Miracle-dz/UniFAR-FTUs huggingface dataset:
Terbium-Based AGuIX-Design Nanoparticle to Mediate X-ray-Induced Photodynamic Therapy

X-ray-induced photodynamic therapy is based on the energy transfer from a nanoscintillator to a photosensitizer molecule, whose activation leads to singlet oxygen and radical species generation, triggering cancer cells to cell death. Herein, we synthesized ultra-small nanoparticle chelated with Terbium (Tb) as a nanoscintillator and 5-(4-carboxyphenyl succinimide ester)-10,15,20-triphenyl porphyrin (P1) as a photosensitizer (AGuIX@Tb-P1). The synthesis was based on the AGuIX@ platform design. AGuIX@Tb-P1 was characterised for its photo-physical and physico-chemical properties. The effect of the nanoparticles was studied using human glioblastoma U-251 MG cells and was compared to treatment with AGuIX@ nanoparticles doped with Gadolinium (Gd) and P1 (AGuIX@Gd-P1). We demonstrated that the AGuIX@Tb-P1 design was consistent with X-ray photon energy transfer from Terbium to P1. Both nanoparticles had similar dark cytotoxicity and they were absorbed in a similar rate within the cells. Pre-treated cells exposure to X-rays was related to reactive species production. Using clonogenic assays, establishment of survival curves allowed discrimination of the impact of radiation treatment from X-ray-induced photodynamic effect. We showed that cell growth arrest was increased (35%-increase) when cells were treated with AGuIX@Tb-P1 compared to the nanoparticle doped with Gd.
Review of NMR Characterization of Pyrolysis Oils

Pyrolysis of renewable biomass has been developed as a method to produce green fuels and chemicals in response to energy security concerns as well as to alleviate environmental issues incurred with fossil fuel usage. However, pyrolysis oils still have limited commercial application, mainly because unprocessed oils cannot be readily blended with current petroleum-based transportation fuels. To better understand these challenges, researchers have applied diverse characterization techniques in the development of bio-oil studies. In particular, nuclear magnetic resonance (NMR) is a key spectroscopic characterization method through analysis of bio-oil components. This review highlights the NMR strategies for pyrolysis oil characterization and critically discusses the applications of 1H, 13C, 31P, 19F, and two-dimensional (2-D NMR) analyses such as heteronuclear single quantum correlation (HSQC) in representative pyrolysis oil studies.
Integrative Analysis of Transcriptome and Metabolome Reveals Salt Stress Orchestrating the Accumulation of Specialized Metabolites in Lycium barbarum L. Fruit

Salt stress seriously affects yield and quality of crops. The fruit of Lycium barbarum (LBF) is extensively used as functional food due to its rich nutrient components. It remains unclear how salt stress influences the quality of LBF. In this study, we identified 71 differentially accumulated metabolites (DAMs) and 1396 differentially expressed genes (DEGs) among ripe LBF with and without 300 mM of NaCl treatment. Pearson correlation analysis indicated that the metabolomic changes caused by salt stress were strongly related to oxidoreductases; hydrolases; and modifying enzymes, in particular, acyltransferases, methyltransferases and glycosyltransferases. Further analysis revealed that salt stress facilitated flavonoid glycosylation and carotenoid esterification by boosting the expression of structural genes in the biosynthetic pathways. These results suggested that salt stress prompts the modification of flavonoids and carotenoids to alleviate ROS damage, which in turn improves the quality of LBF. Our results lay a solid foundation for uncovering the underlying molecular mechanism of salt stress orchestrating LBF quality, and the candidate genes identified will be a valuable gene resource for genetic improvement of L. barbarum.
Tubulin Inhibitors: A Chemoinformatic Analysis Using Cell-Based Data

