Miracle-dz/UniFAR-FTUs huggingface dataset:
UbiNet 2.0: a verified, classified, annotated and updated database of E3 ubiquitin ligase–substrate interactions

Abstract Ubiquitination is an important post-translational modification, which controls protein turnover by labeling malfunctional and redundant proteins for proteasomal degradation, and also serves intriguing non-proteolytic regulatory functions. E3 ubiquitin ligases, whose substrate specificity determines the recognition of target proteins of ubiquitination, play crucial roles in ubiquitin–proteasome system. UbiNet 2.0 is an updated version of the database UbiNet. It contains 3332 experimentally verified E3–substrate interactions (ESIs) in 54 organisms and rich annotations useful for investigating the regulation of ubiquitination and the substrate specificity of E3 ligases. Based on the accumulated ESIs data, the recognition motifs in substrates for each E3 were also identified and a functional enrichment analysis was conducted on the collected substrates. To facilitate the research on ESIs with different categories of E3 ligases, UbiNet 2.0 performed strictly evidence-based classification of the E3 ligases in the database based on their mechanisms of ubiquitin transfer and substrate specificity. The platform also provides users with an interactive tool that can visualize the ubiquitination network of a group of self-defined proteins, displaying ESIs and protein–protein interactions in a graphical manner. The tool can facilitate the exploration of inner regulatory relationships mediated by ubiquitination among proteins of interest. In summary, UbiNet 2.0 is a user-friendly web-based platform that provides comprehensive as well as updated information about experimentally validated ESIs and a visualized tool for the construction of ubiquitination regulatory networks available at http://awi.cuhk. edu.cn/~ubinet/index.php.
An Asian-specific MPL genetic variant alters JAK-STAT signaling and influences platelet count in the population.

Genomic discovery efforts for hematological traits have been successfully conducted through genome-wide association study (GWAS) on samples of predominantly European ancestry. We sought to conduct unbiased genetic discovery for coding variants that influence hematologic traits in a Han Chinese population. A total of 5257 Han Chinese subjects from Beijing, China were included in the discovery cohort and analyzed by an Illumina ExomeChip array. Replication analyses were conducted in 3827 independent Chinese subjects. We analyzed 12 hematological traits and identified 22 exome-wide significant SNP-trait associations with 15 independent SNPs. Our study provides replication for two associations previously reported but not replicated. Further, one association was identified and replicated in the current study, of a coding variant in the myeloproliferative leukemia (MPL) gene, c.793C > T, p.Leu265Phe (L265F) with increased platelet count (β = 20.6 109 cells/L, Pmeta-analysis = 2.6x10-13). This variant is observed at ~ 2% population frequency in East Asians, whereas it has not been reported in gnomAD European or African populations. Functional analysis demonstrated that expression of MPL L265F in Ba/F3 cells resulted in enhanced phosphorylation of Stat3 and ERK1/2 as compared to the reference MPL allele, supporting altered activation of the JAK-STAT signal transduction pathway as the mechanism underlying the novel association between MPL L265F and platelet count.
Kinetics of reduction of iron oxide with carbon monoxide and hydrogen

