cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1569754.v1
title: Dynein prevents erroneous kinetochore-microtubule attachments in mitosis

description: Equal distribution of the genetic material during cell division relies on efficient congression of chromosomes to the metaphase plate. Prior to their alignment, the Dynein motor recruited to kinetochores transports a fraction of laterally-attached chromosomes along microtubules towards the spindle poles. By doing that, Dynein not only contributes to chromosome movements, but also prevents premature stabilization of end-on kinetochore-microtubule attachments. This is achieved by two parallel mechanisms: 1) Dynein-mediated poleward movement of chromosomes counteracts opposite polar-ejection forces (PEFs) on chromosome arms by the microtubule plus-end-directed motors chromokinesins, which could otherwise stabilize erroneous syntelic kinetochore-microtubule attachments and lead to the random ejection of chromosomes away from the spindle poles; and 2) By transporting chromosomes to the spindle poles, Dynein brings the former to the zone of highest Aurora A kinase activity, further destabilizing kinetochore-microtubule attachments. Thus, Dynein plays an important role in keeping chromosome segregation error-free by preventing premature stabilization of kinetochore-microtubule attachments near the spindle poles.
DOI: 10.6084/m9.figshare.1569746
title: Serological proteome analysis reveals new specific biases in the IgM and IgG autoantibody repertoires in autoimmune polyendocrine syndrome type 1

description: <i>Objective</i>: Autoimmune polyendocrine syndrome type 1 (APS 1) is caused by mutations in the <i>AIRE</i> gene that induce intrathymic T-cell tolerance breakdown, which results in tissue-specific autoimmune diseases. <i>Design</i>: To evaluate the effect of a well-defined T-cell repertoire impairment on humoral self-reactive fingerprints, comparative serum self-IgG and self-IgM reactivities were analyzed using both one- and two-dimensional western blotting approaches against a broad spectrum of peripheral tissue antigens. <i>Methods</i>: Autoantibody patterns of APS 1 patients were compared with those of subjects affected by other autoimmune endocrinopathies (OAE) and healthy controls. <i>Results</i>: Using a Chi-square test, significant changes in the Ab repertoire were found when intergroup patterns were compared. A singular distortion of both serum self-IgG and self-IgM repertoires was noted in APS 1 patients. The molecular characterization of these antigenic targets was conducted using a proteomic approach. In this context, autoantibodies recognized more significantly either tissue-specific antigens, such as pancreatic amylase, pancreatic triacylglycerol lipase and pancreatic regenerating protein 1α, or widely distributed antigens, such as peroxiredoxin-2, heat shock cognate 71-kDa protein and aldose reductase. As expected, a well-defined self-reactive T-cell repertoire impairment, as described in APS 1 patients, affected the tissue-specific self-IgG repertoire. Interestingly, discriminant IgM reactivities targeting both tissue-specific and more widely expressed antigens were also specifically observed in APS 1 patients. Using recombinant targets, we observed that post translational modifications of these specific antigens impacted upon their recognition. <i>Conclusions</i>: The data suggest that T-cell-dependent but also T-cell-independent mechanisms are involved in the dynamic evolution of autoimmunity in APS 1.
DOI: 10.6084/m9.figshare.1569742
title: The Contribution of Attached Bacteria to Microcystis Bloom: Evidence From Field Investigation and Microcosm Experiment

description: The research of the relationships among free-living bacteria, attached bacteria and different algal species can provide valuable evidence for understanding the reason of algal bloom development under nutrient limitations. Significantly positive relationships between chlorophyll a and attached bacteria in Microcystis-bloom ponds and between chlorophyll a and free-living bacteria in other algal bloom ponds were observed. Microcosm experiments further confirmed the synchronized growth of Microcystis and attached bacteria as well as Pediastrum and free-living bacteria. Carbon and bacteria stimulation experiments suggested that extracellular organic carbon from Microcystis was more complex, inducing specific attached bacterial communities and markedly high extracellular enzymes, which can strongly fuelled Microcystis development. On the contrary, dissolved organic carbon from Pediastrum was simple and suitable for free-living bacteria, which can made a distinct effect on Pediastrum growth depending on the degree of nutrients uptake by free-living bacteria. Based on the above results, it can be proposed that the reason of Microcystis bloom breakout in Chinese shallow lakes should be attributed to the close nutrient complementary relationship between Microcystis and specific attached bacteria mediated by dissolved organic carbon and extracellular enzymes at the development of bloom, which might provide scientific support for the research of Microcystis bloom control.
DOI: 10.6084/m9.figshare.1569745
title: Fláajökull (north lobe), Iceland: active temperate piedmont lobe glacial landsystem

