cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4754500.v2
title: AZD1775 induces toxicity through double-stranded DNA breaks independently of chemotherapeutic agents in p53-mutated colorectal cancer cells

description: AZD1775 is a small molecule WEE1 inhibitor used in combination with DNA-damaging agents to cause premature mitosis and cell death in p53-mutated cancer cells. Here we sought to determine the mechanism of action of AZD1775 in combination with chemotherapeutic agents in light of recent findings that AZD1775 can cause double-stranded DNA (DS-DNA) breaks. AZD1775 significantly improved the cytotoxicity of 5-FU in a p53-mutated colorectal cancer cell line (HT29 cells), decreasing the IC<sub>50</sub> from 9.3 μM to 3.5 μM. Flow cytometry showed a significant increase in the mitotic marker pHH3 (3.4% vs. 56.2%) and DS-DNA break marker γH2AX (5.1% vs. 50.7%) for combination therapy compared with 5-FU alone. Combination therapy also increased the amount of caspase-3 dependent apoptosis compared with 5-FU alone (4% vs. 13%). The addition of exogenous nucleosides to combination therapy significantly rescued the increased DS-DNA breaks and caspase-3 dependent apoptosis almost to the levels of 5-FU monotherapy. In conclusion, AZD1775 enhances 5-FU cytotoxicity through increased DS-DNA breaks, not premature mitosis, in p53-mutated colorectal cancer cells. This finding is important for designers of future clinical trials when considering the optimal timing and duration of AZD1775 treatment.
DOI: 10.7910/dvn/pkjufn/uinn2x
title: FCC2002.310.ran

description: :unav
DOI: 10.6084/m9.figshare.4754500.v1
title: AZD1775 Induces Toxicity Through Double-Stranded DNA Breaks Independently of Chemotherapeutic Agents in p53-Mutated Colorectal Cancer Cells

description: AZD1775 is a small molecule WEE1 inhibitor used in combination with DNA-damaging agents to cause premature mitosis and cell death in p53-mutated cancer cells. Here we sought to determine the mechanism of action of AZD1775 in combination with chemotherapeutic agents in light of recent findings that AZD1775 can cause double-stranded DNA (DS-DNA) breaks. AZD1775 significantly improved the cytotoxicity of 5-FU in a p53-mutated colorectal cancer cell line (HT29 cells), decreasing the IC<sub>50</sub> from 9.3 μM to 3.5 μM. Flow cytometry showed a significant increase in the mitotic marker pHH3 (3.4% vs. 56.2%) and DS-DNA break marker γH2AX (5.1% vs. 50.7%) for combination therapy compared to 5-FU alone. Combination therapy also increased the amount of caspase-3 dependent apoptosis compared to 5-FU alone (4% vs. 13%). The addition of exogenous nucleosides to combination therapy significantly rescued the increased DS-DNA breaks and caspase-3 dependent apoptosis almost to the levels of 5-FU monotherapy. In conclusion, AZD1775 enhances 5-FU cytotoxicity through increased DS-DNA breaks, not premature mitosis, in p53-mutated colorectal cancer cells. This finding is important for designers of future clinical trials when considering the optimal timing and duration of AZD1775 treatment.
DOI: 10.7910/dvn/pkjufn/x8f1nj
title: FCC2002.004.ran

description: :unav
DOI: 10.6084/m9.figshare.4754473
title: Alane adsorption on SI(100): ELF plots

description: VASP ELFCAR output, MATLAB graphics
DOI: 10.7910/dvn/pkjufn/w2xmx7
title: FCC2001.069.ran

description: :unav
DOI: 10.6084/m9.figshare.4754473.v1
title: Alane adsorption on SI(100): ELF plots

description: VASP ELFCAR output, MATLAB graphics
DOI: 10.6084/m9.figshare.4754470
title: Genome-wide identification and characterization of small RNAs in <i>Rhodobacter capsulatus</i> and identification of small RNAs affected by loss of the response regulator CtrA

