Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of the natural compound inhibitors against Plasmodium falciparum plasmepsin-II via common feature based screening and molecular dynamics simulations

Abstract Malaria is counted amongst the deadly disease caused by Plasmodium falciparum. Recently, plasmepsin-II enzyme has gained much importance as an attractive drug target for the exploration of antimalarials. Therefore, the common feature pharmacophore models were generated from the crystallized complexes of the plasmepsin-II proteome. These models were subjected to a series of validation procedures, i.e. test set and Güner Henry studies to enlist the representative models. The selected representative hypotheses incorporating the most essential chemical features (common ZHHA) were screened against the natural product database to retrieve the potential candidates. To ensure the selection of the drug-like candidates, prior to screening, filtering steps (Drug-likeness and ADMET filters) were employed on the selected database. To study the interaction pattern of the candidates within the protein, these molecules were advanced to the molecular docking studies. Subsequently, based on the selected cut-off criteria obtained via redocking of the reference (4Z22), 15 compounds showed higher docking score (> −16.05 kcal/mol), and displayed the presence of hydrogen bonding with the crucial amino acids, i.e. Asp34 and Asp214. Further, the stability of the docked molecules was scrutinized via molecular dynamics simulations, and the results were compared with the reference compound 4Z22. All the docked compounds showed stable dynamics behaviour. Thus, in the present contribution, the combination of screening and stability procedures resulted in the identification of 15 hits that can serve as a new chemical space in the designing of the novel antimalarials. Communicated by Ramaswamy H. Sarma
The n–Si/p–CVD Diamond Heterojunction

Due to the possible applications, materials with a wide energy gap are becoming objects of interest for researchers and engineers. In this context, the polycrystalline diamond layers grown by CVD methods on silicon substrates seem to be a promising material for engineering sensing devices. The proper tuning of the deposition parameters allows us to develop the diamond layers with varying crystallinity and defect structure, as was shown by SEM and Raman spectroscopy investigations. The cathodoluminescence (CL) spectroscopy revealed defects located just in the middle of the energy gap of diamonds. The current–voltage–temperature, I−V−T characteristics performed in a broad temperature range of 77–500 K yielded useful information about the electrical conduction in this interesting material. The recorded I−V−T in the forward configuration of the n–Si/p–CVD diamond heterojunction indicated hopping trough defects as the primary mechanism limiting conduction properties. The Ohmic character of the carriers flux permitting throughout heterojunction is intensified by charges released from the depletion layer. The magnification amplitude depends on both the defect density and the probability that biasing voltage is higher than the potential barrier binding the charge. In the present work, a simple model is proposed that describes I−V−T characteristics in a wide range of voltage, even where the current saturation effect occurs.
Effects of Combination Denosumab and High‐Dose Teriparatide Administration on Bone Microarchitecture and Estimated Strength: The DATA‐HD HR‐pQCT Study

In postmenopausal women at high risk of fracture, we previously reported that combined denosumab and high‐dose (HD; 40 μg) teriparatide increased spine and hip bone mineral density (BMD) more than combination with standard‐dose teriparatide (SD; 20 μg). To assess the effects of these combinations on bone microarchitecture and estimated bone strength, we performed high‐resolution peripheral quantitative computed tomography (HR‐pQCT) at the distal radius and distal tibia in these women, who were randomized to receive either teriparatide 20 μg (n = 39) or 40 μg (n = 37) during months 0 to 9 overlapped with denosumab 60 mg s.c. given at months 3 and 9, for a 15‐month study duration. The 69 women who completed at least one study visit after baseline are included in this analysis. Over 15 months, increases in total BMD were higher in the HD‐group than the SD‐group at the distal tibia (5.3% versus 3.4%, p = 0.01) with a similar trend at the distal radius (2.6% versus 1.0%, p = 0.06). At 15 months, cortical porosity remained similar to baseline, with absolute differences of −0.1% and −0.7% at the distal tibia and −0.4% and −0.1% at the distal radius in the HD‐group and SD‐group, respectively; p = NS for all comparisons. Tibial cortical tissue mineral density increased similarly in both treatment groups (1.3% [p < 0.0001 versus baseline] and 1.5% [p < 0.0001 versus baseline] in the HD‐group and SD‐group, respectively; p = 0.75 for overall group difference). Improvements in trabecular microarchitecture at the distal tibia and estimated strength by micro‐finite element analysis at both sites were numerically greater in the HD‐group compared with SD‐group but not significantly so. Together, these findings suggest that short‐term treatment combining denosumab with either high‐ or standard‐dose teriparatide improves HR‐pQCT measures of bone density, microstructure, and estimated strength, with greater gains in total bone density observed in the HD‐group, which may be of benefit in postmenopausal women with severe osteoporosis. © 2020 American Society for Bone and Mineral Research (ASBMR).
THE OVIPOSITION BEHAVIOR OF SCAEVA PYRASTRI [HYM.:SURPHIDAE] AND ITS CONTROL EFFECT ON APHIDS IN GREENHOUSES

