cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11452026
title: Toxicity of leachates from pilot reactors simulating a landfill with different concentrations of AgNP

description: ABSTRACT This work’s objective was to verify the leachates toxicity from pilot reactors (PR) simulating a landfill containing different concentrations of silver nanoparticles (AgNP). Acute toxicity tests (48 h) with Daphnia magna were carried out in leachates containing 50, 150 and 450 mg AgNP.kg-1, in addition to a blank for control. Toxicity tests with the pure solution of silver nanoparticle and leachates resulted by the reactors were performed. The acute toxicity tests performed with D. magna confirmed the toxicity of the leachates, as well as confirmed that the silver nanoparticles are toxic, presenting EC50 (48 h) of 0.63 µg.L-1 of pure nanoparticle and ranging from 1.52 to 3.37% for the leachates. Overall, the results from the present study indicate that exposures of aquatic invertebrates to silver nanoparticles could have important ecological effects on lower trophic levels in aquatic ecosystems. The results may contribute to a better understanding of the quality of municipal solid waste (MSW) landfill leachates, with reference to nanoparticle interference and consequent treatment efficiency.
DOI: 10.6084/m9.figshare.11452026.v1
title: Toxicity of leachates from pilot reactors simulating a landfill with different concentrations of AgNP

description: ABSTRACT This work’s objective was to verify the leachates toxicity from pilot reactors (PR) simulating a landfill containing different concentrations of silver nanoparticles (AgNP). Acute toxicity tests (48 h) with Daphnia magna were carried out in leachates containing 50, 150 and 450 mg AgNP.kg-1, in addition to a blank for control. Toxicity tests with the pure solution of silver nanoparticle and leachates resulted by the reactors were performed. The acute toxicity tests performed with D. magna confirmed the toxicity of the leachates, as well as confirmed that the silver nanoparticles are toxic, presenting EC50 (48 h) of 0.63 µg.L-1 of pure nanoparticle and ranging from 1.52 to 3.37% for the leachates. Overall, the results from the present study indicate that exposures of aquatic invertebrates to silver nanoparticles could have important ecological effects on lower trophic levels in aquatic ecosystems. The results may contribute to a better understanding of the quality of municipal solid waste (MSW) landfill leachates, with reference to nanoparticle interference and consequent treatment efficiency.
DOI: 10.6084/m9.figshare.11452029.v1
title: Serving as a bedside surgeon before performing robotic radical prostatectomy improves surgical outcomes

description: ABSTRACT Introduction: To evaluate the influence of previous experience as bedside assistants on patient selection, perioperative and pathological results in robot assisted laparoscopic radical prostatectomy. Materials and Methods: The first 50 cases of two robotic surgeons were reviewed retrospectively. Group 1 consisted of the first 50 cases of the surgeon with previous experience as a robotic bedside assistant between September 2016-July 2018, while Group 2 included the first 50 cases of the surgeon with no bedside assistant experience between February 2009-December 2009. Groups were examined in terms of demographics, prostate volume, presence of median lobe, prostate specific antigen (PSA), preoperative Gleason score, positive core number, clinical stage, console surgery time, estimated blood loss, postoperative Gleason score, pathological stage, positive surgical margin rate, postoperative complications, length of hospital stay and biochemical recurrence rate. Results: Previous abdominal surgery and the presence of median lobe hypertrophy rates were higher in Group 1 than in Group 2 (20% vs. 4%, p=0.014; 24% vs. 6%, p=0.012; respectively). In addition, patients in Group 1 were in a higher clinical stage than those in Group 2 (cT2: 70% vs. 28%, p=0.001). Median console surgery time and median length of hospital stay was significantly shorter in Group 1 than in Group 2 (170 min vs. 240 min, p=0.001; 3 vs. 4, p=0.022; respectively). Clavien grade 3 complication rate was higher in Group 2 but was statistically insignificant. Conclusion: Our findings might reflect that previous bedside assistant experience led to an increase in self-confidence and the ability to manage troubleshooting and made it more likely for surgeons to start with more difficult cases with more challenging patients. It is recommended that novice surgeons serve as bedside assistants before moving on to consoles.
DOI: 10.6084/m9.figshare.11452023
title: Innovation Capabilities in an Inter-Organizational Network in Brazilian Amazon

