cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1569615
title: SelectionOne_proJK1-LGK-CombinedTiles

description: Selection One Combined Tiles Comprehensive Sequence-Flux Mapping of a Levoglucosan Utilization Pathway in E. coli<br>Justin R. Klesmith, John-Paul Bacik, Ryszard Michalczyk, and Timothy A. Whitehead<br>http://pubs.acs.org/doi/full/10.1021/acssynbio.5b00131<br>DOI: 10.1021/acssynbio.5b00131
DOI: 10.6084/m9.figshare.1569618.v1
title: SelectionTwo_proNR2-LGK1-CSV

description: Selection Two - CSV Comprehensive Sequence-Flux Mapping of a Levoglucosan Utilization Pathway in E. coli<br>Justin R. Klesmith, John-Paul Bacik, Ryszard Michalczyk, and Timothy A. Whitehead<br>http://pubs.acs.org/doi/full/10.1021/acssynbio.5b00131<br>DOI: 10.1021/acssynbio.5b00131
DOI: 10.6084/m9.figshare.1569615.v1
title: SelectionOne_proJK1-LGK-CombinedTiles

description: Selection One Combined Tiles Comprehensive Sequence-Flux Mapping of a Levoglucosan Utilization Pathway in E. coli<br>Justin R. Klesmith, John-Paul Bacik, Ryszard Michalczyk, and Timothy A. Whitehead<br>http://pubs.acs.org/doi/full/10.1021/acssynbio.5b00131<br>DOI: 10.1021/acssynbio.5b00131
DOI: 10.6084/m9.figshare.1569603
title: Salarin C inhibits the maintenance of chronic myeloid leukemia progenitor cells

description: We previously showed that incubation of chronic myeloid leukemia (CML) cells in very low oxygen selects a cell subset where the oncogenetic BCR/Abl protein is suppressed and which is thereby refractory to tyrosine kinase inhibitors used for CML therapy. In this study, salarin C, an anticancer macrolide extracted from the <i>Fascaplysinopsis</i> sponge, was tested as for its activity on CML cells, especially after their incubation in atmosphere at 0.1% oxygen. Salarin C induced mitotic cycle arrest, apoptosis and DNA damage. Salarin C also concentration-dependently inhibited the maintenance of stem cell potential in cultures in low oxygen of either CML cell lines or primary cells. Surprisingly, the drug also concentration-dependently enforced the maintenance of BCR/Abl signaling in low oxygen, an effect which was paralleled by the rescue of sensitivity of stem cell potential to IM. These results suggest a potential use of salarin C for the suppression of CML cells refractory to tyrosine kinase inhibitors
DOI: 10.6084/m9.figshare.1569603.v1
title: Salarin C inhibits maintenance of hypoxia-selected Chronic Myeloid Leukemia progenitor cells

description: We previously showed that incubation of chronic myeloid leukemia (CML) cells in very low oxygen selects a cell subset where the oncogenetic BCR/Abl protein is suppressed and which is thereby refractory to tyrosine kinase inhibitors used for CML therapy. In this study, salarin C, an anticancer macrolide extracted from the <i>Fascaplysinopsis</i> sponge, was tested as for its activity on CML cells, especially after their incubation in atmosphere at 0.1% oxygen. Salarin C induced mitotic cycle arrest, apoptosis and DNA damage. Salarin C also concentration-dependently inhibited the maintenance of stem cell potential in cultures in low oxygen of either CML cell lines or primary cells. Surprisingly, the drug also concentration-dependently enforced the maintenance of BCR/Abl signaling in low oxygen, an effect which was paralleled by the rescue of sensitivity of stem cell potential to IM. These results suggest a potential use of salarin C for the suppression of CML cells refractory to tyrosine kinase inhibitors.
DOI: 10.6084/m9.figshare.1569603.v3
title: Salarin C inhibits the maintenance of chronic myeloid leukemia progenitor cells

