Miracle-dz/UniFAR-FTUs huggingface dataset:
De novo 3D models of SARS-CoV-2 RNA elements from consensus experimental secondary structures

Abstract The rapid spread of COVID-19 is motivating development of antivirals targeting conserved SARS-CoV-2 molecular machinery. The SARS-CoV-2 genome includes conserved RNA elements that offer potential small-molecule drug targets, but most of their 3D structures have not been experimentally characterized. Here, we provide a compilation of chemical mapping data from our and other labs, secondary structure models, and 3D model ensembles based on Rosetta's FARFAR2 algorithm for SARS-CoV-2 RNA regions including the individual stems SL1-8 in the extended 5′ UTR; the reverse complement of the 5′ UTR SL1-4; the frameshift stimulating element (FSE); and the extended pseudoknot, hypervariable region, and s2m of the 3′ UTR. For eleven of these elements (the stems in SL1–8, reverse complement of SL1–4, FSE, s2m and 3′ UTR pseudoknot), modeling convergence supports the accuracy of predicted low energy states; subsequent cryo-EM characterization of the FSE confirms modeling accuracy. To aid efforts to discover small molecule RNA binders guided by computational models, we provide a second set of similarly prepared models for RNA riboswitches that bind small molecules. Both datasets (‘FARFAR2-SARS-CoV-2’, https://github.com/DasLab/FARFAR2-SARS-CoV-2; and ‘FARFAR2-Apo-Riboswitch’, at https://github.com/DasLab/FARFAR2-Apo-Riboswitch’) include up to 400 models for each RNA element, which may facilitate drug discovery approaches targeting dynamic ensembles of RNA molecules.
The charge density in dichlorotetrakis(thiourea)nickel(II), [Ni{SC(NH2)2}4Cl2]: a contrast between spectroscopy and diffraction

The charge density observed by X-ray diffraction at 140 K in [Ni(tu)4Cl2](tu = thiourea) is reported. The values for the chloride, thiourea, and NiII fragments closely resemble those of the free ion or molecule, except (a) each chloride σ-donates 0.16(14) e and π-donates 0.35(15) e; (b) each thiourea σ-donates 0.17(20) e to the nickel; (c) NiII, in its 3B1 ground state, has a 3d configuration dxy1.91(14), dxz,yz3.08(18), dx2–y21.12(14), dz21.39(14) with a substantial [1.6(7) e] 4p population. These figures are consistent with a conventional bonding model, in which 3dσ orbitals on NiIIσ-bond almost equally to chlorine and thiourea, and in which 3dπ and 4pπ orbitals π-bond only to chlorine. The residual density maps suggest a differential nephelauxetic effect is occuring, with metal-centred π orbitals larger than σ. A polarisation of the entire NiCl2fragment is also observed, perhaps caused by intermolecular effects. Previous results show that thiourea has a much larger effect on the spectra and magnetism than the chloride. This contrast with the charge-density results is explained by the greater dominance of overlap in spectroscopy, and of ligand energy levels (or crudely, ionisation potentials) in charge densities. This illustrates experimentally the theoretical observation that covalence (i.e. molecular orbital) parameters are best ‘directly’ observed by diffraction, since spectroscopy is often dominated in more ionic complexes by the less interesting terms due to orthogonalisation of metal and ligand orbitals.
Anisotropy of Charge Transport in a Uniaxially Aligned and Chain‐Extended, High‐Mobility, Conjugated Polymer Semiconductor

Charge transport in the ribbon phase of poly(2,5‐bis(3‐alkylthiophen‐2‐yl)thieno[3,2‐b]thiophene) (PBTTT)—one of the most highly ordered, chain‐extended crystalline microstructures available in a conjugated polymer semiconductor—is studied. Ribbon‐phase PBTTT has previously been found not to exhibit high carrier mobilities, but it is shown here that field‐effect mobilities depend strongly on the device architecture and active interface. When devices are constructed such that the ribbon‐phase films are in contact with either a polymer gate dielectric or an SiO2 gate dielectric modified by a hydrophobic, self‐assembled monolayer, high mobilities of up to 0.4 cm2 V−1 s−1 can be achieved, which is comparable to those observed previously in terrace‐phase PBTTT. In uniaxially aligned, zone‐cast films of ribbon‐phase PBTTT the mobility anisotropy is measured for transport both parallel and perpendicular to the polymer chain direction. The mobility anisotropy is relatively small, with the mobility along the polymer chain direction being higher by a factor of 3–5, consistent with the grain size encountered in the two transport directions.
Dynamic Prediction of Wastewater Aeration Basin Temperature

