Miracle-dz/UniFAR-FTUs huggingface dataset:
Editorial: Sprouts, microgreens and edible flowers: Modulation of quality in functional specialty crops

COPYRIGHT © 2022 Kyriacou, Ebert, Samuolienė and Brazaitytė. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. TYPE Editorial PUBLISHED 21 September 2022 DOI 10.3389/fpls.2022. 1033236
Analysis of lncRNA in the skeletal muscle of rabbits at different developmental stages

It is universally acknowledged that lncRNA plays an important role in the regulation of animal skeletal muscle development regulation. However, there is a lack of relevant research on lncRNA in rabbit skeletal muscle development. Thus, we explored the expression profiles of lncRNA in rabbits at three growth stages (2-week-old fetus, 6-week-old post-weaning, and 6-month-old adult) using RNA-seq. A total of 554 differentially expressed lncRNAs (235 up- and 319 down-regulated) were found between the post-weaning and fetus groups and 19 (7 up- and 12 down-regulated) between the post-weaning and adult groups and 429 (115 up- and 314 down-regulated) between the fetus and adult. The enrichment pathways in the post-weaning and fetus groups were mainly concentrated at AMPK and PI3K-Akt signaling pathways, and the co-expression results revealed that LINC-2903, LINC-2374, LINC-8591 plays a role in early maintenance of skeletal muscle development. The enriched pathways in the fetus and adult groups were mainly involved in PI3K-Akt signaling pathways with a strong association found in mTOR signaling pathways. Analysis of the co-expression results suggests that LINC-5617 may be involved in the proliferation of embryonic skeletal muscle cells, and that LINC-8613 and LINC-8705 may provide energy for postnatal skeletal muscle development. The specific roles of different lncRNAs in different developmental stages of New Zealand White rabbits obtained. This will contribute to the subsequent study on the regulatory mechanism of muscle development in New Zealand White rabbits.
Galectin-3 administration drives remyelination after hypoxic-ischemic induced perinatal white matter injury

Hypoxic-ischemic (HI) induced perinatal white matter injury (PWMI) is a major cause of neurologic disabilities characterized by selective oligodendroglial death and myelin disruption. Galectin-3 (Gal-3) modulates postnatal subventricular zone gliogenesis and attenuates ischemic injury. However, the association between Gal-3 and myelin formation still remains unclear. In this study, we first perform Gal-3 knockdown (KD) to identify the importance of Gal-3 on myelin formation. Our results show impeded myelin formation, manifested by Olig2/CC1 (+) mature oligodendrocytes number, expression of oligodendroglial maturation-associated markers (MBP and CNPase), and myelin thickness and integrity. Then we perform recombinant Gal-3 (rGal-3) administration by intracerebroventricular injection. Notably, although rGal-3 administration shows no beneficial effect on oligodendrogenesis and myelin formation under normal condition, our results show that rGal-3 administration attenuates cognitive deficits and drives remyelination after PWMI, which are coupled to signs of enhanced myelin resiliency and cognition. Also, our results indicates that the significant increases in substrates for remyelination of rGal-3 administration are accompanied by enhanced Iba-1 (microglia marker)/ Mrc1 (M2 marker) (+) microglia and decreased Iba-1/ iNOS (M1 marker) (+) microglia. Altogether, our data in this research confirm the association between Gal-3 and myelin formation, underscore its position for the capacity for remyelination and restoration of function, and unveils the efficacy of rGal-3 administration with anti-inflammatory phenotype microglia (M2 microglia) activation. Thus, the findings suggest that Gal-3 plays a significant role in myelin formation and remyelination restoration.
Factors promoting and limiting antimicrobial resistance in the environment – Existing knowledge gaps

The dissemination of multidrug-resistant bacteria strains and genes carrying antibiotic resistance is currently considered to be one of the most important global problem. The WHO calls for the need to contain the spread of Antimicrobial Resistance (AMR) from all possible sources. There have been many international actions grouping scientists studying this phenomenon, and quite a lot of scientific projects devoted to this problem have already been carried out. As well, so far several strategies have been developed that can inhibit the AMR spread. In this mini-review, we highlight overlooked aspects that seem to be crucial for creating a comprehensive picture of AMR, especially in the context of One Health approach.
Contribution of allergy in the acquisition of uncontrolled severe asthma

