Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of van der Waals Interactions on the Adsorption of Olympicene Radical on Cu(111): Characteristics of Weak Physisorption versus Strong Chemisorption

We report the results of Olympicene radical (C19H11) adsorption characteristics on Cu(111) obtained within the density functional framework with and without the inclusion of self-consistent van der Waals (vdW) interactions to evaluate their effects. Our calculations suggest that the vdW interactions enhance the adsorption energies, and the degree of enhancement strongly depends on the implementation. Among the considered configurations, the highest adsorption energy calculated using PBE is found to be 0.24 eV, while those obtained with the inclusion of vdW interactions are 1.32 eV (rPW86), 1.91 eV (optPBE), 2.29 eV (optB88), and 2.65 eV (optB86b). The high energetic contribution obtained using the vdW interactions correlates with the changes in the adsorption heights (from 3.4 A (PBE and rPW86) to 2.24 A (optB86b)), the change in the structural integrity of Olympicene radical upon adsorption, and the changes in the surface electronic structure. Furthermore, our calculations reveal a net charge transfer of.
Can Knowledge of Genetic Distances, Genome Sizes and Chromosome Numbers Support Breeding Programs in Hardy Geraniums?

Breeding programs in ornamentals can be facilitated by integrating knowledge of phylogenetic relatedness of potential parents along with other genomic information. Using AFLP, genetic distances were determined for 59 Geranium genotypes, comprising 55 commercial cultivars of the three subgenera of a total collection of 61 Geranium genotypes. A subgroup of 45 genotypes, including intragroup and intergroup hybrids, were selected and further characterized for genome sizes and chromosome numbers. The variation in genome size ranged from 1.51 ± 0.01 pg/2C to 12.94 ± 0.07 pg/2C. The chromosome numbers ranged from 26 to 108–110 with some hybrids showing an aberrant number of chromosomes based on their parents’ constitution. All chromosome numbers of Geranium are an even number, which presumes that unreduced gametes occur in some cross combinations. Overall, parental difference in genome size and chromosome number were not limiting for cross compatibility. Good crossing compatibility was correlated to a Jaccard similarity coefficient as parameter for parental relatedness of about 0.5. Additionally, parent combinations with high differences in the DNA/chromosome value could not result in a successful cross. We expect that our results will enable breeding programs to overcome crossing barriers and support further breeding initiatives.
Analysis of Kojic Acid Derivatives as Competitive Inhibitors of Tyrosinase: A Molecular Modeling Approach

Tyrosinases belong to the functional copper-containing proteins family, and their structure contains two copper atoms, in the active site, which are coordinated by three histidine residues. The biosynthesis of melanin in melanocytes has two stages depending on the actions of the natural substrates L-DOPA and L-tyrosine. The dysregulation of tyrosinase is involved in skin cancer initiation. In the present study, using molecular modeling tools, we analyzed the inhibition activity of tyrosinase activity using kojic acid (KA) derivatives designed from aromatic aldehydes and malononitrile. All derivatives showed conformational affinity to the enzyme active site, and a favorable distance to chelate the copper ion, which is essential for enzyme function. Molecular dynamics simulations revealed that the derivatives formed promising complexes, presenting stable conformations with deviations between 0.2 and 0.35 Å. In addition, the investigated KA derivatives showed favorable binding free energies. The most stable KA derivatives showed the following binding free energies: −17.65 kcal mol−1 (D6), −18.07 kcal mol−1 (D2), −18.13 (D5) kcal mol−1, and −10.31 kcal mol−1 (D4). Our results suggest that these derivatives could be potent competitive inhibitors of the natural substrates of L-DOPA (−12.84 kcal mol−1) and L-tyrosine (−9.04 kcal mol−1) in melanogenesis.
A Visual and VAE Based Hierarchical Indoor Localization Method

Precise localization and pose estimation in indoor environments are commonly employed in a wide range of applications, including robotics, augmented reality, and navigation and positioning services. Such applications can be solved via visual-based localization using a pre-built 3D model. The increase in searching space associated with large scenes can be overcome by retrieving images in advance and subsequently estimating the pose. The majority of current deep learning-based image retrieval methods require labeled data, which increase data annotation costs and complicate the acquisition of data. In this paper, we propose an unsupervised hierarchical indoor localization framework that integrates an unsupervised network variational autoencoder (VAE) with a visual-based Structure-from-Motion (SfM) approach in order to extract global and local features. During the localization process, global features are applied for the image retrieval at the level of the scene map in order to obtain candidate images, and are subsequently used to estimate the pose from 2D-3D matches between query and candidate images. RGB images only are used as the input of the proposed localization system, which is both convenient and challenging. Experimental results reveal that the proposed method can localize images within 0.16 m and 4° in the 7-Scenes data sets and 32.8% within 5 m and 20° in the Baidu data set. Furthermore, our proposed method achieves a higher precision compared to advanced methods.
Morphological and Metabolite Responses of Potatoes under Various Phosphorus Levels and Their Amelioration by Plant Growth-Promoting Rhizobacteria

