Miracle-dz/UniFAR-FTUs huggingface dataset:
In Silico Prediction of Betulinic Acid Derivatives’ Cytotoxicity: Relationship between Topological Descriptors and CC50 Value

Modeling of the relationship between structure and cytotoxicity has helped in the process of designing safer new drug compounds. In this study, modeling was carried out between the structures of 29 betulinic acid derivatives with their cytotoxicity. The modeling is done by using multiple linear regression (MLR) techniques. In the model, an equation is obtained by involving five descriptors and has statistical parameters as r2training of 0.776; Fcal/Ftab of 4.503; r2test of 0.985; r2m of 0.971. The five descriptors involved in the equation are TDB2e (3D topological distance-based autocorrelation-lag 2/weighted by Sanderson electronegativities), TDB9s (3D topological distance-based autocorrelation-lag 9/weighted by I-state), RDF50m (radial distribution function-050/weighted by relative mass), RDF140m (radial distribution function-140/weighted by relative mass), and RDF10s (radial distribution function-010/weighted by relative I-state). The equation could be used to design the new betulinic acid derivatives with lower predicted cytotoxicities regarding the coefficients of the descriptors. In this case, the new substituent is chosen to enhance the value of RDF140m and RDF10s, while also to make the value of TDB23, TDB9s, and RDF50m getting lower, so the CC50 value will rise (the compound become less toxic to the normal cell).
The Quality Optimization of SiO2/Graphene Material as Sensing Layer for Escherichia coli Bacteria Sensor Application

Escherichia coli bacteria sensors have been broadly developed broadly to overcome a diarrheal disease caused by Escherichia coli on poor hygienic water. Sensing layer, as a main part of the sensor, contacts directly to the analyte on sensors system. Some materials were costly and harmful to detect bacteria. Potentially, graphene is a natural carbon derivative with some excellence properties; easy synthesis, and biocompatible. Hence, the quality of the SiO2/graphene sensing layer was conducted through optical, physical, and electrical characterization to analyze biocompatibility, repeatability, and selectivity. The result showed that Escherichia coli bacterial growth was found around SiO2/graphene after bacterial exposure indicating a biocompatible material. Raman peak also pointed the fingerprint of graphene after 25 times Escherichia coli exposure through G (1584.52 cm–1) and 2D peak (2701.5 cm–1) promising as a repeatable material. The ID/IG ratio increased by the time the bacteria exposure times increased indicating a withstand material from defects and or disorders after bacteria exposure. Through I/V meter, the increasing number of Escherichia coli could increase the resistance value of SiO2/graphene. This sensing layer could detect the presence of Escherichia coli in limit of detection 16 CFU/mL.
Stacking Cell Model Supercapacitor Asymmetry with Multilayer Reduced Graphene Oxide Films Fabricated Using UV Oven Spraying Technique

We report the fabrication of multilayer reduced graphene oxide films using UV oven spraying technique for stacking cell model supercapacitor asymmetry. In report, we used nickel and carbon substrates as asymmetric current collectors. Using UV oven spraying technique, graphene oxide was coated and insitu converted on substrate surfaces forming reduced graphene oxide films that act as active materials in supercapacitor asymmetry. The films consist of 70 layers with delay time between consecutive layer prior to irradiation is 4 minutes to ensure the photoreduction take place on each layer. UV light source using Mercury lamp 125 watt at 30 cm above the substrates. The model structures consist of three cells stacked serial in 1M KCl electrolyte system. Device performance was characterized using charge-discharge technique for constant current at 2, 3, 4, 5, and 10 mA. Performance parameters are the capacitance density, power and energy density. Single cell supercapacitor has energy density in range of 0.072 Wh/kg to 0.256 Wh/kg and power density in range of 123.06 W/kg to 644.14 W/kg. Meanwhile for stacked cell supercapacitor has energy density in range of 0.377 Wh/kg to 0.755 Wh/kg, and power density in range of 169.95 W/kg to 849.79 W/kg. According to Ragone Plot, the results have feature as supercapacitor, even as single cell. Stacked cell has feature better than single cell in all parameter of capacitance density, power and energy density, and electrical working potential.
Introducing Residual Stresses on Sheet Metals by Slide Hardening under Stress Superposition