A dynamic model was developed to predict activated-sludge aeration basin temperature. The model accounts for hourly or more frequent changes in weather conditions and input parameters such as wastewater temperature, aeration, and biological reaction. The model was verified using data from full-scale treatment plants located across the United States. The various heat transfer terms are evaluated, and the relative contribution from each is shown. Evaporation from aeration can be a major component. Surface aerators cool the basin much more than diffused aeration systems. Diffused aeration systems are preferred for cold climates. The heat of biological reaction is small, except for very high rate processes. The effect of changing weather conditions, such as a cold front, can be predicted. Local relative humidity has a major impact on cooling. The impact of design changes, such as covering an aeration basin, insulating walls, or changing retention times, can be determined using the developed model.
Disparities in Experience with Culturally Competent Care and Satisfaction with Care by Sexual Orientation.

Purpose: Prior studies have identified health care providers' lack of cultural competency as a major barrier to care among sexual minority individuals. However, little is known about disparities in experience with culturally competent care by sexual orientation at the population level. This study assessed experiences with culturally competent care and satisfaction with care across sexual orientation groups in the United States. Methods: We analyzed nationally representative data from the 2017 National Health Interview Survey (n = 21,620) with ordinal logit regression models and compared six aspects of health care experiences across sexual orientation groups. These were: preferences for and frequencies of seeing health care providers who understand or share their culture; perceived experiences of being treated with respect by providers and providers asking about their beliefs and opinions; access to easily understood health information from providers; and satisfaction with received care. Results: Relative to heterosexual men, gay men were more likely to consider it important for providers to understand or share their culture (odds ratio [OR] = 1.4, p < 0.05) and to have providers who ask for their opinions or beliefs about care (OR = 1.5, p < 0.01). Relative to heterosexual women, bisexual- and something else-identified women were less likely to report being treated with respect (ORs = 0.4-0.6, p's < 0.01) and satisfaction with care (ORs = 0.5-0.6, p's < 0.05). No statistical differences in health care experiences were found between other sexual minority groups and their heterosexual counterparts. Conclusions: Access to culturally competent care and satisfaction with care varied by sexual orientation and gender. Clinical practices should address the unique health care barriers faced by bisexual- and something else-identified women.
A hybrid genetic algorithm approach to calculating chemical equilibrium and detonation parameters in condensed energetic materials

We discuss the implementation of genetic algorithms for modelling chemical equilibrium and detonation parameters at the Chapman–Jouguet (CJ) state. This strategy has the advantage that no initial estimate of the equilibrium product distribution needs to be made. It is also an efficient method for finding the global minimum, since for highly non-ideal condensed energetic materials, the calculation of the chemical equilibrium using deterministic algorithms can lead to a local minimum being found instead of a global minimum. This can result in an incorrect prediction of the chemical products distribution. The code was tested for several C–H–N–O energetic materials, namely cyclotrimethyline-trinitramine (RDX), nitromethane (NM), 2,4,6-trinitrotoluene (TNT), and pentaerythritol tetranitrate (PETN). The results obtained using these approaches are in good agreement with the experimental data available in the literature. A comparison with results of other modelling approaches is presented.
Electronic and Optical Properties of Some Polysulfone-Polydimethylsiloxane Copolymers in Thin Films

Polysulfone (PSF)-polydimethylsiloxane (PDMS) block copolymers (PSF-b-PDMS) with various compositions were prepared by condensing chloro-terminated polysulfone oligomers with α, ω -dihydrogensilyl-polydimethylsiloxane in refluxing chlorobenzene solution in the presence of urea as a hydrogen chloride acceptor. The temperature dependences of the electrical conductivity and thermoelectric power (Seebeck coefficient) of copolymers were studied using thin films deposited from a dimethylformamide solution (spin coating method) onto glass substrates. It was established that the various copolymers showed typical semiconducting properties. Some correlations between these properties (activation energy, ratio of carrier mobilities, etc) and molecular structure of the copolymers were found. A model based on band gap representation was found to be suitable for explanation of the electronic transport mechanism through the studied copolymers in thin films. The study of the transmission and absorption spectra (in the spectral range from 300 nm to 1400 nm) evidenced that the indirect allowed optical transitions were predominant. The values of the optical energy band gap (ranged between 1.50 eV and 1.70 eV) are in agreement with values of width of the forbidden band calculated from the temperature dependence of the electrical conductivity.
Plasma amino acid concentrations during experimental hyperinsulinemia in 2 laminitis models