description: A 1:6250 map of the foreland of Fláajökull's north lobe as it appeared in 1989, together with a 1:350 scale map of a sample area of recently exposed glacial landforms from 2014, enables an assessment of the spatial and temporal evolution of glacial landform assemblages at the margin of an active temperate piedmont lobe terminating at ice-marginal thickening till wedges. The pattern of landform development captured in these maps indicates that the glacier margin developed strong longitudinal crevassing and well-developed ice-marginal pecten (three-dimensional crenulations) during its historical recession. This is recorded by early recessional phase linear push moraines on well-drained distal slopes of the foreland and the later development of interrelated sawtooth moraines, crevasse squeeze ridges and till eskers, indicative of extending ice flow and poorly drained submarginal conditions. This landform record is a palaeoglaciological signature of a changing process–form regime inherent within the active temperate piedmont lobe landsystem model.
DOI: 10.6084/m9.figshare.1569742.v1
title: The Contribution of Attached Bacteria to Microcystis Bloom: Evidence From Field Investigation and Microcosm Experiment

description: The research of the relationships among free-living bacteria, attached bacteria and different algal species can provide valuable evidence for understanding the reason of algal bloom development under nutrient limitations. Significantly positive relationships between chlorophyll a and attached bacteria in Microcystis-bloom ponds and between chlorophyll a and free-living bacteria in other algal bloom ponds were observed. Microcosm experiments further confirmed the synchronized growth of Microcystis and attached bacteria as well as Pediastrum and free-living bacteria. Carbon and bacteria stimulation experiments suggested that extracellular organic carbon from Microcystis was more complex, inducing specific attached bacterial communities and markedly high extracellular enzymes, which can strongly fuelled Microcystis development. On the contrary, dissolved organic carbon from Pediastrum was simple and suitable for free-living bacteria, which can made a distinct effect on Pediastrum growth depending on the degree of nutrients uptake by free-living bacteria. Based on the above results, it can be proposed that the reason of Microcystis bloom breakout in Chinese shallow lakes should be attributed to the close nutrient complementary relationship between Microcystis and specific attached bacteria mediated by dissolved organic carbon and extracellular enzymes at the development of bloom, which might provide scientific support for the research of Microcystis bloom control.
DOI: 10.6084/m9.figshare.1569745.v1
title: Fláajökull (north lobe), Iceland: active temperate piedmont lobe glacial landsystem

description: A 1:6250 map of the foreland of Fláajökull's north lobe as it appeared in 1989, together with a 1:350 scale map of a sample area of recently exposed glacial landforms from 2014, enables an assessment of the spatial and temporal evolution of glacial landform assemblages at the margin of an active temperate piedmont lobe terminating at ice-marginal thickening till wedges. The pattern of landform development captured in these maps indicates that the glacier margin developed strong longitudinal crevassing and well-developed ice-marginal pecten (three-dimensional crenulations) during its historical recession. This is recorded by early recessional phase linear push moraines on well-drained distal slopes of the foreland and the later development of interrelated sawtooth moraines, crevasse squeeze ridges and till eskers, indicative of extending ice flow and poorly drained submarginal conditions. This landform record is a palaeoglaciological signature of a changing process–form regime inherent within the active temperate piedmont lobe landsystem model.
DOI: 10.6084/m9.figshare.1569746.v1
title: Serological proteome analysis reveals new specific biases in the IgM and IgG autoantibody repertoires in autoimmune polyendocrine syndrome type 1

