Miracle-dz/UniFAR-FTUs huggingface dataset:
A fuzzy logic system for band detection in Raman spectroscopy

Raman spectroscopy can be used to identify artistic materials on the basis of their characteristic Raman spectra. The acquisition of the wavenumber position of the Raman bands is frequently carried out by visual inspection. Obviously this is a slow, imprecise and non-automatic process. In this paper, a fuzzy logic system to locate Raman bands in an automated way, avoiding subjective errors, is presented. The proposed fuzzy logic system is based on a set of rules, which give the processing strategy for detecting the wavenumber position of Raman bands. The fuzzy rule-based system performs the location of Raman bands in a spectrum in the same way as an observer who examines a spectrum visually and tries to localize the Raman bands. That is, he/she compares the possible bands that he has seen with a function that, as known a priori, is representative of a Raman band. Depending on the comparison, he/she establishes that the peak is actually a Raman band. Bearing this in mind, the fuzzy Raman band location system is based on the following statement: when some zone of the spectrum stands out from the nearby background with a characteristic shape, it is established that this zone contains a distinguishable Raman band. In order to know when one zone of the spectrum ‘stands out from the nearby background’, the parabolic approximation of the spectrum in this zone is calculated. The band detection is based on this approximation. The membership functions, which characterize the fuzzy sets at the input and output of the system, and the inference mechanism suitable for the problem are chosen. In the visual process, the knowledge and experience of the observer control the decision-making process; however, fuzzy logic provides a powerful technique in the decision-making environment since it incorporates this knowledge. Copyright © 2004 John Wiley & Sons, Ltd.
A study of (1)benzofuro(3,2-c)pyridine derivatives

Methyl(1)benzofuro(3,2-c)pyridin-1-one 2 was obtained by reaction of the pyridone 1 with NaH followed by methylation with methyl iodide. The reaction of 1 with excess of P4S10 rendered the corresponding thione 3, which was methylated in PTC conditions giving 1- methylsulfanyl(1)benzofuro(3,2-c)pyridine 4. The reactions of 1-chloro(1)benzofuro(3,2- c)pyridine 5 with excess of heterocyclic secondary amines (piperidine, morpholine and pyrrolidine) gave 1-substituted (1)benzofuro(3,2-c)pyridines 6-8. Suzuki coupling reactions were realized with chloro-derivative 5 and phenylboronic or pyridine-3-boronic acids when 1- phenyl(1)benzofuro(3,2-c)pyridine 9 or 1-(pyridin-3-yl)(1)benzofuro(3,2-c)pyridine 10 were obtained. 2-Amino(1)benzofuro(3,2-c)pyridin-2-ium 4-methylbenzene sulfonate 12 was prepared by N-amination of (1)benzofuro(3,2-c)pyridine 11 with 1-((aminooxy)sulfonyl)-4- methylbenzene. Then 12 was transformed into an unisolated zwitterionic N-imide 13, which afforded by 1,3-dipolar cycloaddition reactions with dimethyl but-2-ynedioate (DMBD) or ethyl propiolate the corresponding 1-benzofuro(3,2-c)pyrazolo(1,5-a)pyridine carboxylic acid-esters 14, 15. The reaction of 11 with benzoylnitromethane and DMBD gave benzoyl dimethyl ester 16. The structures of all new compounds were proved by IR and 1 H and 13 C NMR spectra and the structure of 1-phenyl(1)benzofuro(3,2-c)pyridine was proved by X-ray analysis.
Genomic Characterization Provides an Insight into the Pathogenicity of the Poplar Canker Bacterium Lonsdalea populi

