Miracle-dz/UniFAR-FTUs huggingface dataset:
Detection of SARS-CoV-2 genome in the air, surfaces, and wastewater of the referral hospitals, Gorgan, north of Iran

Background and Objectives: Coronavirus disease 2019 (COVID-19) is a pandemic caused by the novel virus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Knowing the virus’s behavior and its persistence in different environments are crucial and will lead to the proper management of the disease. In this study, air, surface, and sewage samples were taken from different parts of referral hospitals for COVID-19. Materials and Methods: Air samples were taken with impinger, surface samples with swabs, and sewage samples were taken from the hospital wastewater treatment plant. After viral genome extraction, a real-time RT-PCR test was applied to confirm the presence of SARS-CoV-2 RNA in the collected samples. Results: The virus genome could be traced in the wards and wastewater related to hospitalized COVID-19 patients. Overally, 29%, 16%, and 37.5% of air, surface, and sewage samples were positive for the SARS-CoV-2 genome, respectively. Conclusion: Findings of such studies provide valuable results regarding the degree of contamination of hospital environments and the risk of virus transmission in different environments and among hospital staff and patients.
Increased serum uric acid level is associated with better outcome after endovascular treatment for acute ischemic stroke—a prospective cohort study

Background The role of serum uric acid (SUA) in affecting outcomes after endovascular treatment (EVT) in patients with ischemic stroke remains unclear. This study investigated the association of SUA with outcomes of patients with acute large vessel occlusion (LVO) who had received EVT. Methods Patients with acute LVO stroke who underwent EVT within 24 hours were enrolled from a prospective, nationwide registry study. Baseline characteristics and SUA level within 24 hours of EVT were collected. The primary outcome was an excellent 90-day functional outcome [modified Rankin Scale (mRS) score 0–1]. Secondary outcomes included a favorable 90-day outcome (mRS score 0–2), symptomatic intracranial hemorrhage (sICH), and 90-day mortality. The SUA level was analyzed in quartiles and as a continuous variable. We investigated the independent association of SUA with the primary outcome using multivariable logistic regression. Results Among 780 patients (mean age 64 years; 66.28% males), 230 (29.49%) had an excellent 90-day outcome. A higher SUA level was significantly associated with an excellent outcome in univariate logistic regression (P=0.045) and after adjusting for confounders in multivariate analysis [adjusted odds ratio (aOR), 0.998; 95% confidence interval (CI), 0.996–1.000; P=0.018]. Multivariate logistic regression analysis showed patients with SUA level in the fourth quartile had an excellent 90-day outcome (aOR, 0.367; 95% CI, 0.154–0.876; P=0.024). There was no significant association for SUA level with favorable 90-day outcome, sICH, or 90-day mortality (P>0.05). Conclusions Among patients with acute LVO type of stroke who received EVT, baseline high SUA level may predict a better 90-day functional outcome.
Personalized Deep Bi-LSTM RNN Based Model for Pain Intensity Classification Using EDA Signal

Automatic pain intensity assessment from physiological signals has become an appealing approach, but it remains a largely unexplored research topic. Most studies have used machine learning approaches built on carefully designed features based on the domain knowledge available in the literature on the time series of physiological signals. However, a deep learning framework can automate the feature engineering step, enabling the model to directly deal with the raw input signals for real-time pain monitoring. We investigated a personalized Bidirectional Long short-term memory Recurrent Neural Networks (BiLSTM RNN), and an ensemble of BiLSTM RNN and Extreme Gradient Boosting Decision Trees (XGB) for four-category pain intensity classification. We recorded Electrodermal Activity (EDA) signals from 29 subjects during the cold pressor test. We decomposed EDA signals into tonic and phasic components and augmented them to original signals. The BiLSTM-XGB model outperformed the BiLSTM classification performance and achieved an average F1-score of 0.81 and an Area Under the Receiver Operating Characteristic curve (AUROC) of 0.93 over four pain states: no pain, low pain, medium pain, and high pain. We also explored a concatenation of the deep-learning feature representations and a set of fourteen knowledge-based features extracted from EDA signals. The XGB model trained on this fused feature set showed better performance than when it was trained on component feature sets individually. This study showed that deep learning could let us go beyond expert knowledge and benefit from the generated deep representations of physiological signals for pain assessment.
Model building for flavor changing Higgs couplings

If $t\rightarrow hq$ ($q=c,u$) or $h\rightarrow\tau\ell$ ($\ell=\mu,e$) decays are observed, it will be a clear signal of new physics. We investigate whether natural and viable flavor models can saturate the present direct upper bounds without violating the indirect constraints from low energy loop processes. We carry out our analysis in two theoretical frameworks: minimal flavor violation (MFV) and Froggatt-Nielsen symmetry (FN). The simplest models in either framework predict flavor changing couplings that are too small to be directly observed. Yet, in the MFV framework, it is possible to have lepton flavor changing Higgs couplings close to the bound if spurions related to heavy singlet neutrinos play a role. In the FN framework, it is possible to have large flavor changing couplings in both the up and the charged lepton sectors if supersymmetry plays a role.
Transition from the macrospin to chaotic behavior by a spin-torque driven magnetization precession of a square nanoelement

