Miracle-dz/UniFAR-FTUs huggingface dataset:
Simulating the Euler equations on multiple GPUs using Python

GPUs have become a household name in High Performance Computing (HPC) systems over the last 15 years. However, programming GPUs is still largely a manual and arduous task, which requires expert knowledge of the physics, mathematics, and computer science involved. Even though there have been large advances in automatic parallelization and GPU execution of serial code, it is still difficult to fully utilize the GPU hardware with such approaches. Many core numeric GPU codes are therefore still mostly written using low level C/C++ or Fortran for the host code. Several studies have shown that using higher level languages, such as Python, can make software development faster and with fewer bugs. We have developed a simulator based on PyCUDA and mpi4py in Python for solving the Euler equations on Cartesian grids. Our framework utilizes the GPU, and can automatically run on clusters using MPI as well as on shared-memory systems. Our framework allows the programmer to implement low-level details in CUDA C/C++, which is important to achieve peak performance, whilst still benefiting from the productivity of Python. We show that our framework achieves good weak and strong scaling. Our weak scaling achieves more than 94% efficiency on a shared-memory GPU system and more than 90% efficiency on a distributed-memory GPU system, and our strong scaling is close to perfect on both shared-memory and distributed-memory GPU systems.
ROS scavenging and ion homeostasis is required for the adaptation of halophyte Karelinia caspia to high salinity

The halophyte Karelinia caspia has not only fodder and medical value but also can remediate saline-alkali soils. Our previous study showed that salt-secreting by salt glands is one of main adaptive strategies of K. caspia under high salinity. However, ROS scavenging, ion homeostasis, and photosynthetic characteristics responses to high salinity remain unclear in K. caspia. Here, physio-biochemical responses and gene expression associated with ROS scavenging and ions transport were tested in K. caspia subjected to 100–400 mM NaCl for 7 days. Results showed that both antioxidant enzymes (SOD, APX) activities and non-enzymatic antioxidants (chlorogenic acid, α-tocopherol, flavonoids, polyamines) contents were significantly enhanced, accompanied by up-regulating the related enzyme and non-enzymatic antioxidant synthesis gene (KcCu/Zn-SOD, KcAPX6, KcHCT, KcHPT1, Kcγ-TMT, KcF3H, KcSAMS and KcSMS) expression with increasing concentrations of NaCl. These responses are beneficial for removing excess ROS to maintain a stable level of H2O2 and O2− without lipid peroxidation in the K. caspia response to high salt. Meanwhile, up-regulating expression of KcSOS1/2/3, KcNHX1, and KcAVP was linked to Na+ compartmentalization into vacuoles or excretion through salt glands in K. caspia. Notably, salt can improve the function of PSII that facilitate net photosynthetic rates, which is helpful to growing normally in high saline. Overall, the findings suggested that ROS scavenging systems and Na+/K+ transport synergistically contributed to redox equilibrium, ion homeostasis, and the enhancement of PSII function, thereby conferring high salt tolerance.
ERK signaling for cell migration and invasion

The RAS - Extracellular signal-regulated kinase (RAS-ERK) pathway plays a conserved role in promoting cell migration and invasion. Growth factors, adhesion, and oncogenes activate ERK. While historically studied with respect to its control of cell proliferation and differentiation, the signaling pattern and effectors specific for cell migration are now coming to light. New advances in pathway probes have revealed how steady-state ERK activity fluctuates within individual cells and propagates to neighboring cells. We review new findings on the different modes of ERK pathway stimulation and how an increased baseline level of activity promotes single cell and collective migration and invasion. We discuss how ERK drives actin polymerization and adhesion turnover for edge protrusion and how cell contraction stimulates cell movement and ERK activity waves in epithelial sheets. With the steady development of new biosensors for monitoring spatial and temporal ERK activity, determining how cells individually interpret the multiple in vivo signals to ERK is within reach.
Myocardial edema during chemotherapy for gynecologic malignancies: A cardiac magnetic resonance T2 mapping study

