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Abstract Ultra-high dose rate FLASH radiotherapy, a promising cancer treatment approach, offers the potential to reduce healthy tissue damage during radiotherapy. As the mechanisms underlying this process remain unknown, several hypotheses have been proposed, including the altered production of radio-induced species under ultra-high dose rate (UHDR) conditions. This study explores realistic irradiation scenarios with various dose-per-pulse and investigates the role of pulse temporal structure. Using the Geant4 toolkit and its Geant4-DNA extension, we modeled the Oriatron eRT6 linac, a FLASH-validated electron beam, and conducted simulations covering four distinct dose-per-pulse scenarios – 0.17 Gy, 1 Gy, 5 Gy, and 10 Gy – all featuring a 1.8 µs pulse duration. Results show close agreement between simulated and experimental dose profiles in water, validating the eRT6 model for Geant4-DNA simulations. We observed important changes in the temporal evolution of certain species, such as the earlier fall in hydroxyl radicals ( $$^{ \bullet } \text{O}\text{H}$$ ) and reduced production and lifetime of superoxide ( $${\text{O}}_{2}^{{\bullet\:}-}$$ ) with higher dose-per-pulse levels. The pulse temporal structure did not influence the long-term evolution of species. Our findings encourage further investigation into different irradiation types, such as multi-pulse configurations, and emphasize the need to add components in water to account for relevant cellular processes.

Abstract Exposure to ionizing radiation can induce genetic aberrations via unrepaired DNA strand breaks. To investigate quantitatively the dose–effect relationship at the molecular level, we irradiated dry pBR322 plasmid DNA with 3 MeV protons and assessed fragmentation yields at different radiation doses using long-read sequencing from Oxford Nanopore Technologies. This technology applied to a reference DNA model revealed dose-dependent fragmentation, as evidenced by read length distributions, showing no discernible radiation sensitivity in specific genetic sequences. In addition, we propose a method for directly measuring the single-strand break (SSB) yield. Furthermore, through a comparative study with a collection of previous works on dry DNA irradiation, we show that the irradiation protocol leads to biases in the definition of ionizing sources. We support this scenario by discussing the size distributions of nanopore sequencing reads in the light of Geant4 and Geant4-DNA simulation toolkit predictions. We show that integrating long-read sequencing technologies with advanced Monte Carlo simulations paves a promising path toward advancing our comprehension and prediction of radiation-induced DNA fragmentation.

We provide sufficient conditions as to when a boundary component of a cocompact convex set in a CAT(0){\rm{CAT}}\left(0)-space is contractible. We then use this to study when the limit set of a quasi-convex, codimension one subgroup of a negatively curved manifold group is “wild” in the boundary. The proof is based on a notion of coarse upper curvature bounds in terms of barycenters and the careful study of interpolation in geodesic metric spaces.

Nas práticas filosófico-espirituais propostas pelos antigos greco-romanos para o cuidado de si (epiméleia heautoû), destacam-se aquelas relacionados à escuta. Escutar caracterizou-se, no interior de uma série de exercícios, como ler, escrever, memorizar e meditar, a forma primeira e mais privilegiada de apropriação da verdade pelo sujeito. Partindo das análises realizadas por Michel Foucault acerca do cuidado de si em sua Hermenêutica do Sujeito e passando por comentadores fundamentais do pensamento de Pitágoras, este trabalho tem por objetivo abordar a escuta, possivelmente em suas orientações mais antigas, como processo de domínio de si e como prática ascética. Atravessado pela exigência da escuta e do silêncio, como exercício obrigatório de introdução e permanência na escola, o discípulo pitagórico era convidado a transformar-se, em vista de buscar constantemente a sabedoria, a exemplo de seu mestre.

