Miracle-dz/UniFAR-FTUs huggingface dataset:
Fungi Occurrence in Ready-to-Eat Hazelnuts (Corylus avellana) From Different Boreal Hemisphere Areas

The present study evaluated the fungal contamination of ready-to-eat dried hazelnuts considering for the first time the application of the same condition drying process of several hazelnut cultivars from different boreal hemisphere areas. Fifty lots of hazelnuts (Corylus avellana), belonging to eight cultivars from seven regions in four countries, were analyzed for fungal microbiota, describing both load levels and species diversity. For this purpose, a polyphasic approach consisting of morphological examination (optical and scanning electron microscope observation) and molecular characterization [PCR-DGGE analysis and sequence analyses of the internal transcribed spacer (ITS)] was performed. The results show that different fungal populations occur in dried hazelnuts regardless of their geographical area of production. Although some varieties appear to be relatively less susceptible, species related to Aspergillus, such as A. commune and A. ochraceus, Penicillium, including P. commune, P. solitum, and P. expansum, and Rhizopus, for instance, R. stolonifer and R. oryzae, have generally been found. A related character “hazelnut cultivar—fungi” was found for species related to the genera Trichoderma and Fusarium, including F. oxyxporum, F. solani, and F. falciforme. All 14 species found are known to host pathogenic strains. Therefore, their presence in a ready-to-eat product, such as dried hazelnuts, can pose a real danger to the consumer. Based on these considerations, the development of new protective strategies seems highly desirable. The species-level description of the contaminating fungal community acquired through this study is the starting point for the development of tailor-made protective biotechnologies.
Impact of Pre-operative Embolization With Onyx for Brain Arteriovenous Malformation Surgery

Objective To clarify the safety and efficacy of pre-operative embolization using Onyx liquid embolic agent (Onyx; ev3) compared with N-butyl cyanoacrylate (NBCA; Cordis Neurovascular, Inc.) or coils in cerebral arteriovenous malformation (AVM) surgery. Methods This was a retrospective review of a prospectively collected clinical database of brain AVMs treated at our institute from January 2005 to March 2021. A total of 38 consecutive patients who underwent AVM resection after pre-operative embolization were included. Based on pre-operative embolization materials, the patients were divided into the pre-Onyx group (n = 16), in which NBCA or coils were used for embolization, and the Onyx group (n = 22). Patient characteristics and treatment results were compared between the two groups. Results Patient characteristics were comparable between the two groups in terms of age, sex, and rupture status. While the Spetzler–Martin grade was also similar between the two groups, the location of the AVM nidus in the eloquent area was slightly higher in patients in the Onyx group (72.7%) than in patients in the pre-Onyx group (43.8%) (P = 0.09). The embolization rate was higher in the pre-Onyx group (mean: 63.0%; range: 12.7–100%) than in the Onyx group (mean: 50.0%; range: 15.8–100%), but the difference was not statistically significant (P = 0.06). The time needed for surgical removal was shorter in the Onyx group (mean: 354.8 min; range: 144–884 min) than in the pre-Onyx group (mean: 457.9 min; range: 240–1,294 min); however, this difference was not statistically significant (P = 0.13). The amount of intraoperative bleeding was significantly lower in the Onyx group (mean: 129.8 ml; range: 20–540 mL) than in the pre-Onyx group (mean: 448.8 mL; range: 120–1,550 ml) (P = 0.0008). The surgical complication rates were comparable between the two groups (pre-Onyx group, 18.8%; Onyx group, 4.5%; P = 0.29). Conclusions Pre-operative embolization with Onyx can significantly reduce the amount of intraoperative bleeding in AVM resection and may contribute to safe AVM surgery.
Fluorescent Microscopy-Based Detection of Chitin in Intact Drosophila melanogaster