Low phosphorus (P) availability is a major limiting factor for potatoes. P fertilizer is applied to enhance P availability; however, it may become toxic when plants accumulate at high concentrations. Therefore, it is necessary to gain more knowledge of the morphological and biochemical processes associated with P deficiency and toxicity for potatoes, as well as to explore an alternative approach to ameliorate the P deficiency condition. A comprehensive study was conducted (I) to assess plant morphology, mineral allocation, and metabolites of potatoes in response to P deficiency and toxicity; and (II) to evaluate the potency of plant growth-promoting rhizobacteria (PGPR) in improving plant biomass, P uptake, and metabolites at low P levels. The results revealed a reduction in plant height and biomass by 60–80% under P deficiency compared to P optimum. P deficiency and toxicity conditions also altered the mineral concentration and allocation in plants due to nutrient imbalance. The stress induced by both P deficiency and toxicity was evident from an accumulation of proline and total free amino acids in young leaves and roots. Furthermore, root metabolite profiling revealed that P deficiency reduced sugars by 50–80% and organic acids by 20–90%, but increased amino acids by 1.5–14.8 times. However, the effect of P toxicity on metabolic changes in roots was less pronounced. Under P deficiency, PGPR significantly improved the root and shoot biomass, total root length, and root surface area by 32–45%. This finding suggests the potency of PGPR inoculation to increase potato plant tolerance under P deficiency.
Reconstruction of a Genome-Scale Metabolic Model of Streptomyces albus J1074: Improved Engineering Strategies in Natural Product Synthesis

Streptomyces albus J1074 is recognized as an effective host for heterologous production of natural products. Its fast growth and efficient genetic toolbox due to a naturally minimized genome have contributed towards its advantage in expressing biosynthetic pathways for a diverse repertoire of products such as antibiotics and flavonoids. In order to develop precise model-driven engineering strategies for de novo production of natural products, a genome-scale metabolic model (GEM) was reconstructed for the microorganism based on protein homology to model species Streptomyces coelicolor while drawing annotated data from databases and literature for further curation. To demonstrate its capabilities, the Salb-GEM was used to predict overexpression targets for desirable compounds using flux scanning with enforced objective function (FSEOF). Salb-GEM was also utilized to investigate the effect of a minimized genome on metabolic gene essentialities in comparison to another Streptomyces species, S. coelicolor.
Pedestrian Detection in Blind Area and Motion Classification Based on Rush-Out Risk Using Micro-Doppler Radar †

Various remote sensing technologies have been applied in intelligent vehicles and robots for surrounding-environment recognition. However, these technologies experience difficulties in detecting pedestrians in blind areas and their motions, such as rush-out behaviors. To address this issue, we present a radar-based technique for the detection of pedestrians in blind areas and the classification of different risks of rush-out behaviors among detected pedestrians. We verify their ability to detect pedestrian motion in blind areas by conducting experiments in two environments with blind areas formed by outdoor cars and indoor walls. Then, the classification of motions with different risks of rush-out behaviors among pedestrians detected in the blind areas is demonstrated. We use the clustering method to accurately classify several types of behaviors with different rush-out risks in both environments.
Identification of Potential Distinguishing Markers for the Use of Cannabis-Based Medicines or Street Cannabis in Serum Samples