The fatigue strength and product life of the components can be improved by introducing compressive residual stresses using mechanical surface treatment. Appling stress superposition is an option to be used in metal forming to reduce the process force. In this work experimental investigations to analyze the influence of stress superposition on residual stresses of sheet metal parts by a slide hardening process were carried out. The flat and elastically pre-bended specimens (i.e. stress-superimposed specimen) were processed with a slide diamond tool under different loading forces. The residual stress generated through the thickness of the sheet metal was similar for the flat and the pre-bended specimens. The superimposed stress by elastic bending of the sheet metal led to higher compressive residual stress compared to the flat specimen under the same loading force. Nevertheless, the contour of the pre-bended specimen showed more bulking compared to the flat specimen. The mechanical characteristics determined by hardness measurements showed no significant improvement when applying stress superposition.
The Effect of Ag Concentration of Core-Shell Fe3O4@Ag Nanoparticles for Sensitivity Enhancement of Surface Plasmon Resonance (SPR) - Based Biosensor

The objective of this research is to advance the affectability of Surface Plasmon Resonance (SPR) biosensor utilizing core-shell Fe3O4@Ag nanoparticles (Fe3O4@Ag NPs) with a variation of Ag concentration (20, 40, 60, 80, 100) mM. Fe3O4@Ag NPs were synthesized by the aqueous solution method. The characterization by utilizing X-ray Diﬀractometer (XRD) depicts that the crystal structure of Fe3O4 compares to the cubic inverse spinel structure and based on Transmission Electron Microscopy (TEM) estimation, the particle size average of Fe3O4@Ag NPs is 14.45 nm. The magnetic properties of Fe3O4@Ag NPs were evaluated by Vibrating Sample Magnetometer (VSM), the result appears that the more concentration of Ag increases, the more remanent magnetization (Mr), saturation magnetization (Ms), and coercitivity field (Hc) diminishes. In this research, a Fe3O4@Ag NPs, a spherical nanoparticle consisting of a spherical Fe3O4 core covered by an Ag shell, was used as an active material to enhance the signal detection of SPR, with a wavelength of 632.8 nm in the Kretschmann configuration. The system consists of a four-layer material, i.e., prism/Au film/ Fe3O4@Ag NPs. The results show that the SPR angle shifted to the larger angle of incident light by using Fe3O4@Ag NPs. However, the effect of Ag concentration appears that the more concentration of Ag extends, the lower angle of SPR shifts. The addition of a core-shell in the conventional SPR-based biosensor leads to the enhancement of the SPR biosensor sensitivity if the fractional volume of the core-shell is large.
Explaining Performance-Limiting Mechanisms in Fluorophosphate Na-Ion Battery Cathodes through Inactive Transition-Metal Mixing and First-Principles Mobility Calculations

Fluorophosphate cathodes are currently one of the most promising polyanionic sodium-ion battery cathodes and exhibit specific energies not far below oxide cathodes. To further improve fluorophosphate cathodes, their capacity must be increased, which might be possible since some sodium (Na) remains unextracted in these cathodes during cycling. In this study we attempt to answer the question of what specific mechanism limits fluorophosphate cathode capacity, which could stem from either redox-limiting or site-limiting behavior. This paper reports the synthesis, electrochemical characterization, and computational examination of Na3GaV(PO4)2F3. This test system, which was designed explicitly for uncovering the limiting factors in these structures, exhibits reversible insertion of Na+ and redox activity for V2+ through V5+ during electrochemical cycling, indicating that fluorophosphate cathodes are not fundamentally redox-limited and must be site-limited. First-principles calculations indicate that large diffu.
Issue Highlights — May 2021

This May 2021 issue of Cytometry B (Clinical Cytometry) consists of one review paper on cerebrospinal fluid (CSF) analysis by flow cytometry in hematological malignancies, together with nine manuscripts containing original research in the field of clinical cytometry, related to myeloid neoplasms e.g. myelodysplastic syndromes (MDS), myeloproliferative neoplasms (MPN), MDS/MPN and hypereosinophilic syndromes (HES), to the flow cytometric detection of T-cell clonality in the diagnostic work-up of mature/peripheral T cell neoplasms and two technical papers related to the diagnosis of Fanconi anemia and stabilization protocols for flow cytometric evaluation of bronchoalveolar lavage samples. Three letters to the editor and two case reports including a dendritic cell neoplasm arising in a patient also diagnosed of MDS/MPN and a transient red cell aplasia due to parvovirus B19 infection, complete the May issue of Cytometry B.
Determinazione di aflatossina M1 nel latte : Metodologie immunochimiche e cromatografiche a confronto

