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Contribution submitted by Antonella Garzelli for the Public consultation on the draft risk assessment of glycoalkaloids in feed and food, in particular in potatoes and potato-derived products

The European Food Safety Authority (EFSA) carried out a public consultation, from 27 February 2020 until 15 April 2020, to receive input from interested parties – organizations or private citizens - on a draft scientific opinion on the risks for animal and human health related to the presence of glycoalkaloids in feed and food, in particular in potatoes and potato-derived products. The draft scientific opinion was prepared by the EFSA Panel on Contaminants in the Food Chain (CONTAM Panel), supported by the Working Group on Glycoalkaloids in feed and food. EFSA used the EU survey tool to receive comments on the draft scientific opinion, and the way these comments were considered for the finalisation of the opinion is described in the Technical Report available at: <a href="https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fefsa.onlinelibrary.wiley.com%2Fdoi%2F10.2903%2Fsp.efsa.2020.EN-1905&data=02%7C01%7C%7C242adcee21744b01890408d82cba24b4%7C406a174be31548bdaa0acdaddc44250b%7C1%7C0%7C637308525272584775&sdata=97Tc3%2FrT1SXtzIN14PCCvUv0OYyaiSO1H76iezwqvnQ%3D&reserved=0">https://efsa.onlinelibrary.wiley.com/doi/10.2903/sp.efsa.2020.EN-1905</a>. Some contributors also attached files to the comments submitted via the EU survey tool. For transparency reasons these files are made available in the public domain as Zenodo uploads.

Contribution submitted by STARCH EU for the Public consultation on the draft risk assessment of glycoalkaloids in feed and food, in particular in potatoes and potato-derived products

Contribution submitted by Matthew Walker for the Public consultation on the draft risk assessment of glycoalkaloids in feed and food, in particular in potatoes and potato-derived products

opencc-zeroAug 2020View details →

Circulating myeloid-derived suppressor cells facilitate invasion of thyroid cancer cells by repressing miR-486-3p

Background: Myeloid-derived suppressor cells (MDSCs) have become increasingly recognized as facilitators of tumor development. However, the role of MDSCs in papillary thyroid carcinoma (PTC) progression has not been clearly explored. Objective: We aimed to evaluate the levels and function of circulating MDSCs in PTC. Methods: The proportion of circulating polymorphonuclear (PMN)-MDSCs and mononuclearMDSCs from patients with PTC or benign thyroid nodules and healthy controls was measured using flow cytometry. For immunosuppressive activity analysis, sorted circulating MDSCs were cocultured with CD3/CD28-costimulated T lymphocytes and the proliferation of T cells was determined. PTC cell lines (TPC-1 and BC-PAP) were cocultured with PMN-MDSCs, and the effects on cell migration, invasion, proliferation, and apoptosis were evaluated. The differential expressed microribonucleic acids (RNAs) and messenger RNAs and their function were also explored in TPC-1 cells cocultured with or without PMN-MDSCs. Results: PMN-MDSCs were increased in peripheral blood mononuclear cells of patients with PTC. Circulating PMN-MDSCs displayed strong T cell suppressive activity. PTC cells demonstrated enhanced invasive capabilities in vitro and in vivo when cocultured with sorted PMN-MDSCs. PMN-MDSCs decreased expression of miR-486-3p and activated nuclear factor kappa B2 (NF-κB2), a direct target of miR-486-3p. Rescue of miR-486-3p diminished the cell migration and invasion induced by PMN-MDSCs. Conclusion: Collectively, our work indicates that circulating PMN-MDSCs promote PTC progression. By suppressing miR-486-3p, PMN-MDSCs promote the activity of the NF-κB2 signaling pathway, resulting in accelerated invasion of PTC cells, which may provide new therapeutic strategies for treatment of thyroid cancer.

opencc-zeroAug 2020View details →

Supplemental tables from: Antifibrogenic activities of CYP11A1-derived vitamin D3-hydroxyderivatives are dependent on RORγ

