Miracle-dz/UniFAR-FTUs huggingface dataset:
Exploring the druggability of the binding site of aurovertin, an exogenous allosteric inhibitor of FOF1-ATP synthase

In addition to playing a central role in the mitochondria as the main producer of ATP, FOF1-ATP synthase performs diverse key regulatory functions in the cell membrane. Its malfunction has been linked to a growing number of human diseases, including hypertension, atherosclerosis, cancer, and some neurodegenerative, autoimmune, and aging diseases. Furthermore, inhibition of this enzyme jeopardizes the survival of several bacterial pathogens of public health concern. Therefore, FOF1-ATP synthase has emerged as a novel drug target both to treat human diseases and to combat antibiotic resistance. In this work, we carried out a computational characterization of the binding sites of the fungal antibiotic aurovertin in the bovine F1 subcomplex, which shares a large identity with the human enzyme. Molecular dynamics simulations showed that although the binding sites can be described as preformed, the inhibitor hinders inter-subunit communications and exerts long-range effects on the dynamics of the catalytic site residues. End-point binding free energy calculations revealed hot spot residues for aurovertin recognition. These residues were also relevant to stabilize solvent sites determined from mixed-solvent molecular dynamics, which mimic the interaction between aurovertin and the enzyme, and could be used as pharmacophore constraints in virtual screening campaigns. To explore the possibility of finding species-specific inhibitors targeting the aurovertin binding site, we performed free energy calculations for two bacterial enzymes with experimentally solved 3D structures. Finally, an analysis of bacterial sequences was carried out to determine conservation of the aurovertin binding site. Taken together, our results constitute a first step in paving the way for structure-based development of new allosteric drugs targeting FOF1-ATP synthase sites of exogenous inhibitors.
Gut microbiota composition reflects disease progression, severity and outcome, and dysfunctional immune responses in patients with hypertensive intracerebral hemorrhage

Objective In this study, we aimed to explore the alterations in gut microbiota composition and cytokine responses related to disease progression, severity, and outcomes in patients with hypertensive intracerebral hemorrhage (ICH). Methods Fecal microbiota communities of 64 patients with ICH, 46 coronary heart disease controls, and 23 healthy controls were measured by sequencing the V3-V4 region of the 16S ribosomal RNA (16S rRNA) gene. Serum concentrations of a broad spectrum of cytokines were examined by liquid chips and ELISA. Relationships between clinical phenotypes, microbiotas, and cytokine responses were analyzed in the group with ICH and stroke-associated pneumonia (SAP), the major complication of ICH. Results In comparison with the control groups, the gut microbiota of the patients with ICH had increased microbial richness and diversity, an expanded spectrum of facultative anaerobes and opportunistic pathogens, and depletion of anaerobes. Enterococcus enrichment and Prevotella depletion were more significant in the ICH group and were associated with the severity and functional outcome of ICH. Furthermore, Enterococcus enrichment and Prevotella depletion were also noted in the SAP group in contrast to the non-SAP group. Enterococci were also promising factors in the prognosis of ICH. The onset of ICH induced massive, rapid activation of the peripheral immune system. There were 12 cytokines (Eotaxin, GM-CSF, IL-8, IL-9, IL-10, IL-12p70, IL-15, IL-23, IL-1RA, IP-10, RANTES, and TNF-α) changed significantly with prolongation of ICH, and the Th2 responses correlated with the 90-day outcomes. Cytokines TNF-α, IP-10, IL-1RA, IL-8, IL-18, and MIP-1β in SAP group significantly differed from non-SAP group. Among these cytokines, only IP-10 levels decreased in the SAP group. Enterococcus was positively associated with IL-1RA and negatively associated with IP-10, while Prevotella was inversely associated in both the ICH and SAP groups. Conclusion This study revealed that gut dysbiosis with enriched Enterococcus and depleted Prevotella increased the risk of ICH and subsequently SAP. The altered gut microbiota composition and serum cytokine profiles are potential biomarkers that reflect the inciting physiologic insult/stress involved with ICH.
A Natural Human-Drone Embodied Interface: Empirical Comparison With a Traditional Interface

