Miracle-dz/UniFAR-FTUs huggingface dataset:
Health condition assessment of transformers based on cross message passing graph neural networks

A method is proposed to assess the health condition of transformers based on cross message passing graph neural networks (CMPGNNs) in this paper. In order to improve the accuracy of transformer health condition assessment, multiple indicators and their strong correlation are taken into account. The evaluation indicators are divided into four comprehensive state categories, and each category has several indicators. First, the correlation between indicators of a state category is extracted by the health index method and the importance of criteria is analyzed through the inter-criteria correlation (CRITIC) method, and the health index of comprehensive indicators is obtained. Then, a diagram of comprehensive indicators is constructed, and the correlation between indicators of different state categories is extracted. Finally, CMPGNN is constructed to achieve the health assessment. The experimental results show that the proposed method can improve the accuracy of transformer health condition assessment.
The role of distinct electricity sources on pollution abatement: Evidence from a wide global panel

In this study, we examine the contribution of nuclear, fossil (coal, oil, and gas), and renewable (hydro, solar, wind, biofuel) electricity sources to pollution in the globalization era, as measured by total greenhouse gases (GHG) produced by electricity per capita. We conduct an empirical investigation in a global panel of 163 countries which assesses both the concurrent and individual effects of alternative energy sources. Additionally, we implement a second model to assess the roles of various electricity sources on the carbon intensity of electricity generation. Robust GMM estimators show that fossil electricity is a major polluter and a driver of carbon intensity. Furthermore, nuclear and renewable energy reduce pollution on a global scale, with wind emerging as the most efficient energy source in the global fight against pollution and climate change. Moreover, globalization as measured by trade openness tends to reduce the carbon intensity of electricity production (CI), whereas biofuels have an increasing impact on CI. The findings have important policy implications, indicating that shifting to nuclear and renewable energy sources could help countries achieve their sustainable development goals more efficiently.
Max is likely not at the Drosophila histone locus

The histone locus body (HLB) is a conserved nuclear body that regulates histone mRNA production in metazoans. While some HLB components are known, there are likely uncharacterized factors that target the histone locus. We identified the Drosophila melanogaster protein Max, which interacts with known HLB member Myc, as an HLB candidate. We mapped Max ChIP-seq and ChIP-nexus datasets, which revealed encouraging signal over the histone gene array. However, we discovered that Max does not colocalize with HLB components on polytene chromosomes. Therefore, we conclude that Max is likely not at the D. melanogaster histone locus.
Biological and synthetic surfactant exposure increases antimicrobial gene occurrence in a freshwater mixed microbial biofilm environment

Aquatic habitats are particularly susceptible to chemical pollution from domestic, agricultural, and industrial sources. Antimicrobials are commonly used in medical and industrial environments to reduce harmful bacteria and biofilms. This has led to the rapid increase in the prevalence of antimicrobial resistant (AMR) genes. Alternate remedies to fight pathogenic bacteria and biofilms are in development including synthetic and biological surfactants such as sodium dodecyl sulphate (SDS) and rhamnolipids respectively. In the aquatic environment these surfactants are present as pollutants with potential to affect biofilm formation and AMR gene occurrence; however, there is limited research showing the actual environmental impact of such exposure. We tested the effects of rhamnolipid and SDS on natural aquatic biofilms in a freshwater stream in Northern Ireland. We grew biofilms on contaminant exposure substrata deployed within the stream over four weeks, and then carried out shotgun sequencing to determine microbial community composition, through 16s rRNA analyses (64,678 classifiable reads identified), and AMR gene occurrence (81 instances of AMR genes over 9 AMR gene classes) through a metagenomic analysis. There were no significant changes in community composition within all systems; however, biofilm exposed to rhamnolipid had a greater number of unique taxa as compared to our SDS treatments and controls. AMR gene prevalence was higher in surfactant-treated biofilms, with biofilm exposed to rhamnolipids having the highest presence of AMR genes and classes compared to the control or SDS treatments, in which genes encoding for rifampin resistance were detected. Our results suggest that the presence of rhamnolipid, and to a lesser extent SDS, encourages an increase in the prevalence of AMR genes in biofilms produced in mixed use water bodies.
Two gustatory receptors involved in host plant recognition of silkworm larvae