The surveillance of aflatoxin M 1 residues in milk requires simple, rapid, sensitive and quantitative analytical methods. ELISA method fairly complies with such requirements, but meanwhile is subjected to interferences from sample components, thus affecting precision and accuracy. Therefore an intra-laboratory comparative assessment was carried out between an immunochemical method (ELISA) and a chromatographic method (IAC-HPLC). The ELISA results do not turn out to be reliable, failing a confirmation method, for instance the IAC-HPLC technique. In particular, this lack of reliability seems to get importance from an aflatoxin M 1 concentration quite close to the suggested limit of 50 ng/L.
Removal of Hazardous Air Pollutant Precursors by Advanced Coal Preparation

The 1990 Clean Air Act Amendment contains provisions that will establish new emission standards for 189 potentially hazardous air pollutants. Several of these, such as arsenic, mercury and selenium, are present as trace elements in run-of-mine coals. Research conducted at Virginia Tech suggests that many of these elements can be efficiently rejected prior to coal combustion using a two-stage physical cleaning circuit that combines advanced froth notation with an enhanced gravity separator. Flotation is a surface-based process that efficiently rejects trace elements associated with ash-forming minerals such as clay, while the enhanced gravity separator is a density-based process that efficiently rejects trace elements associated with high-density middlings containing pyrite. By combining both units in a single circuit, improved rejections of a wide variety of trace elements can be achieved. This paper describes the findings of recent pilot-scale test work conducted to evaluate the capabilities of this nove.
Single cell analysis of RA synovial B cells reveals a dynamic spectrum of ectopic lymphoid B cell activation and hypermutation characterized by NR4A nuclear receptor expression

Ectopic lymphoid structures (ELS) can develop in rheumatoid arthritis (RA) synovial tissue, but the precise pathways of B cell activation and selection are not well understood. Here, we identified a unique B cell population in the synovium characterized by co-expression of a family of orphan nuclear receptors, NR4A1 (also known as NUR77), NR4A2 (NURR1) and NR4A3 (NOR1), that is highly enriched at both early and late stages of RA. NR4A B cells are rare in healthy peripheral blood, RA blood, and SLE kidney, but share markers with blood transcriptomic signatures that peak during RA disease flare. Using combined single cell transcriptomics and B cell receptor (BCR) sequencing, we demonstrate that NR4A synovial B cells have an activated transcriptomic profile that significantly overlaps with germinal center (GC) light zone (LZ) B cells and an accrual of somatic hypermutation that correlates with loss of naïve B cell status. NR4A B cells uniquely co-express lymphotoxin β and IL6, supporting important functions in ELS promotion and pro-inflammatory cytokine production. Further, the presence of shared clones in this activated B cell state and NR4A expressing synovial plasma cells (PC) and the rapid up-regulation with BCR stimulation points to in situ differentiation. Taken together, we identified a dynamic progression of B cell activation in RA synovial ELS, with NR4A transcription factors having an important role in antigen activation and local adaptive immune responses. One sentence summary B cells in the rheumatoid arthritis synovium undergo a spectrum of in situ activation, with the NR4A family of transcription factors having an important role in antigen stimulation, local adaptive immunity, and pathological B cell responses.
Optimization of Polysaccharide Extraction from Polygonatum odoratum by Response Surface Methodology and Evaluation of its Antitumor Activity