description: Small non-coding RNAs (sRNAs) are involved in the control of numerous cellular processes through various regulatory mechanisms, and in the past decade many studies have identified sRNAs in a multitude of bacterial species using RNA sequencing (RNA-seq). Here, we present the first genome-wide analysis of sRNA sequencing data in <i>Rhodobacter capsulatus</i>, a purple nonsulfur photosynthetic alphaproteobacterium. Using a recently developed bioinformatics approach, sRNA-Detect, we detected 422 putative sRNAs from <i>R. capsulatus</i> RNA-seq data. Based on their sequence similarity to sRNAs in a sRNA collection, consisting of published putative sRNAs from 23 additional bacterial species, and RNA databases, the sequences of 124 putative sRNAs were conserved in at least one other bacterial species; and, 19 putative sRNAs were assigned a predicted function. We bioinformatically characterized all putative sRNAs and applied machine learning approaches to calculate the probability of a nucleotide sequence to be a bona fide sRNA. The resulting quantitative model was able to correctly classify 95.2% of sequences in a validation set. We found that putative <i>cis-</i>targets for antisense and partially overlapping sRNAs were enriched with protein-coding genes involved in primary metabolic processes, photosynthesis, compound binding, and with genes forming part of macromolecular complexes. We performed differential expression analysis to compare the wild type strain to a mutant lacking the response regulator CtrA, an important regulator of gene expression in <i>R. capsulatus</i>, and identified 18 putative sRNAs with differing levels in the two strains. Finally, we validated the existence and expression patterns of four novel sRNAs by Northern blot analysis.
DOI: 10.7910/dvn/pkjufn/wpp9vo
title: FCC2003.312.ran

description: :unav
DOI: 10.6084/m9.figshare.4754461
title: A cell based screening approach for identifying protein degradation regulators

description: Cellular transitions are achieved by the concerted actions of regulated degradation pathways. In the case of the cell cycle, ubiquitin mediated degradation ensures unidirectional transition from one phase to another. For instance, turnover of the cell cycle regulator cyclin B1 occurs after metaphase to induce mitotic exit. To better understand pathways controlling cyclin B1 turnover, the N-terminal domain of cyclin B1 was fused to luciferase to generate an N-cyclin B1-luciferase protein that can be used as a reporter for protein turnover. Prior studies demonstrated that cell-based screens using this reporter identified small molecules inhibiting the ubiquitin ligase controlling cyclin B1-turnover. Our group adapted this approach for the G2-M regulator Wee1 where a Wee1-luciferase construct was used to identify selective small molecules inhibiting an upstream kinase that controls Wee1 turnover. In the present study we present a screening approach where cell cycle regulators are fused to luciferase and overexpressed with cDNAs to identify specific regulators of protein turnover. We overexpressed approximately 14,000 cDNAs with the N-cyclin B1-luciferase fusion protein and determined its steady-state level relative to other luciferase fusion proteins. We identified the known APC/C regulator Cdh1 and the F-box protein Fbxl15 as specific modulators of N-cyclin B1-luciferase steady-state levels and turnover. Collectively, our studies suggest that analyzing the steady-state levels of luciferase fusion proteins in parallel facilitates identification of specific regulators of protein turnover.
DOI: 10.6084/m9.figshare.4754470.v1
title: Genome-wide identification and characterization of small RNAs in <i>Rhodobacter capsulatus</i> and identification of small RNAs affected by loss of the response regulator CtrA

description: Small non-coding RNAs (sRNAs) are involved in the control of numerous cellular processes through various regulatory mechanisms, and in the past decade many studies have identified sRNAs in a multitude of bacterial species using RNA sequencing (RNA-seq). Here, we present the first genome-wide analysis of sRNA sequencing data in <i>Rhodobacter capsulatus</i>, a purple nonsulfur photosynthetic alphaproteobacterium. Using a recently developed bioinformatics approach, sRNA-Detect, we detected 422 putative sRNAs from <i>R. capsulatus</i> RNA-seq data. Based on their sequence similarity to sRNAs in a sRNA collection, consisting of published putative sRNAs from 23 additional bacterial species, and RNA databases, the sequences of 124 putative sRNAs were conserved in at least one other bacterial species; and, 19 putative sRNAs were assigned a predicted function. We bioinformatically characterized all putative sRNAs and applied machine learning approaches to calculate the probability of a nucleotide sequence to be a bona fide sRNA. The resulting quantitative model was able to correctly classify 95.2% of sequences in a validation set. We found that putative <i>cis-</i>targets for antisense and partially overlapping sRNAs were enriched with protein-coding genes involved in primary metabolic processes, photosynthesis, compound binding, and with genes forming part of macromolecular complexes. We performed differential expression analysis to compare the wild type strain to a mutant lacking the response regulator CtrA, an important regulator of gene expression in <i>R. capsulatus</i>, and identified 18 putative sRNAs with differing levels in the two strains. Finally, we validated the existence and expression patterns of four novel sRNAs by Northern blot analysis.
DOI: 10.7910/dvn/pkjufn/dfifty
title: FCC2003.136.ran

description: :unav
DOI: 10.6084/m9.figshare.4754431
title: Extent of Occurrence and Area of Occupancy of Psyllocarpus sp. nov.

