cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1569567.v4
title: Photothermal confocal multicolor microscopy of nanoparticles and nanodrugs in live cells

description: Growing biomedical applications of non-fluorescent nanoparticles (NPs) for molecular imaging, disease diagnosis, drug delivery, and theranostics require new tools for real-time detection of nanomaterials, drug nano-carriers, and NP-drug conjugates (nanodrugs) in complex biological environments without additional labeling. Photothermal (PT) microscopy (PTM) has enormous potential for absorption-based identification and quantification of non-fluorescent molecules and NPs at a single molecule and 1.4 nm gold NP level. Recently, we have developed confocal PTM providing three-dimensional (3D) mapping and spectral identification of multiple chromophores and fluorophores in live cells. Here, we summarize recent advances in the application of confocal multicolor PTM for 3D visualization of single and clustered NPs, alone and in individual cells. In particular, we demonstrate identification of functionalized magnetic and gold–silver NPs, as well as graphene and carbon nanotubes in cancer cells and among blood cells. The potential to use PTM for super-resolution imaging (down to 50 nm), real-time NP tracking, guidance of PT nanotherapy, and multiplex cancer markers targeting, as well as analysis of non-linear PT phenomena and amplification of nanodrug efficacy through NP clustering and nano-bubble formation are also discussed.
DOI: 10.6084/m9.figshare.1569553.v3
title: Quantitative large scale gene expression profiling from human stem cell culture micro samples using multiplex pre-amplification

description: Transcriptional profiling is a powerful tool to study biological mechanisms during stem cell differentiation and reprogramming. Genome-wide methods like microarrays or next generation sequencing are expensive, time consuming, and require special equipment and bioinformatics expertise. Quantitative RT-PCR remains one of today’s most widely accepted and used methods for analyzing gene expression in biological samples. However, limitations in the amount of starting materials often hinder the quantity and quality of information that could be obtained from a given sample. Here, we present a fast 4-step workflow allowing direct, column-free RNA isolation from limited human pluripotent stem cell (hPSC) cultures that is directly compatible with subsequent reverse transcription, target specific multiplex pre-amplification, and standard SYBR-Green quantitative PCR (qPCR) analysis. The workflow delivers excellent correlations in normalized gene-expression data obtained from different samples of hPSCs over a wide range of cell numbers (500–50,000 cells). We demonstrate accurate and unbiased target gene quantification in limiting stem cell cultures which allows for monitoring embryoid body differentiation and induced pluripotent stem cell (iPSC) reprogramming. This method highlights a rapid and cost effective screening process, allowing reduction of culture formats and increase of processing throughputs for various stem cell applications.
DOI: 10.6084/m9.figshare.1569567.v3
title: Photothermal confocal multicolor microscopy of nanoparticles and nanodrugs in live cells

description: Growing biomedical applications of non-fluorescent nanoparticles (NPs) for molecular imaging, disease diagnosis, drug delivery, and theranostics require new tools for real-time detection of nanomaterials, drug nano-carriers, and NP-drug conjugates (nanodrugs) in complex biological environments without additional labeling. Photothermal (PT) microscopy (PTM) has enormous potential for absorption-based identification and quantification of non-fluorescent molecules and NPs at a single molecule and 1.4 nm gold NP level. Recently, we have developed confocal PTM providing three-dimensional (3D) mapping and spectral identification of multiple chromophores and fluorophores in live cells. Here, we summarize recent advances in the application of confocal multicolor PTM for 3D visualization of single and clustered NPs, alone and in individual cells. In particular, we demonstrate identification of functionalized magnetic and gold–silver NPs, as well as graphene and carbon nanotubes in cancer cells and among blood cells. The potential to use PTM for super-resolution imaging (down to 50 nm), real-time NP tracking, guidance of PT nanotherapy, and multiplex cancer markers targeting, as well as analysis of non-linear PT phenomena and amplification of nanodrug efficacy through NP clustering and nano-bubble formation are also discussed.
DOI: 10.6084/m9.figshare.1569553.v2
title: Quantitative large scale gene expression profiling from human stem cell culture micro samples using multiplex pre-amplification