Objective Myocardial edema is an early manifestation of chemotherapy-related myocardial injury. In this study, we used cardiac magnetic resonance (CMR) T2 mapping to assess myocardial edema and its changes during chemotherapy for gynecologic malignancies. Methods We enrolled 73 patients receiving chemotherapy for gynecologic malignancies, whose the latest cycle was within one month before the beginning of this study, and 41 healthy volunteers. All participants underwent CMR imaging. Of the 73 patients, 35 completed CMR follow-up after a median interval of 6 (3.3 to 9.6) months. The CMR sequences included cardiac cine, T2 mapping, and late gadolinium enhancement. Results Myocardial T2 was elevated in patients who were treated with chemotherapy compared with healthy volunteers [41ms (40ms to 43ms) vs. 41ms (39ms to 41ms), P = 0.030]. During follow-up, myocardial T2 rose further [40ms (39ms to 42ms) vs. 42.70 ± 2.92ms, P < 0.001]. Multivariate analysis showed that the number of chemotherapy cycles was associated with myocardial T2 elevation (β = 0.204, P = 0.029). After adjustment for other confounders, myocardial T2 elevation was independently associated with a decrease in left ventricular mass (β = −0.186; P = 0.024). Conclusion In patients with gynecologic malignancies, myocardial edema developed with chemotherapy cycles increase, and was associated with left ventricular mass decrease. T2 mapping allows the assessment of myocardial edema and monitoring of its change during chemotherapy.
Impact of and recovery from seabed trawling in soft-bottom benthic communities under natural disturbance of summer hypoxia: A case study in subtropical Hong Kong

Bottom trawling has widespread impact on the structure and composition of benthic communities. In this study, soft-bottom macrofauna in a heavily trawled area and an adjacent marine park that has been closed to bottom trawling for more than ten years were sampled, allowing to investigate the impact of and recovery from trawling. Both areas were equally affected by seasonal summer hypoxia. Polychaetes were the most abundant at trawled (78-86%) and non-trawled (85-94%) sites in both summer and winter. The non-trawled sites inside the marine park area had a lower level of species composition and abundance as compared to the trawled sites in summer, whereas in winter the benthic communities at these trawled and non-trawled sites appeared much similar with the majority of the identified taxa being dominated by new recruiting juveniles in both sampling areas. Results of permutational multivariate analysis of variance (PERMANOVA) on transformed infaunal abundance and biomass data revealed significant differences (p<0.05) between trawled and non-trawled treatments and seasons, as well as their interactions. Pair-wise a posteriori PERMANOVA further indicated significant differences for the abundance and biomass data in summer but insignificant differences in winter. PERMANOVA of the biological traits of infauna weighted with transformed biomass also confirmed significant difference for seasons only. Such findings imply that the effect of season was more important than that of trawling especially on the biological trait structure of the benthic communities. In addition, bottom trawling may contribute to a higher level of dissolved oxygen when the area suffered from hypoxia, resulting a higher biodiversity in the trawled area in summer. By comparing data taken prior to closure of the marine park from trawling, the recovery of infaunal community has been slow over the 12 years as a trawl-free area. Apart from natural disturbance of summer hypoxia, such recovery could also be complicated with the presence of artificial reefs deployed within the marine park, which may affect the hydrodynamics of the benthic environment and modify the community structure and function.
A colorimetric, sensitive, rapid, and simple diagnostic kit for the HLB putative causal agent detection

Huanglongbing (HLB) is one of the most devastating diseases in citrus worldwide. The Gram-negative bacterial plant pathogen “Candidatus Liberibacter spp. ” is phloem-limited and vectored by citrus psyllids. The species “Candidatus Liberibacter asiaticus” (C.Las) has been detected in Argentina, and its vector has been found in at least nine provinces. Early detection of C.Las is critical for a successful management of HLB disease. Currently, HLB molecular diagnosis is carried out by PCR, nested PCR, real-time PCR, or another combination of these techniques, which require purification of genomic DNA, sophisticated equipment, and highly trained personnel. We have developed a prototype of a sensitive colorimetric kit to detect C.Las based on the specific DNA isothermal amplification of this microorganism. The reaction buffer contains hydroxynaphthol blue (HNB), an indicator dye that turns from violet to blue/light blue when the DNA amplification reaction is positive. Similar sensitivity to visualize a positive reaction was observed between HNB loop-mediated isothermal amplification and agarose gel electrophoresis analysis. The detection of C.Las-infected plants was up to 8 ng of total infected plant genomic DNA, similar to quantitative PCR. A blind validation test of the prototype kit was performed with purified DNA extracted from healthy or C.Las-infected midrib plants. Our kit showed 100% concordance with the results of a gold-standard quantitative PCR technique applied by the Laboratorio de Biología Molecular de EEA Montecarlo. The analysis of samples, without DNA purification to detect C.Las, showed a similar sensitivity to the analysis of the same samples in which C.Las DNA was previously purified.
AMERICAN DEMOCRACY IN THE 21ST CENTURY: A RETROSPECTIVE