description: Kml file for conservation status assessment of <i>Psyllocarpus sp. nov. <br></i>
DOI: 10.7910/dvn/pkjufn/hgdu5n
title: FCC2002.355.ran

description: :unav
DOI: 10.6084/m9.figshare.4754431.v1
title: Extent of Occurrence and Area of Occupancy of Psyllocarpus sp. nov.

description: Kml file for conservation status assessment of <i>Psyllocarpus sp. nov. <br></i>
DOI: 10.6084/m9.figshare.4754428
title: Extent of Occurrence and Area of Occupancy of Psyllocarpus sp. nov.

description: Kml file for conservation status assessment of <i>Psyllocarpus </i><i>sp. nov.<br></i>
DOI: 10.7910/dvn/pkjufn/sl5a3a
title: FCC2003.263.ran

description: :unav
DOI: 10.6084/m9.figshare.4754428.v1
title: Extent of Occurrence and Area of Occupancy of Psyllocarpus sp. nov.

description: Kml file for conservation status assessment of <i>Psyllocarpus </i><i>sp. nov.<br></i>
DOI: 10.7910/dvn/pkjufn/92deia
title: FCC2002.016.ran

description: :unav
DOI: 10.6084/m9.figshare.4754308
title: Alane adsorption on Si(100): VASP CONTCAR xyz

description: VASP structure file after optimization, in xyz format
DOI: 10.7910/dvn/pkjufn/jjtois
title: FCC2002.193.ran

description: :unav
DOI: 10.7910/dvn/pkjufn/upgpwh
title: FCC2002.173.ran

description: :unav
DOI: 10.6084/m9.figshare.4754302
title: Table S2 from How (much) do flowers vary?: unbalanced disparity among flower functional modules and a mosaic pattern of morphospace occupation in the order Ericales

description: Dataset
DOI: 10.7910/dvn/pkjufn/2kcif1
title: FCC2003.104.ran

description: :unav
DOI: 10.6084/m9.figshare.4754308.v1
title: Alane adsorption on Si(100): VASP CONTCAR xyz

description: VASP structure file after optimization, in xyz format
DOI: 10.7910/dvn/pkjufn/ugjljg
title: FCC2003.267.ran

description: :unav
DOI: 10.7910/dvn/pkjufn/zzqlk7
title: FCC2003.165.ran

description: :unav
DOI: 10.7910/dvn/pkjufn/uvbdhc
title: FCC2001.046.ran

description: :unav
DOI: 10.6084/m9.figshare.4754287
title: Supplementary Material 1: Dataset from Human infectious disease burdens decrease with urbanization but not with biodiversity

description: Meta-data for dataset assembled to test potential drivers of country-level human infectious disease burden.
DOI: 10.7910/dvn/pkjufn/ustwgb
title: FCC2001.087.ran

description: :unav
DOI: 10.6084/m9.figshare.4754266
title: Alane adsorption on Si(100): VASP CONTCAR

description: VASP structure file after optimization, in native format
DOI: 10.6084/m9.figshare.4754275
title: Supplementary dataset.xlsx from The mountains of giants: an anthropometric survey of male youths in Bosnia and Herzegovina

description: Raw individual data.
DOI: 10.6084/m9.figshare.4754287.v2
title: Supplementary Material 1: Dataset from Human infectious disease burdens decrease with urbanization but not with biodiversity

description: Meta-data for dataset assembled to test potential drivers of country-level human infectious disease burden.
DOI: 10.7910/dvn/pkjufn/vfokiz
title: FCC2002.357.ran

description: :unav
DOI: 10.6084/m9.figshare.4754287.v1
title: Supplementary Material 1: Dataset from Human infectious disease burdens decrease with urbanization but not with biodiversity

description: Meta-data for dataset assembled to test potential drivers of country-level human infectious disease burden.
DOI: 10.7910/dvn/pkjufn/e6iexw
title: FCC2003.132.ran

description: :unav
DOI: 10.6084/m9.figshare.4754251
title: Genome annotation of the oleaginous yeast Rhodotorula toruloides strain CGMCC 2.1609

