Miracle-dz/UniFAR-FTUs huggingface dataset:
Perspectives of using Illumina MiSeq for identification of arbuscular mycorrhizal fungi

Arbuscular mycorrhiza fungi (AMF) form one of the most common symbiosis with the majority of land plants. AMF supply the plant with various mineral elements, primarily phosphorus, and improve the water supply. The search for the most effective AMF strains for symbiosis and the creation of microbial preparations on that basis is an important task for modern biology. Owing to the difficulties of cultivation without a host plant and their high genetic polymorphism, identifying AMF is very difficult. A high number of cryptic species often makes morphological identification unreliable. Recent years have seen a growth in the number of AMF biodiversity studies performed by modern NGS-based methods, Illumina MiSeq in particular. Currently, there are still many questions that remain for the identification of AМF. The most important are whether conservative or variable sequences should be used to select a marker for barcoding and whether universal primers or those specific to AMF should be used. In our work, we have successfully used universal primers ITS3 and ITS4 for the sequencing in Illumina MiSeq of the 5.8S rDNA – ITS2 region of the 35S rRNA genes, which contain both a conservative and variable regions. The molecular genetic approach for AMF identification was quite effective and allowed us to reliably identify eight of nine isolates to the species level: five isolates of Rhizophagus irregularis, and one isolate of R. invermaius, Paraglomus laccatum, and Claroideoglomus etunicatum, respectively. For all five R. irregularis isolates, high variability in the ITS region and the absence of ecotopic-related molecular characters in the ITS2 region were demonstrated. The NCBI data is still insufficient for accurate AMF identification of Acaulospora sp. isolates from the genus to the species level.
Inflammatory Microenvironment and Specific T Cells in Myeloproliferative Neoplasms: Immunopathogenesis and Novel Immunotherapies

The Philadelphia-negative myeloproliferative neoplasms (MPNs) are malignancies of the hematopoietic stem cell (HSC) arising as a consequence of clonal proliferation driven by somatically acquired driver mutations in discrete genes (JAK2, CALR, MPL). In recent years, along with the advances in molecular characterization, the role of immune dysregulation has been achieving increasing relevance in the pathogenesis and evolution of MPNs. In particular, a growing number of studies have shown that MPNs are often associated with detrimental cytokine milieu, expansion of the monocyte/macrophage compartment and myeloid-derived suppressor cells, as well as altered functions of T cells, dendritic cells and NK cells. Moreover, akin to solid tumors and other hematological malignancies, MPNs are able to evade T cell immune surveillance by engaging the PD-1/PD-L1 axis, whose pharmacological blockade with checkpoint inhibitors can successfully restore effective antitumor responses. A further interesting cue is provided by the recent discovery of the high immunogenic potential of JAK2V617F and CALR exon 9 mutations, that could be harnessed as intriguing targets for innovative adoptive immunotherapies. This review focuses on the recent insights in the immunological dysfunctions contributing to the pathogenesis of MPNs and outlines the potential impact of related immunotherapeutic approaches.
Further Insights on the Migration Biology of Monarch Butterflies, Danaus plexippus (Lepidoptera: Nymphalidae) from the Pacific Northwest

