cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.31116369
title: Accurate quantification of anti-drug antibodies against each unique Fab of a bispecific antibody using an ECL bridging assay

description: To develop an anti-drug antibody (ADA) assay for a bispecific antibody (bsAb) we will refer to as Drug-1, and to quantify the ADAs against each specific fragment antigen-binding (Fab) site of Drug-1. Here we use two additional unlabeled monoclonal antibodies (mAbs) Drug-2 & Drug-3 in an ADA confirmation assay format. Drugs-2 & −3 have the same targets as the two Fabs of Drug-1, facilitating our aim to measure and quantify the anti-drug Abs against each specific Fab of Drug-1 by signal inhibition. By using the combination of a screening and a dual confirmation assay format, we were able to accurately quantify the ADAs against each specific Fab of the bsAb Drug-1. Many new medicines are biologics – they’re made from proteins similar to those our bodies make. Most biologics are antibodies. To make antibody medicines, scientists give living cells (usually CHO cells) the antibody’s genetic instructions. The cells then produce the antibody and add small changes like those that happen in humans. Most antibodies bind to one target. Bispecific antibodies are different because they have two separate binding parts (called Fabs) and can attach to two different targets at the same time. Because biologics are large proteins, the immune system can see them as foreign and make anti-drug antibodies (ADAs). Regulators require testing to see if patients make ADAs and whether those ADAs affect safety or how well the drug works. We developed a test that: Detects all ADAs a patient makes against a bispecific antibody, Identifies which of the two Fabs the ADAs bind to, and Measures how much binds to each Fab. This ADA information, together with safety and efficacy data, can help decide whether and how to use those Fabs in future drug projects.
DOI: 10.6084/m9.figshare.31116369.v1
title: Accurate quantification of anti-drug antibodies against each unique Fab of a bispecific antibody using an ECL bridging assay

description: To develop an anti-drug antibody (ADA) assay for a bispecific antibody (bsAb) we will refer to as Drug-1, and to quantify the ADAs against each specific fragment antigen-binding (Fab) site of Drug-1. Here we use two additional unlabeled monoclonal antibodies (mAbs) Drug-2 & Drug-3 in an ADA confirmation assay format. Drugs-2 & −3 have the same targets as the two Fabs of Drug-1, facilitating our aim to measure and quantify the anti-drug Abs against each specific Fab of Drug-1 by signal inhibition. By using the combination of a screening and a dual confirmation assay format, we were able to accurately quantify the ADAs against each specific Fab of the bsAb Drug-1. Many new medicines are biologics – they’re made from proteins similar to those our bodies make. Most biologics are antibodies. To make antibody medicines, scientists give living cells (usually CHO cells) the antibody’s genetic instructions. The cells then produce the antibody and add small changes like those that happen in humans. Most antibodies bind to one target. Bispecific antibodies are different because they have two separate binding parts (called Fabs) and can attach to two different targets at the same time. Because biologics are large proteins, the immune system can see them as foreign and make anti-drug antibodies (ADAs). Regulators require testing to see if patients make ADAs and whether those ADAs affect safety or how well the drug works. We developed a test that: Detects all ADAs a patient makes against a bispecific antibody, Identifies which of the two Fabs the ADAs bind to, and Measures how much binds to each Fab. This ADA information, together with safety and efficacy data, can help decide whether and how to use those Fabs in future drug projects.
DOI: 10.6084/m9.figshare.31205271
title: Extracellular vesicle proteomics and metabolomics: analytical frameworks and translational insights

