Miracle-dz/UniFAR-FTUs huggingface dataset:
A 3D Structural Interactome to Explore the Impact of Evolutionary Divergence, Population Variation, and Small-molecule Drugs on SARS-CoV-2-Human Protein-Protein Interactions

The recent COVID-19 pandemic has sparked a global public health crisis. Vital to the development of informed treatments for this disease is a comprehensive understanding of the molecular interactions involved in disease pathology. One lens through which we can better understand this pathology is through the network of protein-protein interactions between its viral agent, SARS-CoV-2, and its human host. For instance, increased infectivity of SARS-CoV-2 compared to SARS-CoV can be explained by rapid evolution along the interface between the Spike protein and its human receptor (ACE2) leading to increased binding affinity. Sequence divergences that modulate other protein-protein interactions may further explain differences in transmission and virulence in this novel coronavirus. To facilitate these comparisons, we combined homology-based structural modeling with the ECLAIR pipeline for interface prediction at residue resolution, and molecular docking with PyRosetta. This enabled us to compile a novel 3D structural interactome meta-analysis for the published interactome network between SARS-CoV-2 and human. This resource includes docked structures for all interactions with protein structures, enrichment analysis of variation along interfaces, predicted ΔΔG between SARS-CoV and SARS-CoV-2 variants for each interaction, predicted impact of natural human population variation on binding affinity, and a further prioritized set of drug repurposing candidates predicted to overlap with protein interfaces†. All predictions are available online† for easy access and are continually updated when new interactions are published. † Some sections of this pre-print have been redacted to comply with current bioRxiv policy restricting the dissemination of purely in silico results predicting potential therapies for SARS-CoV-2 that have not undergone thorough peer-review. The results section titled “Prioritization of Candidate Inhibitors of SARS-CoV-2-Human Interactions Through Binding Site Comparison,” Figure 4, Supplemental Table 9, and all links to our web resource have been removed. Blank headers left in place to preserve structure and item numbering. Our full manuscript will be published in an appropriate journal following peer-review.
Enhancing the nutritional value of soybeans for poultry through supplementation with new-generation feed enzymes

Soybean meal (SBM) remains the most important and preferred protein feed source for poultry. However, the supply and quality of SBM fluctuates, and the meal is expensive due to processing and transportation costs. Although there is a growing interest in the use of raw SBM for birds, its nutritive value is negatively affected by the presence of anti-nutritive factors (ANF). Heat treatment is applied to alleviate some ANF, such as trypsin inhibitors and lectins, but both under- and over-processing of soybeans can reduce the digestibility of key components in the meal. Feed supplementation with exogenous enzymes, such as phytase and protease enzymes, is a biotechnological option for improving the nutritional values of SBM and other protein-rich ingredients. Proteases break down both stored proteins and proteinaceous anti-nutrients in feeds. Various studies have shown that the performance of birds can be improved through dietary supplementation with new-generation protease enzymes. Phytase is also effective in breaking down phytate (phytic acid), which chelates with mineral cations and other nutrients in soybeans. Recent in vitro and in vivo studies have shown that an enzyme cocktail (combined use of protease and phytase) is more effective in reducing ANF in soybean meal for birds than the use of single enzyme products. This review provides information on how microbial enzymes, particularly protease and phytase, contribute to the improvement of the nutritional values of different types of SBM for poultry.
Efficiency of intracavernosal alprostadil and oral clomiphene citrate combination treatment in penile vasculogenic erectile dysfunction patients accompanied by late‐onset hypogonadism