In Beijing area, naturally occurring scaeva pyrastri overwinters as mated female adult in deep stone crevices. When moved into a rearing room of 25±1℃, 70-80% RH, 16 hr photoperiod and provided with aphid infested bean seedlings, the overwintering females began oviposition within 24 hr. When they were provided with a "Pollen Health Food" as supplementary diet, each overwintered female adult laid an average of 235.0±59.5 eggs with 64.7% hatching rate. In the greenhouses of ornamental flowers, the females showed a preference "of plants or plant parts infested by large number, of aphids to lay their eggs. On Flameray gerbera, for example, the eggs were mostly found on the flowers. In the experiment conducted in a greenhouse of 14m2, two releases of a total of 13 overwintered femalfe adults resulted in an effective control of the aphids on F. qerbera. The number of aphids on the flowers and leaves reduced by 88,4% and 92.6%, respectively in 25 days after the releases. In comparison, the number of aphid on tomato seedlings in the control greenhouse without releasing the predator increased 133.3% in 12 days. In this case, chemical control became necessary.
Short-Term Effects of Air Pollution on Coronary Events in Strasbourg, France—Importance of Seasonal Variations

The aim of this study, is to investigate the effects of a short-term exposure to air pollutants, as assessed by Nitrogen dioxide (NO2), Particulate Matter PM2,5 and PM10 concentrations, on coronary event onsets in Strasbourg, France. An observational, analytical, retrospective, epidemiological study was conducted in Strasbourg between 1 January 2012 and 31 December 2014. Higher daily coronary events rates were evidenced when NO2 concentrations were measured above 40 µg/m3 (1.258 (95% CI 1.142–1.374) vs. 1.110 (95% CI 1.033–1.186); p = 0.015). The NO2 concentration was higher than 30 µg/m3 for 677 days (61.8%). Higher daily coronary events rates were evidenced when NO2 concentrations were measured above 30 µg/m3 (1.208 (95% CI 1.128–1.289) vs. 1.067 (95% CI 0.961–1.172) p = 0.009). A marked seasonality of NO2, PM2.5, and PM10 concentrations characterized by an increase during winter and a decrease during the summer could be established. The seasonality of coronary events was evidenced simultaneously. After adjustments were made to account for the time and the month, no independent impact of NO2, PM2.5 or PM10 on daily coronary events could be demonstrated.
Multidimensional Correlates of Parental Self-Efficacy in Managing Adolescent Internet Use among Parents of Adolescents with Attention-Deficit/Hyperactivity Disorder

Given the growing concerns of problematic Internet use and online safety, it is critical to address parental self-efficacy in managing adolescent Internet use and to examine associated factors, especially in parents of adolescents with attention-deficit/hyperactivity disorder (ADHD). We examined the roles of adolescents’ hyperactivity/impulsivity, inattention and oppositional defiant disorder (ODD) symptoms, parents’ depressive symptoms, parenting behavior (parental care and indifference), and child behavior (Internet addiction) in relation to parental self-efficacy in managing adolescent Internet use. We recruited 237 Taiwanese parents of adolescents with ADHD (ages 11–18). Hierarchical linear regression was performed in four steps to test the study hypotheses. The results indicated that child’s age, ODD symptoms, and Internet addiction of adolescents were negatively associated, and parental care was positively associated with parental self-efficacy in managing adolescent Internet use. The final model was significant and explained 43% of the variance. The present study demonstrated that parenting and child behaviors contribute to parental self-efficacy in managing adolescent Internet use. Moreover, children’s ODD symptoms were identified as the risk factor for reduced parental self-efficacy.
The regulation of ethylene biosynthesis: a complex multilevel control circuitry