Despite the importance of usability in human-machine interaction (HMI), most commonly used devices are not usable by all potential users. In particular, users with low or null technological experience, or with special needs, require carefully designed systems and easy-to-use interfaces supporting recognition over recall. To this purpose, Natural User Interfaces (NUIs) represent an effective strategy as the user's learning is facilitated by features of the interface that mimic the human “natural” sensorimotor embodied interactions with the environment. This paper compares the usability of a new NUI (based on an eye-tracker and hand gesture recognition) with a traditional interface (keyboard) for the distal control of a simulated drone flying in a virtual environment. The whole interface relies on “dAIsy”, a new software allowing the flexible use of different input devices and the control of different robotic platforms. The 59 users involved in the study were required to complete two tasks with each interface, while their performance was recorded: (a) exploration: detecting trees embedded in an urban environment; (b) accuracy: guiding the drone as accurately and fast as possible along a predefined track. Then they were administered questionnaires regarding the user's background, the perceived embodiment of the device, and the perceived quality of the virtual experience while either using the NUI or the traditional interface. The results appear controversial and call for further investigation: (a) contrary to our hypothesis, the specific NUI used led to lower performance than the traditional interface; (b) however, the NUI was evaluated as more natural and embodied. The final part of the paper discusses the possible causes underlying these results that suggest possible future improvements of the NUI.
Computational costs of data definition at the quantum - classical interface

Model-independent semantic requirements for user specification and interpretation of data before and after quantum computations are characterized. Classical computational costs of assigning classical data values to quantum registers and to run-time parameters passed across a classical-to-quantum application programming interface are derived. It is shown that the classical computational costs of data definition equal or exceed the classical computational cost of solving the problem of interest for all applications of quantum computing except computations defined over the integers and the simulation of linear systems with linear boundary conditions.
Internalized homophobia and sexual risk behavior in men who have sex with men: The mediational role of sexual self-concept

Men who have sex with men (MSM) are one of the populations most likely to be infected with human immunodeficiency virus (HIV) and acquired immunodeficiency syndrome (AIDS) worldwide. Sexual risk behaviors (SRB) are the main route of HIV transmission. Among the factors associated with SRB, internalized homophobia (rejection of one’s sexuality) is a risk factor unique for MSM. However, how this factor influences SRB is not clear. Therefore, the present study attempts to clarify the mechanism of action of the relationship between internalized homophobia on SRB based on the mediating effects of sexual self-concept. A study was conducted with 124 MSM living in Chile over 18 years of age (M = 24.4 and SD = 4.19). Through path analysis, it was observed that internalized homophobia has slight inverse effects on SRBs (multiple sexual partners and sexual activity under the influence of alcohol or drugs) when the sexual self-efficacy dimension acts as a mediating variable. These findings suggest that developing sexually transmitted infections (STIs) and HIV/AIDS prevention campaigns focused on MSM must highlight the development of a healthy sexual self-concept and address self-stigma.
Canny algorithm: A new estimator for primordial non-Gaussianities

We utilize the Canny edge detection algorithm as an estimator for primordial non-Gaussianities. In preliminary tests on simulated sky patches with a window size of 57 degrees and multipole moments $l$ up to 1024, we find a $3\sigma$ distinction between maps with local non-Gaussianity $f_{NL}=350$ (or $f_{NL}=-700$) and Gaussian maps. We present evidence that high resolution CMB studies will strongly enhance the sensitivity of the Canny algorithm to non-Gaussianity, making it a promising technique to estimate primordial non-Gaussianity.
Graph Representations of News Articles for Background Linking

Context deﬁnes the circumstances in which things happen and is crucial to fully understand complicated events. This applies especially to news articles, in which an adjustment in context can change the perspective of a story dramatically. To better understand an article, news sites can provide a list of background recommendations. To advance in the development of these systems and to investigate how news is represented online, the Text and REtrieval Conference started a track dedicated to information retrieval and news. This work investigates the performance of a graph-based retrieval method for the task of background linking. That is, the retrieval of context enriching background articles for a speciﬁc topic article. In order to do so, we explored the representation of news articles in graph form, looked at the application of named entities in the news domain and examined relevance measures to increase ranking performance. The proposed models were compared to a state-of-the-art “bag-of-words” baseline, but no signiﬁcant improvements in effectiveness were found.
Increased Risk of Generalized Anxiety Disorder According to Frequent Sedentary Times Based on the 16th Korea Youth Risk Behavior Web-Based Survey

