cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5067724.v1
title: sept_tool_analyzers_20170602.txt

description: Documents the 59 different software engineering research paper analysers and the summary tags they contribute for a research paper in submission. Each row has the name of an analysers/extractor followed by the tags it contributes evidence to.
DOI: 10.6084/m9.figshare.5067742.v1
title: Calcium Dobesilate Prevents Neurodegeneration and Vascular Leakage in Experimental Diabetes

description: <i>Purpose</i>: The mechanisms involved in the reported beneficial effects of Calcium dobesilate monohydrate (CaD) for the treatment of diabetic retinopathy (DR) remain to be elucidated. The main aim of the present study is to examine whether CaD prevents early events in the pathogenesis of DR such as neurodegeneration and vascular leakage. In addition, putative mediators of both neurodegeneration (glutamate/GLAST, ET-1/ETB receptor) and early microvascular impairment (ET-1/ETA receptor, oxidative stress, VEGF, and the PKC-delta-p38 MAPK pathway) have been examined. <i>Methods</i>: Diabetic (db/db) mice were randomly assigned to daily oral treatment with CaD (200 mg/Kg/day) (<i>n</i> = 12) or vehicle (<i>n</i> = 12) for 14 days. In addition, 12 non-diabetic (db/+) mice matched by age were used as the control group. Functional abnormalities were assessed by electroretinography. Neurodegeneration and microvascular abnormalities were evaluated by immunohistochemistry and Western blot. Glutamate was determined by HPLC. <i>Results</i>: CaD significantly decreased glial activation and apoptosis and produced a significant improvement in the electroretinogram parameters. Mechanistically, CaD prevented the diabetes-induced up-regulation of ET-1 and its cognate receptors (ETA-R and ETB-R), which are involved in microvascular impairment and neurodegeneration, respectively. In addition, treatment with CaD downregulated GLAST, the main glutamate transporter, and accordingly prevented the increase in glutamate. Finally, CaD prevented oxidative stress, and the upregulation of VEGF and PKC delta-p38 MAPK pathway induced by diabetes, thus resulting in a significant reduction in vascular leakage. <i>Conclusions</i>: Our findings demonstrate for the first time that CaD exerts neuroprotection in an experimental model of DR. In addition, we provide first evidence that CaD prevents the overexpression of ET-1 and its receptors in the diabetic retina. These beneficial effects on the neurovascular unit could pave the way for clinical trials addressed to confirm the effectiveness of CaD in very early stages of DR.
DOI: 10.6084/m9.figshare.5067727.v1
title: Synthesis of Two Closely Spaced Cysteine Barbiturates Containing Peptides by Copper Catalyzed Oxidation of Contryphan Disulfide

description: In this report, we are documenting synthesis of peptide barbiturate through copper catalyzed oxidation of peptide disulfide. Single disulfide containing contryphans are used as models to access possibility of anchoring of barbituric acid on to the peptide disulfide. Current method permits anchoring of two molecules of barbituric acid on to the polypeptide and yield of peptide barbiturates varies from 59-84%. Formation of cysteine sulfenic acid (Cys-SOH) during oxidation of disulfide was confirmed using chemical probe of Cys-SOH dimedone. Mass spectrometric studies have confirmed presence of cysteine barbiturate in anchored peptides. Based on nature of reactive oxygen species involved in oxidation of peptide disulfide, possible mechanisms were proposed for anchoring of barbituric acid on to the peptide disulfide through Cys-SOH. This is first report on anchoring of two molecules of barbituric acid on to the closely spaced cysteine residues of single polypeptide.
DOI: 10.6084/m9.figshare.5071288.v1
title: Cell Differentiation Processes as Spatial Networks: identifyingfour-dimensional structure in embryogenesis

