Miracle-dz/UniFAR-FTUs huggingface dataset:
Unusual Stylar-End Breakdown and Sour Rot on Key Lime (Citrus aurantiifolia) in Pre-Harvest Condition in Italy

Key lime (Citrus aurantiifolia) is an emerging crop in Italy, especially in the Southern regions, where the environmental conditions are suitable for its cultivation. A field survey in Sicily in a commercial orchard of Key lime revealed the widespread presence of water-soaked spots and sunken/dry lesions at the stylar-end, mainly in pre-harvest condition. Water-soaked spots were attributed to Geotrichum citri-aurantii, an agent of sour rot on Citrus spp. , whereas the sunken/dry lesion was attributed to the physiological disorder known as stylar-end breakdown. Sour rot and stylar-end breakdown are usually considered post-harvest diseases and rarely found in the field on fruit still attached to the tree. Although Geotrichum citri-aurantii is not responsible for the stylar-end breakdown, its association with this alteration reveals the importance of the environmental conditions and the agronomic practices in diseases/disorders development. In addition, to our knowledge, this is the first report of Geotrichum citri-aurantii on Key lime in Europe.
Inhibition of Lysine 63 Ubiquitination Prevents the Progression of Renal Fibrosis in Diabetic DBA/2J Mice

Diabetic nephropathy (DN) is the most frequent cause of end-stage renal disease. Tubulointerstitial accumulation of lysine 63 (K63)-ubiquitinated (Ub) proteins is involved in the progression of DN fibrosis and correlates with urinary miR-27b-3p downregulation. We explored the renoprotective effect of an inhibitor of K63-Ub (NSC697923), alone or in combination with the ACE-inhibitor ramipril, in vitro and in vivo. Proximal tubular epithelial cells and diabetic DBA/2J mice were treated with NSC697923 and/or ramipril. K63-Ub protein accumulation along with α-SMA, collagen I and III, FSP-1, vimentin, p16INK4A expression, SA-α Gal staining, Sirius Red, and PAS staining were measured. Finally, we measured the urinary albumin to creatinine ratio (uACR), and urinary miR-27b-3p expression in mice. NSC697923, both alone and in association with ramipril, in vitro and in vivo inhibited hyperglycemia-induced epithelial to mesenchymal transition by significantly reducing K63-Ub proteins, α-SMA, collagen I, vimentin, FSP-1 expression, and collagen III along with tubulointerstitial and glomerular fibrosis. Treated mice also showed recovery of urinary miR-27b-3p and restored expression of p16INK4A. Moreover, NSC697923 in combination with ramipril demonstrated a trend in the reduction of uACR. In conclusion, we suggest that selective inhibition of K63-Ub, when combined with the conventional treatment with ACE inhibitors, might represent a novel treatment strategy to prevent the progression of fibrosis and proteinuria in diabetic nephropathy and we propose miR-27b-3p as a biomarker of treatment efficacy.
Regulation of Fructose 1,6-Bisphosphatase in Procyclic Form Trypanosoma brucei

Glycolysis is well described in Trypanosoma brucei, while the importance of gluconeogenesis and one of the key enzymes in that pathway, fructose 1,6-bisphosphatase, is less understood. Using a sensitive and specific assay for FBPase, we demonstrate that FBPase activity in insect stage, procyclic form (PF), parasite changes with parasite cell line, extracellular glucose levels, and cell density. FBPase activity in log phase PF 2913 cells was highest in high glucose conditions, where gluconeogenesis is expected to be inactive, and was undetectable in low glucose, where gluconeogenesis is predicted to be active. This unexpected relationship between FBPase activity and extracellular glucose levels suggests that FBPase may not be exclusively involved in gluconeogenesis and may play an additional role in parasite metabolism. In stationary phase cells, the relationship between FBPase activity and extracellular glucose levels was reversed. Furthermore, we found that monomorphic PF 2913 cells had significantly higher FBPase levels than pleomorphic PF AnTat1.1 cells where the activity was undetectable except when cells were grown in standard SDM79 media, which is glucose-rich and commonly used to grow PF trypanosomes in vitro. Finally, we observed several conditions where FBPase activity changed while protein levels did not, suggesting that the enzyme may be regulated via post-translational modifications.
Comparison of the Virome of Quarantined Sugarcane Varieties and the Virome of Grasses Growing near the Quarantine Station