Although the pathological significance of myeloid cell heterogeneity is still poorly understood, new evidence indicates that distinct macrophage subsets are characterized by specific metabolic programs that influence disease onset and progression. Within this scenario, distinct subsets of macrophages, endowed with high rates of heme catabolism by the stress-responsive enzyme heme oxygenase-1 (HO-1), play critical roles in physiologic and pathological conditions. Of relevance, the substrates of HO-1 activity are the heme groups that derive from cellular catabolism and are converted into carbon monoxide (CO), biliverdin and Fe2+, which together elicit anti-apoptotic, anti-inflammatory activities and control oxidative damage. While high levels of expression of HO-1 enzyme by specialized macrophage populations (erythrophagocytes) guarantee the physiological disposal of senescent red blood cells (i.e. erythrocateresis), the action of HO-1 takes on pathological significance in various diseases, and abnormal CO metabolism has been observed in cancer, hematological diseases, hypertension, heart failure, inflammation, sepsis, neurodegeneration. Modulation of heme catabolism and CO production is therefore a feasible therapeutic opportunity in various diseases. In this review we discuss the role of HO-1 in different pathological contexts (i.e. cancer, infections, cardiovascular, immune-mediated and neurodegenerative diseases) and highlight new therapeutic perspectives on the modulation of the enzymatic activity of HO-1.

In this contribution, we propose machine learning techniques to predict zombie firms. First, we derive the risk of failure by training and testing our algorithms on disclosed financial information and nonrandom missing values of 304,906 firms active in Italy from 2008 to 2017. We then identify the highest financial distress conditional on predictions that lie above a threshold for which a combination of the false positive rate (false prediction of firm failure) and the false negative rate (false prediction of active firms) is minimized. Therefore, we identify zombies as firms that remain in financial distress, i.e. whose forecasts fall into the risk category above the threshold for at least three consecutive years. To this end, we implement a gradient boosting algorithm (XGBoost) that exploits information about missing values. The inclusion of missing values in our prediction model is crucial because patterns of undisclosed accounts are correlated with firm failure. Finally, we show that our preferred machine learning algorithm outperforms (i) proxy models such as Z -scores and the distance-to-default, (ii) traditional econometric methods, and (iii) other widely used machine learning techniques. We provide evidence that zombies are less productive and smaller on average and that they tend to increase in times of crisis. Finally, we argue that our application can help financial institutions and public authorities design evidence-based policies—e.g. optimal bankruptcy laws and information disclosure policies. [ABSTRACT FROM AUTHOR]

PURPOSE: Track structure Monte Carlo (MC) codes have achieved successful outcomes in the quantitative investigation of radiation-induced initial DNA damage. The aim of the present study is to extend a Geant4-DNA radiobiological application by incorporating a feature allowing for the prediction of DNA rejoining kinetics and corresponding cell surviving fraction along time after irradiation, for a Chinese hamster V79 cell line, which is one of the most popular and widely investigated cell lines in radiobiology. METHODS: We implemented the Two-Lesion Kinetics (TLK) model, originally proposed by Stewart, which allows for simulations to calculate residual DNA damage and surviving fraction along time via the number of initial DNA damage and its complexity as inputs. RESULTS: By optimizing the model parameters of the TLK model in accordance to the experimental data on V79, we were able to predict both DNA rejoining kinetics at low linear energy transfers (LET) and cell surviving fraction. CONCLUSION: This is the first study to demonstrate the implementation of both the cell surviving fraction and the DNA rejoining kinetics with the estimated initial DNA damage, in a realistic cell geometrical model simulated by full track structure MC simulations at DNA level and for various LET. These simulation and model make the link between mechanistic physical/chemical damage processes and these two specific biological endpoints.

Purpose: Glioblastoma is an aggressive brain tumor with high mortality and a median survival of about 15 months. Starting from our previous published compound, MV1035 that inhibited migration and invasiveness of glioblastoma U87 cells, and also exhibited a synergic effect in combination with the alkylating agent Temozolomide, we identified new active molecules, with the aim to understand the key motifs responsible for MV1035 activity against the DNA repair protein ALKBH2 and the RNA demethylase ALKBH5. Materials and methods: We modified the original structure of MV1035, synthesizing new molecules that have been tested through MTT assay, cell-free ALKBH2 assay and cell-free ALKBH5 assay. Results: We found that compound 6 is able to reduce the activity of both ALKBH2 and ALKBH5. Conclusion: We obtained important information about the key motifs responsible for the activity of these inhibitors. However, considering the complexity, heterogeneity and plasticity of GBM and GSC cells, the new identified compound will need to be validated in vivo.