This study aimed to identify the association between sedentary behavior and anxiety disorders in 53,510 Korean adolescents. It analyzed data from the 16th (2020) Korea Youth Risk Behavior Web-based Survey (KYRBS). The dependent variable was the generalized anxiety disorder-7 (GAD-7). The GAD-7 scores were divided into normal, mild, moderate, and severe levels. The independent variables were sedentary time for learning, other sedentary times, total sedentary time, and regular physical activity. The confounding variables were sex, grade, stress, depression, substance abuse, suicidal thoughts, violent victimization, drinking, smoking, sleep satisfaction, and smartphone addiction. A chi-squared test, one-way analysis of variance, and logistic regression analysis were used for analysis. After adjusting for all confounding variables, the risk of severe level in GAD-7 increased by 1.045 times each time the sedentary time for learning based on increased by one hour. In other sedentary time and total sedentary time, the risk of severe level in GAD-7 increased by 1.025 times and 1.045 times per hour, respectively. However, in regular physical activity, after adjusting for the confounding variables, there was no significant association with the GAD-7 levels. Therefore, to prevent generalized anxiety disorders in Korean adolescents, it is necessary to reduce the overall sedentary times including sedentary time for learning.
The Gas Kinematics of High Mass Star Forming Regions

The mechanism by which massive stars form is not nearly as well understood as it is for lower mass stars. For instance, at the onset of massive star formation, it is still not clear whether the mass for a given massive star comes from the turbulent collapse of a dense core (i.e McKee & Tan, 2003) or whether the star continues to accrete material from the cores environment as it grows (i.e. Bonnell et al., 1998) . From this point , it is suggested that the cold, massive core (an Infrared Dar Cloud) begins to heat up and form a Hot Core. Later in its protostellar evolution, an HII region forms from the ionizing radiation being produced by the massive star. How, or even whether, accretion onto the massive protostar can continue in the presence of the large outward thermal and radiation pressures from the star is also quite uncertain. Can the star continue to accrete ionized gas (i.e. Keto & Wood, 2006)? Are the accretion rates high enough early on to account for the final observed masses (i.e. Klaassen et al., 2006)? Or , is there some way of minimizing the radiation pressure affecting the infalling gas (i.e. McKee & Ostriker , 2007, and references therein). Here, we present observations which suggest that there is a statistically significant, although short, period in which rotation and infall of molecular gas (which powers a bipolar outflow) continue after the formation of an HII region. This continued infall of material is seen on both large and small scales, and appears to be continuing to produce outflows in many of the sources observed in this study. That it is not seen in all sources suggests that this stage is short lived.
Non-Gaussian Minkowski functionals and extrema counts in redshift space

In the context of upcoming large-scale structure surveys such as Euclid, it is of prime importance to quantify the effect of peculiar velocities on geometric probes. Hence the formalism to compute in redshift space the geometrical and topological one-point statistics of mildly non-Gaussian 2D and 3D cosmic fields is developed. Leveraging the partial isotropy of the target statistics, the Gram-Charlier expansion of the joint probability distribution of the field and its derivatives is reformulated in terms of the corresponding anisotropic variables. In particular, the cosmic non-linear evolution of the Minkowski functionals, together with the statistics of extrema are investigated in turn for 3D catalogues and 2D slabs. The amplitude of the non-Gaussian redshift distortion correction is estimated for these geometric probes. In 3D, gravitational perturbation theory is implemented in redshift space to predict the cosmic evolution of all relevant Gram-Charlier coefficients. Applications to the estimation of the cosmic parameters sigma(z) and beta=f/b1 from upcoming surveys is discussed. Such statistics are of interest for anisotropic fields beyond cosmology.
Changes in the characteristics of dry-wet periods in Xinjiang, China based on the SPEI index