This investigation was undertaken to determine the rate controlling step in the reduction of iron oxides with hydrogen and carbon monoxide. For the reduction of porous hematite pellets, and bars it was found that the reduction rate is controlled by the counterdiffusion of reactant gas and product gas between the reaction zone and the main gas stream. The reduction specimens were spheres ranging in size from 1.5- to 4.4-cm. diameter and 5.1- by 7.6-cm. bars either 0.69 or 1.24 cm. thick. They were prepared from electrolytic iron powder, partially oxidized in a rotary kiln. The final oxidation of the specimens to hematite was accomplished by firing them at 1,149°C. in an oxidizing atmosphere. The bulk density was 3.5 g. /cc. The specific surface area was 0.08 sq.m. /g. and the void faction was 0.31. The oxide specimens were reduced in streams of pure hydrogen or carbon monoxide at temperatures between 700° and 1,200°C. The reduction was followed by measuring the sample weight during the reaction. Reduction rates were studied at system pressures of 1 and 2 at. The samples reduced step by step, to magnetite, to wustite, and finally to iron. A shell of reduction, clearly visible in sections of partially reduced specimens, moved concentrically into the core of the samples. Ahead of the receding interface the specimens were known to be pervious to the reactant gases. This led to the conclusion that the gas composition at the interface was in equilibrium with the oxide phases present. Except for the removal of the last portions of oxygen at the lower reduction temperatures, the course of the reduction followed Fick's first law of diffusion. Values of the diffusion co-efficients, determined from the experimental data, were in close agreement with values predicted from empirical equations. Varying the total pressure of the system had no effect on the rate of reduction, which is consistent with the equations developed from Fick's law for the diffusion-controlled reaction under investigation. It is speculated that the retarding of the reduction reaction at the lower reduction temperatures is due to the entrapment of oxide inside shells of iron, which are impervious to the reducing gas. Reduction of the trapped oxide then proceeds by solid state diffusion in a manner proposed by Edstrom (6).
Development of a novel in vitro assay to screen for neuroprotective drugs against iatrogenic neurite shortening

This work tries to help overcome the lack of relevant translational screening assays, as a limitation for the identification of novel analgesics for neuropathic pain. Hyperexcitability and neurite shortening are common adverse effects of antiviral and antitumor drugs, leading to neuropathic pain. Now, as seen in the drug screening that we developed here, a high-content microscopy-based assay with immortalized dorsal root ganglia (DRG) neurons (differentiated F11 cells) allowed to identify drugs able to protect against the iatrogenic neurite shortening induced by the antitumor drug vincristine and the antiviral drug rilpivirine. We observed that vincristine and rilpivirine induced a significant reduction in the neurite length, which was reverted by α-lipoic acid. We had also evidenced protective effects of pregabalin and melatonin, acting through the α2δ-2 subunit of the voltage-dependent calcium channels and the MT1 receptor, respectively. Additionally, two hits originated from a previous primary screening aimed to detect inhibitors of hyperexcitability to inflammatory mediators in DRG neurons (nitrendipine and felodipine) also prevented neurite shortening in our model. In summary, in this work we developed a novel secondary assay for identifying hits with neuroprotective effect against iatrogenic neurite shortening, consistent with the anti-hyperexcitability action previously tested: highlighting nitrendipine and felodipine against iatrogenic damage in DRG neurons.
Low-Temperature CO Oxidation over Co3O4/Al2O3

Abstract The oxidation of CO over Co 3 O 4 /γ-Al 2 O 3 at room temperature (21°C) has been studied in a continuous-flow reactor system with oxidising and reducing pretreatment, at varying stoichiometric ratios, and by using isotope-labeled 18 O 2 . The fresh catalyst was characterised by temperature-programmed reduction and temperature-programmed oxidation. CO deactivates the oxidised catalyst but the rate of deactivation can be suppressed by having a high O 2 /CO ratio. The isotope study showed that the oxygen participating in the oxidation of CO comes from oxygen bound to the cobalt oxide surface. Finally, a mechanism for the CO oxidation over Co 3 O 4 /γ-Al 2 O 3 is proposed.
Ontogenetic diversity buffers communities against consequences of species loss.