description: We previously showed that incubation of chronic myeloid leukemia (CML) cells in very low oxygen selects a cell subset where the oncogenetic BCR/Abl protein is suppressed and which is thereby refractory to tyrosine kinase inhibitors used for CML therapy. In this study, salarin C, an anticancer macrolide extracted from the <i>Fascaplysinopsis</i> sponge, was tested as for its activity on CML cells, especially after their incubation in atmosphere at 0.1% oxygen. Salarin C induced mitotic cycle arrest, apoptosis and DNA damage. Salarin C also concentration-dependently inhibited the maintenance of stem cell potential in cultures in low oxygen of either CML cell lines or primary cells. Surprisingly, the drug also concentration-dependently enforced the maintenance of BCR/Abl signaling in low oxygen, an effect which was paralleled by the rescue of sensitivity of stem cell potential to IM. These results suggest a potential use of salarin C for the suppression of CML cells refractory to tyrosine kinase inhibitors
DOI: 10.6084/m9.figshare.1569603.v2
title: Salarin C inhibits the maintenance of chronic myeloid leukemia progenitor cells

description: We previously showed that incubation of chronic myeloid leukemia (CML) cells in very low oxygen selects a cell subset where the oncogenetic BCR/Abl protein is suppressed and which is thereby refractory to tyrosine kinase inhibitors used for CML therapy. In this study, salarin C, an anticancer macrolide extracted from the <i>Fascaplysinopsis</i> sponge, was tested as for its activity on CML cells, especially after their incubation in atmosphere at 0.1% oxygen. Salarin C induced mitotic cycle arrest, apoptosis and DNA damage. Salarin C also concentration-dependently inhibited the maintenance of stem cell potential in cultures in low oxygen of either CML cell lines or primary cells. Surprisingly, the drug also concentration-dependently enforced the maintenance of BCR/Abl signaling in low oxygen, an effect which was paralleled by the rescue of sensitivity of stem cell potential to IM. These results suggest a potential use of salarin C for the suppression of CML cells refractory to tyrosine kinase inhibitors
DOI: 10.6084/m9.figshare.1569590
title: A minute ostracod (Crustacea: Cytheromatidae) from the Miocene Solimões Formation (western Amazonia, Brazil): evidence for marine incursions?

description: A huge wetland (the ‘Pebas system’) covered western Amazonia during the Miocene, hosting a highly diverse and endemic aquatic fauna. One of the most contentious issues concerns the existence, potential pathways and effects of marine incursions on this ecosystem. Palaeontological evidences (body fossils) are rare. The finding of a new, presumably marine ostracod species (<i>Pellucistoma curupira</i> sp. nov.) in the upper middle Miocene Solimões Formation initiated a taxonomic, ecological and biogeographical review of the genus <i>Pellucistoma</i>. We demonstrate that this marine (sublittoral, euhaline), subtropical–tropical taxon is biogeographically confined to the Americas. The biogeographical distribution of <i>Pellucistoma</i> largely depends on geographical, thermal and osmotic barriers (e.g. land bridges, deep and/or cold waters, sea currents, salinity). We assume an Oligocene/early Miocene, Caribbean origin for <i>Pellucistoma</i> and outline the dispersal of hitherto known species up to the Holocene. <i>Pellucistoma curupira</i> sp. nov. is dwarfed in comparison to all other species of this genus and extremely thin-shelled. This is probably related to poorly oxygenated waters and, in particular, to strongly reduced salinity. The associated ostracod fauna (dominated by the eurypotent <i>Cyprideis</i> and a few, also stunted ostracods of possibly marine ancestry) supports this claim. Geochemical analyses (δ<sup>18</sup>O, δ<sup>13</sup>C) on co-occurring ostracod valves (<i>Cyprideis</i> spp.) yielded very light values, indicative of a freshwater setting. These observations point to a successful adaptation of <i>P. curupira</i> sp. nov. to freshwater conditions and therefore do not signify the presence of marine water. <i>Pellucistoma curupira</i> sp. nov. shows closest affinities to Caribbean species. We hypothesize that <i>Pellucistoma</i> reached northern South America (Llanos Basin) during marine incursions in the early Miocene. While larger animals of marine origin (e.g. fishes, dolphins, manatees) migrated actively into the Pebas wetland via fluvial connections, small biota (e.g. <i>P. curupira</i> sp. nov.) were phoretically freighted and developed freshwater tolerance over long timescales.http://zoobank.org/urn:lsid:zoobank.org:pub:886C6476-393D-4323-8C0E-06BB8BD02FD9
DOI: 10.6084/m9.figshare.1569590.v1
title: A minute ostracod (Crustacea: Cytheromatidae) from the Miocene Solimões Formation (western Amazonia, Brazil): evidence for marine incursions?