Abstract Protocadherin-19 (PCDH19) developmental and epileptic encephalopathy causes an early-onset epilepsy syndrome with limbic seizures, typically occurring in clusters and variably associated with intellectual disability and a range of psychiatric disorders including hyperactive, obsessive-compulsive and autistic features. Previous quantitative neuroimaging studies revealed abnormal cortical areas in the limbic formation (parahippocampal and fusiform gyri) and underlying white-matter fibers. In this study, we adopted morphometric, network-based and multivariate statistical methods to examine the cortex and substructure of the hippocampus and amygdala in a cohort of 20 PCDH19-mutated patients and evaluated the relation between structural patterns and clinical variables at individual level. We also correlated morphometric alterations with known patterns of PCDH19 expression levels. We found patients to exhibit high-significant reductions of cortical surface area at a whole-brain level (left/right p value = 0.045/0.084), and particularly in the regions of the limbic network (left/right parahippocampal gyri p value = 0.230/0.016; left/right entorhinal gyri p value = 0.002/0.327), and bilateral atrophy of several subunits of the amygdala and hippocampus, particularly in the CA regions (head of the left CA3 p value = 0.002; body of the right CA3 p value = 0.004), and differences in the shape of hippocampal structures. More severe psychiatric comorbidities correlated with more significant altered patterns, with the entorhinal gyrus (p value = 0.013) and body of hippocampus (p value = 0.048) being more severely affected. Morphometric alterations correlated significantly with the known expression patterns of PCDH19 (r value = -0.26, p spin = 0.092). PCDH19 encephalopathy represents a model of genetically determined neural network based neuropsychiatric disease in which quantitative MRI-based findings correlate with the severity of clinical manifestations and had have a potential predictive value if analyzed early.

Polysomnography (PSG) is the gold standard for the diagnosis of pediatric obstructive sleep apnea (OSA); however, high costs and limited availability restrict its use for routine screening. This systematic review and meta-analysis investigated the accuracy of overnight oximetry for the diagnosis of pediatric OSA. Studies evaluating overnight oximetry against PSG-derived apnea-hypopnea index (AHI) in subjects aged ≤18 years were considered in the qualitative analysis and evaluated with the QUADAS-2 tool. Only oximetry parameters adopted by at least four studies using the currently accepted diagnostic thresholds for pediatric OSA (AHI of 1, 5 and 10 events/h) were included for quantitative analyses. A bivariate meta-analysis was used to estimate sensitivity and specificity, as well as to construct summary receiver operator characteristic curves. The positive and negative predictive values were calculated. A total of 28 studies (9122 participants) were included in qualitative analyses. Only 3% oxygen desaturation index (ODI3) was eligible for the quantitative analyses (six studies, 1276 participants). As OSA severity increases sensitivity, specificity and the negative predictive value also increase, reaching values of 79%, 84%, and 89% at AHI ≥ 10, respectively. Oximetry displays a good performance as a screening tool for pediatric OSA, especially with moderate-to-severe disease. ODI3 is particularly effective at ruling out OSA in children who test negative.

Trypanosoma cruzi is the etiologic agent of Chagas’ disease, a debilitating and mortal zoonotic illness that threatens the lives of several millions of people in the American continent. The acute phase is underdiagnosed and there is no curative treatment for the chronic stage. This unicellular pathogen colonizes cells from different tissues wherein it replicates and remains hidden from immune recognition. There is an urgent need to develop new chemotherapy, which requires robust screening bioassays against the amastigote, a proliferative and drug-resilient intracellular stage of the parasite. With this aim, here we present the generation and characterization of a bioluminescent reporter cell line of the highly infective strain Dm28c from T. cruzi. Constitutive and stable expression of the reporter gene (a red-shifted luciferase from Photinus pyralis) was achieved in the different developmental stages of the pathogen. The transgene did not affect parasite growth and differentiation. The bioluminescence signal displayed a linear correlation with the parasite number. A 96-well screening assay against the amastigote stage has been established and validated with a small compound library. The bioassay proved sensitive, robust, and amenable for high throughput applications. The reporter cell line may prove highly valuable to address different goals in the early phase of the drug discovery process against American trypanosomiasis.