Herbivorous insects can identify their host plants by sensing plant secondary metabolites as chemical cues. We previously reported the two-factor host acceptance system of the silkworm Bombyx mori larvae. The chemosensory neurons in the maxillary palp (MP) of the larvae detect mulberry secondary metabolites, chlorogenic acid (CGA), and isoquercitrin (ISQ), with ultrahigh sensitivity, for host plant recognition and feeding initiation. Nevertheless, the molecular basis for the ultrasensitive sensing of these compounds remains unknown. In this study, we demonstrated that two gustatory receptors (Grs), BmGr6 and BmGr9, are responsible for sensing the mulberry compounds with attomolar sensitivity for host plant recognition by silkworm larvae. Calcium imaging assay using cultured cells expressing the silkworm putative sugar receptors (BmGr4-10) revealed that BmGr6 and BmGr9 serve as receptors for CGA and ISQ with attomolar sensitivity in human embryonic kidney 293T cells. CRISPR/Cas9-mediated knockout (KO) of BmGr6 and BmGr9 resulted in a low probability of making a test bite of the mulberry leaves, suggesting that they lost the ability to recognize host leaves specifically. Electrophysiological recordings showed that the loss of host recognition ability in the Gr-KO strains was due to a drastic decrease in MP sensitivity toward ISQ in BmGr6-KO larvae and toward CGA and ISQ in BmGr9-KO larvae. Our findings unraveled that the two Grs, which have been regarded as sugar receptors, are molecules responsible for detecting plant phenolics in host plant recognition.
Multivariate Nonparametric Regression and Visualization: With R and Applications to Finance

The book then introduces and examines various tested and proven visualization techniques for learning samples and functions. Multivariate Nonparametric Regression and Visualization identifies risk management, portfolio selection, and option pricing as the main areas in which statistical methods may be implemented in quantitative finance. The book provides coverage of key statistical areas including linear methods, kernel methods, additive models and trees, boosting, support vector machines, and nearest neighbor methods. Exploring the additional applications of nonparametric and semiparametric methods, Multivariate Nonparametric Regression and Visualization features:
Chemokine Signaling Caused by Mycobacterium avium Biofilms in the Lung Airway Increases Bacterial Loads by Spatially Diverting Macrophages

Mycobacterium avium Complex (MAC) are ubiquitous environmental biofilm-forming microbes that can colonize and infect patient lungs. Incidence and prevalence of MAC infections are increasing globally, and reinfection is common. Thus, MAC infections present a significant public health challenge. MAC infections are notoriously difficult to treat and there is an urgent need for MAC-targeted therapeutics. To identify potential drug targets, we quantify the impact of MAC biofilms and repeated exposure on infection progression using a computational model of MAC infection in lung airways. MAC biofilms aid epithelial cell invasion, cause premature macrophage apoptosis, and limit antibiotic efficacy. We develop an agent-based model that incorporates the interactions between bacteria, biofilm and immune cells. We perform virtual knockouts to quantify the effects of the sources of biofilm (biofilm simultaneously deposited with bacteria vs. formed in the airway after initial bacterial deposition), and their effects on macrophages (inducing apoptosis and slowing phagocytosis). We also quantify the effects of repeated bacterial exposure to assess the impact of reinfection on infection progression. Our results show that chemokines released by biofilm-induced apoptosis bias macrophage chemotaxis towards pockets of infected and apoptosed macrophages. This bias results in fewer macrophages finding extracellular bacteria, allowing the extracellular planktonic bacteria to replicate freely. These spatial macrophage trends are further exacerbated with repeated deposition of bacteria. Our model indicates that interventions to either abrogate macrophages’ apoptotic responses to bacterial biofilms and/or reduce frequency of patient exposure to bacteria will lower bacterial load, and likely overall risk of infection.
SARS-CoV-2 Protein Nsp2 Stimulates Translation Under Normal and Hypoxic Conditions