description: Transcriptional profiling is a powerful tool to study biological mechanisms during stem cell differentiation and reprogramming. Genome-wide methods like microarrays or next generation sequencing are expensive, time consuming, and require special equipment and bioinformatics expertise. Quantitative RT-PCR remains one of today’s most widely accepted and used methods for analyzing gene expression in biological samples. However, limitations in the amount of starting materials often hinder the quantity and quality of information that could be obtained from a given sample. Here, we present a fast 4-step workflow allowing direct, column-free RNA isolation from limited human pluripotent stem cell (hPSC) cultures that is directly compatible with subsequent reverse transcription, target specific multiplex pre-amplification, and standard SYBR-Green quantitative PCR (qPCR) analysis. The workflow delivers excellent correlations in normalized gene-expression data obtained from different samples of hPSCs over a wide range of cell numbers (500–50,000 cells). We demonstrate accurate and unbiased target gene quantification in limiting stem cell cultures which allows for monitoring embryoid body differentiation and induced pluripotent stem cell (iPSC) reprogramming. This method highlights a rapid and cost effective screening process, allowing reduction of culture formats and increase of processing throughputs for various stem cell applications.
DOI: 10.6084/m9.figshare.1569539
title: Abundance and #RTU’s of Insects Captured in Sweep Net along a 20 Meter Length in Grassland Area

description: The objective of this lab was to determine the total number of insects and number of different species (#RTU’s) caught along a specified area by using a sweep net. Methods: A transect was laid in a grassland region, measuring a total distance of 20 meters. A sweep net was used to catch any insects along the transect line. The experimenter walked at slow to normal pace along the 20 meter line, vigorously moving the sweep net back and forth in a horizontal “8” formation at stomach-chest height. At the end of the 20 meter walk, the net was quickly held shut to prevent any insects from escaping. While still holding the net shut, the total number of individuals caught was counted and recorded. The number of individuals were grouped into number of different species (#RTU’s) and recorded. When all the needed data was collected, the caught species were allowed to escape. At the beginning of each new trial, the transect was placed into a new, undisturbed location. This was done to ensure that the experimenter’s activity from the previous trial did not interfere with the new trial’s results. This entire process was performed for a total of 10 times (n=10). All the data collected was recorded in a chart. The experiment was conducted by Hannan Fayyaz, Gopaul Parbatie, Albert Lin and Gajamugan Rajavarothayan on Thursday Obtober 1st-2015 during the lab hours of 2:30pm-5:30pm on a grassland region located on Keele Campus of York University. The temperature during the experiment was observed to be 15oC. The tools used to conduct the experiment were a 20 meter long transect and a sweep net.
DOI: 10.6084/m9.figshare.1569539.v2
title: Abundance and #RTU’s of Insects Captured in Sweep Net along a 20 Meter Length in Grassland Area

description: The objective of this lab was to determine the total number of insects and number of different species (#RTU’s) caught along a specified area by using a sweep net. Methods: A transect was laid in a grassland region, measuring a total distance of 20 meters. A sweep net was used to catch any insects along the transect line. The experimenter walked at slow to normal pace along the 20 meter line, vigorously moving the sweep net back and forth in a horizontal “8” formation at stomach-chest height. At the end of the 20 meter walk, the net was quickly held shut to prevent any insects from escaping. While still holding the net shut, the total number of individuals caught was counted and recorded. The number of individuals were grouped into number of different species (#RTU’s) and recorded. When all the needed data was collected, the caught species were allowed to escape. At the beginning of each new trial, the transect was placed into a new, undisturbed location. This was done to ensure that the experimenter’s activity from the previous trial did not interfere with the new trial’s results. This entire process was performed for a total of 10 times (n=10). All the data collected was recorded in a chart. The experiment was conducted by Hannan Fayyaz, Gopaul Parbatie, Albert Lin and Gajamugan Rajavarothayan on Thursday Obtober 1st-2015 during the lab hours of 2:30pm-5:30pm on a grassland region located on Keele Campus of York University. The temperature during the experiment was observed to be 15oC. The tools used to conduct the experiment were a 20 meter long transect and a sweep net.
DOI: 10.6084/m9.figshare.1569539.v1
title: Abundance and #RTU’s of Insects Captured in Sweep Net along a 20 Meter Length in Grassland Area