description: In recent years, the study of extracellular vesicles (EVs) has gained increasing attention due to their pivotal role in intercellular communication and their potential as noninvasive biomarkers and innovative therapeutic tools. Their molecular cargo, shaped by the source cell and its microenvironment, offers an accurate mirror of cellular states and pathophysiological dynamics. Characterizing this content provides critical insights into disease mechanisms, while paving the way for novel diagnostic, prognostic and therapeutic strategies. Among their components, proteins and metabolites stand out for their functional relevance and biomarker potential. In this context, proteomics and metabolomics have emerged as key approaches to unravel the molecular complexity of EVs and clarify their biological functions, thereby advancing their translation into clinical applications. This review highlights the contributions of these disciplines, outlines associated analytical workflows, and discusses major technical challenges. A systematic literature search was conducted in PubMed, Web of Science, Scopus, and Google Scholar for studies published between 2012 and 2025, focusing on proteomic and metabolomic analyses of EVs. Emphasis is placed on the need for methodological consensus to standardize protocols, improve inter-laboratory reproducibility, and support the successful clinical application of EV-based strategies.
DOI: 10.6084/m9.figshare.31205271.v1
title: Extracellular vesicle proteomics and metabolomics: analytical frameworks and translational insights

description: In recent years, the study of extracellular vesicles (EVs) has gained increasing attention due to their pivotal role in intercellular communication and their potential as noninvasive biomarkers and innovative therapeutic tools. Their molecular cargo, shaped by the source cell and its microenvironment, offers an accurate mirror of cellular states and pathophysiological dynamics. Characterizing this content provides critical insights into disease mechanisms, while paving the way for novel diagnostic, prognostic and therapeutic strategies. Among their components, proteins and metabolites stand out for their functional relevance and biomarker potential. In this context, proteomics and metabolomics have emerged as key approaches to unravel the molecular complexity of EVs and clarify their biological functions, thereby advancing their translation into clinical applications. This review highlights the contributions of these disciplines, outlines associated analytical workflows, and discusses major technical challenges. A systematic literature search was conducted in PubMed, Web of Science, Scopus, and Google Scholar for studies published between 2012 and 2025, focusing on proteomic and metabolomic analyses of EVs. Emphasis is placed on the need for methodological consensus to standardize protocols, improve inter-laboratory reproducibility, and support the successful clinical application of EV-based strategies.
DOI: 10.15468/dl.t479w8
title: Occurrence Download

description: A dataset containing 96 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Occurrence evidence)",
 "Geometry POLYGON((-110.48028 31.2701,-107.87355 31.2701,-107.87355 32.66589,-110.48028 32.66589,-110.48028 31.2701))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Heterodon kennerlyi",
 "Year 2015-2026"
 ]
}

 The dataset includes 96 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029618-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.30999075
title: Mitigating ADA matrix interferences: semiquantitative double immunoprecipitation for anti-bevacizumab antibody in plasma

description: Hybrid LC – MS/MS methodology offers orthogonal ADA quantitation but is limited by endogenous immunoglobulin matrix interference challenges. We developed a novel semi-quantitative LC-MS/MS isotyping assay for rabbit IgG/IgM immunogenicity in K<sub>2</sub>EDTA plasma using double immunoprecipitation with double acid dissociation. As compared to single immunoprecipitation, double immunoprecipitation reduced endogenous IgG by ≥90% and IgM by &gt;95% (W1B1) or &gt;55% (W3B2), improved peak-area ratios, and achieved an LLOQ of 100 ng/mL, with acceptable accuracy and precision. Double immunoprecipitation plus acid dissociation mitigates matrix interference and enables robust semi-quantitative hybrid LC-MS/MS ADA isotyping in rabbit plasma.
DOI: 10.6084/m9.figshare.30999075.v1
title: Mitigating ADA matrix interferences: semiquantitative double immunoprecipitation for anti-bevacizumab antibody in plasma

description: Hybrid LC – MS/MS methodology offers orthogonal ADA quantitation but is limited by endogenous immunoglobulin matrix interference challenges. We developed a novel semi-quantitative LC-MS/MS isotyping assay for rabbit IgG/IgM immunogenicity in K<sub>2</sub>EDTA plasma using double immunoprecipitation with double acid dissociation. As compared to single immunoprecipitation, double immunoprecipitation reduced endogenous IgG by ≥90% and IgM by &gt;95% (W1B1) or &gt;55% (W3B2), improved peak-area ratios, and achieved an LLOQ of 100 ng/mL, with acceptable accuracy and precision. Double immunoprecipitation plus acid dissociation mitigates matrix interference and enables robust semi-quantitative hybrid LC-MS/MS ADA isotyping in rabbit plasma.
DOI: 10.25549/rbm-c58-5102
title: Eland trotting