description: <i>Objective</i>: Autoimmune polyendocrine syndrome type 1 (APS 1) is caused by mutations in the <i>AIRE</i> gene that induce intrathymic T-cell tolerance breakdown, which results in tissue-specific autoimmune diseases. <i>Design</i>: To evaluate the effect of a well-defined T-cell repertoire impairment on humoral self-reactive fingerprints, comparative serum self-IgG and self-IgM reactivities were analyzed using both one- and two-dimensional western blotting approaches against a broad spectrum of peripheral tissue antigens. <i>Methods</i>: Autoantibody patterns of APS 1 patients were compared with those of subjects affected by other autoimmune endocrinopathies (OAE) and healthy controls. <i>Results</i>: Using a Chi-square test, significant changes in the Ab repertoire were found when intergroup patterns were compared. A singular distortion of both serum self-IgG and self-IgM repertoires was noted in APS 1 patients. The molecular characterization of these antigenic targets was conducted using a proteomic approach. In this context, autoantibodies recognized more significantly either tissue-specific antigens, such as pancreatic amylase, pancreatic triacylglycerol lipase and pancreatic regenerating protein 1α, or widely distributed antigens, such as peroxiredoxin-2, heat shock cognate 71-kDa protein and aldose reductase. As expected, a well-defined self-reactive T-cell repertoire impairment, as described in APS 1 patients, affected the tissue-specific self-IgG repertoire. Interestingly, discriminant IgM reactivities targeting both tissue-specific and more widely expressed antigens were also specifically observed in APS 1 patients. Using recombinant targets, we observed that post translational modifications of these specific antigens impacted upon their recognition. <i>Conclusions</i>: The data suggest that T-cell-dependent but also T-cell-independent mechanisms are involved in the dynamic evolution of autoimmunity in APS 1.
DOI: 10.6084/m9.figshare.1569735
title: Role of the bradykinin B2 receptor in a rat model of local heart irradiation

description: <i>Purpose</i>: Radiation-induced heart disease (RIHD) is a delayed effect of radiotherapy for cancers of the chest, such as breast, esophageal, and lung. Kinins are small peptides with cardioprotective properties. We previously used a rat model that lacks the precursor kininogen to demonstrate that kinins are involved in RIHD. Here, we examined the role of the kinin B2 receptor (B2R) in early radiation-induced signaling in the heart.<i>Materials and methods</i>: Male Brown Norway rats received the B2R-selective antagonist HOE-140 (icatibant) via osmotic minipump from 5 days before until 4 weeks after 21 Gy local heart irradiation. At 4 weeks, signaling events were measured in left ventricular homogenates and nuclear extracts using western blotting and real-time polymerase chain reaction. Numbers of CD68<b>-</b>positive (monocytes/macrophages), CD2<b>-</b>positive (T-lymphocytes), and mast cells were measured using immunohistochemistry.<i>Results</i>: Radiation-induced c-Jun phosphorylation and nuclear translocation were enhanced by HOE-140. HOE-140 did not modify endothelial nitric oxide synthase (eNOS) phosphorylation or alter numbers of CD2-positive or mast cells, but enhanced CD68-positive cell counts in irradiated hearts.<i>Conclusions</i>: B2R signaling may regulate monocyte/macrophage infiltration and c-Jun signals in the irradiated heart. Although eNOS is a main target for kinins, the B2R may not regulate eNOS phosphorylation in response to radiation.
DOI: 10.6084/m9.figshare.1569735.v1
title: Role of the bradykinin B2 receptor in a rat model of local heart irradiation

description: <i>Purpose</i>: Radiation-induced heart disease (RIHD) is a delayed effect of radiotherapy for cancers of the chest, such as breast, esophageal, and lung. Kinins are small peptides with cardioprotective properties. We previously used a rat model that lacks the precursor kininogen to demonstrate that kinins are involved in RIHD. Here, we examined the role of the kinin B2 receptor (B2R) in early radiation-induced signaling in the heart.<i>Materials and methods</i>: Male Brown Norway rats received the B2R-selective antagonist HOE-140 (icatibant) via osmotic minipump from 5 days before until 4 weeks after 21 Gy local heart irradiation. At 4 weeks, signaling events were measured in left ventricular homogenates and nuclear extracts using western blotting and real-time polymerase chain reaction. Numbers of CD68<b>-</b>positive (monocytes/macrophages), CD2<b>-</b>positive (T-lymphocytes), and mast cells were measured using immunohistochemistry.<i>Results</i>: Radiation-induced c-Jun phosphorylation and nuclear translocation were enhanced by HOE-140. HOE-140 did not modify endothelial nitric oxide synthase (eNOS) phosphorylation or alter numbers of CD2-positive or mast cells, but enhanced CD68-positive cell counts in irradiated hearts.<i>Conclusions</i>: B2R signaling may regulate monocyte/macrophage infiltration and c-Jun signals in the irradiated heart. Although eNOS is a main target for kinins, the B2R may not regulate eNOS phosphorylation in response to radiation.
DOI: 10.6084/m9.figshare.1569722
title: Comprehensive sequence-flux mapping of a levoglucosan utilization pathway in E. coli

