bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prenatal phthalate exposure and cord blood DNA methylation
Authors: Lee Jooah , Kim Jeeyoung , Zinia Sabrina Shafi , Park Jaehyun , Won Sungho , Kim Woo Jin 
Published: April 2023

AbstractExposure to phthalates has been shown to impede the human endocrine system, resulting in deleterious effects on pregnant women and their children. Phthalates modify DNA methylation patterns in infant cord blood. We examined the association between prenatal phthalate exposure and DNA methylation patterns in cord blood in a Korean birth cohort. Phthalate levels were measured in 274 maternal urine samples obtained during late pregnancy and 102 neonatal urine samples obtained at birth, and DNA methylation levels were measured in cord blood samples. For each infant in the cohort, associations between CpG methylation and both maternal and neonate phthalate levels were analyzed using linear mixed models. The results were combined with those from a meta-analysis of the levels of phthalates in maternal and neonatal urine samples, which were also analyzed for MEOHP, MEHHP, MnBP, and DEHP. This meta-analysis revealed significant associations between the methylation levels of CpG sites near the CHN2 and CUL3 genes, which were also associated with MEOHP and MnBP in neonatal urine. When the data were stratified by the sex of the infant, MnBP concentration was found to be associated with one CpG site near the OR2A2 and MEGF11 genes in female infants. In contrast, the concentrations of the three maternal phthalates showed no significant association with CpG site methylation. Furthermore, the data identified distinct differentially methylated regions in maternal and neonatal urine samples following exposure to phthalates. The CpGs with methylation levels that were positively associated with phthalate levels (particularly MEOHP and MnBP) were found to be enriched genes and related pathways. These results indicate that prenatal phthalate exposure is significantly associated with DNA methylation at multiple CpG sites. These alterations in DNA methylation may serve as biomarkers of maternal exposure to phthalates in infants and are potential candidates for investigating the mechanisms by which phthalates impact maternal and neonatal health.
Clinical implications of somatic allele expansion in female FMR1 premutation carriers
Authors: Aishworiya Ramkumar , Hwang Ye Hyun , Santos Ellery , Hayward Bruce , Usdin Karen , Durbin-Johnson Blythe , Hagerman Randi , Tassone Flora 
Published: April 2023

AbstractCarriers of a premutation allele (PM) in the FMR1 gene are at risk of developing a number of Fragile X premutation asssociated disorders (FXPAC), including Fragile X-associated Tremor/Ataxia Syndrome (FXTAS), Fragile X-associated Primary Ovarian Insufficiency (FXPOI), and Fragile X-associated neuropsychiatric disorders (FXAND). We have recently reported somatic CGG allele expansion in female PM; however, its clinical significance remains unclear. The aim of this study was to examine the potential clinical association between somatic FMR1 allele instability and PM associated disorders. Participants comprised of 424 female PM carriers age 0.3– 90 years. FMR1 molecular measures and clinical information on the presence of medical conditions, were determined for all subjects for primary analysis. Two sub-groups of participants (age ≥ 25, N = 377 and age ≥ 50, N = 134) were used in the analysis related to presence of FXPOI and FXTAS, respectively. Among all participants (N = 424), the degree of instability (expansion) was significantly higher (median 2.5 vs 2.0, P = 0.026) in participants with a diagnosis of attention deficit hyperactivity disorder (ADHD) compared to those without. FMR1 mRNA expression was significantly higher in subjects with any psychiatric disorder diagnosis (P = 0.0017); specifically, in those with ADHD (P = 0.009), and with depression (P = 0.025). Somatic FMR1 expansion was associated with the presence of ADHD in female PM and FMR1 mRNA levels were associated with the presence of mental health disorders. The findings of our research are innovative as they suggest a potential role of the CGG expansion in the clinical phenotype of PM and may potentially guide clinical prognosis and management.
Preliminary investigation on the effect of insect-based chitosan on preservation of coated fresh cherry tomatoes
Authors: Tafi Elena , Triunfo Micaela , Guarnieri Anna , Ianniciello Dolores , Salvia Rosanna , Scieuzo Carmen , Ranieri Annamaria , Castagna Antonella , Lepuri Samuel , Hahn Thomas , Zibek Susanne , De Bonis Angela , Falabella Patrizia 
Published: April 2023