Asthma is a multifactorial, heterogeneous disease that has a challenging management. It can be divided in non-allergic and allergic (usually associated with house dust mites (HDM) sensitization). There are several treatments options for asthma (corticosteroids, bronchodilators, antileukotrienes, anticholinergics,…); however, there is a subset of patients that do not respond to any of the treatments, who can display either a T2 or a non-T2 phenotype. A deeper understanding of the differential mechanisms underlying each phenotype will help to decipher the contribution of allergy to the acquisition of this uncontrolled severe phenotype. Here, we aim to elucidate the biological pathways associated to allergy in the uncontrolled severe asthmatic phenotype. To do so, twenty-three severe uncontrolled asthmatic patients both with and without HDM-allergy were recruited from Hospital Universitario de Gran Canaria Dr. Negrin. A metabolomic fingerprint was obtained through liquid chromatography coupled to mass spectrometry, and identified metabolites were associated with their pathways. 9/23 patients had uncontrolled HDM-allergic asthma (UCA), whereas 14 had uncontrolled, non-allergic asthma (UCNA). 7/14 (50%) of the UCNA patients had Aspirin Exacerbated Respiratory Disease. There were no significant differences regarding gender or body mass index; but there were significant differences in age and onset age, which were higher in UCNA patients; and in total IgE, which was higher in UCA. The metabolic fingerprint revealed that 103 features were significantly different between UCNA and UCA (p < 0.05), with 97 being increased in UCA and 6 being decreased. We identified lysophosphocholines (LPC) 18:2, 18:3 and 20:4 (increased in UCA patients); and deoxycholic acid and palmitoleoylcarnitine (decreased in UCA). These metabolites were related with a higher activation of phospholipase A2 (PLA2) and other phospholipid metabolism pathways. Our results show that allergy induces the activation of specific inflammatory pathways, such as the PLA2 pathway, which supports its role in the development of an uncontrolled asthma phenotype. There are also clinical differences, such as higher levels of IgE and earlier onset ages for the allergic asthmatic group, as expected. These results provide evidences to better understand the contribution of allergy to the establishment of a severe uncontrolled phenotype.
Association of cerebrospinal inflammatory profile with radiological features in newly diagnosed treatment-naïve patients with multiple sclerosis

Objective Multiple sclerosis (MS) is an immune-mediated demyelinating disease of the central nervous system. Without reliable diagnostic biomarkers, the clinical and radiological heterogeneity of MS makes diagnosis difficult. Although magnetic resonance imaging (MRI) is a major diagnostic tool for MS, the association of MRI findings with the inflammatory profile in cerebrospinal fluid (CSF) has been insufficiently investigated. Therefore, we focused on CSF profile of MS patients and examined its association with MRI findings. Methods Concentrations of 26 cytokines and chemokines were determined in CSF of 28 treatment-naïve MS patients and 12 disease-control patients with aquaporin-4 antibody-seropositive neuromyelitis optica spectrum disorder (NMOSD). Results High levels of interleukin (IL)-6, IL-17A, B-cell activating factor (BAFF), a proliferation inducing ligand (APRIL), and CD40 ligand were correlated with the absence of at least one of the following three MRI findings in MS: an ovoid lesion, three or more periventricular lesions, and a nodular and/or ring-shaped contrast-enhancing lesion. The multivariate analysis revealed that elevated IL-17A was an independent predictor of absence of ovoid lesion and periventricular lesions less than three. MS patients were classified into a group with all three MRI findings (MS-full) and a group with less than three (MS-partial). The discriminant analysis model distinguished three groups: MS-full, MS-partial, and NMOSD, with 98% accuracy. Conclusion The CSF inflammatory profile was associated with radiological findings of treatment-naïve MS. This result indicates the possible utility of combined CSF and MRI profiling in identifying different MS phenotypes related to the heterogeneity of underlying immune processes.
Radiomics-based infarct features on CT predict hemorrhagic transformation in patients with acute ischemic stroke