In this study, the efficiency of intracavernosal alprostadil + oral clomiphene citrate (CC) treatment in late‐onset hypogonadism (LOH) accompanied by penile vasculogenic erectile dysfunction (PVED) in patients irresponsive to phosphodiesterase type 5 inhibitor treatment was evaluated. A total of 31 patients with concurrent PVED and LOH were included in the study. The patients were given intracavernosal alprostadil (10–20 μg) and oral CC (50 mg) every day for 12 weeks. Before and after treatment, a 15‐question International Index of Erectile Function (IIEF‐15) questionnaire, Erection Hardness Score (EHS), Sexual Encounter Profile (SEP)2 and SEP3 levels were analysed, and follicle stimulating hormone (FSH), luteinising hormone (LH), total testosterone and prostate‐specific antigen (PSA) levels were measured. In all, 41.9% of patients had pure arterial deficiency, 19.3% had pure venous deficiency, and 38.7% had arterial + venous (mixed) deficiency. A significant increase was detected in total testosterone, FSH, LH and PSA values after treatment when compared to values before treatment (p < .001, p < .001, p < .001 and p = .034 respectively). A significant recovery was observed in IIEF‐15 subscores, EHS and SEP2‐SEP3 results. In PVED patients accompanied by LOH, intracavernosal alprostadil and oral CC combination is an efficient, low cost, safely applicable and tolerable treatment.
Glass fiber/polypropylene composites with potential of bone fracture fixation plates: Manufacturing process and mechanical characterization

Mechanical properties and manufacturing processes of Glass Fiber/Polypropylene (GF/PP) composites for application of flexible internal long bone fracture fixation plates have been investigated. PP/Short Chopped Glass Fiber (PPSCGF), PP/Long Glass Fiber (PPLGF) and PP/Long Glass Fiber Yarn (PPLGFY) were used in fabrication of the fixation plates. The PPSCGF and PPLGF plates were made by the heat-compressing process and Three-dimensional (3D) printing method was used to make the PPLGFY ones. The values of Young’s modulus, tensile strength, flexural modulus and strength, and impact strength of the PPSCGF in the fiber longitudinal direction were found to be 2.35 ± 0.15 GPa, 30 ± 5 MPa, 2.1 ± 0.2 GPa, 27 ± 5 MPa and 22 ± 5 kJ/m2, respectively. Where, these values for the PPLGF were to 20.10 ± 2 GPa, 400 ± 30 MPa, 16.2 ± 0.2 GPa, 185 ± 5 MPa, and 162 ± 5 kJ/m2 and for the PPLGFY were to 7.87 ± 0.5 GPa, 150 ± 20 MPa, 2.3 ± 0.2 GPa, 44 ± 5 MPa and 68 ± 5 kJ/m2. These have been found to be in close agreement with the human bone properties. Furthermore, the strength and modulus values of the plates were reasonable to be used as a bone implant applicable for bone fracture reconstructions. Hence, the study concluded that the GF/PP composites are useful for load-bearing during daily activities and would be recommended as a choice in orthopedic fixation plate applications. It will help the researchers for development of new fixation designs and the clinicians for better patient’s therapy in future.
A study of the association between identity, life engagement and well-being among young Asian adults

ABSTRACT The eudaemonic tradition asserts that life engagement, that is the pursuit of a meaningful way of living, is an important element of well-being. Self-identity theory posits that individuals’ identities significantly contribute to their sense of meaning and belonging, which in turn boost well-being. The present study aimed to establish the extent to which self-identities are predictors of well-being and whether they are subsumed within the life engagement construct. An opportunity sample of Singaporeans (n = 269) aged 18–35 (M = 23.88, SD = 4.52) completed the Aspects of Identity Questionnaire, Warwick-Edinburgh Mental Well-Being Scale and Life Engagement Test. Correlational analysis showed that personal, social, relational and collective identities were significantly associated with life engagement and well-being. However, multiple regressions demonstrated that life-engagement subsumed collective and relational identity almost completely, and also accounted for a significant amount of the variance in personal and social identities in the prediction of well-being, broadly supporting the eudaemonic model. It was shown that social and personal identities were predictors of well-being beyond life engagement, possibly because these identities satisfy some of psychological needs that promote various benefits that are independent of life engagement, yet still important for well-being. It is suggested that these differences in the salience of identity types to well-being may be indicative of changes in the sense of identity among young Singaporeans that have arisen as a result of social policy or possibly changes in the ways of identity expression in the Internet. The implications of the findings are discussed and recommendations made for future research.
Ameliorative Effects of Quercetin and Naringenin on Diethylnitrosamine/2-acetyl aminoflourene-Induced Nephrotoxicity in Male Wistar Rats