description: There are two basic forms of animal development: mosaic (as found in roundworms and sea squirts) and regulative (as found in amphibians and mammals). How might one distinguish between each type of development? Using a four-dimensional spatial representation (<i>x,y,z,t</i>), major features of the developmental process are revealed. To establish the role of mosaic mechanisms, we can map the cell division process to a computational representation of <i>C. elegans</i> embryogenesis using a directed, acyclic graph (DAG) and a differentiation code. Mosaic development is identifiable by observing spatial localization of progenitor and descendent cells. This three-dimensional compartmentalization should be consistent with nesting in the cell lineage tree. Regulative development should demonstrate spatial “smearing”, or deviations from the compartmentalization of the mosaic process. In a complementary manner, complex network statistics should confirm this by providing an approximation of embryo geometry. Characterizing the spatial organization and geometry of embryos in this way allows for heuristic indicators of developmental patterns both within and between organisms.
DOI: 10.6084/m9.figshare.5071288.v4
title: Cell Differentiation Processes as Spatial Networks: identifying four-dimensional structure in embryogenesis

description: There are two basic forms of animal development: mosaic (as found in roundworms and sea squirts) and regulative (as found in amphibians and mammals). How might one distinguish between each type of development? Using a four-dimensional spatial representation (<i>x,y,z,t</i>), major features of the developmental process are revealed. To establish the role of mosaic mechanisms, we can map the cell division process to a computational representation of <i>C. elegans</i> embryogenesis using a directed, acyclic graph (DAG) and a differentiation code. Mosaic development is identifiable by observing spatial localization of progenitor and descendent cells. This three-dimensional compartmentalization should be consistent with nesting in the cell lineage tree. Regulative development should demonstrate spatial “smearing”, or deviations from the compartmentalization of the mosaic process. In a complementary manner, complex network statistics should confirm this by providing an approximation of embryo geometry. Characterizing the spatial organization and geometry of embryos in this way allows for heuristic indicators of developmental patterns both within and between organisms.<br>All raw data used in this study are available at Github. <br>Lineage Tree Raw Data: https://github.com/balicea/DevoWorm/tree/master/Lineage Tree DB, Differentiation Tree<br>Raw Data: https://github.com/balicea/DevoWorm/tree/master/Differentiation Tree Dataset. <br>All processed data (used in the analyses) are available from the Open Science Framework: https://osf.io/q9jvb/
DOI: 10.6084/m9.figshare.5071288.v3
title: Cell Differentiation Processes as Spatial Networks: identifying four-dimensional structure in embryogenesis

description: There are two basic forms of animal development: mosaic (as found in roundworms and sea squirts) and regulative (as found in amphibians and mammals). How might one distinguish between each type of development? Using a four-dimensional spatial representation (<i>x,y,z,t</i>), major features of the developmental process are revealed. To establish the role of mosaic mechanisms, we can map the cell division process to a computational representation of <i>C. elegans</i> embryogenesis using a directed, acyclic graph (DAG) and a differentiation code. Mosaic development is identifiable by observing spatial localization of progenitor and descendent cells. This three-dimensional compartmentalization should be consistent with nesting in the cell lineage tree. Regulative development should demonstrate spatial “smearing”, or deviations from the compartmentalization of the mosaic process. In a complementary manner, complex network statistics should confirm this by providing an approximation of embryo geometry. Characterizing the spatial organization and geometry of embryos in this way allows for heuristic indicators of developmental patterns both within and between organisms.<br>All raw data used in this study are available at Github. <br>Lineage Tree Raw Data: https://github.com/balicea/DevoWorm/tree/master/Lineage Tree DB, Differentiation Tree<br>Raw Data: https://github.com/balicea/DevoWorm/tree/master/Differentiation Tree Dataset. <br>All processed data (used in the analyses) are available from the Open Science Framework: https://osf.io/q9jvb/
DOI: 10.6084/m9.figshare.5067496
title: Influence of patch size and resource quantity on litter invertebrate assemblages in dry treeholes

