Miracle-dz/UniFAR-FTUs huggingface dataset:
Reduced-order atomistic cascade method for simulating radiation damage in metals

Atomistic modeling of radiation damage through displacement cascades is deceptively non-trivial. Due to the high energy and stochastic nature of atomic collisions, individual primary knock-on atom (PKA) cascade simulations are computationally expensive and ill-suited for length and dose upscaling. Here, we propose a reduced-order atomistic cascade model capable of predicting and replicating radiation events in metals across a wide range of recoil energies. Our methodology approximates cascade and displacement damage production by modeling the cascade as a core-shell atomic structure composed of two damage production estimators, namely an athermal recombination corrected displacements per atom (arc-dpa) in the shell and a replacements per atom (rpa) representing atomic mixing in the core. These estimators are calibrated from explicit PKA simulations and a standard displacement damage model that incorporates cascade defect production efficiency and mixing effects. We illustrate the predictability and accuracy of our reduced-order atomistic cascade method for the cases of copper and niobium by comparing its results with those from full PKA simulations in terms of defect production as well as the resulting cascade evolution and structure. We provide examples for simulating high energy cascade fragmentation and large dose ion-bombardment to demonstrate its possible applicability. Finally, we discuss the various practical considerations and challenges associated with this methodology especially when simulating subcascade formation and dose effects.
A Simple Method for Anchoring Silver and Copper Nanoparticles on Single Wall Carbon Nanotubes

Single walled carbon nanotubes (SWCNT) were functionalized using the 1,3-dipolar cycloaddition reaction of an azomethine ylide under solvent-free conditions, a one-pot procedure that yields pyrrolidine type of groups at the nanotubes surface. The functionalized SWCNT were further decorated with Ag and Cu nanoparticles by reduction of the corresponding metal salts in dimethylformamide. The extensive reduction of silver from its nitrate was observed, as well as the partial reduction of copper from its acetate. X-ray photoelectron spectroscopy (XPS) confirmed the functionalization of SWCNT with pyrrolidine that provided anchoring sites for the metal nanoparticles. Metal nanoparticles (NP) were formed at the surface of the organically functionalized SWCNT in higher yields as compared to the same procedure carried out with pristine SWCNT. This was observed using scanning electron microscopy (SEM) and quantified by XPS. Raman spectroscopy demonstrated that functionalization and metal decoration of the SWCNT did not induce structural damage to the SWCNT.
DNA methyltransferase inhibitors induce a BRCAness phenotype that sensitizes NSCLC to PARP inhibitor and ionizing radiation

Significance We introduce a key role for low doses of DNA methyltransferase inhibitors (DNMTis) in reprogramming the DNA repair transcriptome and creating a homologous recombination defect (HRD), sensitizing to poly (ADP-ribose) polymerase (PARP) inhibitors (PARPis) in breast cancer gene (BRCA)-proficient nonsmall cell lung cancer (NSCLC), which are not clinically responsive to PARPis. The nonhomologous end-joining pathway is also downregulated by DNMTis, generating sensitivity to radiation therapy (RT). The significant increases in antitumor effects with DNMTi and PARPis in combination with RT suggest a potentially potent therapeutic strategy for patients with BRCA-proficient NSCLC, for whom limited therapy is available. A minority of cancers have breast cancer gene (BRCA) mutations that confer sensitivity to poly (ADP-ribose) polymerase (PARP) inhibitors (PARPis), but the role for PARPis in BRCA-proficient cancers is not well established. This suggests the need for novel combination therapies to expand the use of these drugs. Recent reports that low doses of DNA methyltransferase inhibitors (DNMTis) plus PARPis enhance PARPi efficacy in BRCA-proficient AML subtypes, breast, and ovarian cancer open up the possibility that this strategy may apply to other sporadic cancers. We identify a key mechanistic aspect of this combination therapy in nonsmall cell lung cancer (NSCLC): that the DNMTi component creates a BRCAness phenotype through downregulating expression of key homologous recombination and nonhomologous end-joining (NHEJ) genes. Importantly, from a translational perspective, the above changes in DNA repair processes allow our combinatorial PARPi and DNMTi therapy to robustly sensitize NSCLC cells to ionizing radiation in vitro and in vivo. Our combinatorial approach introduces a biomarker strategy and a potential therapy paradigm for treating BRCA-proficient cancers like NSCLC.
Digital Magnetic Compass Integration with Stationary, Land-Based Electro-Optical Multi-Sensor Surveillance System