Abstract Background Endocrinopathic laminitis develops in association with insulin dysregulation, but the role of insulin in the pathogenesis remains unclear. Hyperinsulinemia can cause hypoaminoacidemia, which is associated with integumentary lesions in other species and therefore warrants investigation as a potential mechanism in laminitis. Objective Evaluate plasma amino acid concentrations in the euglycemic‐hyperinsulinemic clamp (EHC) and prolonged glucose infusion (PGI) laminitis models. Animals Sixteen Standardbred horses. Methods Prospective experimental study. Plasma amino acid concentrations were measured in samples collected every 6 hours from horses that underwent a 48‐hour EHC (n = 8) or 66‐hour PGI (n = 8) after a 24‐ or 6‐hour baseline period in EHC and PGI groups, respectively. Results Fifteen of the 20 measured amino acid concentrations decreased over time in both EHC and PGI horses (P < 0.001). The median percentage change from baseline for these amino acids was: histidine (EHC: 41.5%; PGI: 43.9%), glutamine (EHC: 51.8%; PGI: 35.3%), arginine (EHC: 51.4%; PGI: 41%), glutamic acid (EHC: 52.4%; PGI: 31.7%), threonine (EHC: 62.8%; PGI: 25.2%), alanine (EHC: 48.9%; PGI: 19.5%), proline (EHC: 56.2%; PGI: 30.3%), cystine (EHC: 34.9%; PGI: 31.2%), lysine (EHC: 46.4%; PGI: 27.8%), tyrosine (EHC: 27.5%; PGI: 16.9%), methionine (EHC: 69.3%; PGI: 50.8%), valine (EHC: 50.8%; PGI: 34.4%), isoleucine (EHC: 60.8%; PGI: 38.7%), leucine (EHC: 48.2%; PGI: 36.6%), and phenylalanine (EHC: 16.6%; PGI: 12.1%). Conclusions and Clinical Importance Hypoaminoacidemia develops in EHC and PGI laminitis models. The role of hypoaminoacidemia in the development of hyperinsulinemia‐associated laminitis warrants further investigation.
Effect of Teriparatide on pain relief, and quality of life in postmenopausal females with osteoporotic vertebral compression fractures, a retrospective cohort study.

BACKGROUND Osteoporotic vertebral compression fracture (OVCF) is a common disease in elderly population, which could cause serious back pain and has a substantial impact on patients' health-related quality of life (HRQoL). The aim of this study was to identify the effect of Teriparatide as a conservative treatment on reducing back pain, and improving quality of life for postmenopausal women with osteoporotic vertebral fractures. METHODS In a 12-month, retrospective study, 112 postmenopausal women with OVCFs were assigned to Teriparatide group (20 μg Teriparatide, subcutaneous, once daily, n=38) or control group (500 mg calcium and 400-800 IU Vitamin D per day, oral administration, n=74) according to patients' choices between January 2016 and October 2018. Patient-reported outcomes scores including the visual analogue score (VAS), Oswestry disability index (ODI), and short form 36 questionnaire (SF-36) were assessed at baseline, the 3rd month, the 6th months and 1 year after treatment. RESULTS Treatments with Teriparatide or calcium plus vitamin D supplements had significant effect on improvement of patients' back pain as well as HRQoL, with significantly reduced VAS and ODI and increased SF-36 physical component summary (PCS) and mental component summary (MCS) scores. At the endpoint, Teriparatide showed better therapeutic effect, with greater reductions in VAS and ODI and more increases in SF-36 PCS and MCS scores. However, more adverse events (AEs) were found in Teriparatide group, but symptoms were relatively mild and of short duration. CONCLUSIONS In postmenopausal women with OVCFs, the consequent persistent back pain and impaired HRQoL, treatment with Teriparatide was associated with more profound therapeutic effects and more AEs compared with calcium plus vitamin D supplements.
Is there meaningful influence from situational and environmental factors on the physical and technical activity of elite football players? Evidence from the data of 5 consecutive seasons of the German Bundesliga