description: Abstract This article analyzes innovation capabilities in an inter-organizational network for businesses based on biotechnology applied on biodiversity assets in the Brazilian Amazon. It is a case study about an innovation network for development and commercialization of an antioxidant compounds line of a local fruit called açai (Euterpe oleracea) in the state of Pará. The network is formed by a public university, a small technology-based company that develops high value-added products based on biodiversity, and an agribusiness company that processes, markets, and distributes products made from fruits of the Amazon region. The study shows that the capabilities found in an inter-organizational network produce innovation processes that the network's members would not be able to develop alone. In the case researched, the network connecting the organizations' capabilities enabled the exploration of biotechnological opportunities within the açaí production chain by creating competitive products. However, limitations linked to innovation appropriability prevent those innovative organizations, operating as an inter-organizational network, economically explore this product line.
DOI: 10.6084/m9.figshare.11452023.v1
title: Innovation Capabilities in an Inter-Organizational Network in Brazilian Amazon

description: Abstract This article analyzes innovation capabilities in an inter-organizational network for businesses based on biotechnology applied on biodiversity assets in the Brazilian Amazon. It is a case study about an innovation network for development and commercialization of an antioxidant compounds line of a local fruit called açai (Euterpe oleracea) in the state of Pará. The network is formed by a public university, a small technology-based company that develops high value-added products based on biodiversity, and an agribusiness company that processes, markets, and distributes products made from fruits of the Amazon region. The study shows that the capabilities found in an inter-organizational network produce innovation processes that the network's members would not be able to develop alone. In the case researched, the network connecting the organizations' capabilities enabled the exploration of biotechnological opportunities within the açaí production chain by creating competitive products. However, limitations linked to innovation appropriability prevent those innovative organizations, operating as an inter-organizational network, economically explore this product line.
DOI: 10.6084/m9.figshare.11450799
title: Unannotated R script for the creation of all graphical items and analysis

description: R script for graphical creation and analysis<br>
DOI: 10.6084/m9.figshare.11450799.v1
title: Unannotated R script for the creation of all graphical items and analysis

description: R script for graphical creation and analysis<br>
DOI: 10.6084/m9.figshare.11450793
title: Dataset for Bacterial dominance is due to effective utilisation of secondary metabolites produced by competitors.

description: .csv file containing the data used in this article.<br>
DOI: 10.6084/m9.figshare.11450793.v1
title: Dataset for Bacterial dominance is due to effective utilisation of secondary metabolites produced by competitors.

description: .csv file containing the data used in this article.<br>
DOI: 10.6084/m9.figshare.11450337
title: Lactobacillus murinus Improved the Bioavailability of Orally Administered Glycyrrhizic Acid in Rats

description: <i>L.murinus sequecing raw data</i><br>
DOI: 10.6084/m9.figshare.11450337.v1
title: Lactobacillus murinus Improved the Bioavailability of Orally Administered Glycyrrhizic Acid in Rats

description: <i>L.murinus sequecing raw data</i><br>
DOI: 10.6084/m9.figshare.11450127
title: Genome-wide Association Mapping to Identify Genetic Loci for Cold Tolerance and Cold Recovery during Germination in Rice

description: To investigate cold tolerance during germination in rice (Oryza sativa), we conducted a genome-wide association study (GWAS) using a novel diversity panel of 257 rice accessions and 5,185 SNP markers from a 7K SNP marker array. Genotyping was performed using a 7K Illumina iSelect custom-designed array using the Infinium HD Array Ultra Protocol. The 7K array, called the C7AIR, was designed by Dr. Susan McCouch’s Lab at Cornell University and consists of 7,098 SNPs (Morales et al. 2020, under review). After genotyping 257 rice accessions with the 7K array, poor-performing SNP markers (SNPs of call rate &lt;90%; minor allele frequency &lt;5%; or heterozygosity &gt;20%) were removed from the dataset. A subset of 5,185 high-quality SNP markers obtained after filtering was used to perform the genome-wide association analysis. The genotype data of 5,185 SNP markers by 257 rice accessions is presented here.
DOI: 10.6084/m9.figshare.11450127.v1
title: Genome-wide Association Mapping to Identify Genetic Loci for Cold Tolerance and Cold Recovery during Germination in Rice