Visacane is a sugarcane quarantine station located in the South of France, far away from sugarcane growing areas. Visacane imports up to 100 sugarcane varieties per year, using safe control and confinement measures of plants and their wastes to prevent any risk of pathogen spread outside of the facilities. Viruses hosted by the imported material are either known or unknown to cause disease in cultivated sugarcane. Poaceae viruses occurring in plants surrounding the quarantine glasshouse are currently unknown. These viruses could be considered as a source of new sugarcane infections and potentially cause new sugarcane diseases in cases of confinement barrier failure. The aim of this study was to compare the plant virome inside and outside of the quarantine station to identify potential confinement failures and risks of cross infections. Leaves from quarantined sugarcane varieties and from wild Poaceae growing near the quarantine were collected and processed by a metagenomics approach based on virion-associated nucleic acids extraction and library preparation for Illumina sequencing. While viruses belonging to the same virus genus or family were identified in the sugarcane quarantine and its surroundings, no virus species was detected in both environments. Based on the data obtained in this study, no virus movement between quarantined sugarcane and nearby grassland has occurred so far, and the confinement procedures of Visacane appear to be properly implemented.
Smart Hydrogels Meet Carbon Nanomaterials for New Frontiers in Medicine

Carbon nanomaterials include diverse structures and morphologies, such as fullerenes, nano-onions, nanodots, nanodiamonds, nanohorns, nanotubes, and graphene-based materials. They have attracted great interest in medicine for their high innovative potential, owing to their unique electronic and mechanical properties. In this review, we describe the most recent advancements in their inclusion in hydrogels to yield smart systems that can respond to a variety of stimuli. In particular, we focus on graphene and carbon nanotubes, for applications that span from sensing and wearable electronics to drug delivery and tissue engineering.
Understanding Topological Insulators in Real Space

A real space understanding of the Su–Schrieffer–Heeger model of polyacetylene is introduced thanks to delocalization indices defined within the quantum theory of atoms in molecules. This approach enables to go beyond the analysis of electron localization usually enabled by topological insulator indices—such as IPR—enabling to differentiate between trivial and topological insulator phases. The approach is based on analyzing the electron delocalization between second neighbors, thus highlighting the relevance of the sublattices induced by chiral symmetry. Moreover, the second neighbor delocalization index, δi,i+2, also enables to identify the presence of chirality and when it is broken by doping or by eliminating atom pairs (as in the case of odd number of atoms chains). Hints to identify bulk behavior thanks to δ1,3 are also provided. Overall, we present a very simple, orbital invariant visualization tool that should help the analysis of chirality (independently of the crystallinity of the system) as well as spreading the concepts of topological behavior thanks to its relationship with well-known chemical concepts.
Triple-Band Single-Layer Rectenna for Outdoor RF Energy Harvesting Applications

A triple-band single-layer rectenna for outdoor RF energy applications is introduced in this paper. The proposed rectenna operates in the frequency bands of LoRa, GSM-1800, and UMTS-2100 networks. To obtain a triple-band operation, a modified E-shaped patch antenna is used. The receiving module (antenna) of the rectenna system is optimized in terms of its reflection coefficient to match the RF-to-DC rectifier. The final geometry of the proposed antenna is derived by the application of the Moth Search Algorithm and a commercial electromagnetic solver. The impedance matching network of the proposed system is obtained based on a three-step process, including the minimization of the reflection coefficient versus frequency, as well as the minimization of the reflection coefficient variations and the maximization of the DC output voltage versus RF input power. The proposed RF-to-DC rectifier is designed based on the Greinacher topology. The designed rectenna is fabricated on a single layer of FR-4 substrate. Measured results show that our proposed rectenna can harvest RF energy from outdoor (ambient and dedicated) sources with an efficiency of greater than 52%.
Detection of Quebec Polyomavirus DNA in Samples from Different Patient Groups