description: 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.1569722.v1
title: Comprehensive sequence-flux mapping of a levoglucosan utilization pathway in E. coli

description: 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.1569713
title: The place of Slovakian paternal diversity in the clinal European landscape

description: <i>Background</i>: Several demographic events have been postulated to explain the contemporaneous structure of European genetic diversity. First, an initial settlement of the continent by anatomically modern humans; second, the re-settlement of northern latitudes after the Last Glacial Maximum; third, the demic diffusion of Neolithic farmers from the Near East; and, fourth, several historical events such as the Slavic migration.<i>Aim</i>: The aim of this study was to provide a more integrated picture of male-specific genetic relationships of Slovakia within the broader pan-European genetic landscape.<i>Subjects and methods</i>: This study analysed a new Y-chromosome data-set (156 individuals) for both SNP and STR polymorphisms in population samples from five different Slovakian localities.<i>Results</i>: It was found that the male diversity of Slovakia is embedded in the clinal pattern of the major R1a and R1b clades extending over the continent and a similar pattern of population structure is found with Y-specific SNP or STR variation.<i>Conclusion</i>: The highly significant correlation between the results based on fast evolving STRs on one hand and slow evolving SNPs on the other hand suggests a recent timeframe for the settlement of the area.
DOI: 10.6084/m9.figshare.1569713.v1
title: The place of Slovakian paternal diversity in the clinal European landscape

description: <i>Background</i>: Several demographic events have been postulated to explain the contemporaneous structure of European genetic diversity. First, an initial settlement of the continent by anatomically modern humans; second, the re-settlement of northern latitudes after the Last Glacial Maximum; third, the demic diffusion of Neolithic farmers from the Near East; and, fourth, several historical events such as the Slavic migration.<i>Aim</i>: The aim of this study was to provide a more integrated picture of male-specific genetic relationships of Slovakia within the broader pan-European genetic landscape.<i>Subjects and methods</i>: This study analysed a new Y-chromosome data-set (156 individuals) for both SNP and STR polymorphisms in population samples from five different Slovakian localities.<i>Results</i>: It was found that the male diversity of Slovakia is embedded in the clinal pattern of the major R1a and R1b clades extending over the continent and a similar pattern of population structure is found with Y-specific SNP or STR variation.<i>Conclusion</i>: The highly significant correlation between the results based on fast evolving STRs on one hand and slow evolving SNPs on the other hand suggests a recent timeframe for the settlement of the area.
DOI: 10.6084/m9.figshare.1569694
title: Consistency of QSAR models: Correct split of training and test sets, ranking of models and performance parameters

description: Recent implementations of QSAR modelling software provide the user with numerous models and a wealth of information. In this work, we provide some guidance on how one should interpret the results of QSAR modelling, compare and assess the resulting models, and select the best and most consistent ones. Two QSAR datasets are applied as case studies for the comparison of model performance parameters and model selection methods. We demonstrate the capabilities of sum of ranking differences (SRD) in model selection and ranking, and identify the best performance indicators and models. While the exchange of the original training and (external) test sets does not affect the ranking of performance parameters, it provides improved models in certain cases (despite the lower number of molecules in the training set). Performance parameters for external validation are substantially separated from the other merits in SRD analyses, highlighting their value in data fusion.
DOI: 10.6084/m9.figshare.1569694.v1
title: Consistency of QSAR models: Correct split of training and test sets, ranking of models and performance parameters