We demonstrate (using full-scale micromagnetic simulations) that the spin-injection driven steady-state precession of a thin magnetic nanoelement exhibits a complicated transition from a quasimacrospin to chaotic behavior with increasing element size. For nanoelement parameters and magnetic fields typical of those used experimentally we show that the macrospin approximation is invalid already for very small nanoelement sizes $(\ensuremath{\sim}30\phantom{\rule{0.3em}{0ex}}\mathrm{nm})$.
Equations of Laminar and Turbulent Flows in General Curvilinear Coordinates.

Abstract : Recent developments in computational fluid mechanics and grid generation have made it possible to consider complex three dimensional laminar and turbulent flows using nonorthogonal coordinates. However, the necessary equations in generalized nonorthogonal coordinates. However, the necessary equations in generalized nonorthogonal are not readily available in a single reference. The purpose of this report is to present these equations for an incompressible fluid. Methods of curvilinear tensor analysis are used to develop the most commonly used equations. Their relationship with the more familiar equations in orthogonal coordinates is shown. Finally, the practical problems of evaluating the many geometric coefficients which appear in these equations are examined by considering numerically generated coordinates for flow around three dimensional bodies. Keywords: Tensor analysis; General curvilinear coordinates; Equations of fluid motion; Turbulence models; Body fitted coordinates; and Computational fluid dynamics.
The Sloan Digital Sky Survey Reverberation Mapping Project: The C iv Blueshift, Its Variability, and Its Dependence Upon Quasar Properties

We use the multi-epoch spectra of 362 quasars from the Sloan Digital Sky Survey Reverberation Mapping project to investigate the dependence of the blueshift of C iv relative to Mg ii on quasar properties. We confirm that high-blueshift sources tend to have low C iv equivalent widths (EWs), and that the low-EW sources span a range of blueshift. Other high-ionization lines, such as He ii, also show similar blueshift properties. The ratio of the line width (measured as both the full width at half maximum and the velocity dispersion) of C iv to that of Mg ii increases with blueshift. Quasar variability enhances the connection between the C iv blueshift and quasar properties (e.g., EW). The variability of the Mg ii line center (i.e., the wavelength that bisects the cumulative line flux) increases with blueshift. In contrast, the C iv line center shows weaker variability at the extreme blueshifts. Quasars with the high-blueshift C iv lines tend to have less variable continuum emission, when controlling for EW, luminosity, and redshift. Our results support the scenario that high-blueshift sources tend to have large Eddington ratios.
Effects of sweetpotato (Ipomoea batatas) puree on bread shelf-life

Bioactive compounds in sweet potatoes of different flesh colors possessed potential antioxidant and antimicrobial properties important for human health and food quality. The objective of this study was to determine the levels of bioactive compounds and their inhibitory effects on mold fungi in bread. Composite bread was made by replacing 10, 20, 30 and 40% wheat flour with puree from the sweet potato of different flesh colors. The loaves of bread were incubated over 8-days and analyzed for the fungi load. Physiochemical characteristics: Proximate composition, specific sugars, composites of carotenoids, flavonoids, phenols, and antioxidant activity, as well as ascorbic acid, were analyzed. Orange Fleshed Sweetpotato (OFSP) puree bread, at all levels of wheat flour substitution and Purple Fleshed Sweetpotato (PFSP) puree bread at 10 and 20% wheat flour substitution showed increased shelf-life up to six days, compared to 100% wheat bread that staled at day 3. Microbial inhibition properties exhibited by OFSP and PFSP are attributed to their respective phytochemicals and antioxidant activity of 303.38 and 32.29 mgTE/100 g. Yellow Fleshed Sweetpotato (YFSP) puree bread stayed up to day 4 with antioxidant activity of 64.456 mgTE/100 g whereas White Fleshed Sweetpotato (WFSP) and Cream Fleshed Sweetpotato (CFSP) puree breads had significantly lower (p<0.05) levels of phytochemical contents limiting their inhibition.
Survey for Computer-Aided Tools and Databases in Metabolomics

Metabolomics has advanced from innovation and functional genomics tools and is currently a basis in the big data-led precision medicine era. Metabolomics is promising in the pharmaceutical field and clinical research. However, due to the complexity and high throughput data generated from such experiments, data mining and analysis are significant challenges for researchers in the field. Therefore, several efforts were made to develop a complete workflow that helps researchers analyze data. This paper introduces a review of the state-of-the-art computer-aided tools and databases in metabolomics established in recent years. The paper provides computational tools and resources based on functionality and accessibility and provides hyperlinks to web pages to download or use. This review aims to present the latest computer-aided tools, databases, and resources to the metabolomics community in one place.
SAGE III/ISS ozone and NO2 validation using diurnal scaling factors