I. THE FIRST STEPS . 224 II. THE LABORATORIES OF DEMOCRACY: STATE-LEVEL SOLUTIONS . 226 III. CONGRESS TAKES ACTION . 232 IV. THE PRESIDENTIAL ELECTIONS . 234 V. LESSONS FOR TODAY . 236
ESTIMATING LUMINOSITIES AND STELLAR MASSES OF GALAXIES PHOTOMETRICALLY WITHOUT DETERMINING REDSHIFTS

Large direct imaging surveys usually use a template-fitting technique to estimate photometric redshifts for galaxies, which are then applied to derive important galaxy properties such as luminosities and stellar masses. These estimates can be noisy and suffer from systematic biases because of the possible mis-selection of templates and the propagation of the photometric redshift uncertainty. We introduce an algorithm, the Direct Empirical Photometric method (DEmP), that can be used to directly estimate these quantities using training sets, bypassing photometric redshift determination. DEmP also applies two techniques to minimize the effects arising from the non-uniform distribution of training set galaxy redshifts from a flux-limited sample. First, for each input galaxy, fitting is performed using a subset of the training set galaxies with photometry and colors closest to those of the input galaxy. Second, the training set is artificially resampled to produce a flat distribution in redshift or other properties, e.g., luminosity. To test the performance of DEmP, we use a four filter-band mock catalog to examine its ability to recover redshift, luminosity, stellar mass, and luminosity and stellar mass functions. We also compare the results to those from two publicly available template-fitting methods, finding that the DEmP algorithm outperforms both. We find that resampling the training set to have a uniform redshift distribution produces the best results not only in photometric redshift, but also in estimating luminosity and stellar mass. The DEmP method is especially powerful in estimating quantities such as near-IR luminosities and stellar mass using only data from a small number of optical bands.
Quantum noise eater for a single photonic qubit

We propose a quantum noise eater for a single qubit and experimentally verify its performance for recovery of a superposition carried by a dual-rail photonic qubit. We consider a case when only one of the rails (e.g. one of interferometric arms) is vulnerable to noise. A coherent but randomly arriving photon penetrating into this single rail causes a change of its state, which results in an error in a subsequent quantum information processing. We theoretically prove and experimentally demonstrate a conditional full recovery of the superposition by this quantum noise eater.
BUDHIES II: a phase-space view of H i gas stripping and star formation quenching in cluster galaxies

We investigate the effect of ram-pressure from the intracluster medium on the stripping of H I gas in galaxies in a massive, relaxed, X-ray bright, galaxy cluster at z = 0.2 from the Blind Ultra Deep H I Environmental Survey (BUDHIES). We use cosmological simulations, and velocity versus position phase-space diagrams to infer the orbital histories of the cluster galaxies. In particular, we embed a simple analytical description of ram-pressure stripping in the simulations to identify the regions in phase-space where galaxies are more likely to have been sufficiently stripped of their H I gas to fall below the detection limit of our survey. We find a striking agreement between the model predictions and the observed location of H I-detected and non-detected blue (late-type) galaxies in phase-space, strongly implying that ram-pressure plays a key role in the gas removal from galaxies, and that this can happen during their first infall into the cluster. However, we also find a significant number of gas-poor, red (early-type) galaxies in the infall region of the cluster that cannot easily be explained with our model of ram-pressure stripping alone. We discuss different possible additional mechanisms that could be at play, including the pre-processing of galaxies in their previous environment. Our results are strengthened by the distribution of galaxy colours (optical and UV) in phase-space, that suggests that after a (gas-rich) field galaxy falls into the cluster, it will lose its gas via ram-pressure stripping, and as it settles into the cluster, its star formation will decay until it is completely quenched. Finally, this work demonstrates the utility of phase-space diagrams to analyse the physical processes driving the evolution of cluster galaxies, in particular H I gas stripping.
A constructive method for computing generalized Manley--Rowe constants of motion