description: The objective of this lab was to determine the total number of insects and number of different species (#RTU’s) caught along a specified area by using a sweep net. Methods: A transect was laid in a grassland region, measuring a total distance of 20 meters. A sweep net was used to catch any insects along the transect line. The experimenter walked at slow to normal pace along the 20 meter line, vigorously moving the sweep net back and forth in a horizontal “8” formation at stomach-chest height. At the end of the 20 meter walk, the net was quickly held shut to prevent any insects from escaping. While still holding the net shut, the total number of individuals caught was counted and recorded. The number of individuals were grouped into number of different species (#RTU’s) and recorded. When all the needed data was collected, the caught species were allowed to escape. At the beginning of each new trial, the transect was placed into a new, undisturbed location. This was done to ensure that the experimenter’s activity from the previous trial did not interfere with the new trial’s results. This entire process was performed for a total of 10 times (n=10). All the data collected was recorded in a chart. This experiment was conducted by Hannan Fayyaz, Gopaul Parbatie, Albert Lin and Gajamugan Rajavarothayan on Thursday Obtober 1st-2015 during the lab hours of 2:30pm-5:30pm on a grassland region located on Keele Campus of York University
DOI: 10.6084/m9.figshare.1569533
title: Evaluation of a newly developed quantitative heart-type fatty acid binding protein assay based on fluorescence immunochromatography using specific monoclonal antibodies

description: <b><i>Objectives.</i></b> To develop a rapid, sensitive and specific assay for quantification of serum heart-type fatty acid binding protein (H-FABP) based on immunofluorescence of specific monoclonal antibodies. <b><i>Design and Methods.</i></b> We generated novel H-FABP-directed monoclonal antibodies by cloning of spleen cells of mice immunized with H-FABP. Epitopes were mapped and antigen affinity was assessed by surface plasmon resonance (SPR). The H-FABP specific monoclonal antibodies were coupled to fluorescent beads and sprayed onto a nitrocellulose membrane facilitating quantification of H-FABP by immunofluorescence. Reagent cross-reactivity, interference resistance, accuracy and sensitivity were examined. A total of 103 clinical samples were used to compare the sensitivity and specificity of the new assay to a commercially available Randox kit. <b><i>Results.</i></b> This new assay could be finished within 15 min, with sensitivity reaching 1 ng/ml. In a trial of 103 clinical serum samples, the new testing kit results were highly correlated with those from the Randox kit (R<sup>2</sup> = 0.9707). Using the Randox kit as the reference kit, the sensitivity of the new assay was 98.25%, and specificity was 100%. <b><i>Conclusions.</i></b> An immunofluorescence-based H-FABP assay employing novel monoclonal antibodies could rapidly, specifically and sensitively detect H-FABP in serum samples, providing an effective method for rapid clinical assessment of H-FABP index in the clinic.
DOI: 10.6084/m9.figshare.1569546.v1
title: Petrogenesis of Early Cretaceous volcanic rocks of the Manketouebo Formation in the Wuchagou region, central Great Xing’an Range, NE China, and tectonic implications: geochronological, geochemical, and Hf isotopic evidence

