Miracle-dz/UniFAR-FTUs huggingface dataset:
Prevalence and genotype distribution of caprine papillomavirus in peripheral blood of healthy goats in farms from three European countries

Caprine papillomaviruses (ChPVs, Capra hircus papillomaviruses) were detected and quantified for the first time using droplet digital polymerase chain reaction (ddPCR) in blood samples of 374 clinically healthy goats from farms located in Italy, Romania, and Serbia. Overall, ddPCR revealed ChPV DNA in 78 of the 374 examined samples, indicating that ~21% of the goats harbored circulating papillomavirus DNA. In particular, in Italian goat farms, ChPV genotypes were detected and quantified in 58 of 157 blood samples (~37%), 11 of 117 samples from Serbian farms (~9.4%), and 9 of 100 from Romanian blood samples (9%). Blood samples from Italian goat farms showed a high prevalence of ChPV1, which was detected in 45 samples (28.6%). The ChPV2 genotype was detected in 13 samples (~8.3%). Therefore, significant differences in prevalence and genotype distributions were observed. On Serbian and Romanian farms, no significant differences were observed in the genotype prevalence of ChPVs. Molecular findings are consistent with ChPV prevalence, characterized by a territorial distribution similar to that of papillomaviruses in other mammalian species. Furthermore, this study showed that ddPCR is a very sensitive and accurate assay for ChPV detection and quantification. The ddPCR may be the molecular diagnostic tool of choice, ultimately providing useful insights into the molecular epidemiology and field surveillance of ChPV.
Comprehensive transcript-level analysis reveals transcriptional reprogramming during the progression of Alzheimer’s disease

Background Alzheimer’s disease (AD) is a common neurodegenerative disorder that has a multi-step disease progression. Differences between moderate and advanced stages of AD have not yet been fully characterized. Materials and methods Herein, we performed a transcript-resolution analysis in 454 AD-related samples, including 145 non-demented control, 140 asymptomatic AD (AsymAD), and 169 AD samples. We comparatively characterized the transcriptome dysregulation in AsymAD and AD samples at transcript level. Results We identified 4,056 and 1,200 differentially spliced alternative splicing events (ASEs) that might play roles in the disease progression of AsymAD and AD, respectively. Our further analysis revealed 287 and 222 isoform switching events in AsymAD and AD, respectively. In particular, a total of 163 and 119 transcripts showed increased usage, while 124 and 103 transcripts exhibited decreased usage in AsymAD and AD, respectively. For example, gene APOA2 showed no expression changes between AD and non-demented control samples, but expressed higher proportion of transcript ENST00000367990.3 and lower proportion of transcript ENST00000463812.1 in AD compared to non-demented control samples. Furthermore, we constructed RNA binding protein (RBP)-ASE regulatory networks to reveal potential RBP-mediated isoform switch in AsymAD and AD. Conclusion In summary, our study provided transcript-resolution insights into the transcriptome disturbance of AsymAD and AD, which will promote the discovery of early diagnosis biomarkers and the development of new therapeutic strategies for patients with AD.
High-quality genome assembly and multi-omics analysis of pigment synthesis pathway in Auricularia cornea

Owing to its great market potential for food and health care, white Auricularia cornea, a rare edible fungus, has received increased attention in recent years. This study presents a high-quality genome assembly of A. cornea and multi-omics analysis of its pigment synthesis pathway. Continuous Long Reads libraries, combined with Hi-C-assisted assembly were used to assemble of white A. cornea. Based on this data, we analyzed the transcriptome and metabolome of purple and white strains during the mycelium, primordium, and fruiting body stages. Finally, we obtained the genome of A.cornea assembled from 13 clusters. Comparative and evolutionary analysis suggests that A.cornea is more closely related to Auricularia subglabra than to Auricularia heimuer. The divergence of white/purple A.cornea occurred approximately 40,000 years ago, and there were numerous inversions and translocations between homologous regions of the two genomes. Purple strain synthesized pigment via the shikimate pathway. The pigment in the fruiting body of A. cornea was γ-glutaminyl-3,4-dihydroxy-benzoate. During pigment synthesis, α-D-glucose-1P, citrate, 2-Oxoglutarate, and glutamate were four important intermediate metabolites, whereas polyphenol oxidase and other 20 enzyme genes were the key enzymes. This study sheds light on the genetic blueprint and evolutionary history of the white A.cornea genome, revealing the mechanism of pigment synthesis in A.cornea. It has important theoretical and practical implications for understanding the evolution of basidiomycetes, molecular breeding of white A.cornea, and deciphering the genetic regulations of edible fungi. Additionally, it provides valuable insights for the study of phenotypic traits in other edible fungi.
Comprehensive bibliometric research in neuroscience: focusing on ophthalmology