description: To investigate cold tolerance during germination in rice (Oryza sativa), we conducted a genome-wide association study (GWAS) using a novel diversity panel of 257 rice accessions and 5,185 SNP markers from a 7K SNP marker array. Genotyping was performed using a 7K Illumina iSelect custom-designed array using the Infinium HD Array Ultra Protocol. The 7K array, called the C7AIR, was designed by Dr. Susan McCouch’s Lab at Cornell University and consists of 7,098 SNPs (Morales et al. 2020, under review). After genotyping 257 rice accessions with the 7K array, poor-performing SNP markers (SNPs of call rate &lt;90%; minor allele frequency &lt;5%; or heterozygosity &gt;20%) were removed from the dataset. A subset of 5,185 high-quality SNP markers obtained after filtering was used to perform the genome-wide association analysis. The genotype data of 5,185 SNP markers by 257 rice accessions is presented here.
DOI: 10.6084/m9.figshare.11450082
title: Analysis Code from Experimental translocations to low predation lead to non-parallel increases in relative brain size

description: Supplementary material
DOI: 10.6084/m9.figshare.11450082.v1
title: Analysis Code from Experimental translocations to low predation lead to non-parallel increases in relative brain size

description: Supplementary material
DOI: 10.6084/m9.figshare.11450070.v1
title: HT1080 from Mathematical deconvolution of CAR T-cell proliferation and exhaustion from real-time killing assay data

description: Chimeric antigen receptor (CAR) T-cell therapy has shown promise in the treatment of haematological cancers and is currently being investigated for solid tumours, including high-grade glioma brain tumours. There is a desperate need to quantitatively study the factors that contribute to the efficacy of CAR T-cell therapy in solid tumours. In this work, we use a mathematical model of predator–prey dynamics to explore the kinetics of CAR T-cell killing in glioma: the chimeric antigen receptor T-cell treatment response in GliOma (CARRGO) model. The model includes rates of cancer cell proliferation, CAR T-cell killing, CAR T-cell proliferation and exhaustion, and CAR T-cell persistence. We use patient-derived and engineered cancer cell lines with an <i>in vitro</i> real-time cell analyser to parameterize the CARRGO model. We observe that CAR T-cell dose correlates inversely with the killing rate and correlates directly with the net rate of proliferation and exhaustion. This suggests that at a lower dose of CAR T-cells, individual T-cells kill more cancer cells but become more exhausted when compared with higher doses. Furthermore, the exhaustion rate was observed to increase significantly with tumour growth rate and was dependent on level of antigen expression. The CARRGO model highlights nonlinear dynamics involved in CAR T-cell therapy and provides novel insights into the kinetics of CAR T-cell killing. The model suggests that CAR T-cell treatment may be tailored to individual tumour characteristics including tumour growth rate and antigen level to maximize therapeutic benefit.
DOI: 10.6084/m9.figshare.11450004
title: Table S1: Software packages discussed in this review from Mobile genomics: tools and techniques for tackling transposons

description: Software packages and associated manuscript reference.
DOI: 10.6084/m9.figshare.11450004.v1
title: Table S1: Software packages discussed in this review from Mobile genomics: tools and techniques for tackling transposons

description: Software packages and associated manuscript reference.
DOI: 10.6084/m9.figshare.11449998
title: Table S1. Primers for quality control qPCR from Human transposon insertion profiling by sequencing (TIPseq) to map LINE-1 insertions in single cells

description: Long interspersed element-1 (LINE-1, L1) sequences, which comprise about 17% of human genome, are the product of one of the most active types of mobile DNAs in modern humans. LINE-1 insertion alleles can cause inherited and de novo genetic diseases, and LINE-1-encoded proteins are highly expressed in some cancers. Genome-wide LINE-1 mapping in single cells could be useful for defining somatic and germline retrotransposition rates, and for enabling studies to characterize tumour heterogeneity, relate insertions to transcriptional and epigenetic effects at the cellular level or describe cellular phylogenies in development. Our laboratories have reported a genome-wide LINE-1 insertion site mapping method for bulk DNA, named transposon insertion profiling by sequencing (TIPseq). There have been significant barriers applying LINE-1 mapping to single cells, due to the chimeric artefacts and features of repetitive sequences. Here, we optimize a modified TIPseq protocol and show its utility for LINE-1 mapping in single lymphoblastoid cells. Results from single-cell TIPseq experiments compare well to known LINE-1 insertions found by whole-genome sequencing and TIPseq on bulk DNA. Among the several approaches we tested, whole-genome amplification by multiple displacement amplification followed by restriction enzyme digestion, vectorette ligation and LINE-1-targeted PCR had the best assay performance.This article is part of the discussion meeting issue ‘Crossroads between transposons and gene regulation’.
DOI: 10.6084/m9.figshare.11449998.v1
title: Table S1. Primers for quality control qPCR from Human transposon insertion profiling by sequencing (TIPseq) to map LINE-1 insertions in single cells