Biodiversity can be measured at multiple organizational scales. While traditional studies have focused at taxonomic diversity, recent studies have emphasized the ecological importance of diversity within populations. However, it is unclear how these different scales of diversity interact to determine the consequence of species loss. Here we asked how predator diversity and presence of ontogenetic diversity within predator populations influences community structure. Ontogenetic diversity arises from shifts in the traits and ecology of individuals during ontogeny and it is one of the biggest sources of intraspecific diversity. However, whether it dampens or strengthens the negative consequences of with species loss is poorly understood. To study this interaction of species diversity and ontogenetic diversity, we experimentally manipulated predator species diversity and diversity of developmental stages within focal predator species and analyzed their joint effect on predator and prey survival, biomass, and prey community structure in experimental pond systems. While individual effects of ontogenetic diversity were often species-specific, losing predator species from the community often had a much smaller or no effect on prey survival, biomass, or community structure when all predator populations had high ontogenetic diversity. Thus, ontogenetic diversity within populations buffered against some of the consequences of biodiversity loss at higher organizational levels. Because the experiment controlled mean per capita size and biomass across structured vs. unstructured populations, this pattern was not driven by differences in biomass of predators. Instead, results suggest that effects were driven by changes in the functional roles and indirect interactions across and within species. This indicates that even if all environmental conditions are similar, differences in the intrinsic structure of populations can modify the consequences of biodiversity loss. Together, these results revealed the importance of ontogenetic diversity within species for strengthening the resilience of natural communities to consequences of biodiversity loss and emphasize the need to integrate biodiversity patterns across organizational scales.
Methylation of softwood kraft lignin with dimethyl carbonate

The reactivity and functionality of technical lignin requires reliable modulation in order to be used as a precursor for a variety of applications. A green alternative for lignin methylation using dimethyl carbonate (DMC) is reported and this paper discusses our efforts toward optimization and structural elucidation for such reactions. It is demonstrated that softwood kraft lignin can be progressively and reproducibly methylated to different extents using DMC in the presence of sodium hydroxide or cesium carbonate as bases with the latter requiring milder reaction conditions. 13C NMR, FT-IR, and quantitative 31P NMR spectroscopic analyses were used to document and understand the structural changes occurring within the methylated lignin derivatives. While the phenolic hydroxyl groups of lignin are methylated, the reduction in aliphatic –OHs is also observed in control and methylation reactions, most likely via a solvent mediated intramolecular rearrangement reaction. As anticipated, the methylation induced thermal stability, elimination of thermally induced crosslinking and lowering of the glass transition temperature. Overall, the developed chemistry offers a green alternative to a much sought derivatization reaction that adds value to an otherwise intractable and underutilized biopolymer.
Enzymatic Hydrolysis of Defatted Antheraea pernyi (Lepidoptera: Saturniidae) Pupa Protein by Combined Neutral Protease Yield Peptides With Antioxidant Activity

Abstract In this study, peptides were prepared from defatted Antheraea pernyi (Lepidoptera: Saturniidae) pupa protein via hydrolysis with combined neutral proteases. Single-factor tests and response surface methodology (RSM) were used to determine the optimal hydrolysis condition suitable for industrial application. Optimal hydrolysis of the defatted pupa protein was found to occur at an enzyme concentration of 4.85 g/liter, a substrate concentration of 41 g/liter, a hydrolysis temperature of 55°C, and a hydrolysis time of 10 h and 40 min. Under these conditions, the predicted and actual rates of hydrolysis were 45.82% and 45.75%, respectively. Peptides with a molecular weight of less than 2,000 Da accounted for 90.5% of the total peptides generated. Some of the peptides were antioxidant peptides as revealed by sequencing and functional analysis. The antioxidant activity of the mixed peptides was subsequently confirmed by an antioxidant activity assay. The results showed that peptides with high antioxidant activity could be obtained from the hydrolysis of A. pernyi pupa protein.
Novel Hückel stabilised azole ring-based lithium salts studied by ab initio Gaussian-3 theory

Gaussian-3 theory calculations have been performed for a new family of lithium salts with heterocyclic anions–Li+[N5C2n]− (0 ≤ n ≤ 5). Eight different anions and the most stable 1∶1 lithium ion pairs have been studied for each anion. The lithium ion affinity of the anions decreases with the gradual CN-substitution and is thus lowest for the [N5C10]− anion. The stability vs. oxidation, inferred from the HOMO values, is large for all anions. In addition, the volume and aromaticity of the anions have been evaluated.
Thermographic findings related to facial pain – a survey of 40 subjects