This work established a microwave-assisted procedure for polysaccharide extraction from Polygonatum odoratum. Response surface methodology was used to optimize microwave-assisted extraction parameters (extraction temperature, water-to-raw material ratio, microwave power, and extraction time) by implementing a three-level, fourvariable Box–Behnken experimental design in a single-factor investigation. Three-dimensional response surfaces were plotted by Design-Expert, and result indicated the absence of interaction effects of extraction temperature and microwave power. A polysaccharide yield of approximately 17.49% was obtained under the following optimized conditions: temperature of 57°C, microwave power of 300 W, extraction time of 10 min, and water-to-raw material ratio of 23:1. The results of preliminary in vitro antitumor activity tests showed that polysaccharides derived from P. odoratum could inhibit growth of A549 cells in a dose-dependent manner. Moreover, 4-400 μg/mL of these polysaccharides exerted no significant cytotoxicity to Panc-1 cells.
Chromatin accessibility of primary human cancers ties regional mutational processes with tissues of origin

Regional mutagenesis in cancer genomes associates with DNA replication timing (RT) and chromatin accessibility (CA) of normal cells, however human cancer epigenomes remain uncharacterized in this context. Here we model megabase-scale mutation frequencies in 2517 cancer genomes with 773 CA and RT profiles of cancers and normal cells. We find that CA profiles of matching cancers, rather than normal cells, predict regional mutagenesis and mutational signatures, indicating that most passenger mutations follow the epigenetic landscapes of transformed cells. Carcinogen-induced and unannotated signatures show the strongest associations with epigenomes. Associations with normal cells in melanomas, lymphomas and SBS1 signatures suggest earlier occurrence of mutations in cancer evolution. Frequently mutated regions unexplained by CA and RT are enriched in cancer genes and developmental pathways, reflecting contributions of localized mutagenesis and positive selection. These results underline the complex interplay of mutational processes, genome function and evolution in cancer and tissues of origin.
Heritability and phenotypic plasticity of biting time behaviors in the major African malaria vector Anopheles arabiensis

Use of Insecticide Treated Nets for malaria control has been associated with shifts in mosquito vector feeding behavior including earlier and outdoor biting on humans. The relative contribution of phenotypic plasticity and heritability to these behavioural shifts is unknown. Elucidation of the mechanisms behind these shifts is crucial for anticipating impacts on vector control. We used a novel portable semi-field system (PSFS) to experimentally measure heritability of biting time in the malaria vector Anopheles arabiensis in Tanzania. In PSFS assays, the biting time of F2 offspring (early: 18:00-21:00, mid: 22:00-04:00 or late: 05:00-07:00) was significantly associated with that of their wild-caught F0 grandmothers, corresponding to an estimated heritability of 0.30 (95% CI: 0.20, 0.41). F2 from early-biting F0 were more likely to bite early than F2 from mid or late late-biting F0. Similarly, the probability of biting late was higher in F2 derived from mid and late-biting F0 than from early-biting F0. Our results indicate that variation in biting time is attributable to additive genetic variation. Selection can therefore act efficiently on mosquito biting times, highlighting the need for control methods that target early and outdoor biting mosquitoes.
Runaway evolution from male‐male competition

Wondrously elaborate weapons and displays that appear to be counter to ecological optima are widespread features of male contests for mates across the animal kingdom. To understand how such diverse traits evolve, here we develop a quantitative genetic model of sexual selection for a male signaling trait that mediates aggression in male-male contests and show that an honest indicator of aggression can generate selection on itself by altering the social environment. This can cause selection to accelerate as the trait is elaborated, leading to runaway evolution. Thus, an evolving source of selection provided by the social environment is the fundamental unifying feature of runaway sexual selection driven by either male-male competition or female mate choice. However, a key difference is that runaway driven by male-male competition requires signal honesty. Our model identifies simple conditions that provide clear, testable predictions for empirical studies using standard quantitative genetic methods.
Genetic diversity and population structure of cowpea [Vigna unguiculata (L.) Walp.] accessions from Togo using SSR markers