description: Long interspersed element-1 (LINE-1, L1) sequences, which comprise about 17% of human genome, are the product of one of the most active types of mobile DNAs in modern humans. LINE-1 insertion alleles can cause inherited and de novo genetic diseases, and LINE-1-encoded proteins are highly expressed in some cancers. Genome-wide LINE-1 mapping in single cells could be useful for defining somatic and germline retrotransposition rates, and for enabling studies to characterize tumour heterogeneity, relate insertions to transcriptional and epigenetic effects at the cellular level or describe cellular phylogenies in development. Our laboratories have reported a genome-wide LINE-1 insertion site mapping method for bulk DNA, named transposon insertion profiling by sequencing (TIPseq). There have been significant barriers applying LINE-1 mapping to single cells, due to the chimeric artefacts and features of repetitive sequences. Here, we optimize a modified TIPseq protocol and show its utility for LINE-1 mapping in single lymphoblastoid cells. Results from single-cell TIPseq experiments compare well to known LINE-1 insertions found by whole-genome sequencing and TIPseq on bulk DNA. Among the several approaches we tested, whole-genome amplification by multiple displacement amplification followed by restriction enzyme digestion, vectorette ligation and LINE-1-targeted PCR had the best assay performance.This article is part of the discussion meeting issue ‘Crossroads between transposons and gene regulation’.
DOI: 10.6084/m9.figshare.11449992
title: Table S2 from Human transposon insertion profiling by sequencing (TIPseq) to map LINE-1 insertions in single cells

description: All potential LINE-1 insertions. Each row is an insertion site that is either in the ’gold standard’ list or predicted with probability at least 0.1 in one experiment. Insertion sites within 100bp are merged. Columns D-V are the probability score of the insertion in each experiment. Column W indicates whether an insertion is in the gold standard list and if yes, whether it is a part of the reference genome assembly. Column X indicates if the insertion is in gold standard list. Column Y indicates whether the insertion is in a RepeatMasker annotated repeat and if so, which repeat family. Column Z indicates the distance to the nearest L1Hs in euL1db. Column AA indicates the distance to the nearest L1Hs on same strand in euL1db. Column AB indicates if the insertion is in or within 25bp of L1PA2 to L1PA4. Column AC indicates if the insertion is in a segmental duplication with over 95% identity.
DOI: 10.6084/m9.figshare.11449992.v1
title: Table S2 from Human transposon insertion profiling by sequencing (TIPseq) to map LINE-1 insertions in single cells

description: All potential LINE-1 insertions. Each row is an insertion site that is either in the ’gold standard’ list or predicted with probability at least 0.1 in one experiment. Insertion sites within 100bp are merged. Columns D-V are the probability score of the insertion in each experiment. Column W indicates whether an insertion is in the gold standard list and if yes, whether it is a part of the reference genome assembly. Column X indicates if the insertion is in gold standard list. Column Y indicates whether the insertion is in a RepeatMasker annotated repeat and if so, which repeat family. Column Z indicates the distance to the nearest L1Hs in euL1db. Column AA indicates the distance to the nearest L1Hs on same strand in euL1db. Column AB indicates if the insertion is in or within 25bp of L1PA2 to L1PA4. Column AC indicates if the insertion is in a segmental duplication with over 95% identity.
DOI: 10.6084/m9.figshare.11449977
title: Table S1: Sequencing Statistics and availability from <i>Arabidopsis</i> RNA polymerase IV generates 21–22 nucleotide small RNAs that can participate in RNA-directed DNA methylation and may regulate genes