description: Eland trotting. This is plate 696, captioned "Eland trotting" from Eadweard Muybridge. Animal locomotion: an electro-photographic investigation of consecutive phases of animal movements. 1872-1885 / published under the auspices of the University of Pennsylvania. Plates. The plates printed by the Photo-Gravure Company. Philadelphia, 1887.
DOI: 10.6084/m9.figshare.31048816
title: FALCON-qPCR: a new method for the quantification of oxidative lesions in mitochondrial DNA

description: Accurate quantification of oxidative mitochondrial DNA (mtDNA) lesions remains technically challenging due to the limitations of existing assays, which often require large sample inputs, multi-day workflows, and offer limited sensitivity. Here we introduce FALCON-qPCR (Fpg-assisted Long-PCR), a streamlined, high-sensitivity method for quantifying oxidative damage in mtDNA. FALCON-qPCR couples digestion with formamidopyrimidine [fapy]-DNA glycosylase (Fpg) to long-range PCR and qPCR-based normalization, enabling precise lesion quantification from as few as 10,000 cells (~300 ng total DNA) within a single day. The assay provides a robust dynamic range and reproducibility across diverse biological systems, including human cell lines, hepatocellular carcinoma biopsies, and <i>Caenorhabditis elegans</i>. Compared with established methods, FALCON-qPCR exhibits markedly higher sensitivity in detecting mtDNA damage induced by hydrogen peroxide, antimycin A, and rotenone. Its performance was further demonstrated in assessing mitochondrial toxicity of ruthenium-based compounds, highlighting its potential for pharmacological screening. By integrating enzymatic lesion recognition with quantitative amplification in a unified workflow, FALCON-qPCR eliminates the need for mitochondrial isolation. This methodological advance provides a rapid, accurate, and scalable platform for studying oxidative DNA damage, with broad applicability in mitochondrial research and translational toxicology. Mitochondria are tiny structures inside our cells that produce energy. When they work, they also create reactive molecules called ROS (reactive oxygen species). If ROS levels get too high, they can damage mitochondrial DNA (mtDNA), which may lead to diseases such as cancer and neurodegeneration. Measuring this damage is important, but current methods are slow, need large samples, and are not very sensitive. We developed a new method called FALCON-qPCR that measures mtDNA damage quickly and accurately. It uses a special enzyme to mark damaged DNA and then applies two types of PCR (a technique to copy DNA) to calculate how much damage is present. Unlike older methods, FALCON-qPCR works with very small samples – just 10,000 cells – and gives results in one day. We tested FALCON-qPCR on human cells, liver biopsies from cancer patients, and even tiny worms (<i>C.</i> <i>elegans</i>). In short, FALCON-qPCR is a fast, reliable, and versatile tool for studying mitochondrial DNA damage in research and clinical settings.
DOI: 10.6084/m9.figshare.31048816.v1
title: FALCON-qPCR: a new method for the quantification of oxidative lesions in mitochondrial DNA