Chitin is the major scaffolding component of the insect cuticle. Ultrastructural analyses revealed that chitin adopts a quasi-crystalline structure building sheets of parallel running microfibrils. These sheets called laminae are stacked either helicoidally or with a preferred orientation of the microfibrils. Precise control of chitin synthesis is mandatory to ensure the correct chitin assembly and in turn proper function of cuticular structures. Thus, evaluation of chitin-metabolism deficient phenotypes is a key to our understanding of the function of the proteins and enzymes involved in cuticle architecture and more generally in cuticle biology in insects. Usually, these phenotypes have been assessed using electron microscopy, which is time-consuming and labor intensive. This stresses the need for rapid and straightforward histological methods to visualize chitin at the whole tissue level. Here, we propose a simple method of chitin staining using the common polysaccharide marker Fluorescent brightener 28 (FB28) in whole-mount Drosophila melanogaster. To overcome the physical barrier of FB28 penetration into the cuticle, staining is performed at 65°C without affecting intactness. We quantify FB28 fluorescence in three functionally different cuticular structures namely wings, dorsal abdomens and forelegs by fluorescence microscopy. We find that, as expected, cuticle pigmentation may interfere with FB28 staining. Down-regulation of critical genes involved in chitin metabolism, including those coding for chitin synthase or chitinases, show that FB28 fluorescence reflects chitin content in these organs. We think that this simple method could be easily applied to a large variety of intact insects.
Quantifying Iron Oxide Mineral Contents in Miocene Oceanic Red Beds for the Deep-Sea Oxidation Evolution in the South China Sea

The International Ocean Discovery Program (IODP) Expedition 349 recovered Miocene oceanic red beds overlying the basaltic basement in the South China Sea. The occurrence of oceanic red beds provides an opportunity to understand the deep-sea redox conditions when the South China Sea was open to the western Pacific during the Miocene. Here, we investigated iron oxide mineral contents along with major element compositions of the oceanic red beds at Site U1433 to reveal the Miocene deep-sea oxidation environment of the South China Sea and its interaction with the western Pacific. The results show that these samples contain 0.20–1.48% hematite (average 0.50%) and 0.30–2.98% goethite (average 1.20%). Their contents have good linear correlations with color reflectance a* (red) and b* (yellow), respectively, implying that the reddish-brown color of the Miocene oceanic red beds resulted from a mixture of hematite and goethite. Compared to other oceanic red beds worldwide, the occurrence of hematite and goethite in the South China Sea is considered to form under an oxic bottom water environment with an extremely low sedimentation rate. The (hematite + goethite)/(100%—Al2O3) ratio is adopted to reconstruct the evolution of bottom water oxidation during the Early–Middle Miocene. A continuously decreased oxidation trend from 18.4 to 11.6 Ma, along with two strengthened oxidation events occurring at around 15 Ma and 14 Ma, is observed to dominate the environment evolution of the abyssal South China Sea. We infer that this long-term decreased oxidation trend was caused by the gradual blocking of oxygen-rich bottom water from the western Pacific since the Early Miocene, while the two oxidation events were likely attributed to the rapid thermal subsidence of the South China Sea and the global cooling during the Middle Miocene climate transition, respectively.
The Beneficial Effect of Pollen on Varroa Infested Bees Depends on Its Influence on Behavioral Maturation Genes

Honey bees collect nectar and pollen to fulfill their nutritional demands. In particular, pollen can influence longevity, the development of hypopharyngeal glands, and immune-competence of bees. Pollen can also mitigate the deleterious effects caused by the parasitic mite Varroa destructor and related deformed wing virus (DWV) infections. It has been shown that V. destructor accelerates the physiological and behavioral maturation of honey bees by influencing the interaction between two core physiological factors, Vitellogenin and juvenile hormone. In this study, we test the hypothesis that the beneficial effects of pollen on Varroa-infested bees are related to the hormonal control underpinning behavioral maturation. By analyzing the expression of genes associated to behavioral maturation in pollen-fed mite-infested bees, we show that treatment with pollen increases the lifespan of mite-infested bees by reversing the faster maturation induced by the parasite at the gene expression level. As expected, from the different immune-competence of nurse and forager bees, the lifespan extension triggered by pollen is also correlated with a positive influence of antimicrobial peptide gene expression and DWV load, further reinforcing the beneficial effect of pollen. This study lay the groundwork for future analyses of the underlying evolutionary processes and applications to improve bee health.
Virulence and Host Range of Fungi Associated With the Invasive Plant Ageratina adenophora