Background This study aimed to comprehensively summarize the knowledge structure and research hotspots of ophthalmology in the field of neuroscience through bibliometric and visual analysis. Methods We searched the Web of Science Core Collection database for articles from 2002 to 2021 related to ophthalmology in the field of neuroscience. Using VOSviewer and CiteSpace, bibliometric analysis was conducted on the number of annual ophthalmology publications, authors, organizations, countries, journals, cited references, keywords, and burst keywords. Results A total of 9,179 articles were published from 34,073 authors, 4,987 organizations, and 87 countries. The cited references in these articles were published in 23,054 journals. Moreover, there were 30,864 keywords among the 9,179 articles. Notably, scholars have increasingly begun paying attention to ophthalmology in the field of neuroscience in the past 20 years. Claudio Babiloni published the most articles. The University of Washington had the greatest number of articles. The United States, Germany, and England led in the number of articles published. The Journal of Neuroscience was the most cited. The article with the highest outbreak intensity was an article published by Maurizio Corbetta in Nature Reviews Neuroscience in 2002 entitled “Control of goal-directed and stimulus-driven attention in the brain. ” The most important keyword was the brain, and the top burst keyword was functional connectivity. Conclusion This study visualized ophthalmology research in the field of neuroscience through bibliometric analysis and predicted potential research trends in future to help clinicians and basic researchers provide diversified perspectives and further carry out in-depth research on ophthalmology.
Exploring the selectivity and engineering potential of an NRPS condensation domain involved in the biosynthesis of the thermophilic siderophore fuscachelin

In nonribosomal peptide synthesis, condensation (C) domains are key catalytic domains that most commonly link carrier protein bound substrates to form peptides or depsipeptides. While adenylation domains have been well characterized due to their role in the selection of monomers and hence as gate keepers in nonribosomal peptide biosynthesis, C-domains have been the subject of debate as they do not have apparent “A-domain like” side chain selectivity for their acceptor substrates. To probe the selectivity and specificity of C-domains, here we report our biochemical and structural characterization of the C3-domain from the biosynthesis of the siderophore fusachelin. Our results show that this C-domain is not broadly flexible for monomers bearing significantly alternated side chains or backbones, which suggests there can be a need to consider C-domain specificity for acceptor substrates when undertaking NRPS engineering.
ChatGPT in society: emerging issues

We review and critically assess several issues arising from the potential -large-scale- implementation or deployment of Large Language Models (LLMs) in society. These include security, political, economic, cultural, and educational issues as well as issues concerning social biases, creativity, copyright, and freedom of speech. We argue, without a preconceived pessimism toward these tools, that they may bring about many benefits. However, we also call for a balance assessment of their downsides. While our work is only preliminary and certainly partial it nevertheless holds some value as one of the first exploratory attempts in the literature.
Electron beams near surfaces: the concept of partial intensities for surface analysis and perspective on the low energy regime