When viruses like SARS-CoV-2 infect cells, they reprogram the repertoire of cellular and viral transcripts that are being translated to optimize their strategy of replication, often targeting host translation initiation factors, particularly eIF4F complex consisting of eIF4E, eIF4G and eIF4A. A proteomic analysis of SARS-CoV-2/human proteins interaction revealed viral Nsp2 and initiation factor eIF4E2, but a role of Nsp2 in regulating translation is still controversial. HEK293T cells stably expressing Nsp2 were tested for protein synthesis rates of synthetic and endogenous mRNAs known to be translated via cap- or IRES-dependent mechanism under normal and hypoxic conditions. Both cap- and IRES-dependent translation were increased in Nsp2-expressing cells under normal and hypoxic conditions, especially mRNAs that require high levels of eIF4F. This could be exploited by the virus to maintain high translation rates of both viral and cellular proteins, particularly in hypoxic conditions as may arise in SARS-CoV-2 patients with poor lung functioning.
Effects of ancient anthropogenic clam gardens on the growth, survival, and transcriptome of Pacific littleneck clams (Leukoma staminea)

Clam gardens traditionally established and maintained by coastal Indigenous Peoples of northwest North America are habitat modifications that enhance intertidal clam productivity and therefore provide secure and reliable local food resources. In this study, transcriptomic and phenotypic responses of Pacific littleneck clams (Leukoma staminea) were investigated in relation to transplantation to either clam gardens or unmodified clam beaches and growth for 16 weeks. Sediment characteristics (e.g., grain-size, carbonate, and organic content) were also evaluated and considered in the response. Large differences in phenotypic and abiotic characteristics were observed among beaches but did not differ based on unmaintained clam garden presence. A de novo transcriptome for L. staminea containing 52,000 putative transcripts was assembled and used to identify differential expression in response to the clam gardens. This identified a relatively small effect, but found two transcripts that were differentially expressed in both the gill and digestive gland tissues. In addition, differential expression along survival gradients, as well a tissue-specific expression analysis provide insight into the characteristics of the transcriptome and its ecological associations of this non-model organism. Across the beaches, abiotic characteristics with negative effects on growth and/or survival included small rocks, very fine sand, silt, carbonate, and organic content, whereas positive effects were observed from coarse sand, sand and fine sand. In conclusion, here it was found that localized environmental factors are likely to have a greater influence on Pacific littleneck clam physiology, growth, and survival than the presence or absence of unmaintained clam gardens.
A possible genomic footprint of polygenic adaptation on population divergence in seed beetles?

Efforts to unravel the genomic basis of incipient speciation are hampered by a mismatch between our toolkit and our understanding of the ecology and genetics of adaptation. While the former is focused on detecting selective sweeps involving few independently acting or linked speciation genes, the latter states that divergence typically occurs in polygenic traits under stabilizing selection. Here, we ask whether a role of stabilizing selection on polygenic traits in population divergence may be unveiled by using a phenotypically informed integrative approach, based on genome-wide variation segregating in divergent populations. We compare three divergent populations of seed beetles (Callosobruchus maculatus) where previous work has demonstrated a prominent role for stabilizing selection on, and population divergence in, key life history traits that reflect rate-dependent metabolic processes. We derive and assess predictions regarding the expected pattern of covariation between genetic variation segregating within populations and genetic differentiation between populations. Population differentiation was considerable (mean FST = 0.23 - 0.26) and was primarily built by genes showing high selective constraints and an imbalance in inferred selection in different populations (positive Tajima’s DNS in one and negative in one) and this set of genes was enriched with genes with a metabolic function. Repeatability of relative population differentiation was low at the level of individual genes but higher at the level of broad functional classes, again spotlighting metabolic genes. Absolute differentiation (dXY) showed a very different general pattern at this scale of divergence, more consistent with an important role for genetic drift. Although our exploration is consistent with stabilizing selection on polygenic metabolic phenotypes as an important engine of genome-wide relative population divergence and incipient speciation in our study system, we note that it is exceedingly difficult to firmly exclude other scenarios.
Anatomical and neurophysiological data on primary visual cortex 1 suffice for reproducing brain-like robust multiplexing of visual 2 function