Multi-sensor imaging systems using the global navigation satellite system (GNSS) and digital magnetic compass (DMC) for geo-referencing have an important role and wide application in long-range surveillance systems. To achieve the required system heading accuracy, the specific magnetic compass calibration and compensation procedures, which highly depend on the application conditions, should be applied. The DMC compensation technique suitable for the operation environment is described and different technical solutions are studied. The application of the swinging procedure was shown as a good solution for DMC compensation in a given application. The selected DMC was built into a system to be experimentally evaluated, both under laboratory and field conditions. The implementation of the compensation procedure and magnetic sensor integration in systems is described. The heading accuracy measurement results show that DMC could be successfully integrated and used in long-range surveillance systems providing required geo-referencing data.
FACTCK.BR: a new dataset to study fake news

Machine learning algorithms can be used to combat fake news propagation. For the news classification, labeled datasets are required, however, among the existing datasets, few separate verified false from skewed ones with a good variety of sources. This work presents FACTCK.BR, a new dataset to study Fake News in Portuguese, presenting a supposedly false News along with their respective fact check and classification. The data is collected from the ClaimReview, a structured data schema used by fact check agencies to share their results in search engines, enabling data collect in real time.
SemanticSefaz: an ontology-based semantic portal for the government spending

Supervision in the public procurement process is considered essential for society as a means of promoting greater security and control against possible fraud and illegal actions. However, the data available on government procurement alone does not allow for the identification of possible signed contracts or bidding processes won by unfit or suspended companies, making it difficult to analyze and supervise by employees of tax agencies such as SEFAZ. In addition, data are often not available in the same common format and differ in their vocabulary, making it difficult for these professionals to find interesting information. As a means of solving these problems, the present work presents SemanticSefaz, a semantic portal for integration between heterogeneous bases focused on the domain of public procurement through a homogeneous view, allowing for semantic queries and subsequent discovery of information that priori were not possible. As a case study, the databases with data on government procurement (SIASG), unhealthy and suspenseful companies (CEIS) and punished companies (CNEP) were used to construct semantic integration. Subsequently, queries of interest to the tax domain were conducted through SemanticSefaz, demonstrating its efficiency for performing faceted queries and semantic navigation. In the end, SemanticSefaz is characterized as a timely tool for integration, visualization, discovery of knowledge to facilitate the work of tax professionals.
Potential of the Biogas Fermentation of Rumex L.

Using self-designed anaerobic fermentation experimental device,under(30±1)℃ constant temperature condition,the Rumex L.of different raw material concentration was studied under the single-phase anaerobic fermentation batch.The results showed that the three kinds of raw materials concentration all had two peaks of gas production,the duration of producing gas under the raw material concentration of 6% was longer than the others.The cumulative gas production under three kinds of raw materials concentration was 10 544.0,15 870.5 and 13 019.5 mL respectively,and the average daily production of them was 234.3,352.7 and 289.3 mL/d,respectively.During the fermentation process,pH value decreased firstly then went up.With the extension of fermentation time,the CH4 concentration of gas increased significantly,and all them of three kinds of materials was more than 40%. In addition,the average CH4 concentration of all three treatments were more than 40% and peaked at more than 50%.
Forming Dream Teams: A Chemistry-Oriented Approach in Social Networks