description: ABSTRACTThis study presents new whole-rock major and trace element geochemistry, zircon U–Pb ages, and Hf-isotope compositions for volcanic rocks from the Manketouebo Formation of the central Great Xing’an Range, NE China. These data provide precise ages and information on the petrogenesis and source of the magmas that formed this formation, furthering our understanding of the geodynamic setting of the large-scale late Mesozoic magmatism in the Great Xing’an Range and other areas in NE China. The Manketouebo Formation in the study area is dominated by rhyolites and rhyolitic tuffs with minor trachydacites. The LA-ICP-MS zircon U–Pb dating indicates that these volcanic rocks formed between 143 and 139 Ma. The volcanic rocks contain high silica (66.70–79.91 wt.%) and total alkali (5.93–9.72 wt.%) concentrations, and low concentrations of MgO (0.08–1.15 wt.%), total FeO (0.68–4.50 wt.%), and CaO (0.10–2.56 wt.%). They are enriched in large-ion lithophile elements (LILEs; e.g. Rb, Th, and U) and light rare earth elements (LREEs), and depleted in high field strength elements (HFSEs; e.g. Nb, Ta, Ti, and P) and heavy rare earth elements (HREEs), indicating that they are similar to highly fractionated I-type igneous rocks. All of the magmatic zircons from the analysed samples have high initial <sup>176</sup>Hf/<sup>177</sup>Hf ratios (0.282900–0.283093), positive <i>ε</i><sub>Hf</sub>(<i>t</i>) values (7.48–14.19), and young Hf two-stage model ages (954–344 Ma) that suggest the primary magma that formed the volcanic rocks of the Manketouebo Formation was derived from the partial melting of Neoproterozoic to Phanerozoic juvenile crustal material, indicating in turn that significant crustal growth occurred at this time within the Xing’an Terrane. These data, combined with previous research into the spatial–temporal distribution of Mesozoic volcanic rocks in NE China, suggest that the Early Cretaceous magmatism in the Great Xing’an Range was influenced by both the subduction of the Palaeo-Pacific Plate and the closure of the Mongol–Okhotsk Ocean. This was a crucial period in the transformation from the Mongol–Okhotsk Ocean to the Palaeo-Pacific tectonic regimes. In summary, the early stages of Early Cretaceous magmatism in this area were related to the closure of the Mongol–Okhotsk Ocean, whereas the later stages of magmatism in this area and elsewhere in NE China were related to the subduction of the Palaeo-Pacific Plate.
DOI: 10.6084/m9.figshare.1569533.v2
title: Evaluation of a newly developed quantitative heart-type fatty acid binding protein assay based on fluorescence immunochromatography using specific monoclonal antibodies

description: <b><i>Objectives.</i></b> To develop a rapid, sensitive and specific assay for quantification of serum heart-type fatty acid binding protein (H-FABP) based on immunofluorescence of specific monoclonal antibodies. <b><i>Design and Methods.</i></b> We generated novel H-FABP-directed monoclonal antibodies by cloning of spleen cells of mice immunized with H-FABP. Epitopes were mapped and antigen affinity was assessed by surface plasmon resonance (SPR). The H-FABP specific monoclonal antibodies were coupled to fluorescent beads and sprayed onto a nitrocellulose membrane facilitating quantification of H-FABP by immunofluorescence. Reagent cross-reactivity, interference resistance, accuracy and sensitivity were examined. A total of 103 clinical samples were used to compare the sensitivity and specificity of the new assay to a commercially available Randox kit. <b><i>Results.</i></b> This new assay could be finished within 15 min, with sensitivity reaching 1 ng/ml. In a trial of 103 clinical serum samples, the new testing kit results were highly correlated with those from the Randox kit (R<sup>2</sup> = 0.9707). Using the Randox kit as the reference kit, the sensitivity of the new assay was 98.25%, and specificity was 100%. <b><i>Conclusions.</i></b> An immunofluorescence-based H-FABP assay employing novel monoclonal antibodies could rapidly, specifically and sensitively detect H-FABP in serum samples, providing an effective method for rapid clinical assessment of H-FABP index in the clinic.
DOI: 10.6084/m9.figshare.1569546.v3
title: Petrogenesis of Early Cretaceous volcanic rocks of the Manketouebo Formation in the Wuchagou region, central Great Xing’an Range, NE China, and tectonic implications: geochronological, geochemical, and Hf isotopic evidence