Electron beam techniques are indispensable tools for the analysis of surfaces in fundamental as well as applied fields of science and technology. Significant improvements have been made in the past decades in the quantitative understanding of electron spectra, particularly with respect to the near-surface transport of signal electrons. The concept of partial intensities is a simple approach providing physical insight into transport of electrons in solids, a numerically convenient means for spectrum modelling and an essential ingredient for spectrum interpretation. The energy-dissipation process of energetic electrons in solids is discussed from the perspective of the partial intensities, offering a unified model for any type of electron beam technique, be it in the quasi-elastic (QE) or the continuous slowing down (CSD) regime. Examples are given for modelling and analysis of electron spectra such as X-ray photoelectron spectra (XPS), Elastic peak electron spectra (EPES) and electron energy-loss spectra (EELS). The physical model as well as the quantities for electron beam interaction with solids are reviewed, and methods for spectrum modelling and analysis are presented. The examples considered demonstrate the high level of accuracy nowadays attainable for characterisation of surfaces and nanostructures employing techniques using medium energy electrons ( > 100 eV). This is in contrast to the low energy regime, where a number of problems prevent a similar level of understanding. The topic of low energy electrons (LEEs) is rapidly gaining importance since in this energy range the involved electrons not only act as signal carriers, but also actively participate in electrochemical processes of importance in fields ranging from nanotechnology to life sciences. Issues of future importance in the field of LEEs are discussed and recent developments such as the 2-dimensional electron cascade in the scanning field electron microscope are highlighted.
An overview of the material science and knowledge of nanomedicine, bioscaffolds, and tissue engineering for tendon restoration

Tendon wounds are a worldwide health issue affecting millions of people annually. Due to the characteristics of tendons, their natural restoration is a complicated and lengthy process. With the advancement of bioengineering, biomaterials, and cell biology, a new science, tissue engineering, has developed. In this field, numerous ways have been offered. As increasingly intricate and natural structures resembling tendons are produced, the results are encouraging. This study highlights the nature of the tendon and the standard cures that have thus far been utilized. Then, a comparison is made between the many tendon tissue engineering methodologies proposed to date, concentrating on the ingredients required to gain the structures that enable appropriate tendon renewal: cells, growth factors, scaffolds, and scaffold formation methods. The analysis of all these factors enables a global understanding of the impact of each component employed in tendon restoration, thereby shedding light on potential future approaches involving the creation of novel combinations of materials, cells, designs, and bioactive molecules for the restoration of a functional tendon.
Supporting employability through sport: what kind of training?

Training, as a core device in the projects that use sport to increase employability, is today a much-cited element in papers in the sector. However, there seems to be little research that specifically delves into training processes. This contribution analyses the state of the art on the subject, focusing on the characteristics of the training courses mentioned in literature, highlighting some recurring critical issues. A proposal, which considers the limitations discussed above, is formulated as a result of this analysis. More specifically, we introduce, as a contribution to the debate, a training model for team sports coaches developed within the EU Erasmus + sport project SBSMED. Theoretical assumptions, methodology, contents and assessment methods of training effectiveness will be explained, highlighting valuable elements and the open issues that emerge from this experience.
Proteome-wide comparison of tertiary protein structures reveals molecular mimicry in Plasmodium-human interactions

Introduction Molecular mimicry is a strategy used by parasites to evade the host’s immune system and facilitate transmission to a new host. To date, high-throughput examples of molecular mimicry have been limited to comparing protein sequences. However, recent advances in the prediction of tertiary structural models, led by Deepmind’s AlphaFold, enable the comparison of thousands of proteins from parasites and their hosts at the structural level, allowing for the identification of more mimics. Here, we present the first proteome-level search for tertiary structure similarity between proteins from Plasmodium falciparum, a malaria-causing parasite, and humans. Methods We assembled a database of experimentally-characterized protein tertiary structures (from the Protein Data Bank) and AlphaFold-generated protein tertiary structures from P. falciparum, human, and 15 negative control species, i.e., species not infected by P. falciparum. We aligned human and control structures to the parasite structures using Foldseek. Results We identified molecular mimicry in three proteins that have been previously proposed as mediators of Plasmodium-human interactions. By extending this approach to all P. falciparum proteins, we identified an additional 41 potential mimics that are supported by additional experimental data. Discussion Our findings demonstrate a valuable application of AlphaFold-derived tertiary structural models, and we discuss key considerations for its effective use in other host-parasite systems.
Isolation, identification, and antibacterial evaluation of endophytic fungi from Gannan navel orange