Previous studies showed that non-calcemic 20(OH)D3, a product of CYP11A1 action on vitamin D3, has antifibrotic activity in human dermal fibroblasts and in a bleomycin mouse model of scleroderma. In this study we tested the role of RORγ, which is expressed in skin, in the action of CYP11A1-derived secosteroids using murine fibroblasts isolated from the skin of wild type (RORg+/+), knock out (RORg-/-) and heterozygote (RORg+/-) mice. CYP11A1-derived 20(OH)D3, 20,23(OH)2D3, 1,20(OH)2D3, and 1,20,23(OH)3D3 inhibited proliferation of RORγ+/+ fibroblasts in a dose-dependent manner with a similar potency to 1,25(OH)2D3. Surprisingly, this effect was reversed in RORγ+/- and RORγ-/- fibroblasts with the most pronounced stimulatory effect seen in RORγ-/- fibroblasts. All of the analogs tested inhibited TGF-β1-induced collagen synthesis in RORγ+/+ fibroblasts and the expression of other fibrosis-related genes. This effect was curtailed or reversed in RORγ-/- fibroblasts. These results show that the antiproliferative and antifibrotic activities of the vitamin D hydroxy-derivatives are dependent on a functional RORγ. The dramatic changes in the transcriptomes of fibroblasts of RORg-/- versus wild type mice following treatment with 20(OH)D3 or 1,20(OH)2D3 provide a molecular basis to explain, at least in part, the observed phenotypic differences

AI-Derived West Nile Virus Determinants Maps - 2018 Europe - Data

Data for AI-Derived West Nile Virus Determinants Maps 2018 Europe <ol> <li>Original (nominal value) data</li> <li>SHAP-derived effect data </li> </ol>

opencc-zeroAug 2020View details →

Data from: The propagation of admixture-derived adaptive radiation potential

Adaptive radiations frequently show remarkable repeatability where single lineages undergo multiple independent episodes of adaptive radiation in distant places and long separate timepoints. Increasing evidence suggests that genetic variation generated through hybridization between distantly related lineages can promote adaptive radiation. This mechanism, however, requires rare coincidence in space and time between the hybridization event and opening of ecological opportunity, because hybridization generates large genetic variation only in the site where it occurred and the elevated genetic variation will persist only for a short period. Hence, hybridization seems unlikely to explain recurrent adaptive radiation in the same lineage. Contrary to these expectations, our evolutionary computer simulations demonstrate that admixture variation can geographically spread and persist for long periods if certain conditions are present such that ecological and/or geographic mechanisms split the hybrid population into isolated sub-lineages. Subsequent secondary hybridization of some of these can reestablish genetic polymorphisms from the ancestral hybridization in places far from the birthplace of the hybrid-clade and long after the ancestral hybridization event. Consequently, simulations revealed conditions where exceptional genetic variation, once generated through a rare and unlikely hybridization event, can facilitate multiple adaptive radiations exploiting ecological opportunities available at distant points in time and space.

opencc-zeroSep 2020View details →

Data from: Paleolimnological assessment of wildfire-derived atmospheric deposition of trace metal(loid)s and major ions to subarctic lakes (Northwest Territories, Canada)

Wildfires release terrestrial elements to the atmosphere as aerosols, and these events are becoming more frequent and intense in the Arctic boreal forest as the climate is warming. We quantified the impact of atmospheric deposition of aerosols from local wildfires on metal(loid) fluxes using macroscopic charcoal accumulation rates, historical fire mapping, and element concentrations in 210Pb‐dated lake sediment from five subarctic lakes with small catchments. Lake sediments showed small but significant increases in fluxes (median = 5–10%) for 22 trace metals, metalloids, or major ions following fire events. The impact of wildfire aerosols on element fluxes was mostly due to short‐term (≤2 years) increasing sedimentation rate (6 ± 41% increase), whereas sediment element concentrations were not strongly impacted. Wildfire‐associated deposition to lake sediments was mainly composed of Ca, Al, Fe, Mg, K, Mn, and Na, which are major constituents of ash from burned biomass, but changes in sediment flux were greatest for Sb, As, Ni, Ba, Mn, Mo, and Sr compared to pre‐disturbance conditions. Compared to anthropogenic sources of pollution, wildfire‐associated atmospheric fluxes of metal contaminants to the lakes (e.g., Hg, Pb, As, Sb, and Cd) were low. This study provides quantitative estimates of wildfire impacts on atmospheric geochemical fluxes to subarctic lakes, which can be used for modeling larger‐scale impacts under changing fire regimes.

opencc-zeroSep 2020View details →

Results from: Angiogenic property of silk fibroin scaffolds with adipose-derived stem cells on chick chorioallantoic membrane