ABSTRACT Objective The purpose of this study was to assess how thermography findings relate painful symptoms and signs of temporomandibular disorders (TMD). Methods Thermography, combined with chewing of paraffin wax, was performed on 40 subjects. The results were analyzed according to gender and pain-related TMD symptoms and clinical signs. Results The overall temperatures after chewing were higher in TMD patients than in controls. For females, the most significant findings were the thermal increase between the relaxed state and subjects’ state after chewing in temporal and temporomandibular joint (TMJ) regions. For males, all calculated parameters demonstrated a poor ability to discriminate TMD from controls. Conclusion Thermography could be a potential tool in diagnostics of female TMD patients. The results suggest that the thermal information assessed in specific facial areas could help to discriminate TMD patients from non-TMD patients and could be used to quantify the pain associated with TMD.
Determination of Femtogram Quantities of Protactinium in Geologic Samples by Thermal Ionization Mass Spectrometry

We describe a procedure for measurement of [sup 231]Pa in geologic samples by isotope dilution thermal ionization mass spectrometry, using [sup 233]Pa as a spike isotope, which provides marked improvements in precision and sample size relative to established decay counting techniques. This method allows determination of as little as a few tens of femtograms of [sup 231]Pa (approximately 10[sup 3] atoms) with a conservative estimated uncertainty of [+-]1% (95% confidence level). Applications of [sup 231]Pa-[sup 235]U systematics to uranium-series geochemistry and geochronology should be greatly enhanced by this approach. 31 refs., 4 figs., 1 tab.
Theoretical and experimental study of the effects of scale-up on mixing time for a stirred-tank bioreactor

Mixing time is one of the criteria most widely used to characterize mixing intensity in bioprocesses. In bioreactors, mixing mainly depends on amount of energy consumed, reactor and stirrer shapes, airing speed and the rheology of the medium. In this work we experimentally determined the mixing times for a lab-scale bioreactor equipped with a stirrer propelled by two Rushton turbines. From these experiments we could obtain expressions to evaluate the effects of stirring speed, superficial gas velocity, specific power consumption and system geometry on mixing times under various flow regimes. The resulting correlations were employed to analyze the effect of scale-up on mixing times for the production of Staphylococcus aureus Smith.
Synthesis and X-ray diffraction data of 1-[N-(methyl)-(3,5-dimethylphenylamino)]methylnaphthalene

The 1-[N-(methyl)-(3,5-dimethylphenylamino)]methylnaphthalene (chemical formula C20H21N) was prepared by means of a condensation between alpha-naphthylaldehyde and 3,5-dimethylaniline in anhydrous ethanol to obtain the aldimine (1) which was reduced with NaBH4 to afford the 1-[N-(3,5-dimethylphenylamino)]methylnaphtalene (2), and finally, the compound (3) was obtained by N-alkylation reaction of (2) with methyl iodine (CH3I) and potassium carbonate (K2CO3) in acetone. Final compound (3) was purified by chromatographic column. The XRPD pattern for the new compound, 1-[N-(methyl)-(3,5-dimethylphenylamino)]methylnaphthalene, was obtained. This compound crystallizes in monoclinic system with space group P21/a (No. 14) and refined unit-cell parameters a=13.260(4) Å, b=15.495(5) Å, c=7.719(5) Å, β=90.19(6), and V=1586(1) Å3.
A general dynamical theory of the X‐ray Laue diffraction from a homogeneously bent crystal

General properties of the rigorous solution of the problem of the X-ray dynamical Laue diffraction from a bent crystal are discussed. The solution based on the Takagi equations is formulated in the form of the Huygens-Fresnel principle. Special attention is paid to the behaviour of the quasi-classical asymptotic expansion of the exact dynamical wave fields and to the comparison of the results with those obtained by the eikonal theory. The eikonal theory is developed as a result of the application of the stationary-phase method for the evaluation of the Kirchhoff integral in accordance with the Huygens-Fresnel principle. The focusing of X-rays (the intersection of the ray trajectories and the formation of a caustic) is analysed. The generalized eikonal theory when elaborated yields that the integrated diffracted intensity from a bent crystal tends to the correct kinematical value as the strain gradient increases. For practical purposes, a simple numerical method of calculation of the integrated intensity applied in a general case of asymmetric Laue diffraction is proposed.
Effectiveness and perceptions of using templates in long-term condition reviews: a systematic synthesis of quantitative and qualitative studies