The standardized precipitation evapotranspiration index (SPEI), calculated from 55 stations over the period 1961-2015, was used to analyze the spatial and temporal variability of the dry and wet climate in Xinjiang on a three and six-month time scale, so as to help to actively deal with the negative effects of climate change and reduce disaster losses. The obtained results show that precipitation and temperature in Xinjiang have an increasing trend, with rates of 8.90 mm and 0.39 ºC per decade, respectively. SPEI-3 and SPEI-6 show the same Xinjiang had a moistening trend. The spectra of wavelet coherence and cross wavelet transform showed that the SPEI values in Xinjiang have resonance periods of different time scales with the Atlantic Multidecadal Oscillation (AMO), El Nino Southern Oscillation (ENSO), North Atlantic Oscillation (NAO), and Pacific Decadal oscillation (PDO), but shows differences in different time-domain correlations. Among them, AMO is the main atmospheric circulation factor that affects SPEI in the region.
EXTINCTION AND DUST GEOMETRY IN M83 H ii REGIONS: AN HUBBLE SPACE TELESCOPE/WFC3 STUDY

We present Hubble Space Telescope/WFC3 narrow-band imaging of the starburst galaxy M83 targeting the hydrogen recombination lines (Hβ, Hα, and Paβ), which we use to investigate the dust extinction in the H ii regions. We derive extinction maps with 6 pc spatial resolution from two combinations of hydrogen lines (Hα/Hβ and Hα/Paβ), and show that the longer wavelengths probe larger optical depths, with AV values larger by ≳1 mag than those derived from the shorter wavelengths. This difference leads to a factor ≳2 discrepancy in the extinction-corrected Hα luminosity, a significant effect when studying extragalactic H ii regions. By comparing these observations to a series of simple models, we conclude that a large diversity of absorber/emitter geometric configurations can account for the data, implying a more complex physical structure than the classical foreground “dust screen” assumption. However, most data points are bracketed by the foreground screen and a model where dust and emitters are uniformly mixed. When averaged over large (≳100–200 pc) scales, the extinction becomes consistent with a “dust screen,” suggesting that other geometries tend to be restricted to more local scales. Moreover, the extinction in any region can be described by a combination of the foreground screen and the uniform mixture model with weights of 1/3 and 2/3 in the center (≲2 kpc), respectively, and 2/3 and 1/3 for the rest of the disk. This simple prescription significantly improves the accuracy of the dust extinction corrections and can be especially useful for pixel-based analyses of galaxies similar to M83.
Holographic nuclei: supersymmetric examples

We provide a dual gravity description of a supersymmetric heavy nucleus, following the idea of our previous paper arXiv/0809.3141. The supersymmetric nucleus consists of a merginal bound state of A baryons distributed over a ball in 3 dimensions. In the gauge/string duality, the baryon in = 4 super Yang-Mills (SYM) theory corresponds to a D5-brane wrapping S5 of the AdS5×S5 spacetime, so the nucleus corresponds to a collection of A D5-branes. We take a large A and a near horizon limits of a back-reacted geometry generated by the wrapped A D5-branes, where we find a gap in the supergravity fluctuation spectrum. This spectrum is a gravity dual of giant resonances of heavy nuclei, in the supersymmetric toy example of QCD.
Granger-causality between islamic banks and conventional banks: evidence from Malaysia

This paper explores the Granger-causal relationship between Islamic banks ’ non-performing financing (NPF) and conventional banks ’ non-performing loans (NPL) for the banking industry in Malaysia. To further understand these asset quality variables, we added domestic macroeconomic variables namely domestic credit, real lending rate and exchange rate for the period January 2007 to January 2017. All variables are I(1) in nature on the basis Augmented Dicker Fuller (ADF) and Philips-Perron (PP) unit root test. Using time series cointegrating VAR models, coupled with the Long Run Structural Modelling (LRSM), Vector Error Correction Model (VECM) and Variance Decomposition (VDC), the results tend to suggest that NPF leads NPL. Contrary to expectation, the VDC results suggest that NPF and NPL variables are exogenous and endogenous respectively. This unexpected result gave rise to many interesting arguments especially within the Islamic banking perspectives. Apart from providing important insights into the causality between NPF and NPL, our results contribute to the policy implications. Interest rate variable being the most exogenous variable can affect both NPFs and NPLs. The CUSUM and CUSUMSQ tests substantiate the stability of the functions. _____________________________________
Parallelistic Convolution Neural Network Approach for Brain Tumor Diagnosis