description: Accurate quantification of oxidative mitochondrial DNA (mtDNA) lesions remains technically challenging due to the limitations of existing assays, which often require large sample inputs, multi-day workflows, and offer limited sensitivity. Here we introduce FALCON-qPCR (Fpg-assisted Long-PCR), a streamlined, high-sensitivity method for quantifying oxidative damage in mtDNA. FALCON-qPCR couples digestion with formamidopyrimidine [fapy]-DNA glycosylase (Fpg) to long-range PCR and qPCR-based normalization, enabling precise lesion quantification from as few as 10,000 cells (~300 ng total DNA) within a single day. The assay provides a robust dynamic range and reproducibility across diverse biological systems, including human cell lines, hepatocellular carcinoma biopsies, and <i>Caenorhabditis elegans</i>. Compared with established methods, FALCON-qPCR exhibits markedly higher sensitivity in detecting mtDNA damage induced by hydrogen peroxide, antimycin A, and rotenone. Its performance was further demonstrated in assessing mitochondrial toxicity of ruthenium-based compounds, highlighting its potential for pharmacological screening. By integrating enzymatic lesion recognition with quantitative amplification in a unified workflow, FALCON-qPCR eliminates the need for mitochondrial isolation. This methodological advance provides a rapid, accurate, and scalable platform for studying oxidative DNA damage, with broad applicability in mitochondrial research and translational toxicology. Mitochondria are tiny structures inside our cells that produce energy. When they work, they also create reactive molecules called ROS (reactive oxygen species). If ROS levels get too high, they can damage mitochondrial DNA (mtDNA), which may lead to diseases such as cancer and neurodegeneration. Measuring this damage is important, but current methods are slow, need large samples, and are not very sensitive. We developed a new method called FALCON-qPCR that measures mtDNA damage quickly and accurately. It uses a special enzyme to mark damaged DNA and then applies two types of PCR (a technique to copy DNA) to calculate how much damage is present. Unlike older methods, FALCON-qPCR works with very small samples – just 10,000 cells – and gives results in one day. We tested FALCON-qPCR on human cells, liver biopsies from cancer patients, and even tiny worms (<i>C.</i> <i>elegans</i>). In short, FALCON-qPCR is a fast, reliable, and versatile tool for studying mitochondrial DNA damage in research and clinical settings.
DOI: 10.5281/zenodo.18700218
title: Linked collectors and determiners for: A taxonomic revision of Stenoglottis (Orchideae, Orchidoideae, Orchidaceae).

description: Natural history specimen data linked to collectors and determiners held within, "A taxonomic revision of Stenoglottis (Orchideae, Orchidoideae, Orchidaceae)". Claims or attributions were made on Bionomia by volunteer Scribes, https://bionomia.net/dataset/e20afa6a-b9b0-40d6-922a-349da64e1a5b using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, https://gbif.org/dataset/e20afa6a-b9b0-40d6-922a-349da64e1a5b. Formatted as a Frictionless Data package.
DOI: 10.5281/zenodo.18700219
title: Linked collectors and determiners for: A taxonomic revision of Stenoglottis (Orchideae, Orchidoideae, Orchidaceae).

description: Natural history specimen data linked to collectors and determiners held within, "A taxonomic revision of Stenoglottis (Orchideae, Orchidoideae, Orchidaceae)". Claims or attributions were made on Bionomia by volunteer Scribes, https://bionomia.net/dataset/e20afa6a-b9b0-40d6-922a-349da64e1a5b using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, https://gbif.org/dataset/e20afa6a-b9b0-40d6-922a-349da64e1a5b. Formatted as a Frictionless Data package.
DOI: 10.6084/m9.figshare.30963310
title: Refined ADA testing strategy to overcome sRANKL interference in denosumab/FKS518 immunogenicity assessment