An emerging poplar canker caused by the gram-negative bacterium, Lonsdalea populi, has led to high mortality of hybrid poplars Populus × euramericana in China and Europe. The molecular bases of pathogenicity and bark adaptation of L. populi have become a focus of recent research. This study revealed the whole genome sequence and identified putative virulence factors of L. populi. A high-quality L. populi genome sequence was assembled de novo, with a genome size of 3,859,707 bp, containing approximately 3434 genes and 107 RNAs (75 tRNA, 22 rRNA, and 10 ncRNA). The L. populi genome contained 380 virulence-associated genes, mainly encoding for adhesion, extracellular enzymes, secretory systems, and two-component transduction systems. The genome had 110 carbohydrate-active enzyme (CAZy)-coding genes and putative secreted proteins. The antibiotic-resistance database annotation listed that L. populi was resistant to penicillin, fluoroquinolone, and kasugamycin. Analysis of comparative genomics found that L. populi exhibited the highest homology with the L. britannica genome and L. populi encompassed 1905 specific genes, 1769 dispensable genes, and 1381 conserved genes, suggesting high evolutionary diversity and genomic plasticity. Moreover, the pan genome analysis revealed that the N-5-1 genome is an open genome. These findings provide important resources for understanding the molecular basis of the pathogenicity and biology of L. populi and the poplar-bacterium interaction.
Oxidative Stress Boosts the Uptake of Cerium Oxide Nanoparticles by Changing Brain Endothelium Microvilli Pattern

Vascular oxidative stress is considered a worsening factor in the progression of Alzheimer’s disease (AD). Increased reactive oxygen species (ROS) levels promote the accumulation of amyloid-β peptide (Aβ), one of the main hallmarks of AD. In turn, Aβ is a potent inducer of oxidative stress. In early stages of AD, the concomitant action of oxidative stress and Aβ on brain capillary endothelial cells was observed to compromise the blood–brain barrier functionality. In this context, antioxidant compounds might provide therapeutic benefits. To this aim, we investigated the antioxidant activity of cerium oxide nanoparticles (CNP) in human cerebral microvascular endothelial cells (hCMEC/D3) exposed to Aβ oligomers. Treatment with CNP (13.9 ± 0.7 nm in diameter) restored basal ROS levels in hCMEC/D3 cells, both after acute or prolonged exposure to Aβ. Moreover, we found that the extent of CNP uptake by hCMEC/D3 was +43% higher in the presence of Aβ. Scanning electron microscopy and western blot analysis suggested that changes in microvilli structures on the cell surface, under pro-oxidant stimuli (Aβ or H2O2), might be involved in the enhancement of CNP uptake. This finding opens the possibility to exploit the modulation of endothelial microvilli pattern to improve the uptake of anti-oxidant particles designed to counteract ROS-mediated cerebrovascular dysfunctions.
Attitudes of Costa Rican individuals towards donation of personal genetic data for research

Aim: We explore attitudes from the public in Costa Rica regarding willingness to donate DNA data for research. Materials & methods: A total of 224 Costa Rican individuals answered the anonymous online survey ‘Your DNA, Your Say’. It covers attitudes toward DNA and medical data donation, trust in research professionals and concerns about consequences of reidentification. Results & conclusion: Most individuals (89%) are willing to donate their information for research purposes. When confronted with different potential uses of their data, participants are significantly less likely to donate data to for-profit researchers (34% willingness to donate). The most frequently cited concerns regarding donation of genetic data relate to possible discrimination by health/life insurance companies and employers. For the participants in the survey, the most trusted professionals are their own medical doctor and nonprofit researchers from their country. This is the first study regarding attitudes toward genetic data donation in Costa Rica.
Molecular Phylogeny and Global Diversity of the Genus Haploporus (Polyporales, Basidiomycota)

Phylogeny and taxonomy of the genus Haploporus were carried out based on a larger number of samples covering a wider geographic range including East Asia, South Asia, Europe, and America, and the species diversity of the genus is updated. Four species, Haploporus bicolor, H. longisporus, H. punctatus and H. srilankensis, are described as new species based on morphology and molecular phylogenetic analyses inferred from the internal transcribed spacer (ITS), the large subunit nuclear ribosomal RNA gene (nLSU), and the small subunit mitochondrial rRNA gene (mtSSU). Haploporus bicolor is characterized by the distinctly different colors between the pore surface and the tubes, small pores measuring 5–7 per mm, and narrow basidiospores measuring 10.5–11.9 × 4.5–5 µm; H. longisporus differs from other species in the genus by its large pores measuring 2–3 per mm, hyphae at dissepiment edge with simple septum, and the long basidiospores (up to 22 µm); H. punctatus is distinguished by its cushion-shaped basidiocarps, wide fusiform cystidioles with a simple septum at the tips, the absence of dendrohyphidia and the cylindrical to slightly allantoid basidiospores measuring 9–10.8 × 3.8–5 µm; H. srilankensis is characterized by its perennial habit, small pores measuring 4–5 per mm, dextrinoid skeletal hyphae, the presence of cystidioles and dendrohyphidia. An identification key to accepted species of Haploporus is provided.
DeepIDA: Predicting Isoform-Disease Associations by Data Fusion and Deep Neural Networks