description: A huge wetland (the ‘Pebas system’) covered western Amazonia during the Miocene, hosting a highly diverse and endemic aquatic fauna. One of the most contentious issues concerns the existence, potential pathways and effects of marine incursions on this ecosystem. Palaeontological evidences (body fossils) are rare. The finding of a new, presumably marine ostracod species (<i>Pellucistoma curupira</i> sp. nov.) in the upper middle Miocene Solimões Formation initiated a taxonomic, ecological and biogeographical review of the genus <i>Pellucistoma</i>. We demonstrate that this marine (sublittoral, euhaline), subtropical–tropical taxon is biogeographically confined to the Americas. The biogeographical distribution of <i>Pellucistoma</i> largely depends on geographical, thermal and osmotic barriers (e.g. land bridges, deep and/or cold waters, sea currents, salinity). We assume an Oligocene/early Miocene, Caribbean origin for <i>Pellucistoma</i> and outline the dispersal of hitherto known species up to the Holocene. <i>Pellucistoma curupira</i> sp. nov. is dwarfed in comparison to all other species of this genus and extremely thin-shelled. This is probably related to poorly oxygenated waters and, in particular, to strongly reduced salinity. The associated ostracod fauna (dominated by the eurypotent <i>Cyprideis</i> and a few, also stunted ostracods of possibly marine ancestry) supports this claim. Geochemical analyses (δ<sup>18</sup>O, δ<sup>13</sup>C) on co-occurring ostracod valves (<i>Cyprideis</i> spp.) yielded very light values, indicative of a freshwater setting. These observations point to a successful adaptation of <i>P. curupira</i> sp. nov. to freshwater conditions and therefore do not signify the presence of marine water. <i>Pellucistoma curupira</i> sp. nov. shows closest affinities to Caribbean species. We hypothesize that <i>Pellucistoma</i> reached northern South America (Llanos Basin) during marine incursions in the early Miocene. While larger animals of marine origin (e.g. fishes, dolphins, manatees) migrated actively into the Pebas wetland via fluvial connections, small biota (e.g. <i>P. curupira</i> sp. nov.) were phoretically freighted and developed freshwater tolerance over long timescales.http://zoobank.org/urn:lsid:zoobank.org:pub:886C6476-393D-4323-8C0E-06BB8BD02FD9
DOI: 10.6084/m9.figshare.1569590.v3
title: A minute ostracod (Crustacea: Cytheromatidae) from the Miocene Solimões Formation (western Amazonia, Brazil): evidence for marine incursions?