Objective To develop and validate a model based on the radiomics features of the infarct areas on non-contrast-enhanced CT to predict hemorrhagic transformation (HT) in acute ischemic stroke. Materials and methods A total of 118 patients diagnosed with acute ischemic stroke in two centers from January 2019 to February 2022 were included. The radiomics features of infarcted areas on non-contrast-enhanced CT were extracted using 3D-Slicer. A univariate analysis and the least absolute shrinkage and selection operator (LASSO) were used to select features, and the radiomics score (Rad-score) was then constructed. The predictive model of HT was constructed by analyzing the Rad-score and clinical and imaging features in the training cohort, and it was verified in the validation cohort. The model was evaluated with the receiver operating characteristic curve, calibration curve and decision curve, and the prediction performance of the model in different scenarios was further discussed hierarchically. Results Of the 118 patients, 52 developed HT, including 21 cases of hemorrhagic infarct (HI) and 31 cases of parenchymal hematoma (PH). The Rad-score was constructed from five radiomics features and was the only independent predictor for HT. The predictive model was constructed from the Rad-score. The area under the curve (AUCs) of the model for predicting HT in the training and validation cohorts were 0.845 and 0.750, respectively. Calibration curve and decision curve analyses showed that the model performed well. Further analysis found that the model predicted HT for different infarct sizes or treatment methods in the training and validation cohorts with 78.3 and 71.4% accuracy, respectively. For all samples, the model predicted an AUC of 0.754 for HT in patients within 4.5 h since stroke onset, and predicted an AUC of 0.648 for PH. Conclusion This model, which was based on CT radiomics features, could help to predict HT in the setting of acute ischemic stroke for any infarct size and provide guiding suggestions for clinical treatment and prognosis evaluation.
DIAGNOSING THE BURST INFLUENCE ON ACCRETION IN THE CLOCKED BURSTER GS 1826-238

Type I X-ray bursts on the surface of a neutron star are a unique probe into accretion in X-ray binary systems. However, we know little about the feedback of the burst emission on accretion. Hard X-ray shortages and enhancements of the persistent emission at soft X-rays have been observed. To put these findings in context with the aim of understanding the possible mechanism underneath, we investigated 68 bursts seen by the Rossi X-ray Timing Explorer from the clocked burster GS 1826-238. We diagnosed jointly the burst influence of both soft and hard X-rays, and we found that the observations can be described by the CompTT model with variable normalization, electron temperature, and optical depth. Putting these results in a scenario of coronal Compton cooling via the burst emission would lead to a shortage of cooling power, which may suggest that additional considerations, like the influence of the burst on corona formation, should be accounted for as well.
Resting-state brain network in Parkinson’s disease with different degrees of depression

Objective The aim of this study is to explore the neural network mechanism of Parkinson’s disease (PD) with different degrees of depression using independent component analysis (ICA) of the functional connectivity changes in the forehead, limbic system, and basal ganglia regions. Methods A total of 106 patients with PD were divided into three groups: PD with moderate-severe depression (PDMSD, n = 42), PD with mild depression (PDMD, n = 29), and PD without depression (PDND, n = 35). Fifty gender- and age-matched healthy subjects were recruited as a control group (HC). Three-dimensional T1-weighted image and resting-state functional magnetic resonance imaging (RS-fMRI) data were collected. Results Different functional connectivity was observed in the left precentral gyrus, right precuneus, right inferior frontal gyrus, right medial and paracingulate gyrus, left supplementary motor area, right brain insula, and the inferior frontal gyrus of the left orbit among the four groups (ANOVA, P < 0.05, Voxel size > 5). Both PDMD and PDMSD exhibited increased functional connectivity in the superior-posterior default-mode network (spDMN) and left frontoparietal network (LFPN); they also exhibited a decreased functional connectivity in the interior Salience Network (inSN) when compared with the PDND group. The functional connectivity within the inSN network was decreased in the PDMSD group when compared with the PDMD group (Alphasim correction, P < 0.05, voxel size > 5). Conclusion PD with different degrees of depression has abnormal functional connectivity in multiple networks, which is an important neurobiological basis for the occurrence and development of depression in PD. The degree of decreased functional connectivity in the inSN network is related to the degree of depression in patients with PD-D, which can be an imaging marker for PD to judge the severity of depression.
Amygdalin as a chemoprotective agent in co-treatment with cisplatin