Alternative splicing produces different isoforms from the same gene locus, it is an important mechanism for regulating gene expression and proteome diversity. Although the prediction of gene(ncRNA)-disease associations has been extensively studied, few (or no) computational solutions have been proposed for the prediction of isoform-disease association (IDA) at a large scale, mainly due to the lack of disease annotations of isoforms. However, increasing evidences confirm the associations between diseases and isoforms, which can more precisely uncover the pathology of complex diseases. Therefore, it is highly desirable to predict IDAs. To bridge this gap, we propose a deep neural network based solution (DeepIDA) to fuse multi-type genomics and transcriptomics data to predict IDAs. Particularly, DeepIDA uses gene-isoform relations to dispatch gene-disease associations to isoforms. In addition, it utilizes two DNN sub-networks with different structures to capture nucleotide and expression features of isoforms, Gene Ontology data and miRNA target data, respectively. After that, these two sub-networks are merged in a dense layer to predict IDAs. The experimental results on public datasets show that DeepIDA can effectively predict IDAs with AUPRC (area under the precision-recall curve) of 0.9141, macro F-measure of 0.9155, G-mean of 0.9278 and balanced accuracy of 0.9303 across 732 diseases, which are much higher than those of competitive methods. Further study on sixteen isoform-disease association cases again corroborates the superiority of DeepIDA. The code of DeepIDA is available at http://mlda.swu. edu.cn/codes.php? name=DeepIDA.
cAMP Biosensors Based on Genetically Encoded Fluorescent/Luminescent Proteins

Cyclic adenosine monophosphate (cAMP) plays a key role in signal transduction pathways as a second messenger. Studies on the cAMP dynamics provided useful scientific insights for drug development and treatment of cAMP-related diseases such as some cancers and prefrontal cortex disorders. For example, modulation of cAMP-mediated intracellular signaling pathways by anti-tumor drugs could reduce tumor growth. However, most early stage tools used for measuring the cAMP level in living organisms require cell disruption, which is not appropriate for live cell imaging or animal imaging. Thus, in the last decades, tools were developed for real-time monitoring of cAMP distribution or signaling dynamics in a non-invasive manner. Genetically-encoded sensors based on fluorescent proteins and luciferases could be powerful tools to overcome these drawbacks. In this review, we discuss the recent genetically-encoded cAMP sensors advances, based on single fluorescent protein (FP), Föster resonance energy transfer (FRET), single luciferase, and bioluminescence resonance energy transfer (BRET) for real-time non-invasive imaging.
Subacute cutaneous lupus erythematosus triggered after measles vaccination

Subacute cutaneous lupus erythematosus (SCLE) is a subtype of cutaneous lupus erythematosus that can be triggered by endogenous or exogenous factors. Among the exogenous factors are some medications, drugs, tobacco, infections, and vaccines. In this context, the benefits of vaccination are questioned because although it is important to prevent infections in immunosuppressed patients a theoretical risk of developing systemic lupus erythematosus (SLE) remains in these patients. This report presents a case of a previously healthy female patient who developed SCLE after measles vaccination and progressed to SLE and thereby suggests a possible trigger of the disease.
Chronic and Gradual-Onset Injuries and Conditions in the Sport of Surfing: A Systematic Review