To determine whether disease-mediated invasion of exotic plants can occur and whether this increases the risk of disease transmission in local ecosystems, it is necessary to characterize the species composition and host range of pathogens accumulated in invasive plants. In this study, we found that Didymellaceae, a family containing economically important plant fungal pathogens, is commonly associated with the invasive plant Ageratina adenophora. Accordingly, we characterized its phylogenetic position through multi-locus phylogenetic analysis, as well as its environmental distribution, virulence, and host range. The results indicated that 213 fungal collections were from 11 genera in Didymellaceae, ten of which are known, and one is potentially new. Didymella, Epicoccum, Remotididymella, and Mesophoma were the dominant genera, accounting for 93% of total isolates. The virulence and host ranges of these fungi were related to their phylogenetic relationship. Boeremia exigua, Epicoccum latusicollum, and E. sorghinum were found to be strongly virulent toward all tested native plants as well as toward A. adenophora; M. speciosa and M. ageratinae were weakly virulent toward native plants but strongly virulent toward A. adenophora, thus displaying a narrow host range. Co-evolution analysis showed no strong phylogenetical signal between Didymellaceae and host plants. Isolates S188 and Y122 (belonging to M. speciosa and M. ageratinae, respectively) showed strong virulence toward A. adenophora relative to native plants, highlighting their potential as biocontrol agents for A. adenophora invasion. This study provides new insights into the understanding of the long-term ecological consequences of disease transmission driven by plant invasion.
MIMIC-SBDH: A Dataset for Social and Behavioral Determinants of Health

Social and Behavioral Determinants of Health (SBDHs) are environmental and behavioral factors that have a profound impact on health and related outcomes. Given their importance, physicians document SBDHs of their patients in Electronic Health Records (EHRs). However, SBDHs are mostly documented in unstructured EHR notes. Determining the status of the SBDHs requires manually reviewing the notes which can be a tedious process. Therefore, there is a need to automate identifying the patients' SBDH status in EHR notes. In this work, we created MIMIC-SBDH, the first publicly available dataset of EHR notes annotated for patients' SBDH status. Specifically, we annotated 7,025 discharge summary notes for the status of 7 SBDHs as well as marked SBDH-related keywords. Using this annotated data for training and evaluation, we evaluated the performance of three machine learning models (Random Forest, XGBoost, and Bio-ClinicalBERT) on the task of identifying SBDH status in EHR notes. The performance ranged from the lowest 0.69 F1 score for Drug Use to the highest 0.96 F1 score for Community-Present. In addition to standard evaluation metrics such as the F1 score, we evaluated four capabilities that a model must possess to perform well on the task using the CheckList tool (Ribeiro et al., 2020). The results revealed several shortcomings of the models. Our results highlighted the need to perform more capability-centric evaluations in addition to standard metric comparisons.
A Detailed Review Investigating the Mathematical Modeling of Solar Stills

In recent years providing potable water for humans has become a major problem, especially in rural and remote regions. In the last few decades, methods of providing potable water using solar radiation have proved that there are methods without negative impacts. Solar is a solution and attractive alternative to still non-potable water without adverse consequences on ecosystems. Researchers have presented the results of their investigations in journals, using experimental, numerical, and analytical forms through the study of solar still performance in native climatic conditions. This paper undertakes an extensive review of recent modeling processes in solar stills and the thermal models proposed and derived for different types of solar stills and the modifications recommended to enhance efficiency and performance. During the selection of appropriate geometry and belonging components, this evaluation demonstrates that numerous designs and characteristics are useful in terms of productivity and efficiency. According to the reviewed results, the definition of concentration ratio is a fundamental concept for evaluating the evaporative heat transfer coefficient in relation to the convective heat transfer coefficient. Employing phase change materials, the results reveal that a large mass of PCM produces less solar still productivity, whereas increasing the PCM to water mass ratio from 10 to 100 reduces productivity by up to 30%. Using a parabolic concentrator, results show that productivity can be increased by 56 and 38.5% in the winter and summer, respectively.
Optimisation and Application of a Novel Method to Identify Bacteriophages in Maternal Milk and Infant Stool Identifies Host-Phage Communities Within Preterm Infant Gut