Increasing prescription numbers of cannabis-based medicines raise the question of whether uptake of these medicines can be distinguished from recreational cannabis use. In this pilot study, serum cannabinoid profiles after use of cannabis-based medicines were investigated, in order to identify potential distinguishing markers. Serum samples after use of Sativex®, Dronabinol or medical cannabis were collected and analyzed for 18 different cannabinoids, using a validated liquid chromatography-tandem mass spectrometry (LC-MS/MS) method. Analytes included delta-9-tetrahydrocannabinol, 11-hydroxy-tetrahydrocannabinol, 11-nor-9-carboxy-tetrahydrocannabinol, cannabidiol, cannabinol, cannabigerol, cannabichromene, cannabicyclol, tetrahydrocannabivarin, cannabidivarin, tetrahydocannabinolic acid A, cannabidiolic acid, cannabinolic acid, cannabigerolic acid, cannabichromenic acid, cannabicyclolic acid, tetrahydrocannabivarinic acid and cannabidivarinic acid. Cannabinoid profiles of study samples were compared to profiles of street cannabis user samples via principal component analysis and Kruskal–Wallis test. Potential distinguishing markers for Dronabinol and Sativex® intake were identified, including 11-hydroxy-tetrahydrocannabinol/delta-9-tetrahydrocannabinol ratios ≥1 and increased concentrations of 11-nor-9-carboxy-tetrahydrocannabinol, cannabidiol or cannabichromene. Larger quantities of minor cannabinoids suggested use of cannabis. Use of medical and street cannabis could not be distinguished, except for use of a cannabidiol-rich strain with higher cannabidiol/delta-9-tetrahydrocannabinol and cannabichromene/delta-9-tetrahydrocannabinol ratios. Findings of the study were used to classify forensic serum samples with self-reported use of cannabis-based medicines.
Choline-Sigma-1R as an Additional Mechanism for Potentiation of Orexin by Cocaine

Orexin A, an endogenous peptide involved in several functions including reward, acts via activation of orexin receptors OX1 and OX2, Gq-coupled GPCRs. We examined the effect of a selective OX1 agonist, OXA (17-33) on cytosolic calcium concentration, [Ca2+]i, in neurons of nucleus accumbens, an important area in the reward circuit. OXA (17-33) increased [Ca2+]i in a dose-dependent manner; the effect was prevented by SB-334867, a selective OX1 receptors antagonist. In Ca2+-free saline, the OXA (17-33)-induced increase in [Ca2+]i was not affected by pretreatment with bafilomycin A1, an endo-lysosomal calcium disrupter, but was blocked by 2-APB and xestospongin C, antagonists of inositol-1,4,5-trisphosphate (IP3) receptors. Pretreatment with VU0155056, PLD inhibitor, or BD-1047 and NE-100, Sigma-1R antagonists, reduced the [Ca2+]i response elicited by OXA (17-33). Cocaine potentiated the increase in [Ca2+]i by OXA (17-33); the potentiation was abolished by Sigma-1R antagonists. Our results support an additional signaling mechanism for orexin A-OX1 via choline-Sigma-1R and a critical role for Sigma-1R in the cocaine–orexin A interaction in nucleus accumbens neurons.
Improving Care for Childhood Obesity: A Quality Improvement Initiative

Introduction: Obesity affected 13.7 million children in the United States in 2015. The American Academy of Pediatrics (AAP) offers an evidence-based approach to obesity management, but adherence to recommendations is suboptimal. Our objective was to improve provider adherence to the AAP recommendations for care of patients with obesity by making systematic changes in our practice for patients of ages > 2 and younger than 19 years with a BMI > 95th percentile. Methods: We performed a retrospective chart review of 417 qualifying encounters to assess adherence in the six months preceding the initiative. We measured adherence as a proportion of eligible patients who had (1) obesity on the problem list; (2) laboratory work offered; (3) counseling provided; (4) early follow-up recommended; (5) referral to a weight management program. In 2018, a multidisciplinary QI team conducted plan-do-study-act cycles to educate providers on the AAP recommendations and improve obesity-related care systems. The initiative lasted 18 months. Results: During the initiative, we tracked 885 patient encounters via chart review. We witnessed continued improvement in 4 out of 5 measures. For early follow-up offered, we saw improvement after PDSA 1, followed by a decline after PDSA 3. Providers ordered laboratory tests in only 13% of encounters for eligible children ages younger than 6 years versus 45% for ages older than 6 years, an age-dependent disparity that persisted despite the QI initiative. Conclusion: Our pediatric practice sustained improvement in adherence to AAP recommendations. There is a need to assess the reasons behind the care disparity based on patient ages.
Magnetic Resonance Spectroscopy of Hepatic Fat from Fundamental to Clinical Applications

The number of individuals suffering from fatty liver is increasing worldwide, leading to interest in the noninvasive study of liver fat. Magnetic resonance spectroscopy (MRS) is a powerful tool that allows direct quantification of metabolites in tissue or areas of interest. MRS has been applied in both research and clinical studies to assess liver fat noninvasively in vivo. MRS has also demonstrated excellent performance in liver fat assessment with high sensitivity and specificity compared to biopsy and other imaging modalities. Because of these qualities, MRS has been generally accepted as the reference standard for the noninvasive measurement of liver steatosis. MRS is an evolving technique with high potential as a diagnostic tool in the clinical setting. This review aims to provide a brief overview of the MRS principle for liver fat assessment and its application, and to summarize the current state of MRS study in comparison to other techniques.
Ultrasonic Synthesis and Biomedical Application of Mn0.5Zn0.5ErxYxFe2−2xO4 Nanoparticles