Today, Magnetic Resonance Imaging (MRI) is a prominent technique used in medicine, produces a significant and varied range of tissue contrasts in each imaging modalities, and is frequently employed by medical professionals to identify brain malignancies. With brain tumor being a very deadly disease, early detection will help increase the likelihood that the patient will receive the appropriate medical care leading to either a full elimination of the tumor or the prolongation of the patient’s life. However, manually examining the enormous volume of magnetic resonance imaging (MRI) images and identifying a brain tumor or cancer is extremely time-consuming and requires the expertise of a trained medical expert or brain doctor to manually detect and diagnose brain cancer using multiple Magnetic Resonance images (MRI) with various modalities. Due to this underlying issue, there is a growing need for increased efforts to automate the detection and diagnosis process of brain tumor without human intervention. Another major concern most research articles do not consider is the low quality nature of MRI images which can be attributed to noise and artifacts. This article presents a Contrast Limited Adaptive Histogram Equalization (CLAHE) algorithm to precisely handle the problem of low quality MRI images by eliminating noisy elements and enhancing the visible trainable features of the image. The enhanced image is then fed to the proposed PCNN to learn the features and classify the tumor using sigmoid classifier. To properly train the model, a publicly available dataset is collected and utilized for this research. Additionally, different optimizers and different values of dropout and learning rates are used in the course of this study. The proposed PCNN with Contrast Limited Adaptive Histogram Equalization (CLAHE) algorithm achieved an accuracy of 98.7%, sensitivity of 99.7%, and specificity of 97.4%. In comparison with other state-of-the-art brain tumor methods and pre-trained deep transfer learning models, the proposed PCNN model obtained satisfactory performance.
The Link Between Magnetic Fields and Cloud/Star Formation

The question whether magnetic fields play an important role in the processes of molecular cloud and star formation has been debated for decades. Recent observations have revealed a simple picture that may help illuminate these questions: magnetic fields have a tendency to preserve their orientation at all scales that have been probed - from 100-pc scale inter-cloud media down to sub-pc scale cloud cores. This ordered morphology has implications for the way in which self-gravity and turbulence interact with magnetic fields: both gravitational contraction and turbulent velocities should be anisotropic, due to the influence of dynamically important magnetic fields. Such anisotropy is now observed. Here we review these recent observations and discuss how they can improve our understanding of cloud/star formation.
THE VERTICAL-CURRENT APPROXIMATION NONLINEAR FORCE-FREE FIELD CODE—DESCRIPTION, PERFORMANCE TESTS, AND MEASUREMENTS OF MAGNETIC ENERGIES DISSIPATED IN SOLAR FLARES

In this work we provide an updated description of the Vertical-Current Approximation Nonlinear Force-Free Field (VCA-NLFFF) code, which is designed to measure the evolution of the potential, non-potential, free energies, and the dissipated magnetic energies during solar flares. This code provides a complementary and alternative method to existing traditional NLFFF codes. The chief advantages of the VCA-NLFFF code over traditional NLFFF codes are the circumvention of the unrealistic assumption of a force-free photosphere in the magnetic field extrapolation method, the capability to minimize the misalignment angles between observed coronal loops (or chromospheric fibril structures) and theoretical model field lines, as well as computational speed. In performance tests of the VCA-NLFFF code, by comparing with the NLFFF code of Wiegelmann, we find agreement in the potential, non-potential, and free energy within a factor of , but the Wiegelmann code yields in the average a factor of 2 lower flare energies. The VCA-NLFFF code is found to detect decreases in flare energies in most X, M, and C-class flares. The successful detection of energy decreases during a variety of flares with the VCA-NLFFF code indicates that current-driven twisting and untwisting of the magnetic field is an adequate model to quantify the storage of magnetic energies in active regions and their dissipation during flares. The VCA-NLFFF code is also publicly available in the Solar SoftWare.