Human milk oligosaccharides, proteins, such as lactoferrin, and bacteria represent just some of the bioactive components of mother's breast milk (BM). Bacteriophages (viruses that infect bacteria) are an often-overlooked component of BM that can cause major changes in microbial composition and metabolism. BM bacteriophage composition has been explored in term and healthy infants, suggesting vertical transmission of bacteriophages occurs between mothers and their infants. Several important differences between term and very preterm infants (<30 weeks gestational age) may limit this phenomenon in the latter. To better understand the link between BM bacteriophages and gut microbiomes of very preterm infants in health and disease, standardised protocols are required for isolation and characterisation from BM. In this study, we use isolated nucleic acid content, bacteriophage richness and Shannon diversity to validate several parameters applicable during bacteriophage isolation from precious BM samples. Parameters validated include sample volume required; centrifugal sedimentation of microbes; hydrolysis of milk samples with digestive enzymes; induction of temperate bacteriophages and concentration/purification of isolated bacteriophage particles in donor milk (DM). Our optimised method enables characterisation of bacteriophages from as little as 0.1 mL BM. We identify viral families that were exclusively identified with the inclusion of induction of temperate bacteriophages (Inoviridae) and hydrolysis of milk lipid processes (Iridoviridae and Baculoviridae). Once applied to a small clinical cohort we demonstrate the vertical transmission of bacteriophages from mothers BM to the gut of very preterm infants at the species level. This optimised method will enable future research characterising the bacteriophage composition of BM in very preterm infants to determine their clinical relevance in the development of a healthy preterm infant gut microbiome.
Insights Into Persistent HIV-1 Infection and Functional Cure: Novel Capabilities and Strategies

Although HIV-1 replication can be efficiently suppressed to undetectable levels in peripheral blood by combination antiretroviral therapy (cART), lifelong medication is still required in people living with HIV (PLWH). Life expectancies have been extended by cART, but age-related comorbidities have increased which are associated with heavy physiological and economic burdens on PLWH. The obstacle to a functional HIV cure can be ascribed to the formation of latent reservoir establishment at the time of acute infection that persists during cART. Recent studies suggest that some HIV reservoirs are established in the early acute stages of HIV infection within multiple immune cells that are gradually shaped by various host and viral mechanisms and may undergo clonal expansion. Early cART initiation has been shown to reduce the reservoir size in HIV-infected individuals. Memory CD4+ T cell subsets are regarded as the predominant cellular compartment of the HIV reservoir, but monocytes and derivative macrophages or dendritic cells also play a role in the persistent virus infection. HIV latency is regulated at multiple molecular levels in transcriptional and post-transcriptional processes. Epigenetic regulation of the proviral promoter can profoundly regulate the viral transcription. In addition, transcriptional elongation, RNA splicing, and nuclear export pathways are also involved in maintaining HIV latency. Although most proviruses contain large internal deletions, some defective proviruses may induce immune activation by expressing viral proteins or producing replication-defective viral-like particles. In this review article, we discuss the state of the art on mechanisms of virus persistence in the periphery and tissue and summarize interdisciplinary approaches toward a functional HIV cure, including novel capabilities and strategies to measure and eliminate the infected reservoirs and induce immune control.
Identifying Pupylation Proteins and Sites by Incorporating Multiple Methods