Abstract. We developed a set of solar zenith angle, latitude- and altitude-dependent scaling factors to account for the diurnal variability in ozone (O3) and nitrogen dioxide (NO2) when comparing Stratospheric Aerosol and Gas Experiment (SAGE) III/ISS observations to observations from other times of day. The scaling factors are calculated as a function of solar zenith angle from the four-dimensional output of a global atmospheric chemistry model simulation of 2017–2020 that shows good agreement with observed vertical profiles. Using a global atmospheric chemistry model allows us to account for both chemically and dynamically driven variability. Both year-specific scale factors and a multi-year monthly climatology are available to decrease the uncertainty in inter-instrument comparisons and allow consistent comparisons between observations from different times of day. We describe the variability in the diurnal scale factors as a function of space and time. The quasi-biennial oscillation (QBO) appears to be a contributing factor to interannual variability in the NO2 scaling factors, leading to differences between years that switch sign with altitude. We show that application of these scaling factors improves the comparison between SAGE III/ISS and OSIRIS NO2 and between SAGE III/ISS and OMPS LP, OSIRIS, and ACE-FTS O3 observations. The comparisons between SAGE III/ISS O3 for sunrise or sunset vs. Microwave Limb Sounder (MLS) daytime or nighttime observations are also more consistent when we apply the diurnal scaling factors. There is good agreement between SAGE III/ISS V5.2 ozone and correlative measurements, with differences within 5 % between 20 and 50 km when corrected for diurnal variability. Similarly, the SAGE III/ISS V5.2 NO2 agreement with correlative measurement is mostly within 10 %. While the scale factors were designed for use with SAGE III/ISS observations, they can easily be applied to other observation intercomparisons as well.
Spacecraft Charging Model - Two Maxwellian Approximation.

Abstract : The ambient plasma environment at geosynchronous orbit is assumed to be represented by a two-component Maxwell-Boltzmann particle distribution. Given this, the equations for ambient electron and ion currents to the spacecraft are easily integrated. Likewise, the secondary and backscattered currents can be expressed as integrals. The potential at which the currents balance gives the potential between the spacecraft and ambient plasma. The model is compared with actual data from ATS-5 and is found to agree within plus or minus 1, 200 V over a range of 0 to minus 10,000 V. The model is readily applicable to the simple environmental model of Garrett and DeForest (1979) and can be calibrated to any given satellite. Simple algorithmic expressions are also developed for the backscattered and secondary currents as a function of temperature and potential which promise a significant decrease in computer time without a significant loss in accuracy. (Author)
Revealing a Head-on Major Merger in the Nearby NGC 6338 Group with Chandra and VLA Observations

By analyzing the Chandra archival data of the nearby NGC 6338 galaxy group, we identify two X-ray bright clumps (N-clump and S-clump) within the central kpc, and detect an arc-like X-ray brightness discontinuity at the south boundary of the N-clump, which is defined as a cold front with a gas flow Mach number of . Furthermore, at the northeast boundary of the S-clump (dominated by galaxy NGC 6338) another X-ray edge is detected that corresponds to a weaker cold front. Therefore, the two clumps are approaching each other approximately from opposite directions, and the group is undergoing a head-on collision that is in a stage of pre-core passage. This merger scenario is also supported by the study of the line-of-sight velocity distribution of the group member galaxies. The merger mass ratio is about 1:1.8 as estimated from the central gas temperature of the two clumps, which suggests the merger is most likely to be a major merger. We also analyze the Very Large Array 1.4 and 4.9 GHz radio data, but we do not detect any extended radio emission that is associated with the merger.
Improvement of Ultrasound Image Quality Using Non-Local Means Noise-Reduction Approach for Precise Quality Control and Accurate Diagnosis of Thyroid Nodules

This study aimed to improve the quality of ultrasound images by modeling an algorithm using a non-local means (NLM) noise-reduction approach to achieve precise quality control and accurate diagnosis of thyroid nodules. An ATS-539 multipurpose phantom was used to scan the dynamic range and gray-scale measurement regions, which are most closely related to the noise level. A convex-type 3.5-MHz frequency probe is used for scanning according to ATS regulations. In addition, ultrasound images of human thyroid nodules were obtained using a linear probe. An algorithm based on the NLM noise-reduction approach was modeled based on the intensity and relative distance of adjacent pixels in the image, and conventional filtering methods for image quality improvement were designed as a comparison group. When the NLM algorithm was applied to the image, the contrast-to-noise ratio and coefficient of variation values improved by 28.62% and 19.54 times, respectively, compared with those of the noisy images. In addition, the image improvement efficiency of the NLM algorithm was superior to that of conventional filtering methods. Finally, the applicability of the NLM algorithm to human thyroid images using a high-frequency linear probe was validated. We demonstrated the efficiency of the proposed algorithm in ultrasound images and the possibility of capturing improved images in the dynamic range and gray-scale region for quality control parameters.
Production and Characterization of a Novel Exopolysaccharide from Ramlibacter tataouinensis