Amygdalin is a naturally occurring glycoside used in traditional Chinese medicine and is known to have anti-cancer properties. Even though the anti-cancer properties of amygdalin are well known, its effect on normal cells has not been thoroughly investigated. The aim of the present study was to investigate a possible chemo-protective role of amygdalin against the cytotoxic effects of chemotherapy for normal human cells. Specifically, it was tested in combination with a strong chemotherapeutic drug cisplatin. Human non-tumorigenic MCF12F epithelial cell line, human fibroblasts cells, human breast cancer MCF7 and MDA-MB-231 cells were treated with cisplatin in a dose- and time-depended manner in the absence or presence of amygdalin. When MCF12F cells and fibroblasts underwent pre-treatment with amygdalin followed by cisplatin treatment (24 h amygdalin + 24 h cisplatin), the cell viability was increased (22%, p < 0.001) as indicated using MTT assay. As attested by flow cytometry, combination treatment was associated with decreased the percentage of late apoptotic cells compared with monotherapy (fold-change of decrease = 1.6 and 4.5 for 15 and 20 μΜ, respectively). Also, the proteins expression of PUMA, p53, phospho-p53 and Bax decreased, when a combination treatment was used vs. cisplatin alone, while the proapoptotic proteins Bcl-2 and Bcl-xL exhibited an increased tendency in the presence of amygdalin. Moreover, the levels of pro-apoptotic genes PUMA, p53, and BAX mRNA were significantly downregulated (∼83%, ∼66%, and ∼44%, respectively) vs. cisplatin alone, while the mRNA levels of anti-apoptotic genes BCl-2 and Bcl-XL were upregulated (∼44.5% and ∼51%, respectively), vs. cisplatin alone after 24 h of combination treatment. The study on the Combination index (CI) assay indicated that amygdalin could be possibly considered as an antagonist to cisplatin (2.2 and 2.3) for MCF12F and fibroblast cells, respectively. In contrast, for the breast cancer MCF7 and MDA-MB-231 cells, amygdalin and cisplatin indicated a synergistic effect (0.8 and 0.65), respectively. Our present findings suggest that amygdalin has chemo-modulatory effect when used in co-treatment with cisplatin and is able to protect normal breast cells as well as the fibroblasts during chemotherapy treatment, indicating a strong selective chemoprotective ability and may contribute to a better quality of life for cancer patients.
Leprosy and leprostigma: A review from the past through COVID-19

COPYRIGHT © 2022 Shin and Oh. This is an openaccess article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. TYPE Opinion PUBLISHED 20 September 2022 DOI 10.3389/fitd.2022. 827102
Variability and controls of stable carbon isotopic fractionation during aerobic methane oxidation in temperate lakes

The aerobic oxidation of methane (CH4) by methanotrophic bacteria (MOB) is the major sink of this highly potent greenhouse gas in freshwater environments. Yet, CH4 oxidation is one of the largest uncertain components in predicting the current and future CH4 emissions from these systems. While stable carbon isotopic mass balance is a powerful approach to estimate the extent of CH4 oxidation in situ, its applicability is constrained by the need of a reliable isotopic fractionation factor (αox), which depicts the slower reaction of the heavier stable isotope (13C) during CH4 oxidation. Here we explored the natural variability and the controls of αox across the water column of six temperate lakes using experimental incubation of unamended water samples at different temperatures. We found a large variability of αox (1.004–1.038) with a systematic increase from the surface to the deep layers of lake water columns. Moreover, αox was strongly positively coupled to the abundance of MOB in the γ-proteobacteria class (γ-MOB), which in turn correlated to the concentrations of oxygen and CH4, and to the rates of CH4 oxidation. To enable the applicability in future isotopic mass balance studies, we further developed a general model to predict αox using routinely measured limnological variables. By applying this model to δ13C-CH4 profiles obtained from the study lakes, we show that using a constant αox value in isotopic mass balances can largely misrepresent and undermine patterns of the extent of CH4 oxidation in lakes. Our αox model thus contributes towards more reliable estimations of stable carbon isotope-based quantification of CH4 oxidation and may help to elucidate large scale patterns and drivers of the oxidation-driven mitigation of CH4 emission from lakes.
Metabolomic and transcriptomic analyses reveal a MYB gene, CsAN1, involved in anthocyanins accumulation separation in F1 between ‘Zijuan’ (Camellia sinensis var. assamica) and ‘Fudingdabaicha’ (C. sinensis var. sinensis) tea plants