Polyomaviruses infect many species, including humans. So far, 15 polyomaviruses have been described in humans, but it remains to be established whether all of these are genuine human polyomaviruses. The most recent polyomavirus to be detected in a person is Quebec polyomavirus (QPyV), which was identified in a metagenomic analysis of a stool sample from an 85-year-old hospitalized man. We used PCR to investigate the presence of QPyV DNA in urine samples from systemic lupus erythematosus (SLE) patients (67 patients; 135 samples), multiple sclerosis patients (n = 35), HIV-positive patients (n = 66) and pregnant women (n = 65). Moreover, cerebrospinal fluid from patients with suspected neurological diseases (n = 63), nasopharyngeal aspirates from patients (n = 80) with respiratory symptoms and plasma samples from HIV-positive patients (n = 65) were examined. QPyV DNA was found in urine from 11 (16.4%), 10 (15.4%) and 5 (14.3%) SLE patients, pregnant women, and multiple sclerosis patients, respectively. No QPyV DNA could be detected in the other samples. Alignment with the only available QPyV sequence in the GenBank revealed amino acid substitutions in the HI-loop of capsid protein VP1 in 6/28 of the isolates. Our results show that QPyV viruria can occur, but whether it may cause clinical symptoms in the patients remains to be determined.
Classification of Diffuse Glioma Subtype from Clinical-Grade Pathological Images Using Deep Transfer Learning

Diffuse gliomas are the most common primary brain tumors and they vary considerably in their morphology, location, genetic alterations, and response to therapy. In 2016, the World Health Organization (WHO) provided new guidelines for making an integrated diagnosis that incorporates both morphologic and molecular features to diffuse gliomas. In this study, we demonstrate how deep learning approaches can be used for an automatic classification of glioma subtypes and grading using whole-slide images that were obtained from routine clinical practice. A deep transfer learning method using the ResNet50V2 model was trained to classify subtypes and grades of diffuse gliomas according to the WHO’s new 2016 classification. The balanced accuracy of the diffuse glioma subtype classification model with majority voting was 0.8727. These results highlight an emerging role of deep learning in the future practice of pathologic diagnosis.
Fish Oil Increases Diet-Induced Thermogenesis in Mice

Increasing energy expenditure (EE) is beneficial for preventing obesity. Diet-induced thermogenesis (DIT) is one of the components of total EE. Therefore, increasing DIT is effective against obesity. We examined how much fish oil (FO) increased DIT by measuring absolute values of DIT in mice. C57BL/6J male mice were given diets of 30 energy% fat consisting of FO or safflower oil plus butter as control oil (Con). After administration for 9 days, respiration in mice was monitored, and then the data were used to calculate DIT and EE. DIT increased significantly by 1.2-fold in the FO-fed mice compared with the Con-fed mice. Body weight gain was significantly lower in the FO-fed mice. FO increased the levels of uncoupling protein 1 (Ucp1) mRNA and UCP1 protein in brown adipose tissue (BAT) by 1.5- and 1.2-fold, respectively. In subcutaneous white adipose tissue (subWAT), the levels of Ucp1 mRNA and UCP1 protein were increased by 6.3- and 2.7-fold, respectively, by FO administration. FO also significantly increased the expression of markers of browning in subWAT such as fibroblast growth factor 21 and cell death-inducing DNA fragmentation factor α-like effector a. Thus, dietary FO seems to increase DIT in mice via the increased expressions of Ucp1 in BAT and induced browning of subWAT. FO might be a promising dietary fat in the prevention of obesity by upregulation of energy metabolism.
Missing Diagnoses during the COVID-19 Pandemic: A Year in Review