Simple Summary Monarch butterflies, Danaus plexippus, are known the world over for their iconic long-distance migration from the eastern United States and Canada to Mexico for overwintering. In this study, we shed more light on the less well-known migration of monarchs in the Pacific Northwest of North America. Utilizing the efforts of citizen scientists who captive-reared monarchs and tagged them, we confirmed that the majority of monarchs in Washington and Oregon migrate hundreds of kilometers south during late July–October to overwinter at sites on the California coast. However, some eastern Washington and most Idaho monarchs tended to migrate towards the southeast and may have an alternative winter destination, possibly Mexico. Overwintering monarchs in coastal California remain at sites for 2–3 months and can live for up to ten months. A small number of fall migrants may eschew overwintering and join winter-breeding populations in inland central and southern California. Wildfire smoke and infection with a protozoan parasite does not appear to greatly interfere with the survival and migration success of migrating monarch. Our data improve our understanding of western monarch migration, serving as a basis for further studies and providing information for conservation planning. Abstract The fall migration of monarch butterflies, Danaus plexippus (L.), in the Pacific Northwest was studied during 2017–2019 by tagging 14,040 captive-reared and 450 wild monarchs. One hundred and twenty-two captive-reared monarchs (0.87%) were recovered at distances averaging 899.9 ± 98.6 km for Washington-released and 630.5 ± 19.9 km for Oregon-released monarchs. The greatest straight-line release to recovery distance was 1392.1 km. A mean travel rate of 20.7 ± 2.2 km/day and maximum travel of 46.1 km/day were recorded. Recovery rates were greater for Oregon-released monarchs (0.92%) than Washington-released (0.34%) or Idaho-released monarchs (0.30%). Most monarchs (106/122) were recovered SSW-S-SSE in California, with 82 at 18 coastal overwintering sites. Two migrants from Oregon were recovered just weeks after release ovipositing in Santa Barbara and Palo Alto, CA. Two migrants released in central Washington recovered up to 360.0 km to the SE, and recoveries from Idaho releases to the S and SE suggests that some Pacific Northwest migrants fly to an alternative overwintering destination. Monarchs released in southern Oregon into smoky, poor quality air appeared to be as successful at reaching overwintering sites and apparently lived just as long as monarchs released into non-smoky, good quality air. Migration and lifespan for monarchs infected with the protozoan parasite, Ophryocystis elektroscirrha (McLaughlin and Myers), appeared to be similar to the migration and survival of uninfected monarchs, although data are limited. Our data improve our understanding of western monarch migration, serving as a basis for further studies and providing information for conservation planning.
Secondary Caries Adjacent to Bulk or Incrementally Filled Composites Placed after Selective Excavation In Vitro

Objectives: selective caries excavation (SE) is recommended for deep carious lesions. Bulk fill composites (BF) may be considered to restore SE-cavities. We compared the susceptibility for secondary caries adjacent to BF versus incrementally filled composites (IF) in SE and non-selectively excavated teeth (NS) in vitro. Methods: in 72 extracted human premolars, artificial caries lesions were induced on pulpo-axial walls of standardized cavities. The lesions were left (SE) or removed (NS), and teeth were restored using two BF, GrandioSO x-tra/Voco (BF-Gra) and SDR/Dentsply (BF-SDR), and an IF, GrandioSO/Voco (IF-Gra) (n = 12/group for SE and NS). After thermo-mechanical cycling (5–55 °C, 8 days), teeth were submitted to a continuous-culture Lactobacillus rhamnosus biofilm model with cyclic loading for 10 days. Mineral loss (ΔZ) of enamel surface lesions (ESL), dentin surface lesions (DSL), and dentin wall lesions (DWL) was analyzed using transversal microradiography. Results: ΔZ was the highest in DSL, followed by ESL, and it was significantly lower in DWL. There were no significant differences in ΔZ between groups in DSL, ESL, and DWL (p > 0.05). Regardless of lesion location, ΔZ did not differ between SE and NS (p > 0.05). Conclusions: BF and IF both showed low risks for DWL (i.e., true secondary caries) after SE in vitro, and surface lesion risk was also not significantly different between materials. SE did not increase secondary caries risk as compared with NS. Clinical Significance: the risk of secondary caries was low after selective excavation in this study, regardless of whether bulk or incrementally filled composites were used
A general purpose package (MADFOMS) for predicting the morphologies and powder X-ray diffraction patterns of molecular crystals

We present a generalised procedure for predicting the morphologies and diffraction patterns of molecular crystals. The general purpose program MADFOMSs (Morphologies and Diffraction For Organic Molecular Solids) is described. The success of the approach is illustrated by application to the polymorphs of 5-methyl-2-[(2-nitrophenyl)amino]-3-thiophenecarbonitrile.
Immunocastration in Gilts: A Preliminary Study of the Effect of the Second Dose Administration Time on Growth, Reproductive Tract Development, and Carcass and Meat Quality