The majority of the previous literature investigating injuries in surfing have focused on acute or traumatic injuries. This systematic review appears to be the first to investigate the literature reporting on chronic and gradual-onset injuries and conditions in surfing populations. A search strategy was implemented on five databases in June 2020 to locate peer-reviewed epidemiological studies on musculoskeletal injuries or non-musculoskeletal conditions in surfing. A modified AXIS Critical Appraisal Tool was used to appraise all included texts. Extracted data included key information relevant to the epidemiology of the injuries and conditions. Twenty journal articles were included with the majority rated as good quality and a substantial agreement between raters (k = 0.724). Spine/back (29.3%), shoulder (22.9%), and head/face/neck (17.5%) were the most frequently reported locations of musculoskeletal injury, whilst the most common mechanism of injury was paddling (37.1%). Exostosis was the most frequently described injury or condition in surfing populations, with the most common grade of severity reported as mild obstruction. The key findings of injury type, location, severity, and mechanism can be used to develop relevant injury management and prevention programs for the surfing population, with an emphasis on chronic or gradual-onset spine/back and shoulder injuries, paddling technique, and education on the development and management of exostosis.
Antioxidant and Anti-Inflammatory Effects of White Mulberry (Morus alba L.) Fruits on Lipopolysaccharide-Stimulated RAW 264.7 Macrophages

In this study, the protective effects of white mulberry (Morus alba) fruits on lipopolysaccharide (LPS)-stimulated RAW 264.7 macrophages were investigated. The ethanol (EtOH) extract of white mulberry fruits and its derived fractions contained adequate total phenolic and flavonoid contents, with good in vitro antioxidant radical scavenging activity. The extract and fractions also markedly inhibited ROS generation and antioxidant activity. After treatment with the EtOH extract and its fractions, LPS stimulation-induced elevated nitric oxide (NO) production was restored, which was primarily mediated by downregulation of inducible NO synthase expression. A total of 20 chemical constituents including flavonoids, steroids, and phenolics were identified in the fractions using ultra-high-performance liquid chromatography (UHPLC)-quadrupole time-of-flight (QTOF) high-resolution mass spectrometry (HRMS). These findings provide experimental evidence of the protective effects of white mulberry fruit extract against oxidative stress and inflammatory responses, suggesting their nutraceutical and pharmaceutical potential as natural antioxidant and anti-inflammatory agents.
Ustilaginaceae Biocatalyst for Co-Metabolism of CO2-Derived Substrates toward Carbon-Neutral Itaconate Production

The family Ustilaginaceae (belonging to the smut fungi) are known for their plant pathogenicity. Despite the fact that these plant diseases cause agricultural yield reduction, smut fungi attracted special attention in the field of industrial biotechnology. Ustilaginaceae show a versatile product spectrum such as organic acids (e.g., itaconate, malate, succinate), polyols (e.g., erythritol, mannitol), and extracellular glycolipids, which are considered value-added chemicals with potential applications in the pharmaceutical, food, and chemical industries. This study focused on itaconate as a platform chemical for the production of resins, plastics, adhesives, and biofuels. During this work, 72 different Ustilaginaceae strains from 36 species were investigated for their ability to (co-) consume the CO2-derived substrates acetate and formate, potentially contributing toward a carbon-neutral itaconate production. The fungal growth and product spectrum with special interest in itaconate was characterized. Ustilago maydis MB215 and Ustilago rabenhorstiana NBRC 8995 were identified as promising candidates for acetate metabolization whereas Ustilago cynodontis NBRC 7530 was identified as a potential production host using formate as a co-substrate enhancing the itaconate production. Selected strains with the best itaconate production were characterized in more detail in controlled-batch bioreactor experiments confirming the co-substrate utilization. Thus, a proof-of-principle study was performed resulting in the identification and characterization of three promising Ustilaginaceae biocatalyst candidates for carbon-neutral itaconate production contributing to the biotechnological relevance of Ustilaginaceae.
The variability of MR axon radii estimates in the human white matter

The noninvasive quantification of axonal morphology is an exciting avenue for gaining understanding of the function and structure of the central nervous system. Accurate non‐invasive mapping of micron‐sized axon radii using commonly applied neuroimaging techniques, that is, diffusion‐weighted MRI, has been bolstered by recent hardware developments, specifically MR gradient design. Here the whole brain characterization of the effective MR axon radius is presented and the inter‐ and intra‐scanner test–retest repeatability and reproducibility are evaluated to promote the further development of the effective MR axon radius as a neuroimaging biomarker. A coefficient‐of‐variability of approximately 10% in the voxelwise estimation of the effective MR radius is observed in the test–retest analysis, but it is shown that the performance can be improved fourfold using a customized along‐tract analysis.
Isocratic Separation of Acetaminophen, Phenylephrine, Chlorpheneramine and Dextromethorphan on Gemini ® C18