Inhibiting the tubulin-microtubules (Tub-Mts) system is a classic and rational approach for treating different types of cancers. A large amount of data on inhibitors in the clinic supports Tub-Mts as a validated target. However, most of the inhibitors reported thus far have been developed around common chemical scaffolds covering a narrow region of the chemical space with limited innovation. This manuscript aims to discuss the first activity landscape and scaffold content analysis of an assembled and curated cell-based database of 851 Tub-Mts inhibitors with reported activity against five cancer cell lines and the Tub-Mts system. The structure–bioactivity relationships of the Tub-Mts system inhibitors were further explored using constellations plots. This recently developed methodology enables the rapid but quantitative assessment of analog series enriched with active compounds. The constellations plots identified promising analog series with high average biological activity that could be the starting points of new and more potent Tub-Mts inhibitors.
Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018–2019

Outbreaks of influenza, which is a contagious respiratory disease, occur throughout the world annually, affecting millions of people with many fatal cases. The D222G/N mutations in the hemagglutinin (HA) gene of A(H1N1)pdm09 are associated with severe and fatal human influenza cases. These mutations lead to increased virus replication in the lower respiratory tract (LRT) and may result in life-threatening pneumonia. Targeted NGS analysis revealed the presence of mutations in major and minor variants in 57% of fatal cases, with the proportion of viral variants with mutations varying from 1% to 98% in each individual sample in the epidemic season 2018–2019 in Russia. Co-occurrence of the mutations D222G and D222N was detected in a substantial number of the studied fatal cases (41%). The D222G/N mutations were detected at a low frequency (less than 1%) in the rest of the studied samples from fatal and nonfatal cases of influenza. The presence of HA D222Y/V/A mutations was detected in a few fatal cases. The high rate of occurrence of HA D222G/N mutations in A(H1N1)pdm09 viruses, their increased ability to replicate in the LRT and their association with fatal outcomes points to the importance of monitoring the mutations in circulating A(H1N1)pdm09 viruses for the evaluation of their epidemiological significance and for the consideration of disease prevention and treatment options.
Ceramic Biomaterial Pores Stereology Analysis by the Use of Microtomography

The main aim of this study was to analyze microtomographic data to determine the geometric dimensions of a ceramic porous material’s internal structure. Samples of a porous corundum biomaterial were the research material. The samples were prepared by chemical foaming and were measured using an X-ray scanner. In the next stage, 3D images of the samples were generated and analyzed using Thermo Scientific Avizo software. The analysis enabled the isolation of individual pores. Then, the parameters characterizing the pore geometry and the porosity of the samples were calculated. The last part of the research consisted of verifying the developed method by comparing the obtained results with the parameters obtained from the microscopic examinations of the biomaterial. The comparison of the results confirmed the correctness of the developed method. The developed methodology can be used to analyze biomaterial samples to assess the geometric dimensions of biomaterial pores.
Sella Turcica Morphology on Cephalometric Radiographs and Dental Abnormalities—Is There Any Association?—Systematic Review

Background: The sella turcica is a saddle-like structure in the middle cranial fossa on the intracranial surface of the sphenoid bone, visible on lateral cephalograms routinely conducted for orthodontic diagnosis. The development of facial structures follows similar traits to the sella turcica: glandular anomalies may be associated with functional disorders, e.g., altered hormonal levels, thus influencing dental development. The aim of this study is to find out if there is any association between the morphology of the sella turcica on cephalometric radiographs and the presence of dental abnormalities. (2) Methods: The search was conducted on 27 January 2021 in four search engines: Medline (PubMed Central), Scopus, Web of Science, Embase. The keywords used in the search strategy were as follows: “sella turcica” AND (“dental abnormalities” OR “dental anomalies” OR “malocclusion”). Since all the studies finally included were retrospective case–control studies, the Newcastle–Ottawa Quality Assessment Form for Case–Control Studies was applied. (3) Results: The search strategy identified 465 articles: 289 from PubMed, 121 from Scopus, 32 from Web of Science and 23 from Embase. Finally, 10 full-text papers were included into qualitative analysis. (4) Conclusions: Sella turcica bridging is very frequent among orthodontic patients. A clear association exists between dental abnormalities and sella turcica bridging.
Risk of Typical Diabetes-Associated Complications in Different Clusters of Diabetic Patients: Analysis of Nine Risk Factors