Simple Summary Nowadays, a significant proportion of pig carcasses destined to high-quality dry-cured ham elaboration are declared unsuitable for this purpose. The main reason is the lack of backfat thickness, affecting females in particular because males are castrated. Moreover, the estrus in gilts is undesirable because it carries out productive losses. Immunocastration could resolve these problems. The protocol of immunocastration in white-breed gilts is not well established, especially in terms of the second injection. Therefore, the objective of the current trial was to evaluate the impact of immunocastration and to determine the optimum time for the second dose application in gilts intended for dry-cured ham production. In this trial, we concluded that gilt immunocastration is positive, increasing carcass fatness and decreasing reproductive tract development. Moreover, the optimum time to administer the second dose of immunocastration for this type of gilt seems to be between 9 and 12 weeks before sacrifice. Abstract Increasing fatness and avoiding puberty are desirable in gilts intended for high-quality dry-cured ham production. A total of 48 Duroc x (Landrace x Large White) females of 26.5 ± 3.70 kg body weight (BW) were used to evaluate the impact of immunocastration and to find the optimum application time of the second dose for immunocastration on growth; sex hormones; reproductive tract development; and carcass, meat, and fat quality. Gilts were allocated to four experimental treatments (n = 12): control (entire gilts, EG) and immunocastrated gilts (IG), providing the second dose at 12, 9, or 7 weeks before slaughter (with approximately 60, 75, or 90 kg BW, respectively). Mean slaughter BW was 125 kg. Immunocastrated gilts had lighter reproductive tracts and greater fat thickness than EG. Fat from IG was more saturated and less polyunsaturated than that from EG. Numerically, gilts immunocastrated 9 and 12 weeks before slaughter presented higher fatness than those immunocastrated 7 weeks before slaughter. In conclusion, immunocastration is a good strategy to improve the fatness of gilts destined to dry-cured ham elaboration, with the optimum time for the second dose application seemingly between 9 and 12 weeks before slaughter.
Metabolomics of Pigmented Rice Coproducts Applying Conventional or Deep Eutectic Extraction Solvents Reveal a Potential Antioxidant Source for Human Nutrition

Rice bran (RB) corresponds to the outer layers of whole grain rice and contains several phenolic compounds (PCs) that make it an interesting functional food ingredient. PC richness is enhanced in pigmented RB varieties and requires effective ways of extraction of these compounds. Therefore, we investigated conventional and deep eutectic solvents (DES) extraction methods to recover a wide array of PCs from red and black RB. The RB were extracted with ethanol/water (60:40, v/v) and two DES (choline chloride/1.2-propanediol/water, 1:1:1 and choline chloride/lactic acid, 1:10, mole ratios), based on Generally Recognized as Safe (GRAS) components. Besides the quantification of the most typical phenolic acids of cereals, nontargeted metabolomic approaches were applied to PCs profiling in the extracts. Globally, metabolomics revealed 89 PCs belonging to flavonoids (52%), phenolic acids (33%), other polyphenols (8%), lignans (6%) and stilbenes (1%) classes. All extracts, whatever the solvents, were highly concentrated in the main phenolic acids found in cereals (37–66 mg/100 g in black RB extracts vs. 6–20 mg/100 g in red RB extracts). However, the PC profile was highly dependent on the extraction solvent and specific PCs were extracted using the acidic DES. The PC-enriched DES extracts demonstrated interesting DPPH scavenging activity, which makes them candidates for novel antioxidant formulations.
Insulin-Like Growth Factor 2 As a Possible Neuroprotective Agent and Memory Enhancer—Its Comparative Expression, Processing and Signaling in Mammalian CNS

A number of studies performed on rodents suggest that insulin-like growth factor 2 (IGF-2) or its analogs may possibly be used for treating some conditions like Alzheimer’s disease, Huntington’s disease, autistic spectrum disorders or aging-related cognitive impairment. Still, for translational research a comparative knowledge about the function of IGF-2 and related molecules in model organisms (rats and mice) and humans is necessary. There is a number of important differences in IGF-2 signaling between species. In the present review we emphasize species-specific patterns of IGF-2 expression in rodents, humans and some other mammals, using, among other sources, publicly available transcriptomic data. We provide a detailed description of Igf2 mRNA expression regulation and pre-pro-IGF-2 protein processing in different species. We also summarize the function of IGF-binding proteins. We describe three different receptors able to bind IGF-2 and discuss the role of IGF-2 signaling in learning and memory, as well as in neuroprotection. We hope that comprehensive understanding of similarities and differences in IGF-2 signaling between model organisms and humans will be useful for development of more effective medicines targeting IGF-2 receptors.
The Oral Microbiota Changes in Orthodontic Patients and Effects on Oral Health: An Overview