Nephrotoxicity is one of the most widespread kidney tribulations. Quercetin and naringenin are natural flavonoids highly enriched in fruits, and vegetables which have a bioactive effect on human health. The current study was designed to evaluate the preventive effects of quercetin and naringenin on Diethylnitrosamine (DEN)/2- Acetylaminofluorene (2AAF)-induced nephrotoxicity in rats. The Wistar rats used in this study were allocated into 4 groups. The 1st group was kept as a normal group while the other 3 groups were intraperitoneally administered DEN (150 mg/kg b.w./week for two weeks) dissolved in 0.9% saline at the beginning of experiment. One week after the last injection of DEN, 2-AAF was orally administrated at dose 20 mg/kg b.w. in 1% tween 80 four days per week for three weeks. One of the three DEN/2AAF-administered groups was kept as control and the others were orally treated with quercetin and naringenin at dose 10 mg/kg b.w. every other day for 20 weeks. DEN/2AAF administration induced kidney injury evidenced by histological alterations as well as significant increases of serum creatinine, urea and uric acid concentrations. There was also a significant increase in the levels of renal lipid peroxidation and nitric oxide. Moreover, renal glutathione content and activities of superoxide dismutase, catalase, glutathione peroxidase and glutathione-s-transferase were significantly declined as a result DEN/2AAF administration. The treatments of DEN/2AAF-administered rats with the two flavonoids quercetin and naringenin successfully amended kidney histological perturbations and improved serum markers related to kidney function in association with alleviation of the deteriorated kidney oxidative stress and anti-oxidant defense system. In conclusion, quercetin and naringenin successfully attenuate the DEN/2AAF-induced nephrotoxicity and this effect may be mediated via suppression of the oxidative stress and stimulation of the antioxidant defense system.
Liste des Cochenilles de France (Hemiptera, Coccoidea)

Ce travail s'inscrit comme une contribution a la connaissance de la biodiversite nationale. Il dresse une liste des 381 especes de Cochenilles de France reparties en 143 genres et 13 familles. Une liste des Cochenilles nuisibles aux plantes cultivees et ornementales est egalement proposee.
HandMorph: a Passive Exoskeleton that Miniaturizes Grasp

We engineered an exoskeleton, which we call HandMorph, that approximates the experience of having a smaller grasping range. It uses mechanical links to transmit motion from the wearer's fingers to a smaller hand with five anatomically correct fingers. The result is that HandMorph miniaturizes a wearer's grasping range while transmitting haptic feedback. Unlike other size-illusions based on virtual reality, HandMorph achieves this in the user's real environment, preserving the user's physical and social contexts. As such, our device can be integrated into the user's workflow, e.g., to allow product designers to momentarily change their grasping range into that of a child while evaluating a toy prototype. In our first user study, we found that participants perceived objects as larger when wearing HandMorph, which suggests that their size perception was successfully transformed. In our second user study, we assessed the experience of using HandMorph in designing a simple toy trumpet for children. We found that participants felt more confident in their toy design when using HandMorph to validate its ergonomics.
Characterization of ovary genes of beet webworm, Loxostege sticticalis, through de novo transcriptome analysis and its potential application in ovary grading

The beet webworm, Loxostege sticticalis (L.) (Lepidoptera: Crambidae), is an important insect pest that infests crops such as sugar beet, maize, and potato in Asia, Europe, and North America. The ovary grade is a reliable factor that can be used to forecast L. sticticalis outbreaks. However, forecasting outbreaks by dissecting female ovaries is tedious and generally impractical. Better methods for outbreak forecasting need to be developed. Molecular information on ovary transcriptomes potentially provides criteria for ovary grade. We constructed a library of female ovaries from L. sticticalis and sequenced the transcriptome with RNA‐Seq technology. We analyzed the gene expression profile with Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Clusters of Orthologous Groups (COG) for eukaryotic complete genome analysis. The RNA‐seq libraries generated over 62 640 808 clean reads, and a total of 22 628 genes were identified. Many genes related to oocyte meiosis, oocyte maturation, cell adhesion, and signal transduction were identified. Twenty‐eight oocyte meiosis‐ and oocyte maturation‐related genes were selected for quantitative real‐time (qRT) PCR and revealed differentially expressed genes among ovary grades (I–IV) of females. Of the 28 genes selected, 12 were highly expressed in one of the four ovary grades. These genes have potential use as molecular markers for ovary grading serve as a resource for forecasting population outbreaks of L. sticticalis.
Survival of Escherichia coli O157:H7 during Fermentation of Apple Cider.