1. These compositions are complex mixtures, each component being effective for a speture, comprising phenylephrine hydrochloride (decongestant), acetaminophen (paracetamol, analgesic/antipyretic), chlorpheneramine maleate (antihistamine) and dextromethorphan hydrobromide (antitussive). The structures of these drugs are shown in Figure 1.
Anti-Inflammatory Effect of Artemisia argyi on Ethanol-Induced Gastric Ulcer: Analytical, In Vitro and In Vivo Studies for the Identification of Action Mechanism and Active Compounds

Artemisia argyi is widely used as traditional medicine in East Asia. However, its effects against inflammation and gastric ulcers have not been reported yet. We analyzed anti-inflammatory activity and its molecular mechanisms of A. argyi using RAW264.7 cells line, then evaluated the curative efficacy in rats with acute gastric ulcers. Nitric oxide and IL-6 production was measured using Griess reagent and an ELISA kit. Inducible nitric oxide synthase (iNOS), interleukin (IL)-6, and mucin (MUC)1, MUC5AC, and MUC6 mRNA were determined by SYBR Green or Taqman qRT-PCR methods. The phosphorylation of ERK, JNK, p38, and c-Jun protein were detected by western blotting. RW0117 inhibited LPS-induced NO and IL-6 production. The mRNA levels of iNOS and IL-6 were strongly suppressed. The phosphorylation of ERK, JNK, and c-Jun decreased by treatment with RW0117. Oral administration of RW0117 recovered the amount of mucin mRNA and protein level that was decreased due to gastric ulcers by HCl-EtOH. A. argyi exhibited strong anti-inflammatory effects and contributed to the modulation of HCl-EtOH-induced gastric ulcer in rats.
Prevalence and Clinical Significance of Drug–Drug and Drug–Dietary Supplement Interactions among Patients Admitted for Cardiothoracic Surgery in Greece

Background: Drug interactions represent a major issue in clinical settings, especially for critically ill patients such as those with cardiovascular disease (CVD) who require cardiothoracic surgery (CTS) and receive a high number of different medications. Methods: A cross-sectional study aimed at evaluating the exposure and clinical significance of drug–drug (DDIs) and drug–dietary supplement interactions (DDSIs) in patients admitted for CTS in the University Hospital of Crete Greece. DDIs were evaluated regarding underlying pharmacological mechanisms upon admission, preoperation, postoperation, and discharge from CTS clinic. Additionally, upon admission, the use of dietary supplements (DSs) and if patients had informed their treating physician that they were using these were recorded with subsequent analysis of potential DDSIs with prescribed medications. Results: The study employed 76 patients who were admitted for CTS and accepted to participate. Overall, 166 unique DDIs were identified, with 32% of them being related to pharmacokinetic (PK) processes and the rest (68%) were related to possible alterations of pharmacodynamic (PD) action. CVD medications and drugs for central nervous system disorders were the most frequently interacting medications. In total, 12% of the identified DDIs were of serious clinical significance. The frequency of PK-DDIs was higher during admission and discharge, whereas PD-DDIs were mainly recorded during pre- and postoperation periods. Regarding DS usage, 60% of patients were using DSs and perceived them as safe, and the majority had not informed their treating physician of this or sought out medical advice. Analysis of medical records showed 30 potential combinations with prescribed medications that could lead in DDSIs due to modulation of PK or PD processes, and grapefruit juice consumption was involved in 38% of them. Conclusions: An increased burden of DDIs and DDSIs was identified mostly upon admission for patients in CTS clinics in Greece. Healthcare providers, especially prescribing physicians in Greece, should always take into consideration the possibility of DDIs and the likely use of DS products by patients to promote their well-being; this should only be undertaken after receiving medical advice and an evidenced-based evaluation.