The Manley--Rowe constants of motion (MRC) are conservation laws written out for a dynamical system describing the time evolution of the amplitudes in resonant triad. In this paper we extend the concept of MRC to resonance clusters of any form yielding generalized Manley--Rowe constants (gMRC) and give a constructive method how to compute them. We also give details of a \emph{Mathematica} implementation of this method. While MRC provide integrability of the underlying dynamical system, gMRC generally do not but may be used for qualitative and numerical study of dynamical systems describing generic resonance clusters.
On The Possible Mechanism Of Energy Dissipation In Shock‐Wave Fronts Driven Ahead Of Coronal Mass Ejections

Analysis of Mark 4 and LASCO C2, C3 coronagraph data shows that, at the distance R⩽0 R⊙ from the center of the Sun, the thickness of a CME‐generated shock‐wave front (δF) may be of order of the proton mean free path. This means that the energy dissipation mechanism in the shock front at these distances is collisional. A new discontinuity (thickness δ*F≪δF) is observed to appear in the anterior part of the front at R⩾10 R⊙. Within the limits of experimental error, the thickness δ*F≈0.1–0.2 R⊙ does not vary with distance and is determined by the spatial resolution of the LASCO C3 instrument. At the initial stage of formation, the discontinuity on the scale of δ*F has rather small amplitude and exists simultaneously with the front having thickness δF. The relative amplitude of the discontinuity gradually increases with distance, and the brightness profile behind it becomes even. Such transformations may be associated with the transition from a collisional shock wave to a collisionless one.
Impact of Digital Face Beautification in Biometrics

Face retouching is a widespread procedure available across a huge spectrum of modern applications. Among them, social media offer different filters to beautify face pictures by performing operations such as skin smoothing, addition of virtual makeup, as well as deforming certain facial features, for instance by widening the eyes or making the nose thinner. In this work, the effect of different facial feature modification filters (FFMF) on face recognition (FR), gender classifiers and a weight estimator are studied. To this end, popular FFMF are applied to face images of the publicly available CALFW and VIP_attribute databases. Such filters distort or modify biometric features, affecting the ability of automatic FR systems to recognize individuals. The results show that the application of FFMF to face images penalizes the accuracy of FR systems and affects the estimation of other facial traits such as gender and weight.
How Electronic Cigarette Affects the Vascular System

The popularity of the electronic cigarette has soared in the last decades. However, the health effect of smoking electronic cigarettes on the vascular system is unclear. This systematic review examines the electronic cigarettes' effect on the vascular system from recent evidence. A systematic search was conducted in MEDLINE (PubMed) database from January 2016 to August 2021 for studies assessing the vascular effect of chronic use of electronic cigarettes on human and animal. The Cochrane Risk of Bias 2, NIH Quality Assessment for Cross-Sectional Study, and SYRCLE's Risk of Bias were used to assess the risk of bias in interventional, observational, and animal study, respectively. A narrative synthesis of evidence is provided to describe results. From 101 retrieved studies related to electronic cigarettes effect on the vascular system, a total of 16 studies are included in this review. The overall results indicated that electronic cigarette use is associated with adverse events in the vascular, including the incident of elevated oxidative stress, endothelial dysfunction, inflammation, arterial stiffness, and the development of atherosclerotic lesion. Further studies should broaden perspectives and reveal more about the mechanism of how electronic cigarettes impact on vascular system.
Contraindicated drug-drug interactions associated with oral antimicrobial agents prescribed in in States