Cowpea [Vigna unguiculata (L.) Walp. ] is a crop with significant agronomic and nutritional potential. I is very appreciate by local people. It is the third food habit in Togo after maize and rice. However, several accessions of cowpea cultivated in Togo are now prone to extinction, creating a risk of genetic erosion. It is therefore urgent to assess the genetic diversity of accessions in order to set up a good conservation program. To achieve this, genetic diversity and phylogenetic relationships among 70 accessions of cowpea collected in the five (5) administrative regions of Togo were assessed using Simple Sequence Repeat (SSR) molecular markers. Twenty-eight out of the thirty-two (32) primer pairs screened for polymorphism were polymorphic, and a total of 164 alleles were detected for the 28 loci with an average of 5.82 alleles per locus. Polymorphic Information Content (PIC) values ranged from 0.18 to 0.895, with an average value of 0.67. Population structure analysis using model-based revealed that the cowpea germplasm was grouped into two subpopulations. The analysis of molecular variance (AMOVA) revealed that 85% of genetic variation existed among individuals within regions. The fixation index (Fst) value, which was 0.018, was low, indicating relatively low population differentiation. The Togolese cowpea germplasm collection was grouped into four groups independently of theirs origins. This study provides a foundation for a Togolese cowpea germplasm conservation program and can serve for the selection of parental material for further studies aimed at the genetic improvement of local germplasm.
Threonine phosphorylation regulates the molecular assembly and signaling of EGFR in cooperation with membrane lipids

The cytoplasmic domain of the receptor tyrosine kinases (RTKs) plays roles as a phosphorylation enzyme and a protein scaffold but the regulation of these two functions is not fully understood. We here analyzed assembly of the transmembrane (TM)- juxtamembrane (JM) region of EGFR, one of the best studied species of RTKs, by combining single-pair FRET imaging and a nanodisc technique. The JM domain of EGFR contains a threonine residue that is phosphorylated after ligand association. We observed that the TM-JM peptides of EGFR form anionic lipid-induced dimers and cholesterol-induced oligomers. The two forms involve distinct molecular interactions, with a bias towards oligomer formation upon threonine phosphorylation. We further analyzed the functions of whole EGFR molecules, with or without a threonine to alanine substitution in the JM domain, in living cells. The results suggested an autoregulatory mechanism in which threonine phosphorylation of the JM domain causes a switch from kinase activation dimers to scaffolding oligomers.
Transcriptome Analysis Reveals Higher Levels of Mobile Element-Associated Abnormal Gene Transcripts in Temporal Lobe Epilepsy Patients

Objective To determine role of abnormal splice variants associated with mobile elements in epilepsy. Methods Publicly available human RNA-seq-based transcriptome data for laser-captured dentate granule cells of post-mortem hippocampal tissues from temporal lobe epilepsy patients with (TLE, N=14 for 7 subjects) and without hippocampal sclerosis (TLE-HS, N=8 for 5 subjects) and healthy individuals (N=51), surgically resected bulk neocortex tissues from TLE patients (TLE-NC, N=17). For each individual sample, de novo transcriptome assembly was performed followed by identification of spliced gene transcripts containing mobile element (ME) sequences (ME-transcripts) to compare the ME-transcript frequency across the sample groups. Enrichment analysis for genes associated with ME-transcripts and detailed sequence examination for representative epileptic genes were performed to analyze the pattern and mechanism of ME-transcripts on gene function. Results We observed significantly higher levels of ME-transcripts in the hippocampal tissues of epileptic patients, particularly in TLE-HS. Among ME classes, SINEs were shown to be the most frequent contributor to ME-transcripts followed by LINEs and DNA transposons. These ME sequences almost in all cases represent older MEs normally located in the intron sequences, leading abnormal splicing variants. For protein coding genes, ME sequences were mostly found in the 3’-UTR regions, with a significant portion also in the coding sequences (CDS) leading to reading frame disruption. Genes associated with ME-transcripts showed enrichment for involvement in the mRNA splicing process in all sample groups, with bias towards neural and epilepsy-associated genes in the epileptic transcriptomes. Significance Our data suggest that abnormal splicing involving MEs, leading to loss of function in critical genes, plays a role in epilepsy, particularly in TLE-HS, providing a novel insight on the molecular mechanisms underlying epileptogenesis. Key points box Significantly higher rates of abnormal splicing variants involving mobile elements (MEs) were observed in the hippocampal tissues of epilepsy patients. SINEs/Alus are most frequently observed in ME-transcripts followed by LINEs and DNA transposons. For protein coding genes, MEs mostly locate in 3’ UTR, but also in coding regions, causing open reading frame disruption, with a bias for neural and epileptic genes. Abnormal splicing involving MEs may be a contributing factor in epileptogenesis.