description: Treeholes are dry or water-filled cavities that occur in the aboveground parts of forest ecosystems and support terrestrial and aquatic invertebrates. Compared with aquatic invertebrate assemblages in water-filled treeholes, little is known about how strongly patch size or resource quantity affects the terrestrial invertebrate assemblages in dry treeholes. Therefore, we examined the factors that affect terrestrial invertebrate assemblages in dry treeholes using a field experiment with artificial treeholes and by investigating natural treeholes, both in broad-leaved forests in central Japan. In the artificial treeholes, final litter density (final litter weight per unit treehole volume), which indicates the extent of resource concentration, was positively correlated with total invertebrate abundance and negatively correlated with the proportion of litter remaining at the end of the experiment. These results suggest that greater litter density results in an increase in both invertebrate abundance and litter decomposition. In natural treeholes, however, the total abundance of terrestrial invertebrates was not significantly correlated with litter density, litter weight, or treehole volume. The quantity of litter, which consisted mainly of fine particulate organic matter, increased with treehole opening size (area) and volume, suggesting that already decomposed litter was filled, depending on the treehole volume. This may have been attributed to the nonsignificant results concerning the abundance of terrestrial invertebrates in natural conditions. Thus, we suggest that both litter weight and density are important factors in determining the abundance of invertebrate in dry treeholes, even though their influence is weakened in natural treeholes by the effects of other factors.<br>
DOI: 10.6084/m9.figshare.5067364
title: Ethical Issues in the Relationship between Medical Students and the Pharmaceutical Industry. A Comparative Study of the Situation in Poland and in the US.

description: SPSS file with the data from 2013.
DOI: 10.6084/m9.figshare.5067496.v2
title: Influence of patch size and resource quantity on litter invertebrate assemblages in dry treeholes

description: Treeholes are dry or water-filled cavities that occur in the aboveground parts of forest ecosystems and support terrestrial and aquatic invertebrates. Compared with aquatic invertebrate assemblages in water-filled treeholes, little is known about how strongly patch size or resource quantity affects the terrestrial invertebrate assemblages in dry treeholes. Therefore, we examined the factors that affect terrestrial invertebrate assemblages in dry treeholes using a field experiment with artificial treeholes and by investigating natural treeholes, both in broad-leaved forests in central Japan. In the artificial treeholes, final litter density (final litter weight per unit treehole volume), which indicates the extent of resource concentration, was positively correlated with total invertebrate abundance and negatively correlated with the proportion of litter remaining at the end of the experiment. These results suggest that greater litter density results in an increase in both invertebrate abundance and litter decomposition. In natural treeholes, however, the total abundance of terrestrial invertebrates was not significantly correlated with litter density, litter weight, or treehole volume. The quantity of litter, which consisted mainly of fine particulate organic matter, increased with treehole opening size (area) and volume, suggesting that already decomposed litter was filled, depending on the treehole volume. This may have been attributed to the nonsignificant results concerning the abundance of terrestrial invertebrates in natural conditions. Thus, we suggest that both litter weight and density are important factors in determining the abundance of invertebrate in dry treeholes, even though their influence is weakened in natural treeholes by the effects of other factors.<br>
DOI: 10.6084/m9.figshare.5067331
title: England highway mean vehicle speed data from UK Government

description: This dataset includes 1/4-hourly average vehicle speed data of England highways from UK Government online public data (see “https://data.gov.uk/dataset/dft-eng-srn-routes-journey-times”). <br><br>Here each node is one section of road between two neighboring junctions. For each node, we consider time periods with length 28 days (2688 time bins) for each considered month (from the 1st to the 28th), and here we focus on January, April, July and October of 2014 as 4 examples. More details regarding the data files can be found in "DataDefinitionsSRN.doc" as a dataset description. Finally, "<strong>l</strong>ink-coordinates_latlng.xls" contains all the geographical locations (latitudes and longitudes) of all nodes.<br><br><br>
DOI: 10.6084/m9.figshare.5067331.v1
title: England highway mean vehicle speed data from UK Government