Objectives: Diabetic patients are often diagnosed with several comorbidities. The aim of the present study was to investigate the relationship between different combinations of risk factors and complications in diabetic patients. Research design and methods: We used a longitudinal, population-wide dataset of patients with hospital diagnoses and identified all patients (n = 195,575) receiving a diagnosis of diabetes in the observation period from 2003–2014. We defined nine ICD-10-codes as risk factors and 16 ICD-10 codes as complications. Using a computational algorithm, cohort patients were assigned to clusters based on the risk factors they were diagnosed with. The clusters were defined so that the patients assigned to them developed similar complications. Complication risk was quantified in terms of relative risk (RR) compared with healthy control patients. Results: We identified five clusters associated with an increased risk of complications. A combined diagnosis of arterial hypertension (aHTN) and dyslipidemia was shared by all clusters and expressed a baseline of increased risk. Additional diagnosis of (1) smoking, (2) depression, (3) liver disease, or (4) obesity made up the other four clusters and further increased the risk of complications. Cluster 9 (aHTN, dyslipidemia and depression) represented diabetic patients at high risk of angina pectoris “AP” (RR: 7.35, CI: 6.74–8.01), kidney disease (RR: 3.18, CI: 3.04–3.32), polyneuropathy (RR: 4.80, CI: 4.23–5.45), and stroke (RR: 4.32, CI: 3.95–4.71), whereas cluster 10 (aHTN, dyslipidemia and smoking) identified patients with the highest risk of AP (RR: 10.10, CI: 9.28–10.98), atherosclerosis (RR: 4.07, CI: 3.84–4.31), and loss of extremities (RR: 4.21, CI: 1.5–11.84) compared to the controls. Conclusions: A comorbidity of aHTN and dyslipidemia was shown to be associated with diabetic complications across all risk-clusters. This effect was amplified by a combination with either depression, smoking, obesity, or non-specific liver disease.
Bone Marrow Adipocytes—Role in Physiology and Various Nutritional Conditions in Human and Animal Models

In recent years, adipose tissue has attracted a lot of attention. It is not only an energy reservoir but also plays important immune, paracrine and endocrine roles. BMAT (bone marrow adipose tissue) is a heterogeneous tissue, found mostly in the medullary canal of the long bones (tibia, femur and humerus), in the vertebrae and iliac crest. Adipogenesis in bone marrow cavities is a consequence of ageing or may accompany pathologies like diabetes mellitus type 1 (T1DM), T2DM, anorexia nervosa, oestrogen and growth hormone deficiencies or impaired haematopoiesis and osteoporosis. This paper focuses on studies concerning BMAT and its physiology in dietary interventions, like obesity in humans and high fat diet in rodent studies; and opposite: anorexia nervosa and calorie restriction in animal models.
A Machine Vision Rapid Method to Determine the Ripeness Degree of Olive Lots

The degree of olive maturation is a very important factor to consider at harvest time, as it influences the organoleptic quality of the final product, for both oil and table use. The Jaén index, evaluated by measuring the average coloring of olive fruits (peel and pulp), is currently considered to be one of the most indicative methods to determine the olive ripening stage, but it is a slow assay and its results are not objective. The aim of this work is to identify the ripeness degree of olive lots through a real-time, repeatable, and objective machine vision method, which uses RGB image analysis based on a k-nearest neighbors classification algorithm. To overcome different lighting scenarios, pictures were subjected to an automatic colorimetric calibration method—an advanced 3D algorithm using known values. To check the performance of the automatic machine vision method, a comparison was made with two visual operator image evaluations. For 10 images, the number of black, green, and purple olives was also visually evaluated by these two operators. The accuracy of the method was 60%. The system could be easily implemented in a specific mobile app developed for the automatic assessment of olive ripeness directly in the field, for advanced georeferenced data analysis.
Increasing Adult Hippocampal Neurogenesis Promotes Resilience in a Mouse Model of Depression