Angiogenesis is a key step in tissue regeneration and repair. Biomaterials that allow or promote angiogenesis are thus beneficial. In this study, angiogenic properties of salt-leached silk fibroin (SF) scaffolds seeded with human adipose stem cells (hADSCs) were studied using chick chorioallantoic membrane (CAM) as a model. The hADSC-seeded SF scaffolds (SF-hADSC) with porosity of 77.34 ± 6.96 % and pore diameter of 513.95 ± 4.99 µm were implanted on CAM of chick embryos that were on embryonic day 8 (E8) of development. The SF-hADSC scaffolds induced a spoke-wheel pattern of capillary network indicative of angiogenesis, which was evident since E11. Moreover, ingrowth of blood vessels into the scaffolds was seen in histological sections. The unseeded scaffolds induced the same extent of angiogenesis later on E14. In contrast, the control group could not induce angiogenesis to the same extent even as late. In vitro cytotoxicity tests and in vivo angioirritative study reaffirmed the biocompatibility of the scaffolds. This work highlighted that the biocompatible SF-hADSC scaffolds accelerates angiogenesis, and hence they can be a promising biomaterial for regeneration of tissues that require angiogenesis.

opencc-zeroOct 2020View details →

The 49,890 SNPgenotype derived from genotyping-by-sequencing strategy for the NIP/9311 backcross inbred lines population

Transmission ratio distortion (TRD) refers to a widespread phenomenon in which one allele is transmitted by heterozygotes more frequently to the progeny than the opposite allele. TRD is considered as a mark suggesting the presence of reproductive barrier. However, the genetic and molecular mechanisms underlying TRD in rice remain largely unknown. In the present study, a population of backcross inbred lines (BILs) derived from the cross of a japonica cultivar Nipponbare and an indica variety 9311 was utilized to study the genetic base of TRD. A total of eighteen genomic regions were identified for TRD in the BILs. Among them, twelve and six regions showed indica (9311) and japonica (Nipponbare) alleles with preferential transmission, respectively. A series of F2 populations were used to confirm the TRD effects, including six genomic regions that were confirmed by chromosome segment substitution line (CSSL)-derived F2 populations from inter-subspecific allelic combinations. However, none of the regions was confirmed by the CSSL-derived populations from intra-subspecific allelic combination. Furthermore, significant epistatic interaction was found between TRD1.3 and TRD8.1 suggesting that TRD could positively contribute to breaking inter-subspecific reproductive barriers. Our results have laid the foundation for identifying the TRD genes and provide an effective strategy to breakdown TRD for breeding wide-compatible lines, which will be further utilized in the inter-subspecific hybrid breeding programs.

opencc-by-4.0Oct 2020View details →

A Tool for Product Derivation and Semi-Automatic Deployment of Web-Based Systems

This paper presents a tool for product derivation and semi-automatic deployment of web-based systems. The tool focuses on cloned webbased systems implemented using the PHP language, which are refactored to become software product lines. The paper also reports the results of a case study of using the tool in the context of a large scale web-based system. Our findings show some preliminary evidence of the benefits of the tool to reduce: (i) the time of product derivation and deployment; and (ii) the manual effort to customize existing cloned web-based systems.

opencc-zeroNov 2020View details →

Data from: Maternally-derived anti-helminth antibodies predict offspring survival in a wild mammal

The transfer of antibodies from mother to offspring provides crucial protection against infection to offspring during early life. However, few studies have tested the consequences of variation in maternal antibody transfer for offspring fitness in the wild. Further, separating out the immunoprotective effects of antibodies from their association with nutritional resources provided by the mother is difficult. Here, we measured plasma levels of total and parasite-specific antibody levels in neonatal (<10 days old) wild Soay sheep over 25 years to quantify variation in maternal antibody transfer and test its association with offspring survival. Maternal antibody transfer was predicted by maternal age and previous antibody responses, and was consistent within mothers across years. Neonatal total IgG antibody levels were positively related to early growth, suggesting they reflected nutritional transfer. Neonatal parasite-specific IgG levels positively predicted first year offspring survival, independent of lamb weight, total IgG levels and subsequent lamb parasite-specific antibody levels. This relationship was in part mediated via an indirect negative association with parasite burden. We show that among-female variation in maternal transfer of immunity can have long-term effects on offspring growth, parasite burden and fitness in the wild, and is likely to impact naturally-occurring host and parasite dynamics.