Extracellular DNA (exDNA) can be actively released by living cells and different putative functions have been attributed to it. Further, homologous exDNA has been reported to exert species-specific inhibitory effects on several organisms. Here, we demonstrate by different experimental evidence, including 1H-NMR metabolomic fingerprint, that the growth rate decline in Saccharomyces cere-visiae fed-batch cultures is determined by the accumulation of exDNA in the medium. Sequencing of such secreted exDNA represents a portion of the en-tire genome, showing a great similarity with extrachromosomal circular DNA (eccDNA) already reported inside yeast cells. The recovered DNA molecules were mostly single strands and specifically associated to the yeast metabolism displayed during cell growth. Flow cytometric analysis showed that the ob-served growth inhibition by exDNA corresponded to an arrest in the S phase of the cell cycle. These unprecedented findings open a new scenario on the func-tional role of exDNA produced by living cells.

Alternative means of control are becoming increasingly relevant to the improvement of safety and the reduction of postharvest losses and waste of fruit and vegetables, especially in view of the application of the EU Greed Deal. A previous study from our research group that focused on the electrolysis process of water and was conducted using NaCl and NaHCO3 as electrolytes proved to efficiently reduce pathogen inoculum in packinghouse washing water. In the present study, we examined the effect of the electrolyzed salt solutions (eNaCl and eNaHCO3) produced in the same experimental conditions previously reported to be used as postharvest treatments during handling and commercialization, and/or at the consumer’s site. We tested the electrolyzed solutions, obtained in the presence or absence of the salts, against five relevant fungal pathogens in terms of conidia viability, and on various hosts in terms of rot incidence/severity. Chemical parameters of electrolyzed and non-electrolyzed solutions were also assessed. Although a different susceptibility to treatments was observed among pathogens, electrolyzed sodium chloride (eNaCl) was the most efficient treatment for preventing spore germination, as well as for minimizing fruit rot. However, a consistent control of fungal viability and consequent rot was also achieved using electrolyzed tap water (eW). The eNaHCO3, although less efficient on fungal viability, provided a significant effect against fruit rot. The investigated electrolyzed solutions seem promising for reducing the waste of fresh fruit and vegetables.

The chemical stage of the Monte Carlo track-structure (MCTS) code Geant4-DNA was extended for its use in DNA strand break (SB) simulations and compared against published experimental data. Geant4-DNA simulations were performed using pUC19 plasmids (2686 base pairs) in a buffered solution of DMSO irradiated by60Co or137Csγ-rays. A comprehensive evaluation of SSB yields was performed considering DMSO, DNA concentration, dose and plasmid supercoiling. The latter was measured using the super helix density value used in a Brownian dynamics plasmid generation algorithm. The Geant4-DNA implementation of the independent reaction times method (IRT), developed to simulate the reaction kinetics of radiochemical species, allowed to score the fraction of supercoiled, relaxed and linearized plasmid fractions as a function of the absorbed dose. The percentage of the number of SB after •OH + DNA and H• + DNA reactions, referred as SSB efficiency, obtained using MCTS were 13.77% and 0.74% respectively. This is in reasonable agreement with published values of 12% and 0.8%. The SSB yields as a function of DMSO concentration, DNA concentration and super helix density recreated the expected published experimental behaviors within 5%, one standard deviation. The dose response of SSB and DSB yields agreed with published measurements within 5%, one standard deviation. We demonstrated that the developed extension of IRT in Geant4-DNA, facilitated the reproduction of experimental conditions. Furthermore, its calculations were strongly in agreement with experimental data. These two facts will facilitate the use of this extension in future radiobiological applications, aiding the study of DNA damage mechanisms with a high level of detail.