Survival of Escherichia coli O157:H7 in fermenting and nonfermenting fresh apple cider was determined. Populations of E. coli O157:H7 were reduced from 6.4 log CFU/ml to undetectable levels (detection limit of 0.5 log CFU/ml) in fermenting cider after 3 days at 20°C and from 6.5 log CFU/ml to 2.9 log CFU/m1 after 10 days at 20°C in nonfermenting cider. After 1 day of incubation, recovery of E. coli O157:H7 from fermenting and nonfermenting cider was statistically (P < 0.01) lower on sorbitol MacConkey agar than on tryptone soya agar supplemented with cycloheximide. These results suggest that substantial portions of the surviving E. coli O157:H7 populations were sublethally injured by cider components (i.e., acid and ethanol). The pH of fermenting cider was not significantly different (P > 0.05) from that of nonfermenting cider throughout the 10-day test period. Final ethanol concentrations in fermenting cider reached 6.01% (vol/vol) after 10 days at 20°C. Inactivation of E. coli O157:H7 in fermenting cider is attributed to the combined effects of pH and ethanol. Results of this study indicate that E. coli O157:H7 is capable of survival in fresh apple cider at 20°C, while alcoholic fermentation of fresh cider is an effective means of destroying this pathogen.
Kinetic Analysis of Lipid Oxidation Data

Lipid oxidation is one of the important reactions in biology. It has deleterious effects on polyunsaturated fatty acids and other lipid substrates, causing significant losses in our food quality, health, and well-being. To design strategies to inhibit the progression of oxidative reactions in foods and biological systems, it is important to understand the nature of these reactions and how they are influenced by controllable chemical and physical factors. This goal may be achieved through a better understanding of the reaction kinetics (Greek, kinein “set in motion or move”) and, whenever possible, the energetic and mechanistic aspects of these reactions. Chemical reaction kinetics considers two aspects: (i) the rate (i.e., the speed) at which the reaction takes place, and (ii) the effective factors (mainly temperature, concentration of reactants and products, and presence of catalysts), and how these two are related. If the kinetic data are appropriately collected and analyzed, one might be able to propose a reasonable mechanism for the reaction and to further develop models able to simulate the oxidation of lipid substrates under given experimental physical conditions. Understanding reaction kinetics is an essential prerequisite for modeling the lipid oxidation cascade, the shelf life of stored foods, durability of functional low density lipoproteins, and so on. To date, only scattered literature is available for trials analyzing lipid oxidation kinetic data. This chapter provides a review of some of these with the aim of highlighting the knowledge achieved in these studies and the remaining gaps awaiting further scientific investigations. The chapter also reviews knowledge about the mechanism of lipid oxidation and points to gray areas of understanding. Finally, the application of this knowledge to the stability of foods and of lipids in biological compartments is discussed briefly.
Learning from the Past - Do Historical Data Help to Improve Progress Indicators in Web Surveys?

As a typical part of the interface of web surveys, progress indicators show the degree of completion for participants. These progress indicators influence the dropout and response behavior as various studies suggest. For this reason, the indicator should be chosen carefully. However, calculating the progress in adaptive surveys with many branches is often difficult. Recently related work has provided algorithms for such surveys based on different prediction strategies and has identified the Root Mean Squared Error as a valuable measure to compare different strategies. However, all previously mentioned strategies have shown poor predictions in some cases. In this paper, we present a new strategy which learns from historical data. A simulation study with 10k randomly generated surveys shows its benefits and its limits. As an example of application, we confirm our results of the simulation by comparing different prediction strategies for two large real-world surveys.
Brain Relevance Feedback for Interactive Image Generation