The study aimed to identify the effects of situational (match location, match outcome and strength of team/opponent team) and environmental (ambient temperature, relative humidity, WBGT, ground and weather condition) factors on the physical and technical activity of elite football on individual playing positions. Physical and technical activity were collected from 779 football players competing in the German Bundesliga during 5 domestic seasons, from 2014/2015 to 2018/2019, totalling 1530 matches. The data on players’ physical and technical activity was taken from the IMPIRE AG system. Based on the available data, 11 variables were selected to quantify the match activity profiles of players. The results showed that situational variables had major effects on the technical performance (especially number of passes performed) but minor effects on physical performance. In turn, among the analysed environmental factors, temperature is the most sensitive, which affects the Total Distance and Sprint Efforts of players in all five positions. This investigation demonstrated that, given that passing is a key technical activity in modern football, players and training staff should be particularly aware that passing maybe affected by situational variables. Professional players are able to react and adapt to various environmental conditions, modifying physical activity depending on the needs in German Bundesliga. These results could help coaches and analysts to better understand the influences of situational and environmental variables on individual playing positions during the evaluation of players’ physical and technical performance.
The effect of inversion of the ester group on the mesophase behaviour of some azo/ester compounds

Five homologous series of 4-substituted phenyl 4′-(4″-alkoxy phenylazo) benzoates (Ina–−e) were prepared in which, within each homologous series, the length of the terminal alkoxy group varies between 8, 10, 12, 14 and 16 carbons, while the other terminal substituent, X, is a polar group that alternatively changed from CH3O, CH3, H, Br, and CN groups. Compounds prepared were characterised by infrared, mass, and H1-NMR spectroscopy and their mesophase behaviour investigated by differential scanning calorimetry (DSC) and polarised light microscopy (PLM). The results were discussed in terms of mesomeric and polarisability effects. Only for the lower group of compounds, I8a-e, that showed a nematic phase, the nematic-to-isotropic transition temperatures (TN–I) were successfully correlated to the polarisability anisotropy of bonds to the substituent X. A comparative study was made between the investigated compounds and two previously prepared isomeric groups. In the first group of isomers, 4-(4′alkoxy phenylazo) phenyl 4″-substituted benzoates (IIna–e), the ester groups are inverted. While in the second, 4-(4′-substituted phenylazo) phenyl 4″-alkoxy benzoates (IIIna–e), two modifications were made, inversion of the COO group, and exchange of the two wing substituents
Reflection of different applications of potassium and iron fertilization on tomato yield and fruit quality in soilless medium

Potassium and iron are the main elements that are of great importance in soilless medium in terms of tomato yield and fruit quality. For this reason, the effects of these elements on yield and fruit quality parameters were investigated. Three different combinations of potassium (150, 300 and 450 mg l -1 ) and iron (1, 2 and 3 mg l -1 ) ratios were evaluated. The experiment was conducted according to completely randomized factorial design with 4 replicates. The interaction between potassium and iron applications was significant in yield, total soluble solids, fruit firmness and a*-value. Moreover, titratable acidity, total soluble solids content and pH of fruit juice showed increase by ascending K applications. There were no effects of K and Fe applications on ascorbic acid, fruit diameter, L* and b* values. These results indicated interactive effects between potassium and iron applications on fruit quality and yield are more complex structure. Therefore, detailed investigations are required in different growing medium, ecological condition and on tomato variety.
(-)-Epicatechin and Anthocyanins Modulate GLP-1 Metabolism: Evidence from C57BL/6J Mice and GLUTag Cells.