AbstractChitosan was produced from Hermetia illucens pupal exuviae by heterogeneous and homogeneous deacetylation. Tomato fruits (Solanum lycopersicum), that are one of the most grown and consumed food throughout the world, were coated with 0.5 and 1% chitosan, applied by dipping or spraying, and stored at room temperature or 4 °C, for a storage period of 30 days. Statistical analysis give different results depending on the analysed parameters: heterogeneous chitosan, indeed, had a better effect than the homogenous one in maintaining more stable physico-chemical parameters, while the homogenous chitosan improved the total phenols, flavonoids and antioxidant activity. Chitosan coatings applied by spraying were more effective in all the analyses. Chitosan derived from H. illucens always performed similarly to the commercial chitosan. However, a general better performance of insect-derived chitosan on the concentration of phenolics and flavonoids, and the antioxidant activity was observed as compared to the commercial one. Chitosan coating has already been successfully used for preservation of fresh fruits, as alternative to synthetic polymers, but this is the first investigation of chitosan produced from an insect for this application. These preliminary results are encouraging regarding the validation of the insect H. illucens as a source of chitosan.
Effect of remote ischemic conditioning on the immune-inflammatory profile in patients with traumatic hemorrhagic shock in a randomized controlled trial
Authors: Leung C. H. , Rizoli S. B. , Trypcic S. , Rhind S. G. , Battista A. P. , Ailenberg M. , Rotstein O. D. 
Published: April 2023

AbstractResuscitation induced ischemia/reperfusion predisposes trauma patients to systemic inflammation and organ dysfunction. We investigated the effect of remote ischemic conditioning (RIC), a treatment shown to prevent ischemia/reperfusion injury in experimental models of hemorrhagic shock/resuscitation, on the systemic immune-inflammatory profile in trauma patients in a randomized trial. We conducted a prospective, single-centre, double-blind, randomized, controlled trial involving trauma patients sustaining blunt or penetrating trauma in hemorrhagic shock admitted to a Level 1 trauma centre. Patients were randomized to receive RIC (four cycles of 5-min pressure cuff inflation at 250 mmHg and deflation on the thigh) or a Sham intervention. The primary outcomes were neutrophil oxidative burst activity, cellular adhesion molecule expression, and plasma levels of myeloperoxidase, cytokines and chemokines in peripheral blood samples, drawn at admission (pre-intervention), 1 h, 3 h, and 24 h post﻿-admission. Secondary outcomes included ventilator, ICU and hospital free days, incidence of nosocomial infections, 24 h and 28 day mortality. 50 eligible patients were randomized; of which 21 in the Sham group and 18 in the RIC group were included in the full analysis. No treatment effect was observed between Sham and RIC groups for neutrophil oxidative burst activity, adhesion molecule expression, and plasma levels of myeloperoxidase and cytokines. RIC prevented significant increases in Th2 chemokines﻿ TARC/CCL17 (P < 0.01) and MDC/CCL22 (P < 0.05) at 24 h post-intervention in comparison to the Sham group. Secondary clinical outcomes were not different between groups. No adverse events in relation to the RIC intervention were observed. Administration of RIC was safe and did not adversely affect clinical outcomes. While trauma itself modified several immunoregulatory markers, RIC failed to alter expression of the majority of markers. However, RIC may influence Th2 chemokine expression in the post resuscitation period. Further investigation into the immunomodulatory effects of RIC in traumatic injuries and their impact on clinical outcomes is warranted.ClinicalTrials.gov number: NCT02071290.
Peristaltic transfer of nanofluid with motile gyrotactic microorganisms with nonlinear thermic radiation
Authors: Mostapha Doaa R. , El-dabe Nabil T. M. 
Published: April 2023