9 10 Neural networks of the brain that process visual information have structural properties that differ 11 significantly from those of neural networks which are commonly used for visual processing in AI, 12 such as Convolutional Neural Networks (CNNs). But it has remained unknown how these structural 13 differences are related to network function. We analyze visual processing capabilities of a large-scale 14 model for area V1 that arguably provides the most comprehensive accumulation of anatomical and 15 neurophysiological data that is currently available. Its network structure turns out to induce a number 16 of characteristic visual processing capabilities of the brain, in particular the capability to multiplex 17 different visual processing tasks, also on temporally dispersed visual information, with remarkable 18 robustness to noise. This V1 model also exhibits a number of characteristic neural coding properties 19 of the brain, which provide explanations for its superior noise robustness. Since visual processing in 20 the brain is substantially more energy-efficient than implementations of CNNs in common computer 21 hardware, such brain-like neural network models are likely to have also an impact on technology: As 22 blueprints for visual processing in more energy-efficient neuromorphic hardware. 23
IL-1β turnover by TRIP12 and AREL1 ubiquitin ligases and UBE2L3 limits inflammation

The cytokine interleukin-1β (IL-1β) has pivotal roles in antimicrobial immunity, but also incites inflammatory pathology. Bioactive IL-1β is released following proteolytic maturation of the pro-IL-1β precursor by caspase-1 inflammasomes. UBE2L3/UBCH7, a conserved ubiquitin conjugating enzyme, promotes pro-IL-1β ubiquitylation and proteasomal disposal. However, UBE2L3 actions in vivo and ubiquitin ligases involved in this process are unknown. Here we report that deletion of Ube2l3 in mice markedly reduces pro-IL-1β turnover in macrophages, leading to excessive mature IL-1β production, neutrophilic inflammation and disease symptoms following inflammasome activation. A family-wide siRNA screen identified two ubiquitin ligases, TRIP12 and AREL1, which we show add K27-, K29- and K33- poly-ubiquitin chains on lysine residues in the ‘pro’ domain and destabilise pro-IL-1β. Mutation of ubiquitylation sites increased pro-IL-1β stability, but did not affect proteolysis by caspase-1. The extent of mature IL-1β production is therefore determined by precursor abundance, and UBE2L3, TRIP12 and AREL1 limit inflammation by shrinking the cellular pool of pro-IL-1β. Our study has uncovered fundamental processes governing IL-1β homeostasis and provided molecular insights that could be exploited to mitigate its adverse actions in disease.
Gene amplifications cause high-level resistance against albicidin in gram-negative bacteria

Antibiotic resistance is a continuously increasing concern for public health care. Understanding resistance mechanisms and their emergence is crucial for the development of new antibiotics and their effective use. Here, we report the discovery of a gene amplification-based mechanism that imparts an up to 1000-fold increase in resistance levels against the antibiotic albicidin. We show that this mechanism protects Salmonella Typhimurium and Escherichia coli by increasing the copy number of the GyrI-like transcription regulator STM3175 (YgiV) which binds albicidin. X-ray crystallography and molecular docking studies reveal a conserved binding motif that can interact with aromatic building blocks of albicidin. Phylogenetic studies suggest that this resistance mechanism is ubiquitous in Gram-negative bacteria and our experiments confirm that STM3175 homologs can convey resistance in pathogens such as Vibrio vulnificus and Pseudomonas aeruginosa.
Phage-Assisted, Active Site-Directed Ligand Evolution of a Potent and Selective Histone Deacetylase 8 Inhibitor

The phage-assisted, active site-directed ligand evolution (PADLE) is a recently developed technique that uses an amber codon-encoded noncanonical amino acid (ncAA) as an anchor to direct phage-displayed peptides to a target for an enhanced ligand identification process. 2-Amino-8-oxodecanoic acid (Aoda) is a ketone-containing ncAA residue in the macrocyclic peptide natural product apicidin that is a pan-inhibitor of Zn2+-dependent histone deacetylases (HDACs). Its ketone serves as an anchoring point to chelate the catalytic zinc ion in HDACs. Using a previously evolved Nε-acetyl-lysyl-tRNA synthetase in combination with tRNAPyl, we showed that Aoda was efficiently incorporated into proteins in Escherichia coli by amber suppression. By propagating an amber codon-obligate phagemid library in E. coli encoding Aoda, we generated an Aoda-containing phage-displayed peptide library. Using this library to conduct PADLE against HDAC8 revealed a 7-mer peptide GH8P01F1 with Aoda-flanking amino acid residues that match existing peptide sequences in identified HDAC8 substrates. Switching Aoda in GH8P01F1 to a more Zn2+-chelating ncAA S-2-amino-8-hydroxyamino-8-oxooctanoic acid (Asuha) led to an extremely potent GH8HA01 that has an HDAC8-inhibition Ki value as 0.67 nM. GH8HA01 and its 5-mer truncation analogue Ac-GH8HA01Δ1Δ7 that has an HDAC8-inhibition Ki value as 0.31 nM represent two most potent HDAC8 inhibitors that have been developed so far and both are highly selective against HDAC8 over the other three tested HDACs, demonstrating the great potential of using PADLE to identify highly potent and selective ligands for targets.
Time-scaled phylogenetic analysis of the Lamiini, its close relatives and some other widely distributed tribes of Lamiinae (Coleoptera, Cerambycidae)