opencc-zeroOct 2020View details →

VCF file of multiple single-cyst-derived Ro1 and Ro2 lines of New York fields on Globodera rostochiensis genome

The potato cyst nematode, Globodera rostochiensis, is a regulated pest posing a serious threat to potato production worldwide. Although the endemic pathotype (Ro1) of G. rostochiensis has been confined to New York State for several decades as a result of quarantine regulations and management with resistant potato cultivars, a virulent pathotype, Ro2, has emerged, for which control measures are scarce. The ability to detect Ro2 early in fields is necessary to sustain the success of G. rostochiensis quarantine in the US. Here, we report the comparative analysis of whole-genome sequences of multiple single-cyst-derived Ro1 and Ro2 lines, propagated from original field populations. The identified discriminant variants are good targets for developing molecular diagnostic tools for differentiating G. rostochiensis pathotypes in NY.

opencc-by-4.0Nov 2020View details →

"Pressure-to-depth conversion models for metamorphic rocks: derivation and applications" (Supplementary material and Figures)

Supporting Information and Figures associated to the paper entitled: "Pressure-to-depth conversion models for metamorphic rocks: derivation and applications" by A. Bauville and P. Yamato. (Geochemistry, Geophysics, Geosystems). These links allow to download: - The figures of the paper in .pdf format - The scripts used to generate the figures - The supporting information file. Please, contact A. Bauville for additional information.

opencc-by-4.0Dec 2019View details →

Results of OLCI-derived Secchi disk depth in lakes across Eastern China

Water clarity, represented by Secchi disk depth (Zsd), is the first-order indicator of water quality. This dataset contains Zsd of 86 major large lakes with an area greater than 30 km2 in East China estimated using a random forest regression (RFR)-based Zsd model. Scientists from optical remote sensing and aquatic sciences can use this dataset for their research.

opencc-by-4.0Nov 2020View details →

Carbene‐Catalyzed Activation of Remote Nitrogen Atoms of (benz)imidazole‐derived aldimines for Enantioselective Synthesis of Heterocycles

This folder /xyz_structures/ contains the geometries (in .xyz format together with the gas-phase energy, E) accompanying the paper "Carbene‐Catalyzed Activation of Remote Nitrogen Atoms of (benz)imidazole‐derived aldimines for Enantioselective Synthesis of Heterocycles" citation: X. Yang, Y. Xie, J. Xu, S. Ren, B. Mondal, L. Zhou, W. Tian, X. Zhang, L. Hao, Z. Jin, Y. R. Chi, Angew. Chem. Int. Ed. 2021, 60, 7906. Where conformers occur, they are always named from the lowest Gibbs energy to the highest in ascending order from c1 (sometimes omitted), c2, c3, ... This folder has the following structure and they correspond to the raw data in the SI: /DFT_optimized_structures/      --> contains DFT-optimized structures for the computational study of the mechanism for the reaction between intermediates IV-3b/IV-3ac and isatin substrate 2b. /DI-AS_analysis/      --> structures along the IRC pathways for Si-ts1 (in subfolder /Si-ts1/) and Re-ts1 (in subfolder /Re-ts1/) taken for distortion interaction-activation strain (DI-AS) model analysis.     --> structures along the IRC points are named p<num>.xyz where <num> denotes number of points along the IRC from the TS; fragments results from each point are denoted p<num>_f1.xyz and p<num>_f2.xyz. For example, the first point along the IRC is named p1.xyz and its component fragments are denoted p1_f1.xyz and p2_f2.xyz.

opencc-by-4.0Dec 2020View details →

B3 Derivatives Prices Historical Data

Historical prices of derivatives obtained from B3 (Bolsa de Valores do Brasil) website. The data are referent to the years 2011 to 2020. The data are separated into 10 .csv files referring to one complete year each.

opencc-by-4.0Dec 2020View details →

Simultaneous readout of multiple FRET pairs using photochromism: cell traces and derived data

All cell traces and derived datasets for our publication on 'Simultaneous readout of multiple FRET pairs using photochromism'.

opencc-byDec 2020View details →

Supporting Information of the article "mesenchymal stem cell-derived exosomes protect trabecular meshwork from oxidative stress"

Supporting Information of the article "mesenchymal stem cell-derived exosomes protect trabecular meshwork from oxidative stress".