Scientific collaboration networks are social networks in which vertices represent scientists and edges typically represent co-authorship. Such networks not only permit research into understanding the characteristics of scientific collaboration, but can also provide a basis for building collaborative research platforms to support research groups with functionality such as, information sharing, data repositories, and communication. Collaboration networks are highly clustered, mapping closely to the real world relationships of individual researchers. However, just as big data constitute a well recognised disruptive change to the way basic research is carried out in many fields, there is an equivalent and largely unexplored change in the collaborative relationships between researchers – which are becoming not only larger in scale, but also more distributed and interdisciplinary. One element in this, which we suggest will play a pivotal role in the future, is the formation of teams for big data projects. This paper presents an innovative algorithm for expert team formation called Chemistry Oriented Team Formation (ChemoTF) based on two new metrics; Chemistry Level and Expertise Level. Chemistry Level measures scale of communication required by the task, while Expertise Level measures the overall expertise among potential teams filtered by Chemistry Level. This approach is tested using a large scholarly corpus containing 472,365 individual authors. The ChemoTF algorithm is able to build teams for median average 90 percent of the expected cost, achieving a 99 percent fit while remaining tractable for teams up to 16 individuals – resulting in the formation of more communicative and cost effective teams with higher expertise level.
Modeling and Characterization of Capacitive Coupling Intrabody Communication in an In-Vehicle Scenario

Intrabody communication (IBC) has drawn extensive attention in the field of ubiquitous healthcare, entertainment, and more. Until now, most studies on the modeling and characterization of capacitive coupling IBC have been conducted in open space, while influences when using metallic-enclosed environments such as a car, airplane, or elevator have not yet been considered. In this paper, we aimed to systematically investigate the grounding effect of an enclosed metal wall of a vehicle on the transmission path loss, utilizing the finite element method (FEM) to model capacitive coupling IBC in an in-vehicle scenario. The results of a simulation and experimental validation indicated that the system gain in an in-vehicle scenario increased up to 7 dB compared to in open space. The modeling and characterization achieved in this paper of capacitive coupling IBC could facilitate an intrabody sensor design and an evaluation with great flexibility to meet the performance needs of an in-vehicle use scenario.
Development of a recombinant replication-deficient rabies virus-based bivalent-vaccine against MERS-CoV and rabies virus and its humoral immunogenicity in mice

Middle East respiratory syndrome-coronavirus (MERS-CoV) is an emerging virus that causes severe disease with fatal outcomes; however, there are currently no approved vaccines or specific treatments against MERS-CoV. Here, we developed a novel bivalent vaccine against MERS-CoV and rabies virus (RV) using the replication-incompetent P-gene-deficient RV (RVΔP), which has been previously established as a promising and safe viral vector. MERS-CoV spike glycoprotein comprises S1 and S2 subunits, with the S1 subunit being a primary target of neutralizing antibodies. Recombinant RVΔP, which expresses S1 fused with transmembrane and cytoplasmic domains together with 14 amino acids from the ectodomains of the RV-glycoprotein (RV-G), was developed using a reverse genetics method and named RVΔP-MERS/S1. Following generation of RVΔP-MERS/S1 and RVΔP, our analysis revealed that they shared similar growth properties, with the expression of S1 in RVΔP-MERS/S1-infected cells confirmed by immunofluorescence and western blot, and the immunogenicity and pathogenicity evaluated using mouse infection experiments. We observed no rabies-associated signs or symptoms in mice inoculated with RVΔP-MERS/S1. Moreover, virus-specific neutralizing antibodies against both MERS-CoV and RV were induced in mice inoculated intraperitoneally with RVΔP-MERS/S1. These findings indicate that RVΔP-MERS/S1 is a promising and safe bivalent-vaccine candidate against both MERS-CoV and RV.
Parasite‐mediated selection in a natural metapopulation of Daphnia magna