AbstractIn situated theoretical article, a study of peristaltic transition of Jeffery nanofluid comprising motile gyrotactic microorganisms is exposed. The movement floods due to anisotropically stenosed endoscope influenced by Hall current, Joule heating during Darcy-Forchheimer feature. Influences of nonlinear thermic radiation, chemical interactions as well as Soret and Dufour scheme are exhibited. To ameliorate the competence of this article, activation energy has been appended to concentration of nano-particles due to the amended Arrhenius scheme and Buongiorno type. The slip stipulation is deemed relative to the speed scheme. Meanwhile, convective stipulation is reckoned for temperature. The proposition of protracted wavelength besides subdued Reynolds numeral is regulated to transit the manner of partial differential formulations that judges the fluid movement to ordinary one. Homotopy perturbation manner is tackled to manage the traditional solutions of generated neutralizations. Influences of assorted factors of the issue are debated and schematically showed with a class of charts. The situated study grants a medication for the malign cells and clogged arteries of the heart by manner of penetrating a slender tube (catheter). Also, this study may represent the depiction of the gastric juice movement in small intestine when an endoscope is permeating across it.
Highly-conserved regulatory activity of the ANR family in the virulence of diarrheagenic bacteria through interaction with master and global regulators
Authors: Rodriguez-Valverde Diana , Giron Jorge A. , Hu Yang , Nataro James P. , Ruiz-Perez Fernando , Santiago Araceli E. 
Published: April 2023

AbstractANR (AraC negative regulators) are a novel class of small regulatory proteins commonly found in enteric pathogens. Aar (AggR-activated regulator), the best-characterized member of the ANR family, regulates the master transcriptional regulator of virulence AggR and the global regulator HNS in enteroaggregative Escherichia coli (EAEC) by protein–protein interactions. On the other hand, Rnr (RegA-negative regulator) is an ANR homolog identified in attaching and effacing (AE) pathogens, including Citrobacter rodentium and enteropathogenic Escherichia coli (EPEC), sharing only 25% identity with Aar. We previously found that C. rodentium lacking Rnr exhibits prolonged shedding and increased gut colonization in mice compared to the parental strain. To gain mechanistic insights into this phenomenon, we characterized the regulatory role of Rnr in the virulence of prototype EPEC strain E2348/69 by genetic, biochemical, and human organoid-based approaches. Accordingly, RNA-seq analysis revealed more than 500 genes differentially regulated by Rnr, including the type-3 secretion system (T3SS). The abundance of EspA and EspB in whole cells and bacterial supernatants confirmed the negative regulatory activity of Rnr on T3SS effectors. We found that besides HNS and Ler, twenty-six other transcriptional regulators were also under Rnr control. Most importantly, the deletion of aar in EAEC or rnr in EPEC increases the adherence of these pathogens to human intestinal organoids. In contrast, the overexpression of ANR drastically reduces bacterial adherence and the formation of AE lesions in the intestine. Our study suggests a conserved regulatory mechanism and a central role of ANR in modulating intestinal colonization by these enteropathogens despite the fact that EAEC and EPEC evolved with utterly different virulence programs.
Sustainable development goals as unifying narratives in large UK firms’ Twitter discussions
Authors: Patuelli Alessia , Saracco Fabio 
Published: April 2023

AbstractTo achieve sustainable development worldwide, the United Nations set 17 Sustainable Development Goals (SDGs) for humanity to reach by 2030. Society is involved in the challenge, with firms playing a crucial role. Thus, a key question is to what extent firms engage with the SDGs. Efforts to map firms’ contributions have mainly focused on analysing companies’ reports based on limited samples and non-real-time data. We present a novel interdisciplinary approach based on analysing big data from an online social network (Twitter) with complex network methods from statistical physics. By doing so, we provide a comprehensive and nearly real-time picture of firms’ engagement with SDGs. Results show that: (1) SDGs themes tie conversations among major UK firms together; (2) the social dimension is predominant; (3) the attention to different SDGs themes varies depending on the community and sector firms belong to; (4) stakeholder engagement is higher on posts related to global challenges compared to general ones; (5) large UK companies and stakeholders generally behave differently from Italian ones. This paper provides theoretical contributions and practical implications relevant to firms, policymakers and management education. Most importantly, it provides a novel tool and a set of keywords to monitor the influence of the private sector on the implementation of the 2030 Agenda.
Tracing the human movements of three thousand years ago by volcanic grinding tools in the Final Bronze Age settlement of Monte Croce Guardia (Arcevia-Marche Region, central Italy)
Authors: Santi P. , Cardarelli A. , Bettelli M. , Di Renzoni A. , Cardarelli L. , Paniccia C. , Renzulli A. 
Published: April 2023