Many studies evaluated the functional role of adult hippocampal neurogenesis (AHN) and its key role in cognitive functions and mood regulation. The effects of promoting AHN on the recovery of stress-induced symptoms have been well studied, but its involvement in stress resilience remains elusive. We used a mouse model enabling us to foster AHN before the exposure to unpredictable chronic mild stress (UCMS) to evaluate the potential protective effects of AHN on stress, assessing the depressive-like phenotype and executive functions. For this purpose, an inducible transgenic mouse model was used to delete the pro-apoptotic gene Bax from neural progenitors four weeks before UCMS, whereby increasing the survival of adult-generated neurons. Our results showed that UCMS elicited a depressive-like phenotype, highlighted by a deteriorated coat state, a higher immobility duration in the tail suspension test (TST), and a delayed reversal learning in a water maze procedure. Promoting AHN before UCMS was sufficient to prevent the development of stressed-induced behavioral changes in the TST and the water maze, reflecting an effect of AHN on stress resilience. Taken together, our data suggest that increasing AHN promotes stress resilience on some depressive-like symptoms but also in cognitive symptoms, which are often observed in MD.
A Novel E2 Glycoprotein Subunit Marker Vaccine Produced in Plant Is Able to Prevent Classical Swine Fever Virus Vertical Transmission after Double Vaccination

The efficacy of a novel subunit vaccine candidate, based in the CSFV E2 glycoprotein produced in plants to prevent classical swine fever virus (CSFV) vertical transmission, was evaluated. A Nicotiana benthamiana tissue culture system was used to obtain a stable production of the E2-glycoprotein fused to the porcine Fc region of IgG. Ten pregnant sows were divided into three groups: Groups 1 and 2 (four sows each) were vaccinated with either 100 μg/dose or 300 μg/dose of the subunit vaccine at 64 days of pregnancy. Group 3 (two sows) was injected with PBS. Groups 1 and 2 were boosted with the same vaccine dose. At 10 days post second vaccination, the sows in Groups 2 and 3 were challenged with a highly virulent CSFV strain. The vaccinated sows remained clinically healthy and seroconverted rapidly, showing efficient neutralizing antibodies. The fetuses from vaccinated sows did not show gross lesions, and all analyzed tissue samples tested negative for CSFV replication. However, fetuses of non-vaccinated sows had high CSFV replication in tested tissue samples. The results suggested that in vaccinated sows, the plant produced E2 marker vaccine induced the protective immunogenicity at challenge, leading to protection from vertical transmission to fetuses.
Bare Iron Oxide Nanoparticles as Drug Delivery Carrier for the Short Cationic Peptide Lasioglossin

New drug delivery systems are a potential solution for administering drugs to reduce common side effects of traditional methods, such as in cancer therapy. Iron oxide nanoparticles (IONs) can increase the drugs’ biological activity through high binding efficiency and magnetically targeted drug delivery. Understanding the adsorption and release process of a drug to the carrier material plays a significant role in research to generate an applicable and controlled drug delivery system. This contribution focuses on the binding patterns of the peptide lasioglossin III from bee venom on bare IONs. Lasioglossin has a high antimicrobial behavior and due to its cationic properties, it has high binding potential. Considering the influence of pH, the buffer type, the particle concentration, and time, the highest drug loading of 22.7% is achieved in phosphate-buffered saline. Analysis of the desorption conditions revealed temperature and salt concentration sensitivity. The nanoparticles and peptide-ION complexes are analyzed with dynamic light scattering, zeta potential, and infrared spectroscopy. Additionally, cytotoxicity experiments performed on Escherichia coli show higher antimicrobial activity of bound lasioglossin than of the free peptide. Therefore, bare IONs are an interesting platform material for the development of drug-delivery carriers for cationic peptides.
Functional Interfaces, Biological Pathways, and Regulations of Interferon-Related DNA Damage Resistance Signature (IRDS) Genes