description: Genome annotation of the oleaginous yeast Rhodotorula toruloides strain CGMCC 2.1609 as a GFF file. Genome sequence and further information is available on NCBI.
DOI: 10.7910/dvn/pkjufn/rbfua8
title: FCC2001.261.ran

description: :unav
DOI: 10.7910/dvn/pkjufn/wq1fzs
title: FCC2002.320.ran

description: :unav
DOI: 10.6084/m9.figshare.4754266.v1
title: Alane adsorption on Si(100): VASP CONTCAR

description: VASP structure file after optimization, in native format
DOI: 10.7910/dvn/pkjufn/ny3fzq
title: FCC2001.175.ran

description: :unav
DOI: 10.6084/m9.figshare.4754038
title: The role of molybdenum in suppressing cold dwell fatigue in titanium alloys

description: This dataset contains supporting data for the publication entitled "The role of molybdenum in suppressing cold dwell fatigue in titanium alloys" by the above authors to be published in Proceedings of the Royal Society A.<br>It contains VASP input files and .xyz relaxed geometries of the DFT supercells used to compute the formation and binding energies in this paper.
DOI: 10.6084/m9.figshare.4754182
title: Leopard camera trap dataset

description: This dataset contains the data and code used in the analysis for Williams, S.T., Williams, K.S., Lewis, B.P. and Hill, R.A. (2017) Population dynamics and threats to an apex predator outside protected areas: Implications for carnivore management. Royal Society Open Science. <br><br>Data were collected in the Soutpansberg Mountains, South Africa, between 2008 and 2016. Data and R code used for the analyses are included in this dataset. Please see the article for further details. If you have any questions contact Sam Williams (samual.t.williams@gmail.com).<br>The files provided in this data set are as follows:<br>Leopard camera trap datasetPublished on 16 Nov 2016 - 21:26 by Sam WilliamsData used in analysis for Williams et al. (2017) Population dynamics and threats to an apex predator outside protected areas: Implications for carnivore management. For full details see article. <br>Details of the files are as follows:<br>"SPACECAP input files.zip" contains SPACECAP input files for 24 surveys of leopard population density in the Soutpansberg Mountains, South Africa from 2012 to 2016. For each survey (for dates see article) the zip archive contains a - capture history file "capture_sXX.csv" - trap deployment file "deployment_sXX.csv" - potential home range centres file "HRC_s01.csv"<br>Details of coding used in SPACECAP input files. In input files ANIMAL_IDs and LOC_IDs must be represented as sequential numbers. - "ANIMAL_ID coding in capture files.csv" shows which ANIMAL_IDs correspond to which individual animals, and - "LOC_ID coding in deployment files.csv" shows which LOC_IDs correspond to which camera station numbers<br>Files used for analysis of SPACECAP results and demographic data: - Input files - "densityInclExcl2008.csv" - "heatmapLeopard.csv" - "individuals.csv" - "leopardTenure.csv"- "cameraTrapAnalysis.R" contains the R code used to analyse the data.- "cameraTrapAnalysis output.pdf" contains the output of the analysis.
DOI: 10.7910/dvn/pkjufn/9gdgcu
title: FCC2003.233.ran

description: :unav
DOI: 10.6084/m9.figshare.4754251.v1
title: Gene annotation of the oleaginous yeast Rhodotorula toruloides strain CGMCC 2.1609

description: Gene annotation of the oleaginous yeast Rhodotorula toruloides strain CGMCC 2.1609 as a GFF file. Genome sequence and further information is available on NCBI.
DOI: 10.6084/m9.figshare.4753975
title: AFM Experimental Data

description: Here included are data sets of AFM images, corresponding cell height profiles for all time points, time stamp, and text describing experimental conditions.
DOI: 10.6084/m9.figshare.4753990
title: Dummy data

description: Fisher's iris
DOI: 10.6084/m9.figshare.4754008
title: Dummy data

description: Fisher's iris
DOI: 10.7910/dvn/pkjufn/fndnll
title: FCC2001.162.ran

description: :unav
DOI: 10.7910/dvn/pkjufn/ij0dna
title: FCC2001.009.ran

description: :unav
DOI: 10.6084/m9.figshare.4753852
title: Dummy data

description: Fisher's iris
DOI: 10.6084/m9.figshare.4753861
title: Supplementary Material for: Communicative Functions Integrate Segments in Prosodies and Prosodies in Segments