The current study examines the desiccation-resistant Ramlibacter tataouinensis TTB310T as a model organism for the production of novel exopolysaccharides and their structural features. This bacterium is able to produce dividing forms of cysts which synthesize cell-bound exopolysaccharide. Initial experiments were conducted on the enrichment of cyst biomass for exopolysaccharide production under batch-fed conditions in a pilot-scale bioreactor, with lactate as the source of carbon and energy. The optimized medium produced significant quantities of exopolysaccharide in a single growth phase, since the production of exopolysaccharide took place during the division of the cysts. The exopolysaccharide layer was extracted from the cysts using a modified trichloroacetic acid method. The biochemical characterization of purified exopolysaccharide was performed by gas chromatography, ultrahigh-resolution mass spectrometry, nuclear magnetic resonance, and Fourier-transform infrared spectrometry. The repeating unit of exopolysaccharide was a decasaccharide consisting of ribose, glucose, rhamnose, galactose, mannose, and glucuronic acid with the ratio 3:2:2:1:1:1, and additional substituents such as acetyl, succinyl, and methyl moieties were also observed as a part of the exopolysaccharide structure. This study contributes to a fundamental understanding of the novel structural features of exopolysaccharide from a dividing form of cysts, and, further, results can be used to study its rheological properties for various industrial applications.
Use of Mobile Laser Scanning (MLS) to Monitor Vegetation Recovery on Linear Disturbances

Seismic lines are narrow, linear corridors cleared through forests for oil and gas exploration. Their inconsistent recovery has led to Alberta’s forests being highly fragmented, resulting in the need for seismic line restoration programs and subsequent monitoring. Light detection and ranging (LiDAR) is becoming an increasingly popular technology for the fast and accurate measurement of forests. Mobile LiDAR scanners (MLS) are emerging as an alternative to traditional aerial LiDAR due to their increased point cloud density. To determine whether MLS could be effective for collecting vegetation data on seismic lines, we sampled 17 seismic lines using the Emesent Hovermap™ in leaf-on and leaf-off conditions. Processing the LiDAR data was conducted with GreenValley International’s LiDAR 360 software, and data derived from the point clouds were compared to physically measured field data. Overall, the tree detection algorithm was unsuccessful at accurately segmenting the point clouds. Complex vegetation environments on seismic lines, including small conifers with obscured stems or extremely dense and tall shrubs with overlapping canopies, posed a challenge for the software’s capacity to differentiate trees As a result, tree densities and diameters were overestimated, while tree heights were underestimated. Exploration of alternative algorithms and software is needed if measuring vegetation data on seismic lines with MLS is to be implemented.
The Quality and Productivity of Strawberry (Fragaria × ananassa Duch.) Improved by the Inoculation of PGPR Bacillus velezensis BS89 in Field Experiments

Efficient plant-growth-promoting rhizobacteria (PGPR) used as biofertilizers and biological control agents are promising substitutes for minimizing the application of synthetic agrochemicals in crop production. We studied the effect of PGPR strain Bacillus velezensis BS89 alone and in combination with three forms of nitrogen fertilizers (ammonium nitrate, carbamide, and ammonium sulfate) on the productivity of two strawberry varieties in three-year field experiments. We first showed that the application of PGPR Bacillus velezensis BS89 on strawberries demonstrated the same effect as the application of nitrogen fertilizers. Use of the strain BS89 increased the chlorophyll content in plant leaves by 2.7–6.8%, and also increased the yield of berries by 6.7–36.4% for cv. Rusich and 7.5–19.3% for cv. Troitskaya depending on the form of nitrogen fertilizer. The best results in the yield of strawberry plants of the cv. Rusich were achieved in the variant BS89 + ammonium nitrate (41.9–57.4%), and the cv. Troitskaya—in the BS89 + carbamide variant (8.1–38.8%). Three-year use of strain BS89 for cv. Rusich resulted in an increase of runner’s weight by 212.1%, and also the weight of the roots by 120%, thereby significantly improving the mineral nutrition of plants. This is mainly associated with the plant growth-promoting activity of Bacillus velezensis BS89, which was able to produce a high amount of IAA—494.1 µg/mL. We believe that the PGPR strain BS89 can be successfully used for growing strawberries. However, each variety requires careful selection of the composition of nitrogen fertilizers and analysis of the compatibility of fertilizers and the PGPR strain.