Nowadays, there is a considerable interest to study the biological and microbiological changes that accompany orthodontic treatment. Growing knowledge on oral microbiota allows, day after day, to identify and characterize the microbial arrangements specifically associated with oral and extra-oral conditions. The aim of the present work is to highlight any further correlations between orthodontic appliances and the qualitative and quantitative modifications of the oral microbiota, such as predisposing factors for the onset of caries, periodontal diseases, and other infections, which can impact the oral and systemic health of the orthodontic patients. When compared with subjects without orthodontic appliances, orthodontic patients reported significant qualitative and quantitative differences in supra- and subgingival plaque during the entire treatment period. Certain components of fixed appliances (mainly bonded molar brackets, ceramic brackets, and elastomeric ligatures) showed high risks of periodontal disease and tooth decay for patients. An unclear prevalence of Candida spp. and the paucity of studies on viruses and protozoas in the oral microbiota of orthodontic patients need to be further investigated. The evidence emerging from this study could guide clinicians in modulating the timing of controls and enhance patient motivation to prevent the formation of mature plaque, thus reducing the risks of oral-plaque-related diseases.
UNDERSTANDING THE EFFECTS OF COMPRESSION AND CONSTRAINTS ON WATER UPTAKE OF FUEL-CELL MEMBRANES

Accurate characterization of polymer-electrolyte fuel cells (PEFCs) requires understanding the impact of mechanical and electrochemical loads on cell components. An essential aspect of this relationship is the effect of compression on the polymer membrane? s water-uptake behavior and transport properties. However, there is limited information on the impact of physical constraints on membrane properties. In this paper, we investigate both theoretically and experimentally how the water uptake of Nafion membrane changes under external compression loads. The swelling of a compressed membrane is modeled by modifying the swelling pressure in the polymer backbone which relies on the changes in the microscopic volume of the polymer. The model successfully predicts the water content of the compressed membrane measured through in-situ swelling-compression tests and neutron imaging. The results show that external mechanical loads could reduce the water content and conductivity of the membrane, especially at lower temperatures, higher humidities, and in liquid water. The modeling framework and experimental data provide valuable insight for the swelling and conductivity of constrained and compressed membranes, which are of interest in electrochemical devices such as batteries and fuel cells.
Anandamide Influences Interleukin-1β Synthesis and IL-1 System Gene Expressions in the Ovine Hypothalamus during Endo-Toxin-Induced Inflammation