Gannan navel orange is a famous brand in China but the isolation of its endophytic fungi was rarely reported. In this study, a total of 54 strains of endophytic fungi were successfully isolated from the pulp, peel, twig, and leaf of Gannan navel orange; they were successfully identified to belong to 17 species of 12 genera. All these strains were fermented using potato-dextrose agar (PDA) medium, and their secondary metabolites were then extracted with ethyl acetate (EtOAc). The antibacterial assays of Escherichia coli (E. coli), methicillin-resistant Staphylococcus aureus (MRSA), and Xanthomonas citri subsp. citri (Xcc) were also performed for the EtOAc extracts of these strains. As a result, the extracts of both Geotrichum sp. (gc-1-127-30) and Diaporthe biconispora (gc-1-128-79) demonstrated significant antibacterial activities against Xcc, and the MIC value for the extract of Colletotrichum gloeosporioides against MRSA was low to 62.5 μg/mL. Moreover, the chemical components of the extracts of Colletotrichum sp. , Diaporthe biconispora, and Annulohypoxylon atroroseum were primarily investigated, and they successfully led to the isolation of 24 compounds involving a new botryane sesquiterpene. Among the isolated products, compound 2 showed significant inhibitory activities toward SA, MRSA, E. coli, and Xcc with MIC values of 12.5, 3.1, 125, and 12.5 μg/mL, respectively. This study revealed that the endophytic fungi of Gannan navel orange showed high potency to produce secondary metabolites with significant antibacterial effects.
Phylogenomics of Lasiodoriforms: reclassification of the South American genus Vitalius Lucas, Silva and Bertani and allied genera (Araneae: Theraphosidae)

Theraphosinae is the most diverse subfamily of Theraphosidae spiders, but their evolutionary history remains unresolved to date. This problem is common in taxonomic groups with phylogenetic hypotheses that have often been based only on qualitative morphological characters and, rarely, on molecular analyses. Phylogenomics has significantly contributed to the understanding of the evolution of many non-model groups, such as spiders. Herein, we employed ultraconserved elements (UCEs) phylogenomics to propose a new hypothesis for a group of Theraphosinae genera, namely Lasiodoriforms: Vitalius, Lasiodora, Eupalaestrus, Pterinopelma, Proshapalopus, and Nhandu. We propose three genera and their respective morphological diagnoses are provided. Our phylogeny supports the transfer of species from the genus Vitalius to Pterinopelma and Proshapalopus and from Proshapalopus to Eupalaestrus. Finally, we describe a new species of Vitalius from Southern Brazil. Based on these three new generic descriptions and transferred species, the Lasiodoriform tarantulas comprise nine genera from Argentina, Brazil, Paraguay, and Uruguay, and the genus Vitalius now includes seven species.
Improving nutrition-sensitive value chains of African indigenous vegetables: current trends in postharvest management and processing

The value chains of African indigenous vegetables (AIVs) are highly constrained by high postharvest losses (up to 50%) along the chain, largely occasioned by poor postharvest management and a lack of optimized processing technologies. The technologies and practices are key technical aspects that can transform the capacity of the chain by enhancing the overall value generated from the system. AIVs have recently experienced an increase in demand due to their high nutritional value and the opportunity they present to enhance rural incomes, since they are predominantly produced by smallholder farmers in rural and peri-urban areas. This implies that they can positively contribute to increased availability and hence supply of nutritious food within local food systems. Furthermore, the fact that half of the economic value of AIVs is potentially lost due to inappropriate postharvest management and inadequate processing demonstrates the potential that related interventions and transformations could have in enhancing and preserving value along AIV value chains. Currently, the approaches applied to reduce food waste, preserve nutritional quality, and add value to AIVs are largely traditional in nature. They require upgrading and need to be aligned toward achieving a nutrition-sensitive value chain. By looking at these as value creation processes, this mini-review examines the current postharvest management practices, highlights relevant new and innovative technologies and related challenges, and suggests potential options to improve the benefits for AIV value chain actors and thus contribute to a sustainable transformation of nutrition-sensitive food systems.
Improvement of the NCEP Global Model over the Tropics: An Evaluation of Model Performance during the 1995 Hurricane Season