Interferon (IFN)-related DNA damage resistant signature (IRDS) genes are a subgroup of interferon-stimulated genes (ISGs) found upregulated in different cancer types, which promotes resistance to DNA damaging chemotherapy and radiotherapy. Along with briefly discussing IFNs and signalling in this review, we highlighted how different IRDS genes are affected by viruses. On the contrary, different strategies adopted to suppress a set of IRDS genes (STAT1, IRF7, OAS family, and BST2) to induce (chemo- and radiotherapy) sensitivity were deliberated. Significant biological pathways that comprise these genes were classified, along with their frequently associated genes (IFIT1/3, IFITM1, IRF7, ISG15, MX1/2 and OAS1/3/L). Major upstream regulators from the IRDS genes were identified, and different IFN types regulating these genes were outlined. Functional interfaces of IRDS proteins with DNA/RNA/ATP/GTP/NADP biomolecules featured a well-defined pharmacophore model for STAT1/IRF7-dsDNA and OAS1/OAS3/IFIH1-dsRNA complexes, as well as for the genes binding to GDP or NADP+. The Lys amino acid was found commonly interacting with the ATP phosphate group from OAS1/EIF2AK2/IFIH1 genes. Considering the premise that targeting IRDS genes mediated resistance offers an efficient strategy to resensitize tumour cells and enhances the outcome of anti-cancer treatment, this review can add some novel insights to the field.
Spatial Transcriptomics: Molecular Maps of the Mammalian Brain.

Maps of the nervous system inspire experiments and theories in neuroscience. Advances in molecular biology over the past decades have revolutionized the definition of cell and tissue identity. Spatial transcriptomics has opened up a new era in neuroanatomy, where the unsupervised and unbiased exploration of the molecular signatures of tissue organization will give rise to a new generation of brain maps. We propose that the molecular classification of brain regions on the basis of their gene expression profile can circumvent subjective neuroanatomical definitions and produce common reference frameworks that can incorporate cell types, connectivity, activity, and other modalities. Here we review the technological and conceptual advances made possible by spatial transcriptomics in the context of advancing neuroanatomy and discuss how molecular neuroanatomy can redefine mapping of the nervous system. Expected final online publication date for the Annual Review of Neuroscience, Volume 44 is July 2021. Please see http://www.annualreviews. org/page/journal/pubdates for revised estimates.
The Effect of Environmental pH during Trichothecium roseum (Pers.:Fr.) Link Inoculation of Apple Fruits on the Host Differential Reactive Oxygen Species Metabolism

Trichothecium roseum is an important postharvest pathogen, belonging to an alkalizing group of pathogens secreting ammonia during fungal growth and colonization of apple fruits. Fungal pH modulation is usually considered a factor for improving fungal gene expression, contributing to its pathogenicity. However, the effects of inoculation with T. roseum spore suspensions at increasing pH levels from pH 3 up to pH 7, on the reactive oxygen species (ROS) production and scavenging capability of the apple fruits, affecting host susceptibility, indicate that the pH regulation by the pathogens also affects host response and may contribute to colonization. The present results indicate that the inoculation of T. roseum spores at pH 3 caused the lowest cell membrane permeability, and reduced malondialdehyde content, NADPH oxidases activity, O2●− and H2O2 production in the colonized fruit. Observations of the colonized area on the 9th day after inoculation at pH 3, showed that the rate of O2●− production and H2O2 content was reduced by 57% and 25%, compared to their activities at pH 7. In contrast, antioxidative activities of superoxide dismutase, catalase and peroxidases of fruit tissue inoculated with spores’ suspension in the presence of a solution at pH 3.0 showed their highest activity. The catalase and peroxidases activities in the colonized tissue at pH 3 were higher by almost 58% and 55.9%, respectively, on the 6th day after inoculation compared to inoculation at pH 7. The activities of key enzymes of the ascorbate-glutathione (AsA-GSH) cycle and their substrates and products by the 9th day after fruit inoculation at pH 3 showed 150%, 31%, 16%, and 110% higher activities of ascorbate peroxidase, monodehydroascorbate reductase, dehydroascorbate reductase and glutathione reductase, respectively, compared to pH 7. A similar pattern of response was also observed in the accumulation of ascorbic acid and dehydroascorbate which showed a higher accumulation at pH 3 compared to the colonization at pH 7. The present results indicate that the metabolic regulation of the pH environment by the T. roseum not only modulates the fungal pathogenicity factors reported before, but it induces metabolic host changes contributing both together to fungal colonization.