Summary The gaseous plant hormone ethylene is produced by a fairly simple two‐step biosynthesis route. Despite this pathway’s simplicity, recent molecular and genetic studies have revealed that the regulation of ethylene biosynthesis is far more complex and occurs at different layers. Ethylene production is intimately linked with the homeostasis of its general precursor S‐adenosyl‐l‐methionine (SAM), which experiences transcriptional and posttranslational control of its synthesising enzymes (SAM synthetase), as well as the metabolic flux through the adjacent Yang cycle. Ethylene biosynthesis continues from SAM by two dedicated enzymes: 1‐aminocyclopropane‐1‐carboxylic (ACC) synthase (ACS) and ACC oxidase (ACO). Although the transcriptional dynamics of ACS and ACO have been well documented, the first transcription factors that control ACS and ACO expression have only recently been discovered. Both ACS and ACO display a type‐specific posttranslational regulation that controls protein stability and activity. The nonproteinogenic amino acid ACC also shows a tight level of control through conjugation and translocation. Different players in ACC conjugation and transport have been identified over the years, however their molecular regulation and biological significance is unclear, yet relevant, as ACC can also signal independently of ethylene. In this review, we bring together historical reports and the latest findings on the complex regulation of the ethylene biosynthesis pathway in plants.
Epigallocatechin Gallate Slows Retinal Degeneration, Reduces Oxidative Damage, and Modifies Circadian Rhythms in P23H Rats

Retinitis pigmentosa (RP) includes a group of genetic disorders that involve the loss of visual function due to mutations mainly in photoreceptors but also in other retinal cells. Apoptosis, retinal disorganization, and inflammation are common in the progression of the disease. Epigallocatechin gallate (EGCG) has been proved as beneficial in different eye diseases. Pigmented heterozygous P23H rat was used as an animal model of RP. Visual function was assessed by optomotor and electroretinogram (ERG) and circadian rhythms were evaluated by telemetry. Hepatic oxidative damage and antioxidant defenses were assessed using biochemical tests. The visual function of the EGCG P23H group was preserved, with a deterioration in the activity period and lower values in the interdaily stability parameter. Control rats treated with EGCG were less active than the sham group. EGCG increased antioxidant levels in P23H rats but reduced total hepatic antioxidant capacity by almost 42% in control rats compared to the sham group. We conclude that treatment with EGCG improves visual function and antioxidant status in P23H rats but diminishes antioxidant defenses in wild-type control animals, and slightly worsens activity circadian rhythms. Further studies are necessary to clarify the beneficial effects in disease conditions and in healthy organisms.
The Influence of the Hybridization Process on the Mechanical and Thermal Properties of Polyoxymethylene (POM) Composites with the Use of a Novel Sustainable Reinforcing System Based on Biocarbon and Basalt Fiber (BC/BF)

The presented work focuses on the assessment of the material performance of polyoxymethylene (POM)-based composites reinforced with the use of a biocarbon/basalt fiber system (BC/BF). The use of BC particles was aimed at eliminating mineral fillers (chalk, talc) by using fully biobased material, while basalt fibers can be considered an alternative to glass fibers (GF). All materials were prepared with the same 20% filler content, the differences concerned the (BC/BF) % ratio. Hybrid samples with (25/75), (50/50), and (75/25) ratios were prepared. Additionally, reference samples were also prepared (POM BC20% and POM BF20%.). Samples prepared by the injection molding technique were subjected to a detailed analysis of mechanical properties (static tensile and Charpy impact tests), thermomechanical characteristics (dynamic mechanical thermal analysis—DMTA, heat deflection temperature - HDT), and thermal and rheological properties (DSC, rotational rheometer tests). In order to assess fiber distribution within the material structure, the samples were scanned by a microtomography method (μCT). The addition of even a significant amount of BC particles did not cause excessive material brittleness, while the elongation and impact strength of all hybrid samples were very similar to the reference POM BF20% sample. The tensile modulus and strength values appear to be strictly dependent on the increasing BF fiber content. Thermomechanical analysis (DMTA, HDT) showed very similar heat resistance for all hybrid samples; the results did not differ from the values for the POM BF20 sample.
Sociotropy, Autonomy and Emotional Symptoms in Patients with Major Depression or Generalized Anxiety: The Mediating Role of Rumination and Immature Defenses