description: A huge wetland (the ‘Pebas system’) covered western Amazonia during the Miocene, hosting a highly diverse and endemic aquatic fauna. One of the most contentious issues concerns the existence, potential pathways and effects of marine incursions on this ecosystem. Palaeontological evidences (body fossils) are rare. The finding of a new, presumably marine ostracod species (<i>Pellucistoma curupira</i> sp. nov.) in the upper middle Miocene Solimões Formation initiated a taxonomic, ecological and biogeographical review of the genus <i>Pellucistoma</i>. We demonstrate that this marine (sublittoral, euhaline), subtropical–tropical taxon is biogeographically confined to the Americas. The biogeographical distribution of <i>Pellucistoma</i> largely depends on geographical, thermal and osmotic barriers (e.g. land bridges, deep and/or cold waters, sea currents, salinity). We assume an Oligocene/early Miocene, Caribbean origin for <i>Pellucistoma</i> and outline the dispersal of hitherto known species up to the Holocene. <i>Pellucistoma curupira</i> sp. nov. is dwarfed in comparison to all other species of this genus and extremely thin-shelled. This is probably related to poorly oxygenated waters and, in particular, to strongly reduced salinity. The associated ostracod fauna (dominated by the eurypotent <i>Cyprideis</i> and a few, also stunted ostracods of possibly marine ancestry) supports this claim. Geochemical analyses (δ<sup>18</sup>O, δ<sup>13</sup>C) on co-occurring ostracod valves (<i>Cyprideis</i> spp.) yielded very light values, indicative of a freshwater setting. These observations point to a successful adaptation of <i>P. curupira</i> sp. nov. to freshwater conditions and therefore do not signify the presence of marine water. <i>Pellucistoma curupira</i> sp. nov. shows closest affinities to Caribbean species. We hypothesize that <i>Pellucistoma</i> reached northern South America (Llanos Basin) during marine incursions in the early Miocene. While larger animals of marine origin (e.g. fishes, dolphins, manatees) migrated actively into the Pebas wetland via fluvial connections, small biota (e.g. <i>P. curupira</i> sp. nov.) were phoretically freighted and developed freshwater tolerance over long timescales.http://zoobank.org/urn:lsid:zoobank.org:pub:886C6476-393D-4323-8C0E-06BB8BD02FD9
DOI: 10.6084/m9.figshare.1569590.v2
title: A minute ostracod (Crustacea: Cytheromatidae) from the Miocene Solimões Formation (western Amazonia, Brazil): evidence for marine incursions?

description: A huge wetland (the ‘Pebas system’) covered western Amazonia during the Miocene, hosting a highly diverse and endemic aquatic fauna. One of the most contentious issues concerns the existence, potential pathways and effects of marine incursions on this ecosystem. Palaeontological evidences (body fossils) are rare. The finding of a new, presumably marine ostracod species (<i>Pellucistoma curupira</i> sp. nov.) in the upper middle Miocene Solimões Formation initiated a taxonomic, ecological and biogeographical review of the genus <i>Pellucistoma</i>. We demonstrate that this marine (sublittoral, euhaline), subtropical–tropical taxon is biogeographically confined to the Americas. The biogeographical distribution of <i>Pellucistoma</i> largely depends on geographical, thermal and osmotic barriers (e.g. land bridges, deep and/or cold waters, sea currents, salinity). We assume an Oligocene/early Miocene, Caribbean origin for <i>Pellucistoma</i> and outline the dispersal of hitherto known species up to the Holocene. <i>Pellucistoma curupira</i> sp. nov. is dwarfed in comparison to all other species of this genus and extremely thin-shelled. This is probably related to poorly oxygenated waters and, in particular, to strongly reduced salinity. The associated ostracod fauna (dominated by the eurypotent <i>Cyprideis</i> and a few, also stunted ostracods of possibly marine ancestry) supports this claim. Geochemical analyses (δ<sup>18</sup>O, δ<sup>13</sup>C) on co-occurring ostracod valves (<i>Cyprideis</i> spp.) yielded very light values, indicative of a freshwater setting. These observations point to a successful adaptation of <i>P. curupira</i> sp. nov. to freshwater conditions and therefore do not signify the presence of marine water. <i>Pellucistoma curupira</i> sp. nov. shows closest affinities to Caribbean species. We hypothesize that <i>Pellucistoma</i> reached northern South America (Llanos Basin) during marine incursions in the early Miocene. While larger animals of marine origin (e.g. fishes, dolphins, manatees) migrated actively into the Pebas wetland via fluvial connections, small biota (e.g. <i>P. curupira</i> sp. nov.) were phoretically freighted and developed freshwater tolerance over long timescales.http://zoobank.org/urn:lsid:zoobank.org:pub:886C6476-393D-4323-8C0E-06BB8BD02FD9
DOI: 10.6084/m9.figshare.1569567
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.1569562
title: Local infiltration analgesia is not improved by postoperative intra-articular bolus injections for pain after total hip arthroplasty