The COVID-19 pandemic has had major impacts on population health not only through COVID-positive cases, but also via the disruption of healthcare services, which in turn has impacted the diagnosis and treatment of all other diseases during this time. We study changes in all new registered diagnoses in ICD-10 groups during 2020 with respect to a 2019 baseline. We compare new diagnoses in 2019 and 2020 based on administrative records of the public primary health system in Central Catalonia, Spain, which cover over 400,000 patients and 3 million patient visits. We study the ratio of new diagnoses between 2019 and 2020 and find an average decline of 31.1% in new diagnoses, with substantial drops in April (61.1%), May (55.6%), and November (52%). Neoplasms experience the largest decline (49.7%), with heterogeneity in the magnitudes of the declines across different types of cancer diagnoses. While we find evidence of temporal variation in new diagnoses, reductions in diagnoses early in the year are not recouped by the year end. The observed decline in new diagnoses across all diagnosis groups suggest a large number of untreated and undetected cases across conditions. Our findings provide a year-end summary of the impact of the pandemic on healthcare activities and can help guide health authorities to design evidence-based plans to target under-diagnosed conditions in 2021.
Pan-Genome miRNomics in Brachypodium

Pan-genomes are efficient tools for the identification of conserved and varying genomic sequences within lineages of a species. Investigating genetic variations might lead to the discovery of genes present in a subset of lineages, which might contribute into beneficial agronomic traits such as stress resistance or yield. The content of varying genomic regions in the pan-genome could include protein-coding genes as well as microRNA(miRNAs), small non-coding RNAs playing key roles in the regulation of gene expression. In this study, we performed in silico miRNA identification from the genomic sequences of 54 lineages of Brachypodium distachyon, aiming to explore varying miRNA contents and their functional interactions. A total of 115 miRNA families were identified in 54 lineages, 56 of which were found to be present in all lineages. The miRNA families were classified based on their conservation among lineages and potential mRNA targets were identified. Obtaining information about regulatory mechanisms stemming from these miRNAs offers strong potential to provide a better insight into the complex traits that were potentially present in some lineages. Future work could lead us to introduce these traits to different lineages or other economically important plant species in order to promote their survival in different environmental conditions.
Synthesis, Characterization, and Specific Localization of Mitochondrial-Targeted Antioxidant Peptide SS31 Probe

The aim of this study is to investigate the targeting efficiency of FITC-SS31 to mitochondria in both normal and H2O2-induced oxidative damaged 661W cells, characterizing the properties of FITC-SS31 in the biological assays. The purity and molecular weight of FITC-SS31 were identified using HPLC and MS. MTT and LDH assays were used to evaluate the cytotoxicity and cell permeability. The binding ability of FITC-SS31 to cells was demonstrated by flow cytometry. The colocalization of FITC-SS31 and MitoTracker both in normal and oxidative cells was analyzed by a laser confocal microscope. We detected the DEGs between SS31+H2O2 and H2O2-alone-treated cells by RNA seq. GO and KEGG analyses were performed to predict the functional gene of SS31. The molecular weight of FITC-SS31 was 1142.2 with the 97.76% purity. The flow cytometry results showed that the MFI (mean fluorescence intensity) of FITC-SS31 in normal cells in the 4 h probe treatment group was higher than that in the 2 h and the 0 h group. The MFI in the 2 h probe treatment group was much higher than that in the 4 h and 0 h groups in damaged cells. The positive rate of 10 μM FITC-SS31 was higher than that of 1 μM and 5 μM. Fluorescein imaging analysis confirmed that FITC-SS31 was overlapped with MitoTracker. Through the analysis, DEGs were highly expressed in “localization, organelle, antioxidant activity, binding” functions and enriched in “AMPK signaling pathway, MAPK targets/nuclear events mediated by MAP kinase pathway and PI3K-Akt signaling pathway. ” It is speculated that SS31 exerts an antioxidant effect through one of these pathways. We hypothesized that SS31 could play a more efficient role in the pathological cells in the half-life period to avoid cell death due to oxidative damage. The functions of the DEGs in SS31+H2O2 and H2O2-alone samples are related to the localization and antioxidant activity of SS31. DEGs are mostly enriched in the AMPK signaling pathway, which needs further studies.
Regulation of Oxalate Metabolism in Spinach Revealed by RNA-Seq-Based Transcriptomic Analysis