BACKGROUND Generated in intestinal L cells through cleavage of proglucagon (Gcg), glucagon-like peptide 1 (GLP-1) is secreted and rapidly inactivated by dipeptidyl peptidase IV (DPP-IV). GLP-1 regulates insulin secretion and overall glucose homeostasis. The capacity of dietary bioactives to increase GLP-1 circulating levels, and therefore increase insulin secretion and glucose metabolism, has gained significant interest of late. OBJECTIVES We evaluated the effects of (-)-epicatechin (EC) and different anthocyanins (ACs) and AC metabolites on GLP-1 metabolism in mice and on GLUTag cells. METHODS We fed 6-week-old C57BL/6J male mice a control diet or a control diet supplemented with either 40 mg AC or 20 mg EC/kg body weight for 14 weeks (AC) or 15 weeks (EC). Intestinal mRNA levels of Gcg and Dpp-iv were measured. In vitro, GLUTag cells were incubated in the presence or absence of different ACs, the AC metabolite protocatechuic acid (PCA), and EC. GLP-1 secretion and the main pathways involved in its release were assessed. RESULTS Long-term supplementation with EC or AC increased mouse GLP-1 plasma concentrations (55% and 98%, respectively; P < 0.05). In mice, 1) EC and AC increased Gcg mRNA levels in the ileum (91%) and colon (41%), respectively (P < 0.05); and 2) AC lowered ileum Dpp-iv mRNA levels (35%), while EC decreased plasma DPP-IV activity (15%; P < 0.05). In GLUTag cells, 1) cyanidin, delphinidin, PCA, and EC increased GLP-1 secretion (53%, 33%, 53%, and 68%, respectively; P < 0.05); and 2) cyanidin, delphinidin, EC, and PCA increased cyclin adenosine monophosphate levels (25-50%; P < 0.05) and activated protein kinase A (PKA; 100%, 50%, 80%, and 86%, respectively; P < 0.05). CONCLUSIONS In mice, EC and ACs regulated different steps in GLP-1 regulation, leading to increased plasma GLP-1. Cyanidin, delphinidin, PCA, and EC promoted GLP-1 secretion from GLUTag cells by activating the PKA-dependent pathway. These findings support the beneficial actions of these flavonoids in sustaining intestinal and glucose homeostasis through the modulation of the GLP-1 metabolism.
The in vitro Effect of Some Commonly Used Fungicides, Insecticides and Herbicides for Their Compatibility with Trichoderma harzianum PBT23

The in-vitro effect of some commonly used fungicides, insecticides and herbicides on the mycelial growth of Trichoderma harzianum PBT 23 were evaluated. Nine fungicides, 6 insecticides and 7 herbicides were tested. A progressive increase in percent inhibition of radial growth in the fungus was observed as the concentrations of the fungicides increased. Among fungicides, Captaf, Thiram, Chlorothalonil and Copper hydroxide were found compatible with the test antagonist up to 100 µg a.i. /ml, while Mancozeb up to 250 µg a.i. /ml, as these did not adversely affect the growth of test antagonist. However, Benomyl, Thiophanate methyl, Bayleton and ipridione were found incompatible with the test antagonist even at 25 µg a.i. /ml. Among insecticides, Monocrotophos, Dichlorvos, Profenophos and Triazophos were found compatible up to 250 µl a.i./ml; while Deltamethrin and Quinalphos up to 100 µl a.i./ml. Seven herbicides, 2, 4-D ethyl ester, Pretilachlor, Aniliofos, Alachlor, Butachlor, Fluchloralin and Pendimethalin were found compatible with the test antagonist even at higher concentration (250 µl a.i. /ml). The present results would be helpful to delineate the possibility of combining T. harzianum PBT 23 as biocontrol agent with agrochemicals under integrated pest management approaches.
Age-related degeneration of lumbar muscle morphology in healthy younger versus older men

Abstract Aim The aim of this study was to evaluate age-related changes in lumbar paravertebral muscle (LPM) morphology in healthy younger and older adult men. Methods T2-weighted axial MRI of the lumbar spine were obtained for 12 healthy older (67.3 ± 6.0 years) and younger (24.7 ± 3.1 years) men. Normalised muscle volume (NMV) and muscle fat infiltrate (MFI) were determined bilaterally for the psoas (PS), quadratus lumborum (QL), erector spinae (ES) and multifidus (MF). MANOVA was used to compare NMV and MFI between age groups. Follow-up ANOVA compared NMV and MFI for each muscle between age groups, with physical activity (PA) as a covariate. Stepwise regression was used to explore the association between muscle morphology. Results NMV of the ES and QL were significantly lower in the older group (OG) (p = 0.040 and p < 0.001, respectively). MFI across all muscles was significantly greater in the OG (p < 0.001). PA did not moderate the relationship between aging and muscle degeneration. Non-dominant handgrip strength was associated with NMV (p = 0.003). Conclusions Age-related atrophy is muscle specific in the lumbar spine; changes in lumbar musculature is independent of PA, handgrip strength may reflect morphological changes in the postural muscles with age. This study supports establishing effective targeted exercise interventions in the lumbar musculature.