description: This dataset includes 1/4-hourly average vehicle speed data of England highways from UK Government online public data (see “https://data.gov.uk/dataset/dft-eng-srn-routes-journey-times”). <br><br>Here each node is one section of road between two neighboring junctions. For each node, we consider time periods with length 28 days (2688 time bins) for each considered month (from the 1st to the 28th), and here we focus on January, April, July and October of 2014 as 4 examples. More details regarding the data files can be found in "DataDefinitionsSRN.doc" as a dataset description. Finally, "<strong>l</strong>ink-coordinates_latlng.xls" contains all the geographical locations (latitudes and longitudes) of all nodes.<br><br><br>
DOI: 10.6084/m9.figshare.5067364.v1
title: Ethical Issues in the Relationship between Medical Students and the Pharmaceutical Industry. A Comparative Study of the Situation in Poland and in the US.

description: SPSS file with the data from 2013.
DOI: 10.6084/m9.figshare.5067283
title: Global daily 2-m air temperture from ECMWF ERA-Interim Reanalysis

description: This dataset includes the global daily mean 2-m air temperature data from the European Centre for Medium-Range Weather Forecasts Interim Re-Analysis (ECMWF ERA-Interim). <br><br>The nodes are selected with a bin width of 2.5 degree for both the latitude and the longitude. Therefore, there are 73 latitude values (from 90 degree north to 90 degree south) and 144 longitude values (from 0 degree east to 360 degree east) in total, as written in each file's name. The length of each record is 35 years (12775 days). The unit of the time series is Kelvin.<br><br><br>
DOI: 10.6084/m9.figshare.5067283.v1
title: Global daily 2-m air temperture from ECMWF ERA-Interim Reanalysis

description: This dataset includes the global daily mean 2-m air temperature data from the European Centre for Medium-Range Weather Forecasts Interim Re-Analysis (ECMWF ERA-Interim). <br><br>The nodes are selected with a bin width of 2.5 degree for both the latitude and the longitude. Therefore, there are 73 latitude values (from 90 degree north to 90 degree south) and 144 longitude values (from 0 degree east to 360 degree east) in total, as written in each file's name. The length of each record is 35 years (12775 days). The unit of the time series is Kelvin.<br><br><br>
DOI: 10.6084/m9.figshare.5067169
title: Analysis of Younger Dryas–Early Holocene pollen in sediments of Paisley Cave 2, south-central Oregon

description: Pollen analysis from Paisley Cave 2 (35LK3400), in Oregon has produced a record of climate change affecting the Summer Lake Sub-basin during a 7000-year period beginning at roughly 14,500 cal. yr. These sediments provide an opportunity to examine questions concerning human–environmental interaction at the end of the Pleistocene Epoch, during the Younger Dryas climatic event. The sediment deposits show a relatively unchanging early Holocene environment of predominantly xeric conditions with subalpine and marsh communities nearby. Additionally, there is little evidence of culturally significant use of any specific plant species. The data shows that the overall climatic conditions in the region were slightly cooler and perhaps wetter, just prior to the end of the Late Glacial, than today. These results provide important perspective on early settlement patterns and human ecology in the far western region of North America.
DOI: 10.6084/m9.figshare.5067160
title: Bird memes present at different fragments (kipukas) in the Big Island of Hawaii

description: This datafile shows the presence or absence of different acoustic memes (i.e. syllables) in a fragmented landscape in the Big Island of Hawaii (USA). The fragments (i.e. kipukas) were formed by lava flows. The data is for four native Hawaiian forest birds: 'i'wi, 'elepaio, 'amakihi and 'apapane. In the files, each row represents a fragment and each column a meme. We show if a meme is vocalized in a fragment. Recordings taken in 2014-2015. See publication in Oikos for more details.
DOI: 10.6084/m9.figshare.5067169.v1
title: Analysis of Younger Dryas–Early Holocene pollen in sediments of Paisley Cave 2, south-central Oregon