AbstractVolcanic rocks were among the most sought-after materials to produce grinding tools in antiquity because lavas lithologies, either mafic or felsic, ensured good wear resistance and grinding capacity with respect to many other kinds of rocks. The interest in findings made of vesciculated lavas, referable to parts of querns, mortars, and/or pestles of the Final Bronze Age site of Monte Croce Guardia (Arcevia) lies in the fact that this settlement was built upon limestones belonging to the sedimentary sequence of the Marche-Umbria Apennines (central Italy) and far away from potential raw materials of volcanic rocks. A petrologic study of 23 grinding tool fragments clearly indicates a provenance from the volcanic provinces of central Italy: Latium and Tuscany Regions. Few leucite tephrites (5) and one leucite phonolite lavas have a clear magmatic affinity with the high-K series of the Roman Volcanic Province (Latium) whereas the most abundant volcanic lithotype (17 samples) is represented by shoshonites (K-series) whose thin section texture, modal mineralogy and major-trace elements contents closely match with the shoshonite lavas from the Radicofani volcanic centre in the Tuscan Magmatic Province. At Radicofani (a volcanic neck in the eastern sector of Tuscany) a Final Bronze Age site coeval to that of Arcevia is present and a potential pathway corridor from that site towards Arcevia (air-line distance of ca. 115 km) is dotted with many settlements of the same age. Through analytical algorithms based on the slope and the different human-dependent cost-functions which can be applied to determine non-isotropic accumulated cost surface, least-cost paths and least-cost corridors, the best route from Radicofani to Monte Croce Guardia, approximately 140 km long, was simulated, with a walking time of 25–30 h, possibly using pack animals and wheel chariots. Three thousand years ago the Apennine Mountains did not thus constitute a barrier for human movements. This study also shed light on some other possible patterns of interactions between Final Bronze Age communities of central Italy through the present-day regions of Tuscany, Umbria and Marche, aimed towards the best performance of strategic economic activities at that time such as that of the transformation of cereals, and accompanied to cultural and social reasons.
The DNA cytosine methylome revealed two methylation motifs in the upstream regions of genes related to morphological and physiological differentiation in Streptomyces coelicolor A(3)2 M145
Authors: Pisciotta Annalisa , Sampino Alessia Maria , Presentato Alessandro , Galardini Marco , Manteca Angel , Alduina Rosa 
Published: April 2023

AbstractDNA methylation is an epigenetic modification detected in both prokaryotic and eukaryotic genomic DNAs. In bacteria, the importance of 5-methylcytosine (m5C) in gene expression has been less investigated than in eukaryotic systems. Through dot-blot analysis employing m5C antibodies against chromosomal DNA, we have previously demonstrated that m5C influences the differentiation of Streptomyces coelicolor A(3)2 M145 in solid sporulating and liquid non-sporulating complex media. Here, we mapped the methylated cytosines of the M145 strain growing in the defined Maltose Glutamate (MG) liquid medium. Sequencing of the M145 genome after bisulfite treatment (BS-sequencing) evidenced 3360 methylated cytosines and the two methylation motifs, GGCmCGG and GCCmCG, in the upstream regions of 321 genes. Besides, the role of cytosine methylation was investigated using the hypo-methylating agent 5′-aza-2′-deoxycytidine (5-aza-dC) in S. coelicolor cultures, demonstrating that m5C affects both growth and antibiotic biosynthesis. Finally, quantitative reverse-transcription polymerase-chain-reaction (RT-qPCR) analysis of genes containing the methylation motifs in the upstream regions showed that 5-aza-dC treatment influenced their transcriptional levels and those of the regulatory genes for two antibiotics. To the best of our knowledge, this is the first study that reports the cytosine methylome of S. coelicolor M145, supporting the crucial role ascribed to cytosine methylation in controlling bacterial gene expression.
Evolution of fairness in the divide-a-lottery game
Authors: Kim Jeong-Yoo , Lee Kyu-Min 
Published: April 2023