In the present study, biocompatible manganese nanoparticles have been linked with zinc and iron molecules to prepare different derivatives of Mn0.5Zn0. 5ErxYxFe2−2xO4 NPs (x = 0.02, 0.04, 0.06, 0.08, 0.10), using an ultrasonication approach. The structure, surface morphology, and chemical compositions of Mn0.5Zn0. 5ErxYxFe2−2xO4 NPs were elucidated by X-ray diffractometer (XRD), High-resolution transmission electron microscopy (HR-TEM), scanning electron microscope (SEM), and Energy Dispersive X-Ray Analysis (EDX) techniques. The bioactivity of Mn0.5Zn0. 5ErxYxFe2−2xO4 NPs on normal (HEK-293) and (HCT-116) colon cancer cell line was evaluated. The Mn0.5Zn0. 5ErxYxFe2−2xO4 NPs treatment post 48 h resulted in a significant reduction in cells (via MTT assay, having an IC50 value between 0.88 µg/mL and 2.40 µg/mL). The specificity of Mn0.5Zn0. 5ErxYxFe2−2xO4 NPs were studied by treating them on normal cells line (HEK-293). The results showed that Mn0.5Zn0. 5ErxYxFe2−2xO4 NPs did not incur any effect on HEK-293, which suggests that Mn0.5Zn0. 5ErxYxFe2−2xO4 NPs selectively targeted the colon cancerous cells. Using Candida albicans, antifungal activity was also studied by evaluating minimum inhibitory/fungicidal concentration (MIC/MFC) and the effect of nanomaterial on the germ tube formation, which exhibited that NPs significantly inhibited the growth and germ tube formation. The obtained results hold the potential to design nanoparticles that lead to efficient bioactivity.
Chemical Interactions at the Interface of Plant Root Hair Cells and Intracellular Bacteria

In this research, we conducted histochemical, inhibitor and other experiments to evaluate the chemical interactions between intracellular bacteria and plant cells. As a result of these experiments, we hypothesize two chemical interactions between bacteria and plant cells. The first chemical interaction between endophyte and plant is initiated by microbe-produced ethylene that triggers plant cells to grow, release nutrients and produce superoxide. The superoxide combines with ethylene to form products hydrogen peroxide and carbon dioxide. In the second interaction between microbe and plant the microbe responds to plant-produced superoxide by secretion of nitric oxide to neutralize superoxide. Nitric oxide and superoxide combine to form peroxynitrite that is catalyzed by carbon dioxide to form nitrate. The two chemical interactions underlie hypothesized nutrient exchanges in which plant cells provide intracellular bacteria with fixed carbon, and bacteria provide plant cells with fixed nitrogen. As a consequence of these two interactions between endophytes and plants, plants grow and acquire nutrients from endophytes, and plants acquire enhanced oxidative stress tolerance, becoming more tolerant to abiotic and biotic stresses.
A Whole-Body Physiologically Based Pharmacokinetic Model Characterizing Interplay of OCTs and MATEs in Intestine, Liver and Kidney to Predict Drug-Drug Interactions of Metformin with Perpetrators

Transmembrane transport of metformin is highly controlled by transporters including organic cation transporters (OCTs), plasma membrane monoamine transporter (PMAT), and multidrug/toxin extrusions (MATEs). Hepatic OCT1, intestinal OCT3, renal OCT2 on tubule basolateral membrane, and MATE1/2-K on tubule apical membrane coordinately work to control metformin disposition. Drug–drug interactions (DDIs) of metformin occur when co-administrated with perpetrators via inhibiting OCTs or MATEs. We aimed to develop a whole-body physiologically based pharmacokinetic (PBPK) model characterizing interplay of OCTs and MATEs in the intestine, liver, and kidney to predict metformin DDIs with cimetidine, pyrimethamine, trimethoprim, ondansetron, rabeprazole, and verapamil. Simulations showed that co-administration of perpetrators increased plasma exposures to metformin, which were consistent with clinic observations. Sensitivity analysis demonstrated that contributions of the tested factors to metformin DDI with cimetidine are gastrointestinal transit rate > inhibition of renal OCT2 ≈ inhibition of renal MATEs > inhibition of intestinal OCT3 > intestinal pH > inhibition of hepatic OCT1. Individual contributions of transporters to metformin disposition are renal OCT2 ≈ renal MATEs > intestinal OCT3 > hepatic OCT1 > intestinal PMAT. In conclusion, DDIs of metformin with perpetrators are attributed to integrated effects of inhibitions of these transporters.
Rehydration before Application Improves Functional Properties of Lyophilized Lactiplantibacillus plantarum HAC03