description: Pollen analysis from Paisley Cave 2 (35LK3400), in Oregon has produced a record of climate change affecting the Summer Lake Sub-basin during a 7000-year period beginning at roughly 14,500 cal. yr. These sediments provide an opportunity to examine questions concerning human–environmental interaction at the end of the Pleistocene Epoch, during the Younger Dryas climatic event. The sediment deposits show a relatively unchanging early Holocene environment of predominantly xeric conditions with subalpine and marsh communities nearby. Additionally, there is little evidence of culturally significant use of any specific plant species. The data shows that the overall climatic conditions in the region were slightly cooler and perhaps wetter, just prior to the end of the Late Glacial, than today. These results provide important perspective on early settlement patterns and human ecology in the far western region of North America.
DOI: 10.6084/m9.figshare.5067148
title: Norwegian mobile downtime dataset from NorNet Edge

description: We use measurements collected by the NorNet Edge measurement infrastructure. NorNet Edge consists of hundreds of measurement nodes that are spread all over Norway. Each node connects to up to 4 mobile operators. We collect all downtime events (time periods without mobile connectivity) for each node on each operator.<br><br>This dataset includes downtime time series of each node (with a fixed Node ID) on each operator ("Net01-04"). The 0-1 time series are defined using 5-min bins, and each bin is marked as "1" if it include a part of a downtime event. The dataset here includes five periods of time with length 3 months: January 1-March 31 ("JFM") of 2014 and 2015, as well as July 1-September 30 ("JAS") of 2013, 2014 and 2015. When the time series in one data file is shorter than the full length of 3 months, it means that there is no more downtime event in the remaining time series (always "0" values).<br><br>Finally, "invalid_final.zip" contains the data of node invalid periods within the considered 5 stages. Each line in the text file includes 4 values of an invalid period: Node ID, Operator ID, starting time (Unix timestamp), and total time length in seconds. When we calculate the Pearson correlation between nodes, invalid periods should be excluded from the 0-1 time series firstly.<br><br><br><br>
DOI: 10.6084/m9.figshare.5066833
title: <i>In silico</i> estimation of basic activity-relevant parameters for a set of drug absorption promoters

description: Finding a balance between a desired drug’s potency and its physicochemical properties that are important for its molecule pharmacokinetic or pharmacodynamics profile is still a challenging issue in rational drug discovery. Quantitative assessment of the lipophilic characteristics of potential drug molecules is indispensable for efficient development of Absorption, Distribution, Metabolism, Excretion, Toxicity-tailored structure–activity models; therefore reliable procedures for deriving log <i>P</i> from molecular structure are desirable. In the current work a range of various software log <i>P</i> predictors for estimation of the numerical lipophilic values for a set of cholic acid derivatives were employed and subsequently cross-compared with the experimental parameters. Thus, the empirical lipophilicity (<i>R</i><sub><i>M</i></sub>) was compared with the corresponding log <i>P</i> characteristics calculated using alternative methods for deducing the lipophilic features. The mean values of the selected molecular descriptors that were averaged over the chosen calculation methods (consensus clog <i>P</i>) were subsequently correlated with the <i>R</i><sub><i>M</i></sub> parameter. As an additional experiment, the iterative variable elimination partial least squares (IVE-PLS) methodology for an ensemble of descriptors retrieved from Dragon 6.0 software was applied for a set of drug transporters. To investigate the variations within the ensemble of cholic acid derivatives principal component analysis (PCA) and self-organizing neural network (SOM) procedures were used to visualize the major differences in the performance of drug promoters with respect to their lipophilic profile.
DOI: 10.6084/m9.figshare.5067160.v1
title: Birds memes present at different fragments (kipukas) in the Big Island of Hawaii

description: This datafile shows the presence or absence of different acoustic memes (i.e. syllables) in a fragmented landscape in the Big Island of Hawaii (USA). The fragments (i.e. kipukas) were formed by lava flows. The data is for four native Hawaiian forest birds: 'i'wi, 'elepaio, 'amakihi and 'apapane. In the files, each row represents a fragment and each column a meme. We show if a meme is vocalized in a fragment. Recordings taken in 2014-2015. See publication in Oikos for more details.