description: Fresenius Kabi developed FKS518, a fully human monoclonal antibody biosimilar to denosumab, that inhibits osteoclast activation by targeting the receptor activator of nuclear factor kappa-Β ligand (RANKL). RANKL exists as a trimeric soluble protein (sRANKL) with high affinity for denosumab. Post-dose, sRANKL levels can rise due to drug–target complex accumulation, creating a risk of interference in bridging anti-drug antibodies (ADA) assays, particularly after acid dissociation. We evaluated sRANKL interference in the ADA bridging assay and, to competitively block sRANKL, we introduced a specificity tier by adding osteoprotegerin (OPG). This approach enabled reanalysis of previously ADA-positive samples to confirm whether signals represented true ADA responses or artifacts caused by sRANKL interference. Acid dissociation significantly exacerbated target interference, resulting in ADA positivity rates of ~96–98% in clinical studies. Introducing a specificity tier corrected incidence to ≤3.9%. OPG incorporation did not change the minimum required dilution (MRD) of the assay and did not affect signals for negative/positive control, confirming assay integrity. These findings underscore the importance of early interference assessment and mitigation. A multi-tiered strategy, encompassing screening, confirmatory, and specificity tiers, provided a robust solution applicable to programs facing similar challenges. This study identified and solved a problem with the laboratory test for measuring immune responses to denosumab or its biosimilar, FKS518, in people treated with these medicines in clinical studies. Sometimes, after treatment, the body can make antibodies against the drug (called anti-drug antibodies or ADAs). Detecting these antibodies is important because they can affect how well the medicine works and its safety. The initial test showed that too many people had ADAs, but this was mostly because a protein called sRANKL, which increases after treatment, was interfering and causing false positives results. To fix this, an extra step was added to the test using a natural protein called osteoprotegerin (OPG), which blocks sRANKL. This made it possible to differentiate between real ADA responses and false results caused by interference. This new approach showed that the actual number of people with anti-drug antibodies was much lower and matched what is known from past studies. These results show that it’s important to check for this kind of interference early when developing tests for measuring ADAs. Adding OPG to the test is a practical way to get reliable results for biosimilar drug development and approval, ensuring that patients and doctors have reliable information about the safety of these medicines.
DOI: 10.6084/m9.figshare.30963310.v2
title: Refined ADA testing strategy to overcome sRANKL interference in denosumab/FKS518 immunogenicity assessment

description: Fresenius Kabi developed FKS518, a fully human monoclonal antibody biosimilar to denosumab, that inhibits osteoclast activation by targeting the receptor activator of nuclear factor kappa-Β ligand (RANKL). RANKL exists as a trimeric soluble protein (sRANKL) with high affinity for denosumab. Post-dose, sRANKL levels can rise due to drug–target complex accumulation, creating a risk of interference in bridging anti-drug antibodies (ADA) assays, particularly after acid dissociation. We evaluated sRANKL interference in the ADA bridging assay and, to competitively block sRANKL, we introduced a specificity tier by adding osteoprotegerin (OPG). This approach enabled reanalysis of previously ADA-positive samples to confirm whether signals represented true ADA responses or artifacts caused by sRANKL interference. Acid dissociation significantly exacerbated target interference, resulting in ADA positivity rates of ~96–98% in clinical studies. Introducing a specificity tier corrected incidence to ≤3.9%. OPG incorporation did not change the minimum required dilution (MRD) of the assay and did not affect signals for negative/positive control, confirming assay integrity. These findings underscore the importance of early interference assessment and mitigation. A multi-tiered strategy, encompassing screening, confirmatory, and specificity tiers, provided a robust solution applicable to programs facing similar challenges. This study identified and solved a problem with the laboratory test for measuring immune responses to denosumab or its biosimilar, FKS518, in people treated with these medicines in clinical studies. Sometimes, after treatment, the body can make antibodies against the drug (called anti-drug antibodies or ADAs). Detecting these antibodies is important because they can affect how well the medicine works and its safety. The initial test showed that too many people had ADAs, but this was mostly because a protein called sRANKL, which increases after treatment, was interfering and causing false positives results. To fix this, an extra step was added to the test using a natural protein called osteoprotegerin (OPG), which blocks sRANKL. This made it possible to differentiate between real ADA responses and false results caused by interference. This new approach showed that the actual number of people with anti-drug antibodies was much lower and matched what is known from past studies. These results show that it’s important to check for this kind of interference early when developing tests for measuring ADAs. Adding OPG to the test is a practical way to get reliable results for biosimilar drug development and approval, ensuring that patients and doctors have reliable information about the safety of these medicines.