separately conduct experiments on binary and multi-class classification and visualize the attention pathways generated by the model. The results prove that LaGAT can better capture semantic relationships and achieves remarkably superior performance over both the classical and state-of-the-art models on DDI prediction. Availabilityand implementation The source code and data are available at https://github.com/Azra3lzz/LaGAT. Supplementary information Supplementary data are available at Bioinformatics online.
CLIC4 localizes to mitochondrial-associated membranes and mediates cardioprotection

Mitochondrial-associated membranes (MAMs) are known to modulate organellar and cellular functions and can subsequently affect pathophysiology including myocardial ischemia-reperfusion (IR) injury. Thus, identifying molecular targets in MAMs that regulate the outcome of IR injury will hold a key to efficient therapeutics. Here, we found chloride intracellular channel protein (CLIC4) presence in MAMs of cardiomyocytes and demonstrate its role in modulating ER and mitochondrial calcium homeostasis under physiological and pathological conditions. In a murine model, loss of CLIC4 increased myocardial infarction and substantially reduced cardiac function after IR injury. CLIC4 null cardiomyocytes showed increased apoptosis and mitochondrial dysfunction upon hypoxia-reoxygenation injury in comparison to wild-type cardiomyocytes. Overall, our results indicate that MAM-CLIC4 is a key mediator of cellular response to IR injury and therefore may have a potential implication on other pathophysiological processes.