Abstract An evaluation of the performance of the National Centers for Environmental Prediction Medium-Range Forecast Model was made for the large-scale tropical forecasts and hurricane track forecasts during the 1995 hurricane season. The assessment of the model was based on changes to the deep convection and planetary boundary layer parameterizations to determine their impact on some of the model deficiencies identified during previous hurricane seasons. Some of the deficiencies in the hurricane forecasts included a weakening of the storm circulation with time that seriously degraded the track forecasts. In the larger-scale forecasts, an upper-level easterly wind bias was identified in association with the failure of the model to maintain the midoceanic upper-tropical upper-tropospheric trough. An overall modest improvement is shown in the large-scale upper-level tropical winds from root-mean-square-error calculations. Within a diagnostic framework, an improved simulation of the midoceanic tropical troug.
Lanatoside C decelerates proliferation and induces apoptosis through inhibition of STAT3 and ROS-mediated mitochondrial membrane potential transformation in cholangiocarcinoma

Introduction: The incidence of cholangiocarcinoma (CCA) has increased worldwide in recent years. Given the poor prognosis associated with the current management approach of CCA, new therapeutic agents are warranted to improve the prognosis of this patient population. Methods: In this study, we extracted five cardiac glycosides (CGs) from natural plants: digoxin, lanatoside A, lanatoside C, lanatoside B, and gitoxin. Follow-up experiments were performed to assess the effect of these five extracts on cholangiocarcinoma cells and compounds with the best efficacy were selected. Lanatoside C (Lan C) was selected as the most potent natural extract for subsequent experiments. We explored the potential mechanism underlying the anticancer activity of Lan C on cholangiocarcinoma cells by flow cytometry, western blot, immunofluorescence, transcriptomics sequencing, network pharmacology and in vivo experiments. Results: We found that Lan C time-dependently inhibited the growth and induced apoptosis of HuCCT-1 and TFK-1 cholangiocarcinoma cells. Besides Lan C increased the reactive oxygen species (ROS) content in cholangiocarcinoma cells, decreased the mitochondrial membrane potential (MMP) and resulted in apoptosis. Besides, Lan C downregulated the protein expression of STAT3, leading to decreased expression of Bcl-2 and Bcl-xl, increased expression of Bax, activation of caspase-3, and initiation of apoptosis. N-acetyl-L-cysteine (NAC) pretreatment reversed the effect of Lan C. In vivo, we found that Lan C inhibited the growth of cholangiocarcinoma xenografts without toxic effects on normal cells. Tumor immunohistochemistry showed that nude mice transplanted with human cholangiocarcinoma cells treated with Lan C exhibited decreased STAT3 expression and increased caspase-9 and caspase-3 expression in tumors, consistent with the in vitro results. Conclusion: In summary, our results substantiates that cardiac glycosides have strong anti-CCA effects. Interestingly the biological activity of Lan C provides a new anticancer candidate for the treatment of cholangiocarcinoma.
Allocation concealment appraisal of clinical therapy trials using the extended Composite Quality Score (CQS-2)—An empirically based update

Objectives The objective of this study was to revise CQS-2/Criterion II concerning allocation concealment appraisal for prospective, controlled clinical therapy trials. Methods Meta-analyses of trials with inadequate allocation concealment were tested for in-between trial heterogeneity (I2 > 0) due to imbalances in baseline variables. Meta-analyses with positive test results were used as a basis to deduce criteria for adequate allocation concealment. The CQS-2/Criterion II was reformulated in line with the findings. Result One suitable meta-analysis was identified. Two forest plots with data from five and four trials with inadequate/unclear allocation concealment were selected for testing. In addition, a total of five trials with adequate allocation concealment were identified. The meta-analysis test results were positive, and keywords for the judgment of adequate allocation concealment were extracted verbatim from the text of the meta-analysis. The extracted keywords indicated “central allocation” as the main criterion for adequate allocation concealment. Criterion II of the CQS-2 was revised accordingly. Conclusion Criterion II of the CQS-2 trial appraisal tool was revised. The revised appraisal tool was specified as version CQS-2B.