description: The plant-specific RNA Polymerase IV (Pol IV) transcribes heterochromatic regions, including many transposable elements (TEs), with the well-described role of generating 24 nucleotide (nt) small interfering RNAs (siRNAs). These siRNAs target DNA methylation back to TEs to reinforce the boundary between heterochromatin and euchromatin. In the male gametophytic phase of the plant life cycle, pollen, Pol IV switches to generating primarily 21–22 nt siRNAs, but the biogenesis and function of these siRNAs have been enigmatic. In contrast to being pollen-specific, we identified that Pol IV generates these 21–22 nt siRNAs in sporophytic tissues, likely from the same transcripts that are processed into the more abundant 24 nt siRNAs. The 21–22 nt forms are specifically generated by the combined activities of DICER proteins DCL2/DCL4 and can participate in RNA-directed DNA methylation. These 21–22 nt siRNAs are also loaded into ARGONAUTE1, which is known to function in post-transcriptional regulation. Like other plant siRNAs and microRNAs incorporated into AGO1, we find a signature of genic mRNA cleavage at the predicted target site of these siRNAs, suggesting that Pol IV-generated 21–22 nt siRNAs may function to regulate gene transcript abundance. Our data provide support for the existing model that in pollen Pol IV functions in gene regulation.This article is part of the discussion meeting issue ‘Crossroads between transposons and gene regulation’.
DOI: 10.6084/m9.figshare.11449977.v1
title: Table S1: Sequencing Statistics and availability from <i>Arabidopsis</i> RNA polymerase IV generates 21–22 nucleotide small RNAs that can participate in RNA-directed DNA methylation and may regulate genes

description: The plant-specific RNA Polymerase IV (Pol IV) transcribes heterochromatic regions, including many transposable elements (TEs), with the well-described role of generating 24 nucleotide (nt) small interfering RNAs (siRNAs). These siRNAs target DNA methylation back to TEs to reinforce the boundary between heterochromatin and euchromatin. In the male gametophytic phase of the plant life cycle, pollen, Pol IV switches to generating primarily 21–22 nt siRNAs, but the biogenesis and function of these siRNAs have been enigmatic. In contrast to being pollen-specific, we identified that Pol IV generates these 21–22 nt siRNAs in sporophytic tissues, likely from the same transcripts that are processed into the more abundant 24 nt siRNAs. The 21–22 nt forms are specifically generated by the combined activities of DICER proteins DCL2/DCL4 and can participate in RNA-directed DNA methylation. These 21–22 nt siRNAs are also loaded into ARGONAUTE1, which is known to function in post-transcriptional regulation. Like other plant siRNAs and microRNAs incorporated into AGO1, we find a signature of genic mRNA cleavage at the predicted target site of these siRNAs, suggesting that Pol IV-generated 21–22 nt siRNAs may function to regulate gene transcript abundance. Our data provide support for the existing model that in pollen Pol IV functions in gene regulation.This article is part of the discussion meeting issue ‘Crossroads between transposons and gene regulation’.
DOI: 10.6084/m9.figshare.11449932
title: Catalogue and Supporting Data

description: This spreadsheet contains the catalogue and supporting data required to visualise constructs.
DOI: 10.6084/m9.figshare.11449671
title: Supplementary tables from Transposable elements have contributed human regulatory regions that are activated upon bacterial infection

description: Transposable elements (TEs) are increasingly recognized as important contributors to mammalian regulatory systems. For instance, they have been shown to play a role in the human interferon response, but their involvement in other mechanisms of immune cell activation remains poorly understood. Here, we investigated the profile of accessible chromatin enhanced in stimulated human macrophages using ATAC-Seq to assess the role of different TE subfamilies in regulating gene expression following an immune response. We found that both previously identified and new repeats belonging to the MER44, THE1, Tigger3 and MLT1 families provide 14 subfamilies that are enriched in differentially accessible chromatin and found near differentially expressed genes. These TEs also harbour binding motifs for several candidate transcription factors, including important immune regulators AP-1 and NF-kB, present in 96% of accessible MER44B and 83% of THE1C instances, respectively. To more directly assess their regulatory potential, we evaluated their presence in regions putatively affecting gene expression, as defined by quantitative trait locus analysis, and found that repeats are also contributing to accessible elements near QTLs. Together, these results suggest that a number of TE families have contributed to the regulation of gene expression in the context of the immune response to infection in humans.This article is part of the discussion meeting issue ‘Crossroads between transposons and gene regulation’.