Lamiinae is a tremendous subfamily of Cerambycidae, with around 20,000 members dispersed across continents. The knowledge of the evolutionary history of the subfamily is scarcely, and there are growing doubts about the phylogenetic relationships due to the recognised illusion caused by the convergence of the morphological characters. The present study contributes to the evolutionary history and phylogenetic relationships of the tribes Acanthocinini, Acanthoderini, Agapanthiini, Batocerini, Dorcadionini, Lamiini, Mesosini, Monochamini, Phytoeciini, Phrynetini, Pogonocherini (including Exocentrini) and Saperdini with Neighbor-Joining (NJ), Maximum Likelihood (ML) and time-scaled Bayesian analyses based on partial mitochondrial COI and 16S rRNA and nuclear 28S rRNA gene regions (2257 base pair alignment length). The most recent common ancestor (MRCA) of the taxa included in the analyses appeared during the Middle or Late Cretaceous, and the MRCAs of the closely related tribes emerged in Paleogene. The MRCA of Dorcadionini, Lamiini and Monochamini was younger than the common ancestors of the other close tribes. The hypothetical ML phylogram was consistent with the Bayesian chronogram in the proximity of Batocerini to Lamiini, Acanthocinini to Acanthoderini, Phyretrini to Pogonocherini, and Phytoeciini to Saperdini, in addition to the affiliation of Lamiini, Dorcadionini and Monochamini. At the COI -based NJ and ML gene trees, Paraleprodera and Lamia (Lamiini) were sisters to Imantocera (Gnomini), Oberea (Obereini) to Phytoecia (Phytoeciini), and Hippopsis (Agapanthiini) to Omosarotes (Acanthomerosternoplini). The present results support Dorcadionini Gnomini and Monochamini as synonyms of Lamiini; and Obereini and Phytoeciini of Saperdini. We suggest that the emergence of the living tribes included in this study was during Paleogene, and the intrageneric diversifications occurred in Cenozoic, mostly during Neogene.
Inorganic phosphate content does not affect oviposition preference in the invasive pest Drosophila suzukii

The broad variation in host use among polyphagous insects is well documented but still poorly understood. In numerous pest insects, the proximate mechanisms responsible for variation in oviposition preference among host plants remain to be elucidated. The invasive crop pest, Drosophila suzukii, attacks a wide range of host fruits. Females prefer ovipositing on particular fruit media (blackberry, cherry, blackcurrant) that are rich in phosphorus. As phosphorus is known to be involved in female reproduction in insect species such as Drosophila, it could drive oviposition preference in D. suzukii. Phosphorus is either present as inorganic or organic phosphate in fruits. As the absolute content in macromolecules associated with phosphate in fruits (i.e. proteins and carbohydrates) do not affect oviposition in D. suzukii, we tested for the effect of inorganic phosphate on oviposition preference. We measured the egg-laying preferences of D. suzukii in a choice environment containing 12 artificial media with increasing content in inorganic phosphate (monopotassium dihydrogen phosphate). In our assay, D. suzukii females did not prefer ovipositing in media with high inorganic phosphate content compared to media with lower inorganic phosphate content. As a confirmation, we verified the previous result of a higher female preference for media made of phosphorus-rich fruits (blackberry, cherry, blackcurrant). The higher preference for phosphorus-rich fruits could be driven by macromolecules containing phosphorus (e.g. phospholipids) or by the presence of one or more molecules that do not contain phosphorus, but that happen to be correlated to fruit phosphorus content. Studying the proximate mechanisms driving host use will ultimately help improve the management of D. suzukii and other crop pests.