description: This study presents new whole-rock major and trace element geochemistry, zircon U–Pb ages, and Hf-isotope compositions for volcanic rocks from the Manketouebo Formation of the central Great Xing’an Range, NE China. These data provide precise ages and information on the petrogenesis and source of the magmas that formed this formation, furthering our understanding of the geodynamic setting of the large-scale late Mesozoic magmatism in the Great Xing’an Range and other areas in NE China. The Manketouebo Formation in the study area is dominated by rhyolites and rhyolitic tuffs with minor trachydacites. The LA-ICP-MS zircon U–Pb dating indicates that these volcanic rocks formed between 143 and 139 Ma. The volcanic rocks contain high silica (66.70–79.91 wt.%) and total alkali (5.93–9.72 wt.%) concentrations, and low concentrations of MgO (0.08–1.15 wt.%), total FeO (0.68–4.50 wt.%), and CaO (0.10–2.56 wt.%). They are enriched in large-ion lithophile elements (LILEs; e.g. Rb, Th, and U) and light rare earth elements (LREEs), and depleted in high field strength elements (HFSEs; e.g. Nb, Ta, Ti, and P) and heavy rare earth elements (HREEs), indicating that they are similar to highly fractionated I-type igneous rocks. All of the magmatic zircons from the analysed samples have high initial <sup>176</sup>Hf/<sup>177</sup>Hf ratios (0.282900–0.283093), positive <i>ε</i><sub>Hf</sub>(<i>t</i>) values (7.48–14.19), and young Hf two-stage model ages (954–344 Ma) that suggest the primary magma that formed the volcanic rocks of the Manketouebo Formation was derived from the partial melting of Neoproterozoic to Phanerozoic juvenile crustal material, indicating in turn that significant crustal growth occurred at this time within the Xing’an Terrane. These data, combined with previous research into the spatial–temporal distribution of Mesozoic volcanic rocks in NE China, suggest that the Early Cretaceous magmatism in the Great Xing’an Range was influenced by both the subduction of the Palaeo-Pacific Plate and the closure of the Mongol–Okhotsk Ocean. This was a crucial period in the transformation from the Mongol–Okhotsk Ocean to the Palaeo-Pacific tectonic regimes. In summary, the early stages of Early Cretaceous magmatism in this area were related to the closure of the Mongol–Okhotsk Ocean, whereas the later stages of magmatism in this area and elsewhere in NE China were related to the subduction of the Palaeo-Pacific Plate.
DOI: 10.6084/m9.figshare.1569546.v2
title: Petrogenesis of Early Cretaceous volcanic rocks of the Manketouebo Formation in the Wuchagou region, central Great Xing’an Range, NE China, and tectonic implications: geochronological, geochemical, and Hf isotopic evidence

description: ABSTRACTThis study presents new whole-rock major and trace element geochemistry, zircon U–Pb ages, and Hf-isotope compositions for volcanic rocks from the Manketouebo Formation of the central Great Xing’an Range, NE China. These data provide precise ages and information on the petrogenesis and source of the magmas that formed this formation, furthering our understanding of the geodynamic setting of the large-scale late Mesozoic magmatism in the Great Xing’an Range and other areas in NE China. The Manketouebo Formation in the study area is dominated by rhyolites and rhyolitic tuffs with minor trachydacites. The LA-ICP-MS zircon U–Pb dating indicates that these volcanic rocks formed between 143 and 139 Ma. The volcanic rocks contain high silica (66.70–79.91 wt.%) and total alkali (5.93–9.72 wt.%) concentrations, and low concentrations of MgO (0.08–1.15 wt.%), total FeO (0.68–4.50 wt.%), and CaO (0.10–2.56 wt.%). They are enriched in large-ion lithophile elements (LILEs; e.g. Rb, Th, and U) and light rare earth elements (LREEs), and depleted in high field strength elements (HFSEs; e.g. Nb, Ta, Ti, and P) and heavy rare earth elements (HREEs), indicating that they are similar to highly fractionated I-type igneous rocks. All of the magmatic zircons from the analysed samples have high initial <sup>176</sup>Hf/<sup>177</sup>Hf ratios (0.282900–0.283093), positive <i>ε</i><sub>Hf</sub>(<i>t</i>) values (7.48–14.19), and young Hf two-stage model ages (954–344 Ma) that suggest the primary magma that formed the volcanic rocks of the Manketouebo Formation was derived from the partial melting of Neoproterozoic to Phanerozoic juvenile crustal material, indicating in turn that significant crustal growth occurred at this time within the Xing’an Terrane. These data, combined with previous research into the spatial–temporal distribution of Mesozoic volcanic rocks in NE China, suggest that the Early Cretaceous magmatism in the Great Xing’an Range was influenced by both the subduction of the Palaeo-Pacific Plate and the closure of the Mongol–Okhotsk Ocean. This was a crucial period in the transformation from the Mongol–Okhotsk Ocean to the Palaeo-Pacific tectonic regimes. In summary, the early stages of Early Cretaceous magmatism in this area were related to the closure of the Mongol–Okhotsk Ocean, whereas the later stages of magmatism in this area and elsewhere in NE China were related to the subduction of the Palaeo-Pacific Plate.