Objective : Antimicrobial agents are commonly used in ambulatory care settings. Our objective 23 was to examine national-level patterns of contraindications between oral antibacterial or 24 antifungal agents and patients’ other oral medications in the U.S ambulatory care setting. 25 Methods : This cross-sectional study included multiple year pooled data (2003-2011) from the 26 National Ambulatory Medical Care Survey (NAMCS) and the National Hospital Ambulatory 27 Medical Care Survey (NHAMCS Outpatient Department). Visits by adults (age ≥ 18 years) in 28 ambulatory settings in US who were prescribed oral antibacterial or antifungal agents were 29 evaluated for potential drug-drug interaction contraindications. Findings with Relative Standard 30 Error > 30% or unweighted sample size < 30 were not reported as these were deemed unreliable 31 estimates. : there were 1,235,000 visits (proportion = 0.52%, 95% combination statin lovastatin) visits, proportion CI quinidine,
Saccharomyces cerevisiae as a Model System for Eukaryotic Cell Biology, from Cell Cycle Control to DNA Damage Response

The yeast Saccharomyces cerevisiae has been used for bread making and beer brewing for thousands of years. In addition, its ease of manipulation, well-annotated genome, expansive molecular toolbox, and its strong conservation of basic eukaryotic biology also make it a prime model for eukaryotic cell biology and genetics. In this review, we discuss the characteristics that made yeast such an extensively used model organism and specifically focus on the DNA damage response pathway as a prime example of how research in S. cerevisiae helped elucidate a highly conserved biological process. In addition, we also highlight differences in the DNA damage response of S. cerevisiae and humans and discuss the challenges of using S. cerevisiae as a model system.
Intelligent System for Personalised Interventions and Early Drop-out Prediction in MOOCs

—In this paper, we propose an approach to early detect students at high risk of drop-out in MOOC (Massive Open Online Course); we design personalised interventions to mitigate that risk. We apply Machine Learning (ML) algorithms and data mining techniques to a dataset extracted from XuetangX MOOC learning platforms and sourced from the KDD cup 2015. Since this dataset contains only raw student log activity records, we perform a hybrid feature selection and dimensionality reduction techniques to extract relevant features, and reduce models complexity and computation time. Besides, we built two models based on: Genetic Algorithms (GA) and Deep Learning (DL) with supervised learning methods. The obtained results, according to the accuracy and the AUC (Area Under Curve)-ROC (Reciever Operator Characteristic) metrics, prove the pertinence of the extracted features and encourage the use of the hybrid features selection. They also proved that GA and DL are outperforming the baseline algorithms used in related works. To assess the generalisation of the approach used in this work, The same process is performed to a second benchmark dataset extracted from the university MOOC. Then, a single web application hosted on the university server, produces an individual weekly drop-out probability, using time series data. It also proposes an approach to personalise and prioritise interventions for at-risk students according to the drop-out patterns.
CBT4Depression: A Cognitive Behaviour Therapy (CBT) Therapeutic Game to Reduce Depression Level among Adolescents

—Dropping out of depression treatment commonly occurs in the current psychotherapy treatment. Adolescents often find it difficult to express their thoughts and feelings clearly due to their developmental constraints. They also have trouble realising their behaviours as unhealthy or problematic. The use of therapeutic games in depression treatment among adolescents can enhance the engagement level. Indirectly, the issue of dropping out can be reduced among the adolescents. Therefore, this study aimed to improve engagement levels and reduce depression level among adolescents with depression by designing a therapeutic game. A prototype named CBT4Depression was developed in this study. A quasi experimental study was conducted to evaluate the developed therapeutic game and 115 adolescents were recruited to measure their depression level using CBT4Depression. Based on the findings from the evaluation process, it can be concluded that the CBT4Depression considered success to engage and reduce the depression level among adolescents.
Can Be Automatically Generated )

The scientific community produces many papers with dull and uninteresting titles. We wanted to explore how researchers break these standards and create memorable names. In this work, we present a coherent view of the current naming conventions of IEEE VIS papers and propose an online tool for their automatic generation. We took advantage of the predictable behavior of the naming habits of the vis community, and we compared them with cultural references and paper titles from other scientific fields. Based on our findings, we formed two iterations of vis naming grammar and used the second one in a publicly available tool. Lastly, inspired by similar works, we created a quiz comprising real and fake vis titles.