Brain-computer interfaces (BCIs) are increasingly used to perform simple operations such as a moving a cursor, but have remained of limited use for more complex tasks. In our new approach to BCI, we use brain relevance feedback to control a generative adversarial network (GAN). We obtained EEG data from 31 participants who viewed face images while concentrating on particular facial features. Following, an EEG relevance classifier was trained and propagated as feedback on the latent image representation provided by the GAN. Estimates for individual vectors matching the relevant criteria were iteratively updated to optimize an image generation process towards mental targets. A double-blind evaluation showed high performance (86.26% accuracy) against random feedback (18.71%), and not significantly lower than explicit feedback (93.30%). Furthermore, we show the feasibility of the method with simultaneous task targets demonstrating BCI operation beyond individual task constraints. Thus, brain relevance feedback can validly control a generative model, overcoming a critical limitation of current BCI approaches.
Evaluating future success of whitebark pine ecosystem restoration under climate change using simulation modeling

Major declines of whitebark pine forests throughout western North America from the combined effects of mountain pine beetle (Dendroctonus ponderosae) outbreaks, fire exclusion policies, and the exotic disease white pine blister rust (WPBR) have spurred many restoration actions. However, projected future warming and drying may further exacerbate the species' decline and possibly compromise long‐term success of today's restoration activities. We evaluated successes of restoration treatments under future climate using a comprehensive landscape simulation experiment. The spatially explicit, ecological process model FireBGCv2 was used to simulate whitebark pine populations on two U.S. Northern Rocky Mountain landscapes over 95 years under two climate, three restoration, and two fire management scenarios. Major findings were that (1) whitebark pine can remain on some high mountain landscapes in a future climate albeit at lower basal areas (50% decrease), (2) restoration efforts, such as thinning and prescribed burning, are vital to ensure future whitebark pine forests, and (3) climate change impacts on whitebark pine vary by local setting. Whitebark pine restoration efforts will mostly be successful in the future but only if future populations are somewhat resistant to WPBR. Results were used to develop general guidelines that address climate change impacts for planning, designing, implementing, and evaluating fine‐scale restoration activities.
Differential performance of two geometrids on previously defoliated Scots pine

We studied the effect of previous defoliations of Pinus sylvestris on the performance of two geometrid moths, Bupalus piniarius and Macaria liturata, using a field experiment. Prior to the experiment, we found defoliationto increase the concentrations of certain secondary chemicals and reduce the N (nitrogen) concentration of needles. Hence, it was predicted that defoliation-induced changes should decrease the performance of geometrids feeding on P. sylvestris. As B. piniarius is a monophagous species on P. sylvestris, and M. liturata is oligophagous feeding also on Larix and Juniperus species, we predicted that M. liturata should suffer more than B. piniarius from defoliation-induced changes in needle chemistry. As predicted, defoliation had a negative effect on the performance, the oligophagous M. liturata being more vulnerable. Defoliation resulted in decreased sex-specific survival of M. liturata, but did not affect the survival of B. piniarius. In M. liturata, no males survived to the pupal stage in previously defoliated trees. Defoliation also resulted in lower pupal weights in both species. We conclude that defoliation-induced changes on the performance of insects with different host ranges merit more attention.
Tetrocarcins N and O, glycosidic spirotetronates from a marine-derived Micromonospora sp. identified by PCR-based screening

Two new glycosidic spirotetronate antibiotics, tetrocarcins N (1) and O (2), were isolated and identified from the marine-derived Micromonospora sp. 5-297 using a PCR-based genetic screening method targeting the dTDP-glucose-4,6-dehydratase gene. Their structures were determined by extensive IR, NMR, and MS spectroscopic analyses. Tetrocarcin O (2) is a derivative of 1 that lacks the terminal L-amicetose moiety at C-9. Compound 1 and 2 exhibited antibacterial activity against Bacillus subtilis with MIC values of 2 and 64 μg mL−1, respectivly. It seems that the sugar moieties at C-9 and the formyl group at C-32 play important roles in the antibacterial activity of the tetrocarcins.