Simple Summary Pro-inflammatory cytokines are considered to be one of the most important mediators affecting the function of central nervous system during an immune/inflammatory challenge. It was found that in acting on different hypothalamic nuclei, pro-inflammatory cytokines influence the centrally regulated processes including reproduction. Recently, it has been shown that the endocannabinoid system and endogenous cannabinoids may attenuate the inflammatory response. Therefore, in our study we examined the influence of anandamide, one of the earliest known endocannabinoids, on the synthesis of interleukin (IL)-1β and IL-1 system gene expressions in the hypothalamic structures involved in gonadotropin-releasing hormone (GnRH)-ergic activity, and thus the central control of reproduction, during immune stress induced by endotoxin injection. It was found that anandamide inhibited lipopolysaccharide (LPS)-stimulated synthesis of IL-1β in the hypothalamus, likely affecting posttranscriptional levels of this cytokine synthesis. Anti-inflammatory effect of anandamide at the level of central nervous system might also result from its stimulating action on IL-1 antagonist and IL-1 type II receptor gene expression. This study suggests the potential of endocannabinoids and/or their metabolites in the inhibition of inflammatory process at the level of the central nervous system, as well as their usefulness in the therapy of inflammation-induced neuroendocrine disorders, but further detailed research is required to investigate this issue. Abstract This study evaluated the effect of anandamide (AEA) on interleukin (IL)-1β synthesis and gene expression of IL-1β, its type I (IL-1R1) and II (IL-1R2) receptors, and IL-1 receptor antagonist (IL-1RN) in the hypothalamic structures, involved in the central control of reproduction, during inflammation. Animals were intravenously (i.v.) injected with bacterial endotoxin-lipopolysaccharide (LPS) (400 ng/kg) or saline, and two hours after LPS administration. , a third group received i.v. injection of AEA (10 μg/kg). Ewes were euthanized one hour later. AEA injection (p < 0.05) suppressed LPS-induced expression of IL-1β protein in the hypothalamus. The gene expression of IL-1β, IL-1RN, and IL-1R2 in the hypothalamic structures was higher (p < 0.05) in animals treated with both LPS and AEA in comparison to other experimental groups. AEA administration did not influence LPS-stimulated IL-1R1 gene expression. Our study shows that AEA suppressed IL-1β synthesis in the hypothalamus, likely affecting posttranscriptional levels of this cytokine synthesis. However, anti-inflammatory effect of AEA might also result from its stimulating action on IL-1RN and IL-1R2 gene expression. These results indicate the potential of endocannabinoids and/or their metabolites in the inhibition of inflammatory process at the level of central nervous system, and therefore their usefulness in the therapy of inflammation-induced neuroendocrine disorders.
Analysing Touchscreen Gestures: A Study Based on Individuals with Down Syndrome Centred on Design for All

There has been a conscious shift towards developing increasingly inclusive applications. However, despite this fact, most research has focused on supporting those with visual or hearing impairments and less attention has been paid to cognitive impairments. The purpose of this study is to analyse touch gestures used for touchscreens and identify which gestures are suitable for individuals living with Down syndrome (DS) or other forms of physical or cognitive impairments. With this information, app developers can satisfy Design for All (DfA) requirements by selecting adequate gestures from existing lists of gesture sets. Twenty touch gestures were defined for this study and a sample group containing eighteen individuals with Down syndrome was used. A tool was developed to measure the performance of touch gestures and participants were asked to perform simple tasks that involved the repeated use of these twenty gestures. Three variables are analysed to establish whether they influence the success rates or completion times of gestures, as they could have a collateral effect on the skill with which gestures are performed. These variables are Gender, Type of Down syndrome, and Socioeconomic Status. Analysis reveals that significant difference is present when a pairwise comparison is performed, meaning individuals with DS cannot perform all gestures with the same ease. The variables Gender and Socioeconomic Status do not influence success rates or completion times, but Type of DS does.
TOTAL NITROGEN STATUS OF SOILS UNDER BUSH FALLOW IN THE FOREST ZONE OF SOUTH WESTERN NIGERIA

Summary A substantial increase of total nitrogen occurred in the top 10 cm of soil profiles during the first ten years under bush fallow but no significant increase occurred in the 10–30 cm layer. The increase of nitrogen in the topsoils is related to soil organic matter content, increase in tree size and in vegetation cover.
Prokaryotic Solute/Sodium Symporters: Versatile Functions and Mechanisms of a Transporter Family †

The solute/sodium symporter family (SSS family; TC 2.A.21; SLC5) consists of integral membrane proteins that use an existing sodium gradient to drive the uphill transport of various solutes, such as sugars, amino acids, vitamins, or ions across the membrane. This large family has representatives in all three kingdoms of life. The human sodium/iodide symporter (NIS) and the sodium/glucose transporter (SGLT1) are involved in diseases such as iodide transport defect or glucose-galactose malabsorption. Moreover, the bacterial sodium/proline symporter PutP and the sodium/sialic acid symporter SiaT play important roles in bacteria–host interactions. This review focuses on the physiological significance and structural and functional features of prokaryotic members of the SSS family. Special emphasis will be given to the roles and properties of proteins containing an SSS family domain fused to domains typically found in bacterial sensor kinases.