Parasite‐mediated selection varying across time and space in metapopulations is expected to result in host local adaptation and the maintenance of genetic diversity in disease‐related traits. However, nonadaptive processes like migration and extinction‐(re)colonization dynamics might interfere with adaptive evolution. Understanding how adaptive and nonadaptive processes interact to shape genetic variability in life‐history and disease‐related traits can provide important insights into their evolution in subdivided populations. Here we investigate signatures of spatially fluctuating, parasite‐mediated selection in a natural metapopulation of Daphnia magna. Host genotypes from infected and uninfected populations were genotyped at microsatellite markers, and phenotyped for life‐history and disease traits in common garden experiments. Combining phenotypic and genotypic data a QST–FST‐like analysis was conducted to test for signatures of parasite mediated selection. We observed high variation within and among populations for phenotypic traits, but neither an indication of host local adaptation nor a cost of resistance. Infected populations have a higher gene diversity (Hs) than uninfected populations and Hs is strongly positively correlated with fitness. These results suggest a strong parasite effect on reducing population level inbreeding. We discuss how stochastic processes related to frequent extinction‐(re)colonization dynamics as well as host and parasite migration impede the evolution of resistance in the infected populations. We suggest that the genetic and phenotypic patterns of variation are a product of dynamic changes in the host gene pool caused by the interaction of colonization bottlenecks, inbreeding, immigration, hybrid vigor, rare host genotype advantage and parasitism. Our study highlights the effect of the parasite in ameliorating the negative fitness consequences caused by the high drift load in this metapopulation.
∆Np63/p40 correlates with the location and phenotype of basal/mesenchymal cancer stem‐like cells in human ER+ and HER2+ breast cancers

ΔNp63, also known as p40, regulates stemness of normal mammary gland epithelium and provides stem cell characteristics in basal and HER2‐driven murine breast cancer models. Whilst ΔNp63/p40 is a characteristic feature of normal basal cells and basal‐type triple‐negative breast cancer, some receptor‐positive breast cancers express ΔNp63/p40 and its overexpression imparts cancer stem cell‐like properties in ER+ cell lines. However, the incidence of ER+ and HER2+ tumours that express ΔNp63/p40 is unclear and the phenotype of ΔNp63/p40+ cells in these tumours remains uncertain. Using immunohistochemistry with p63 isoform‐specific antibodies, we identified a ΔNp63/p40+ tumour cell subpopulation in 100 of 173 (58%) non‐triple negative breast cancers and the presence of this population associated with improved survival in patients with ER−/HER2+ tumours (p = 0.006). Furthermore, 41% of ER+/PR+ and/or HER2+ locally metastatic breast cancers expressed ΔNp63/p40, and these cells commonly accounted for <1% of the metastatic tumour cell population that localised to the tumour/stroma interface, exhibited an undifferentiated phenotype and were CD44+/ALDH−. In vitro studies revealed that MCF7 and T47D (ER+) and BT‐474 (HER2+) breast cancer cell lines similarly contained a small subpopulation of ΔNp63/p40+ cells that increased in mammospheres. In vivo, MCF7 xenografts contained ΔNp63/p40+ cells with a similar phenotype to primary ER+ cancers. Consistent with tumour samples, these cells also showed a distinct location at the tumour/stroma interface, suggesting a role for paracrine factors in the induction or maintenance of ΔNp63/p40. Thus, ΔNp63/p40 is commonly present in a small population of tumour cells with a distinct phenotype and location in ER+ and/or HER2+ human breast cancers.
Detecting Neurodevelopmental Toxicity of Domoic Acid and Ochratoxin A Using Rat Fetal Neural Stem Cells

Currently, animal experiments in rodents are the gold standard for developmental neurotoxicity (DNT) investigations; however, testing guidelines for these experiments are insufficient in terms of animal use, time, and costs. Thus, alternative reliable approaches are needed for predicting DNT. We chose rat neural stem cells (rNSC) as a model system, and used a well-known neurotoxin, domoic acid (DA), as a model test chemical to validate the assay. This assay was used to investigate the potential neurotoxic effects of Ochratoxin A (OTA), of which the main target organ is the kidney. However, limited information is available regarding its neurotoxic effects. The effects of DA and OTA on the cytotoxicity and on the degree of differentiation of rat rNSC into astrocytes, neurons, and oligodendrocytes were monitored using cell-specific immunofluorescence staining for undifferentiated rNSC (nestin), neurospheres (nestin and A2B5), neurons (MAP2 clone M13, MAP2 clone AP18, and Doublecortin), astrocytes (GFAP), and oligodendrocytes (A2B5 and mGalc). In the absence of any chemical exposure, approximately 46% of rNSC differentiated into astrocytes and neurons, while 40% of the rNSC differentiated into oligodendrocytes. Both non-cytotoxic and cytotoxic concentrations of DA and OTA reduced the differentiation of rNSC into astrocytes, neurons, and oligodendrocytes. Furthermore, a non-cytotoxic nanomolar (0.05 µM) concentration of DA and 0.2 µM of OTA reduced the percentage differentiation of rNSC into astrocytes and neurons. Morphometric analysis showed that the highest concentration (10 μM) of DA reduced axonal length. These indicate that low, non-cytotoxic concentrations of DA and OTA can interfere with the differentiation of rNSC.
Pyruvate Substitutions on Glycoconjugates