description: <b>Background and purpose —</b> The effect of postoperative intra-articular bolus injections after total hip arthroplasty (THA) remains unclear. We tested the hypothesis that intra-articular bolus injections administered every 6 hours after surgery during the first 24 hours would significantly improve analgesia after THA.<b>Patients and methods —</b> 80 patients undergoing THA received high-volume local infiltration analgesia (LIA; 200 mg ropivacaine and 30 mg ketorolac) followed by 4 intra-articular injections with either ropivacaine (100 mg) and ketorolac (15 mg) (the treatment group) or saline (the control group). The intra-articular injections were combined with 4 intravenous injections of either saline (treatment group) or 15 mg ketorolac (control group). All patients received morphine as patient-controlled analgesia (PCA). The primary outcome was consumption of intravenous morphine PCA and secondary outcomes were consumption of oral morphine, pain intensity, side effects, readiness for hospital discharge, length of hospital stay, and postoperative consumption of analgesics at 3, 6, and 12 weeks after surgery.<b>Results —</b> There were no statistically significant differences between the 2 groups regarding postoperative consumption of intravenous morphine PCA. Postoperative pain scores during walking were higher in the treatment group from 24–72 hours after surgery, but other pain scores were similar between groups. Time to readiness for hospital discharge was longer in the treatment group. Other secondary outcomes were similar between groups.<b>Interpretation —</b> Postoperative intra-articular bolus injections of ropivacaine and ketorolac cannot be recommended as analgesic method after THA.
DOI: 10.6084/m9.figshare.1569562.v1
title: Local infiltration analgesia is not improved by postoperative intra-articular bolus injections for pain after total hip arthroplasty

description: <b>Background and purpose —</b> The effect of postoperative intra-articular bolus injections after total hip arthroplasty (THA) remains unclear. We tested the hypothesis that intra-articular bolus injections administered every 6 hours after surgery during the first 24 hours would significantly improve analgesia after THA.<b>Patients and methods —</b> 80 patients undergoing THA received high-volume local infiltration analgesia (LIA; 200 mg ropivacaine and 30 mg ketorolac) followed by 4 intra-articular injections with either ropivacaine (100 mg) and ketorolac (15 mg) (the treatment group) or saline (the control group). The intra-articular injections were combined with 4 intravenous injections of either saline (treatment group) or 15 mg ketorolac (control group). All patients received morphine as patient-controlled analgesia (PCA). The primary outcome was consumption of intravenous morphine PCA and secondary outcomes were consumption of oral morphine, pain intensity, side effects, readiness for hospital discharge, length of hospital stay, and postoperative consumption of analgesics at 3, 6, and 12 weeks after surgery.<b>Results —</b> There were no statistically significant differences between the 2 groups regarding postoperative consumption of intravenous morphine PCA. Postoperative pain scores during walking were higher in the treatment group from 24–72 hours after surgery, but other pain scores were similar between groups. Time to readiness for hospital discharge was longer in the treatment group. Other secondary outcomes were similar between groups.<b>Interpretation —</b> Postoperative intra-articular bolus injections of ropivacaine and ketorolac cannot be recommended as analgesic method after THA.
DOI: 10.6084/m9.figshare.1569567.v2
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
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.