The relationships between dimensions of personality (sociotropy and autonomy), coping strategies (rumination: brooding and reflection subtypes, and immature defenses) and symptoms of depression and anxiety were explored in patients with Major Depressive Disorder (MDD) and Generalized Anxiety Disorder (GAD). A total of 279 patients completed questionnaires including measures of personality dimensions, rumination, immature defenses, depression and anxiety. Our findings suggested that sociotropy and autonomy may be associated with both depressive and anxious symptoms in patients with MDD and with GAD. Multiple mediation analyses indicated that brooding always acted as a mediating link between personality vulnerabilities (sociotropy and autonomy) and depressive and anxiety symptoms, independently of the patient group. In addition, in patients with MDD and those with GAD, brooding and immature defenses functioned together by linking sociotropy and autonomy, respectively, with depressive symptoms. Our results also showed that, in patients with GAD, both types of rumination explained the relationship between sociotropy and autonomy and anxiety symptoms. Overall, our findings provided evidence of the transdiagnostic role of the brooding, linking the vulnerability of personality dimensions and emotional symptoms. They also indicated that reflection and immature defenses can operate in conjunction with brooding, depending on the type of vulnerability and emotional context.
Synthetic Aperture Sonar (SAS) without Navigation: Scan Registration as Basis for Near Field Synthetic Imaging in 2D

Sonars are essential for underwater sensing as they can operate over extended ranges and in poor visibility conditions. The use of a synthetic aperture is a popular approach to increase the resolution of sonars, i.e., the sonar with its N transducers is positioned at k places to generate a virtual sensor with kN transducers. The state of the art for synthetic aperture sonar (SAS) is strongly coupled to constraints, especially with respect to the trajectory of the placements and the need for good navigation data. In this article, we introduce an approach to SAS using registration of scans from single arrays, i.e., at individual poses of arbitrary trajectories, hence avoiding the need for navigation data of conventional SAS systems. The approach is introduced here for the near field using the coherent phase information of sonar scans. A Delay and Sum (D&S) beamformer (BF) is used, which directly operates on pixel/voxel form on a Cartesian grid supporting the registration. It is shown that this pixel/voxel-based registration and the coherent processing of several scans forming a synthetic aperture yields substantial improvements of the image resolution. The experimental evaluation is done with an advanced simulation tool generating realistic 2D sonar array data, i.e., with simulations of a linear 1D antenna reconstructing 2D images. For the image registration of the raw sonar scans, a robust implementation of a spectral method is presented. Furthermore, analyses with respect to the trajectories of the sensor locations are provided to remedy possible grating lobes due to the gaping positions of the transmitter devices.
How do undergraduates cope with anxiety resulting from active learning practices in introductory biology?

Active learning pedagogies decrease failure rates in undergraduate introductory biology courses, but these practices also cause anxiety for some students. Classroom anxiety can impact student learning and has been associated with decreased student retention in the major, but little is known about how students cope with anxiety caused by active learning practices. In this study, we investigated student coping strategies for various types of active learning (clickers, volunteering to answer a question, cold calling, and group work) that were used in 13 introductory Biology courses at a large public university in 2016–2017. A survey asked students to rate their anxiety regarding the four active learning practices and over half of the students explained the coping strategies they used to manage their active learning anxieties. Coping responses from 880 students were sorted into pre-defined categories of coping strategies: problem solving, information seeking, self-reliance, support seeking, accommodation, helplessness, escape, delegation, and isolation. We found that a different category of coping was dominant for each type of active learning. The dominant coping strategies for anxiety associated with clickers, cold calling, and group work were adaptive coping strategies of information seeking, self-reliance, and support-seeking, respectively. The dominant coping strategy for volunteering to answer a question was escape, which is a maladaptive strategy. This study provides a detailed exploration of student self-reported coping in response to active learning practices and suggests several areas that could be foci for future psychosocial interventions to bolster student regulation of their emotions in response to these new classroom practices.
Structural basis for transcription inhibition by E. coli SspA