Glycoconjugates are the most diverse biomolecules of life. Mostly located at the cell surface, they translate into cell-specific “barcodes” and offer a vast repertoire of functions, including support of cellular physiology, lifestyle, and pathogenicity. Functions can be fine-tuned by non-carbohydrate modifications on the constituting monosaccharides. Among these modifications is pyruvylation, which is present either in enol or ketal form. The most commonly best-understood example of pyruvylation is enol-pyruvylation of N-acetylglucosamine, which occurs at an early stage in the biosynthesis of the bacterial cell wall component peptidoglycan. Ketal-pyruvylation, in contrast, is present in diverse classes of glycoconjugates, from bacteria to algae to yeast—but not in humans. Mild purification strategies preventing the loss of the acid-labile ketal-pyruvyl group have led to a collection of elucidated pyruvylated glycan structures. However, knowledge of involved pyruvyltransferases creating a ring structure on various monosaccharides is scarce, mainly due to the lack of knowledge of fingerprint motifs of these enzymes and the unavailability of genome sequences of the organisms undergoing pyruvylation. This review compiles the current information on the widespread but under-investigated ketal-pyruvylation of monosaccharides, starting with different classes of pyruvylated glycoconjugates and associated functions, leading to pyruvyltransferases, their specificity and sequence space, and insight into pyruvate analytics.
ROS-based lethality of Caenorhabditis elegans mitochondrial electron transport mutants grown on Escherichia coli siderophore iron release mutants

Significance The animal mitochondrion has a bacterial origin and depends on vitamins and other biochemicals produced by bacteria. In a genetic search for mitochondrial biochemical dependencies when the animal Caenorhabditis elegans is feeding on Escherichia coli as its sole nutritional source, we identified 45 E. coli mutations that disrupt mitochondrial function. Four of these E. coli mutations that disrupt the transport and removal of iron from an iron retrieval cofactor were lethal in combination with C. elegans mitochondrial mutations. Antioxidants strongly suppressed this inviability, suggesting a reactive oxygen toxicity. Iron retrieval cofactors produced by one bacterial species are often hijacked by other bacterial species. The toxicity of this iron retrieval cofactor may be a selected additional function of this biochemical. Caenorhabditis elegans consumes bacteria, which can supply essential vitamins and cofactors, especially for mitochondrial functions that have a bacterial ancestry. Therefore, we screened the Keio Escherichia coli knockout library for mutations that induce the C. elegans hsp-6 mitochondrial damage response gene, and identified 45 E. coli mutations that induce hsp-6::gfp. We tested whether any of these E. coli mutations that stress the C. elegans mitochondrion genetically interact with C. elegans mutations in mitochondrial functions. Surprisingly, 4 E. coli mutations that disrupt the import or removal of iron from the bacterial siderophore enterobactin were lethal in combination with a collection of C. elegans mutations that disrupt particular iron–sulfur proteins of the electron transport chain. Bacterial mutations that fail to synthesize enterobactin are not synthetic lethal with these C. elegans mitochondrial mutants; it is the enterobactin–iron complex that is lethal in combination with the C. elegans mitochondrial mutations. Antioxidants suppress this inviability, suggesting that reactive oxygen species (ROS) are produced by the mutant mitochondria in combination with the bacterial enterobactin–iron complex.