Background Review templates are commonly used in long-term condition (LTC) consultations to standardise care for patients and promote consistent data recording. However, templates may affect interactions during the review and, potentially, inhibit patient-centred care. Aim To systematically review the literature about the impact that LTC review templates have on process and health outcomes, and the views of health professionals and patients on using review templates in consultations. Design and setting Parallel qualitative and quantitative systematic reviews. Method Following Cochrane methodology, nine databases were searched (1995–2019; updated July 2020) for clinical trials and qualitative studies of LTC templates in healthcare settings. Duplicate selection, risk-of-bias assessment, and data extraction were performed. The quantitative and qualitative analyses were conducted in parallel, and findings synthesised narratively. Results In total, 12 qualitative and 14 quantitative studies were included (two studies reported both qualitative and quantitative data, and were included in both analyses). Review templates were well used, but the only study to assess health outcomes showed no effect. Templates can improve documentation of key measures and act as a reminder tool; however, they can restrict the review process, and risk health professionals’ agendas being prioritised over those of patients. Templates may also limit opportunities to discuss individuals’ concerns about living with their condition and act as a barrier to providing patient-centred care. Conclusion Future research should evaluate health, as well as process, outcomes. The potential benefits of templates in improving documentation should be balanced against concerns that ‘tick boxes’ may override patient agendas, unless templates are designed to promote patient-centred care.
The stability of magnetic chitosan beads in the adsorption of Cu2

Magnetic chitosan beads (MCBs) synthesized through a common embedding method and crosslinked with glutaraldehyde were studied for the adsorption of Cu2+ in aqueous solution. MCBs were investigated by means of hysteresis curves, thermo-magnetization curves, TGA, FTIR and XRD. Kinetic, isothermal and thermodynamic studies were applied to investigate the adsorption of Cu2+ by the MCBs. The effects of the pH value and the coexisting ions on the adsorption of Cu2+ were explored. Subsequently, the stability of the MCBs including the adsorption capacity (Qe) and the saturated magnetization (Ms) stability was investigated under various conditions. Simultaneously, FTIR and XRD were utilized to further analyze the change in the MCBs in the stability studies. The results suggested that the MCBs showed good stability without a significant loss in Qe and Ms after regeneration from five sequential cycles. The MCBs presented excellent storage stability while stored in a drying vessel for ten months. For thermal stability, the Qe and Ms of the MCBs presented similar variations after being heated in the atmosphere and in a vacuum at different temperatures for 30 h. The Qe changed slightly after being heated at 50 and 100 °C, and decreased sharply at 150 and 200 °C. The magnetization was stable in the lower temperature range (50–150 °C) and increased slightly at 200 °C. Different magnetic fields had little effect on the stability of the MCBs.
Regulation of the Plant Cell Cycle in Response to Hormones and the Environment.

Developmental and environmental signals converge on cell cycle machinery to achieve proper and flexible organogenesis under changing environments. Studies on the plant cell cycle began 30 years ago, and accumulated research has revealed many links between internal and external factors and the cell cycle. In this review, we focus on how phytohormones and environmental signals regulate the cell cycle to enable plants to cope with a fluctuating environment. After introducing key cell cycle regulators, we first discuss how phytohormones and their synergy are important for regulating cell cycle progression and how environmental factors positively and negatively affect cell division. We then focus on the well-studied example of stress-induced G2 arrest and view the current model from an evolutionary perspective. Finally, we discuss the mechanisms controlling the transition from the mitotic cycle to the endocycle, which greatly contributes to cell enlargement and resultant organ growth in plants. Expected final online publication date for the Annual Review of Plant Biology, Volume 72 is May 2021. Please see http://www.annualreviews. org/page/journal/pubdates for revised estimates.