Pupylation is an important posttranslational modification in proteins and plays a key role in the cell function of microorganisms; an accurate prediction of pupylation proteins and specified sites is of great significance for the study of basic biological processes and development of related drugs since it would greatly save experimental costs and improve work efficiency. In this work, we first constructed a model for identifying pupylation proteins. To improve the pupylation protein prediction model, the KNN scoring matrix model based on functional domain GO annotation and the Word Embedding model were used to extract the features and Random Under-sampling (RUS) and Synthetic Minority Over-sampling Technique (SMOTE) were applied to balance the dataset. Finally, the balanced data sets were input into Extreme Gradient Boosting (XGBoost). The performance of 10-fold cross-validation shows that accuracy (ACC), Matthew’s correlation coefficient (MCC), and area under the ROC curve (AUC) are 95.23%, 0.8100, and 0.9864, respectively. For the pupylation site prediction model, six feature extraction codes (i.e., TPC, AAI, One-hot, PseAAC, CKSAAP, and Word Embedding) served to extract protein sequence features, and the chi-square test was employed for feature selection. Rigorous 10-fold cross-validations indicated that the accuracies are very high and outperformed its existing counterparts. Finally, for the convenience of researchers, PUP-PS-Fuse has been established at https://bioinfo.jcu. edu.cn/PUP-PS-Fuse and http://121.36. 221.79/PUP-PS-Fuse/as a backup.
Capturing the Formation and Regulation of Emotions in Collaborative Learning: The FRECL Coding Procedure

Despite recent increases in research on emotions and regulation in collaborative learning, measuring both constructs remains challenging and often lacks structure. Researchers need a systematic method to measure both the formation of emotions and subsequent regulation in collaborative learning environments. Drawing from the Formation and Regulation of Emotions in Collaborative Learning (FRECL) model, I introduce a new observational coding procedure that provides comprehensive guidelines for coding these phenomena. The FRECL coding procedure has been implemented successfully in other studies and is described here in detail. Specifically, I detail the ideal situations for using the procedure, discuss background information and present a codebook and empirical examples for each stage of the FRECL model, and provide additional considerations that allow researchers flexibility based on their own experiences and preferences. This procedure extends past research by providing an accessible observational protocol that is both systematic and comprehensive. The FRECL coding procedure can benefit future research by providing more organized consistency to the measurement of collaborative emotions and regulation.
Food-Level Analysis to Identify Dietary Choices With the Highest Nutritional Quality and Lowest Greenhouse Gas Emissions and Price

Introduction Food systems are challenged to provide healthy, sustainable and affordable foods. From a consumer perspective, identifying healthy, sustainable and affordable choices based on individual food products rather than diets could promote better shopping choices. Objective To identify foods and drinks with the highest nutritional quality and lowest greenhouse gas emissions (GHGE) and price. We also assessed how a combination of these indicators (e.g., nutritional quality, GHGE and price) for food categories aligned with current United Kingdom dietary recommendations. Materials and Methods We performed a secondary analysis of the National Diet and Nutrition Survey (NDNS) nutrient databank year 11 (2018/2019). Spearman correlation coefficients were used to assess the strength of relationships between nutritional quality, environmental impact and/or prices per 100 kcal. In addition, we developed an optimized nutritional quality, GHGE and price score for each food or drink item based on the overall medians for each of these indicators. Results Median nutritional value was highest for fruit and vegetables, whilst median GHGE and price was lower for starchy carbohydrates, fats and items of which consumption should be limited. The relative proportions of foods considered the most nutritious and with a low GHGE and price in each of the food categories, on a per 100 kcal basis, were comparable to the proportions in the Eatwell Guide, except for the proportion of fruits and vegetables being smaller and the proportion of potatoes, bread, rice, pasta, and other starchy carbohydrates being larger in our analysis. Conclusion Public health efforts should consider the impact of dietary choices not only in terms of nutritional quality but also in terms of environmental and economic impact. Our food-based analysis shows a large variation in nutritional quality, GHGE and price within and across food categories, which provides consumers with opportunities for “food swaps” that are more nutritious and have lower GHGE and price.