AbstractIn this paper, we show that fairness can evolve in the divide-a-lottery game which is more general than the divide-a-dollar game by using an indirect evolutionary approach. In the divide-a-lottery game, the size of a pie is uncertain. Two players sequentially bid for a share and they get their bid if the allocation based on the bids turns out to be feasible and otherwise neither gets anything. In this game, rational players over-compete for a higher share, resulting in a high probability of failure in agreement, whereas fair players who dislike the disparity between shares lower their bids thereby reducing the failure probability and thus increasing the expected payoff. As a result, fairness strictly dominates rationality. This is the mechanism through which fairness evolves. However, this result is not robust against even a slight uncertainty about the opponent’s type. Surprisingly, we show a contrasted simulation result that only rational players who are strictly dominated by fair players survive evolutionarily for most of the parameter values if players have even a slight chance of not knowing the opponent’s type. Our simulation results in a local interaction model in which players only know the type of closer neighbors capture both insights and demonstrate that moderate proportions of both types coexist evolutionarily over time, and that the population average fitness of this polymorphic population is higher than monomorphic population consisting only of fair types or rational types.
Clinical validation for automated geographic atrophy monitoring on OCT under complement inhibitory treatment
Authors: Mai Julia , Lachinov Dmitrii , Riedl Sophie , Reiter Gregor S. , Vogl Wolf-Dieter , Bogunovic Hrvoje , Schmidt-Erfurth Ursula 
Published: April 2023

AbstractGeographic atrophy (GA) represents a late stage of age-related macular degeneration, which leads to irreversible vision loss. With the first successful therapeutic approach, namely complement inhibition, huge numbers of patients will have to be monitored regularly. Given these perspectives, a strong need for automated GA segmentation has evolved. The main purpose of this study was the clinical validation of an artificial intelligence (AI)-based algorithm to segment a topographic 2D GA area on a 3D optical coherence tomography (OCT) volume, and to evaluate its potential for AI-based monitoring of GA progression under complement-targeted treatment. 100 GA patients from routine clinical care at the Medical University of Vienna for internal validation and 113 patients from the FILLY phase 2 clinical trial for external validation were included. Mean Dice Similarity Coefficient (DSC) was 0.86 ± 0.12 and 0.91 ± 0.05 for total GA area on the internal and external validation, respectively. Mean DSC for the GA growth area at month 12 on the external test set was 0.46 ± 0.16. Importantly, the automated segmentation by the algorithm corresponded to the outcome of the original FILLY trial measured manually on fundus autofluorescence. The proposed AI approach can reliably segment GA area on OCT with high accuracy. The availability of such tools represents an important step towards AI-based monitoring of GA progression under treatment on OCT for clinical management as well as regulatory trials.
Synthetic lethality prediction in DNA damage repair, chromatin remodeling and the cell cycle using multi-omics data from cell lines and patients.
Authors: Markowska Magda , Budzinska Magdalena A. , Coenen-Stass Anna , Kang Senbai , Kizling Ewa , Kolmus Krzysztof , Koras Krzysztof , Staub Eike , Szczurek Ewa 
Published: April 2023

AbstractDiscovering synthetic lethal (SL) gene partners of cancer genes is an important step in developing cancer therapies. However, identification of SL interactions is challenging, due to a large number of possible gene pairs, inherent noise and confounding factors in the observed signal. To discover robust SL interactions, we devised SLIDE-VIP, a novel framework combining eight statistical tests, including a new patient data-based test iSurvLRT. SLIDE-VIP leverages multi-omics data from four different sources: gene inactivation cell line screens, cancer patient data, drug screens and gene pathways. We applied SLIDE-VIP to discover SL interactions between genes involved in DNA damage repair, chromatin remodeling and cell cycle, and their potentially druggable partners. The top 883 ranking SL candidates had strong evidence in cell line and patient data, 250-fold reducing the initial space of 200K pairs. Drug screen and pathway tests provided additional corroboration and insights into these interactions. We rediscovered well-known SL pairs such as RB1 and E2F3 or PRKDC and ATM, and in addition, proposed strong novel SL candidates such as PTEN and PIK3CB. In summary, SLIDE-VIP opens the door to the discovery of SL interactions with clinical potential. All analysis and visualizations are available via the online SLIDE-VIP WebApp.