‘Zijuan’ (Camellia sinensis var. assamica), a somatic mutant with purple foliage and stem selected from the Yunnan Daye cultivar, has been well developed owing to abnormal pattern of anthocyanin accumulation. However, the genetic basis for the specific accumulation of phloem glycosides is not clear. Tea plants are self-incompatible, so parents with large differences in foliage color were used for crosses to investigate the genetic mechanism of anthocyanins. In this study, ‘Zijuan’ and green foliage cultivar ‘Fudingdabaicha’ (C. sinensis var. sinensis) were used as female and male parents, respectively, to generated F1 hybrid progenies with various anthocyanin contents. In order to decipher the genetic rules of anthocyanins accumulation, we performed widely targeted metabolic and transcriptomic profiling. The results showed that cyanidin-3-O-galactoside, delphinidin-3-O-galactoside and petunidin-3-O-galactoside were the major types of anthocyanins and factors directly led to the color variation between parents and F1 plants. Transcriptomic analyses suggested the significant up-regulation of anthocyanidin synthase gene (CsANS1) and CsAN1, a MYB family gene positively regulated the expression of CsANS1, in anthocyanin-rich tea plants. Furthermore, the deletion mutation of CsAN1 was found by cloning and alignment in anthocyanin-lacking cultivars. Taken together, the function deficiency of CsAN1 is predominantly responsible for the inability of anthocyanins accumulation, and this trait is heritable in progenies through hybridization. The present study elucidated the molecular basis of leaf purple trait formation in ‘zijuan’ and ‘Fudingdabaicha’ and their F1 plants, which helps to elucidate the genetic mechanism of leaf anthocyanin accumulation regulation in tea plants, and the results provide a research reference for the selection and breeding of high anthocyanin type tea varieties.
Distribution patterns of microplastics in subtidal sediments from the Sado river estuary and the Arrábida marine park, Portugal

Understanding local accumulation patterns of microplastics in subtidal sediments is crucial to assess how available such particles are for ingestion by benthic feeders and to identify the potential pollution sources in the region upon which is urgent to act. The coastal urban centers of Setúbal and Sesimbra (Portugal) and the multiple activities taking place at the contiguous Sado estuary and in the sheltered waters of Professor Luiz Saldanha Marine Park make this a relevant case study about MPs pollution in the seabed. Here, a short-term investigation assessed the spatiotemporal distribution, abundance, and composition of MPs on the nearshore seabed. Sediment samples were monthly collected from summer 2018 to winter 2019, in six stations. Despite the differences observed in rainfall between campaigns, no distinct patterns were detected in the accumulation of MPs throughout the sampled months. Yet, strong variations occurred among stations. The abundance of MPs in the Sado estuary (1042.8 ± 430.8 items kg−1) was higher in comparison to all the stations located along the marine park (52.9 ± 31.9 items kg−1). Fragments comprised 70% of particles found in estuarine sediments, while fibers were the predominant type in marine sediments. The majority of MPs collected in the estuary shared the same size class as the best represented grain size fraction: 0.250–0.500 mm. On average, the ratio between the abundance of MPs and the abundance of meiofauna organisms was higher in the estuary, suggesting more encounter rates, by both meiofauna and their predators, with MPs. The distribution of MPs throughout the study area was moderately correlated with sediment sorting and organic matter content. Also, the distinct mineralogical content of each station indicates a reduced sediment transit between stations and consequently a weak exportation of MPs from the estuary. The majority of the polymers identified by Fourier Transform Infrared Spectroscopy was denser than seawater. Polyethylene terephthalate represented 41% of the items analyzed and was mostly assigned to fibers and fiber bundles. Unveiling the distribution patterns of MPs along this segment of the Portuguese west coast enabled to identify a high-risk area where the implementation of preventive measures is urgent.