description: Recent implementations of QSAR modelling software provide the user with numerous models and a wealth of information. In this work, we provide some guidance on how one should interpret the results of QSAR modelling, compare and assess the resulting models, and select the best and most consistent ones. Two QSAR datasets are applied as case studies for the comparison of model performance parameters and model selection methods. We demonstrate the capabilities of sum of ranking differences (SRD) in model selection and ranking, and identify the best performance indicators and models. While the exchange of the original training and (external) test sets does not affect the ranking of performance parameters, it provides improved models in certain cases (despite the lower number of molecules in the training set). Performance parameters for external validation are substantially separated from the other merits in SRD analyses, highlighting their value in data fusion.
DOI: 10.6084/m9.figshare.1569691
title: Quantification of CT-assessed radiation-induced lung damage in lung cancer patients treated with or without chemotherapy and cetuximab

description: <i>Background and Purpose</i>: Prediction models for radiation-induced lung damage (RILD) are still unsatisfactory, with clinical toxicity endpoints that are difficult to quantify objectively. We therefore evaluated RILD more objectively, quantitatively and on a continuous scale measuring the lung tissue density changes per voxel. <i>Material and methods</i>: Patients treated with radiotherapy (RT) alone, sequential and concurrent chemo-RT with and without the addition of cetuximab were studied. Follow-up computed tomography (CT) scans were co-registered using deformable registration to baseline CT scans. CT density changes were correlated to the RT dose delivered in every part of the lungs. <i>Results</i>: One hundred and seventeen lung cancer patients were included. Mean dose to tumor was 60 Gy (range 45–79.2 Gy). Dose response curves showed a linear increase in the dose region between 0 and 65 Gy having a slope (based on coefficients of the multilevel model) expressed as a lung density increase per dose of 0.86 (95% CI 0.73–0.99), 1.31 (95% CI 1.19–1.43), 1.39 (95% CI 1.28–1.50) and 2.07 (95% CI 1.93–2.21) for patients treated only with RT (N=19), sequential chemo-RT (N=30), concurrent chemo-RT (N=49), and concurrent chemo-RT with cetuximab (N=19), respectively. <i>Conclusions</i>: CT density changes allow quantitative assessment of lung damage after fractionated RT, giving complementary information to standard used clinical endpoints. Patients receiving cetuximab showed a significantly larger dose response compared with other treatments.
DOI: 10.6084/m9.figshare.1569690
title: Diagnostic characters in fossil coralline algae (Corallinophycidae: Rhodophyta) from the Miocene of southern Moravia (Carpathian Foredeep, Czech Republic)

description: Fourteen coralline algal species (Corallinales, Sporolithales) from Early Langhian (Lower Badenian) red-algal limestones of the Carpathian Foredeep (Czech Republic) are described: <i>Sporolithon lvovicum</i> (Maslov) Bassi <i>et al</i>., <i>Lithothamnion roveretoi</i> Airoldi, <i>Lithothamnion moretii</i> Lemoine, ?<i>Lithothamnion</i> sp. 1, ?<i>Lithothamnion</i> sp. 2, <i>Mesophyllum alternans</i> (Foslie) Cabioch & Mendoza, <i>M</i>. cf. <i>erubescens</i> (Foslie) Lemoine, <i>M</i>. cf. <i>printzianum</i> Woelkerling & Harvey, <i>M. curtum</i> Lemoine, <i>Phymatolithon</i> sp., <i>Lithophyllum</i> sp. 1, <i>Lithophyllum</i> sp. 2, <i>Hydrolithon lemoinei</i> (Miranda) Aguirre <i>et al</i>. and <i>Spongites fruticulosa</i> Kützing. The characters used in coralline algal species description and identification are summarized and discussed. Five characters newly used in fossil material are associated with the structure and fate of presumed tetrasporangial, gametangial and carposporangial conceptacles, with the shape, size and organization of roof cells, and with the position of the asexuate conceptacles relative to the surrounding thallus surface. Gametangial conceptacles of <i>Phymatolithon</i> and gametangial and carposporangial plants of <i>Sporolithon lvovicum</i> are described for the first time.