Although spinach (Spinacia oleracea L.) is considered to be one of the most nutrient-rich leafy vegetables, it is also a potent accumulator of anti-nutritional oxalate. Reducing oxalate content would increase the nutritional value of spinach by enhancing the dietary bioavailability of calcium and other minerals. This study aimed to investigate the proposed hypothesis that a complex network of genes associated with intrinsic metabolic and physiological processes regulates oxalate homeostasis in spinach. Transcriptomic (RNA-Seq) analysis of the leaf and root tissues of two spinach genotypes with contrasting oxalate phenotypes was performed under normal physiological conditions. A total of 2308 leaf- and 1686 root-specific differentially expressed genes (DEGs) were identified in the high-oxalate spinach genotype. Gene Ontology (GO) analysis of DEGs identified molecular functions associated with various enzymatic activities, while KEGG pathway analysis revealed enrichment of the metabolic and secondary metabolite pathways. The expression profiles of genes associated with distinct physiological processes suggested that the glyoxylate cycle, ascorbate degradation, and photorespiratory pathway may collectively regulate oxalate in spinach. The data support the idea that isocitrate lyase (ICL), ascorbate catabolism-related genes, and acyl-activating enzyme 3 (AAE3) all play roles in oxalate homeostasis in spinach. The findings from this study provide the foundation for novel insights into oxalate metabolism in spinach.
Insulin-Like Peptide Receptor-Mediated Signaling Pathways Orchestrate Regulation of Growth in the Pacific Oyster (Crassostrea gigas), as Revealed by Gene Expression Profiles

The involvement of insulin/insulin-like growth factor signaling (IIS) pathways in the growth regulation of marine invertebrates remains largely unexplored. In this study, we used a fast-growing Pacific oyster (Crassostrea gigas) variety “Haida No.1” as the material with which to unravel the role of IIS systems in growth regulation in oysters. Systematic bioinformatics analyses allowed us to identify major components of the IIS signaling pathway and insulin-like peptide receptor (ILPR)-mediated signaling pathways, including PI3K-AKT, RAS-MAPK, and TOR, in C. gigas. The expression levels of the major genes in IIS and its downstream signaling pathways were significantly higher in “Haida No.1” than in wild oysters, suggesting their involvement in the growth regulation of C. gigas. The expression profiles of IIS and its downstream signaling pathway genes were significantly altered by nutrient abundance and culture temperature. These results suggest that the IIS signaling pathway coupled with the ILPR-mediated signaling pathways orchestrate the regulation of energy metabolism to control growth in Pacific oysters.
An Overview of the Chemical Characteristics, Bioactivity and Achievements Regarding the Therapeutic Usage of Acetogenins from Annona cherimola Mill.

Annona cherimola Mill. , or the custard apple, is one of the species belonging to the Annonaceae family, is widely used in traditional medicine, and has been reported to be a valuable source of bioactive compounds. A unique class of secondary metabolites derived from this family are Annonaceous acetogenins, lipophilic polyketides considered to be amongst the most potent antitumor compounds. This review provides an overview of the chemical diversity, isolation procedures, bioactivity, modes of application and synthetic derivatives of acetogenins from A. cherimola Mill.