Preservation of probiotics by lyophilization is considered a method of choice for developing stable products. However, both direct consumption and reconstitution of dehydrated probiotic preparations before application “compromise” the survival and functional characteristics of the microorganisms under the stress of the upper gastro-intestinal tract. We evaluated the impact of different food additives on the viability, mucin adhesion, and zeta potential of a freeze-dried putative probiotic, Lactiplantibacillus (Lp.) plantarum HAC03. HAC03-compatible ingredients for the formulation of ten rehydration mixtures could be selected. Elevated efficacy was achieved by the B-active formulation, a mixture of non-protein nitrogen compounds, sugars, and salts. The survival of Lp. plantarum HAC03 increased by 36.36% compared rehydration with distilled water (4.92%) after passing simulated gastro-intestinal stress conditions. Cell viability determined by plate counting was confirmed by flow cytometry. B-active formulation also influenced Lp. plantarum HAC03 functionality by increasing its adherence to a Caco-2 cell-line and by changing the bacterial surface charge, measured as zeta potential.Hydrophobicity, mucin adhesion and immunomodulatory properties of Lp. plantarum HAC03 were not affected by the B-active formulation. The rehydration medium also effectively protected Lp. plantarum ATCC14917, Lp. plantarum 299v, Latilactobacillus sakei (Lt.) HAC11, Lacticaseibacillus (Lc.) paracasei 532, Enterococcus faecium 200, and Lc. rhamnosus BFE5263.
Calibration and Cross-Validation of Accelerometer Cut-Points to Classify Sedentary Time and Physical Activity from Hip and Non-Dominant and Dominant Wrists in Older Adults

Accelerometers’ accuracy for sedentary time (ST) and moderate-to-vigorous physical activity (MVPA) classification depends on accelerometer placement, data processing, activities, and sample characteristics. As intensities differ by age, this study sought to determine intensity cut-points at various wear locations people more than 70 years old. Data from 59 older adults were used for calibration and from 21 independent participants for cross-validation purposes. Participants wore accelerometers on their hip and wrists while performing activities and having their energy expenditure measured with portable calorimetry. ST and MVPA were defined as ≤1.5 metabolic equivalents (METs) and ≥3 METs (1 MET = 2.8 mL/kg/min), respectively. Receiver operator characteristic (ROC) analyses showed fair-to-good accuracy (area under the curve [AUC] = 0.62–0.89). ST cut-points were 7 mg (cross-validation: sensitivity = 0.88, specificity = 0.80) and 1 count/5 s (cross-validation: sensitivity = 0.91, specificity = 0.96) for the hip; 18 mg (cross-validation: sensitivity = 0.86, specificity = 0.86) and 102 counts/5 s (cross-validation: sensitivity = 0.91, specificity = 0.92) for the non-dominant wrist; and 22 mg and 175 counts/5 s (not cross-validated) for the dominant wrist. MVPA cut-points were 14 mg (cross-validation: sensitivity = 0.70, specificity = 0.99) and 54 count/5 s (cross-validation: sensitivity = 1.00, specificity = 0.96) for the hip; 60 mg (cross-validation: sensitivity = 0.83, specificity = 0.99) and 182 counts/5 s (cross-validation: sensitivity = 1.00, specificity = 0.89) for the non-dominant wrist; and 64 mg and 268 counts/5 s (not cross-validated) for the dominant wrist. These cut-points can classify ST and MVPA in older adults from hip- and wrist-worn accelerometers.
Divergent Strategy in Marine Tetracyclic Meroterpenoids Synthesis

The divergent total synthesis strategy can be successfully applied to the preparation of families of natural products using a common late-stage pluripotent intermediate. This approach is a powerful tool in organic synthesis as it offers opportunities for the efficient preparation of structurally related compounds. This article reviews the synthesis of the marine natural product aureol, as well as its use as a common intermediate in the divergent synthesis of other marine natural and non-natural tetracyclic meroterpenoids.