Abstract Stringent starvation protein A (SspA) is an RNA polymerase (RNAP)-associated protein involved in nucleotide metabolism, acid tolerance and virulence of bacteria. Despite extensive biochemical and genetic analyses, the precise regulatory role of SspA in transcription is still unknown, in part, because of a lack of structural information for bacterial RNAP in complex with SspA. Here, we report a 3.68 Å cryo-EM structure of an Escherichia coli RNAP-promoter open complex (RPo) with SspA. Unexpectedly, the structure reveals that SspA binds to the E. coli σ70-RNAP holoenzyme as a homodimer, interacting with σ70 region 4 and the zinc binding domain of EcoRNAP β′ subunit simultaneously. Results from fluorescent polarization assays indicate the specific interactions between SspA and σ70 region 4 confer its σ selectivity, thereby avoiding its interactions with σs or other alternative σ factors. In addition, results from in vitro transcription assays verify that SspA inhibits transcription probably through suppressing promoter escape. Together, the results here provide a foundation for understanding the unique physiological function of SspA in transcription regulation in bacteria.
Modulating the Microbiome and Immune Responses Using Whole Plant Fibre in Synbiotic Combination with Fibre-Digesting Probiotic Attenuates Chronic Colonic Inflammation in Spontaneous Colitic Mice Model of IBD

A probiotic and prebiotic food ingredient combination was tested for synergistic functioning in modulation of the colonic microbiome and remediation of the gastrointestinal immune and inflammatory responses in a spontaneous colitic mouse model. Bacillus coagulans MTCC5856 spores with capability to metabolise complex plant polysaccharides were supplemented with complex whole-plant prebiotic sugarcane fibre (PSCF). The combined and individual efficacies were tested for their influence on the outcomes of chronic inflammation in Muc2 mutant colitic Winnie mice. The mice were fed normal chow diet supplemented with either ingredient or a combination for 21 days. Synbiotic combined supplementation ameliorated clinical symptoms and histological colonic damage scores more effectively than either B. coagulans or PSCF alone. PSCF and B. coagulans alone also induced considerable immunomodulatory effects. Synbiotic supplementation however was the most efficacious in modulating the overall immune profile compared to the unsupplemented Winnie-control. The augmented synbiotic effect could potentially be due to a combination of increased levels of fermentation products, direct immune-modulating abilities of the components, their capability to reduce colonic epithelial damage and/or modulation of the microbiota. The beneficial effects of the supplementation with a complex plant fibre and a fibre-degrading probiotic parallel the effects seen in human microbiota with high plant fibre diets.
Quality of life and spirituality of patients with chronic kidney disease: pre- and post-transplant analysis.

OBJECTIVE to compare the quality of life (QoL) of patients under dialysis and after kidney transplant; correlate the QoL of transplant patients to sociodemographic, morbid and spirituality/religiosity variables. METHOD prospective study with a quantitative approach, with a sample of 27 patients who underwent peritoneal dialysis or dialysis undergoing kidney transplant. QoL and spirituality were assessed by the KDQOL-SF and WHOQOL-SRPB tools, being correlated with sociodemographic and economic variables. RESULTS the dimensions of total mental component, kidney disease effects and kidney disease burden showed significant improvement in the post-transplant period, with p <0.0004. There was a significant correlation between four dimensions of spirituality and seven dimensions of QoL; p ranged from 0.04 to 0.006. CONCLUSION there was a significant improvement in QoL in the post-transplant period. The dimensions of spirituality: wholeness and integration, spiritual connection, wonder and inner peace were positively correlated with seven dimensions of QoL.