description: This paper takes a new look at the traditionally established divide between sounds and prosodies, viewing it as a useful heuristics in language descriptions that focus on the segmental make- up of words. It pleads for a new approach that bridges this reified compartmentalization of speech in a more global communicative perspective. Data are presented from a German perception experiment in the framework of the Semantic Differential that shows interdependence of f0 contours and the spectral characteristics of a following fricative segment, for the expression of semantic functions along the scales questioning – asserting, excited – calm, forceful – not forceful, contrary – agreeable. The results lead to the conclusion that segments shape prosodies and are shaped by them in varying ways in the coding of semantic functions. This implies that the analysis of sentence prosodies needs to integrate the manifestation of segments, just as the analysis of segments needs to consider their prosodic embedding. In communicative interaction, speakers set broad prosodic time windows of varying sizes, and listeners respond to them. So, future phonetic research needs to concentrate on speech analysis in such windows.
DOI: 10.6084/m9.figshare.4753990.v1
title: Dummy data

description: Fisher's iris
DOI: 10.6084/m9.figshare.4753852.v1
title: Dummy data

description: Fisher's iris
DOI: 10.7910/dvn/pkjufn/2lvdsd
title: FCC2003.319.ran

description: :unav
DOI: 10.6084/m9.figshare.4753795
title: A videofluoroscopy-based tracking algorithm for quantifying the time course of human intervertebral displacements

description: The motions of individual intervertebral joints can affect spine motion, injury risk, deterioration, pain, treatment strategies, and clinical outcomes. Since standard kinematic methods do not provide precise time-course details about individual vertebrae and intervertebral motions, information that could be useful for scientific advancement and clinical assessment, we developed an iterative template matching algorithm to obtain this data from videofluoroscopy images. To assess the bias of our approach, vertebrae in an intact porcine spine were tracked and compared to the motions of high-contrast markers. To estimate precision under clinical conditions, motions of three human cervical spines were tracked independently ten times and vertebral and intervertebral motions associated with individual trials were compared to corresponding averages. Both tests produced errors in intervertebral angular and shear displacements no greater than 0.4° and 0.055 mm, respectively. When applied to two patient cases, aberrant intervertebral motions in the cervical spine were typically found to correlate with patient-specific anatomical features such as disc height loss and osteophytes. The case studies suggest that intervertebral kinematic time-course data could have value in clinical assessments, lead to broader understanding of how specific anatomical features influence joint motions, and in due course inform clinical treatments.
DOI: 10.6084/m9.figshare.4753975.v1
title: AFM Experimental Data

description: Here included are data sets of AFM images, corresponding cell height profiles for all time points, time stamp, and text describing experimental conditions.
DOI: 10.7910/dvn/pkjufn/kgl4je
title: FCC2002.178.ran

description: :unav
DOI: 10.6084/m9.figshare.4753780
title: Veteran trees and saproxylic insects in the floodplains of Lower Morava and Dyje rivers, Czech Republic

description: Veteran and solitary trees are key structures supporting biodiversity in many wooded ecosystems. Their global decline threatens numerous organisms associated with them, including several insect species protected by law that serve as umbrella species. The floodplain along the lower Morava and Dyje rivers is considered a hotspot for saproxylic organisms associated with veteran trees. The area is a UNESCO Biosphere Reserve and part of NATURA 2000. Between 2006 and 2015, we mapped 11,596 veteran and habitat trees in the area. The mapping also included the distribution of several insects associated with veteran trees including three beetle species (<i>Cerambyx cerdo, Osmoderma barnabita</i>, and <i>Eurythyrea quercus</i>) and two ant species (<i>Liometopum microcephalum</i> and <i>Lasius fuliginosus</i>). The data on the position, abundance, diameter, forest structure and health of the veteran trees and trees inhabited by the above species are presented in a map created in ArcGIS Online. These data serve as an important source of information for the management of nature conservation of the area.
DOI: 10.6084/m9.figshare.4753795.v1
title: A videofluoroscopy-based tracking algorithm for quantifying the time course of human intervertebral displacements

description: The motions of individual intervertebral joints can affect spine motion, injury risk, deterioration, pain, treatment strategies, and clinical outcomes. Since standard kinematic methods do not provide precise time-course details about individual vertebrae and intervertebral motions, information that could be useful for scientific advancement and clinical assessment, we developed an iterative template matching algorithm to obtain this data from videofluoroscopy images. To assess the bias of our approach, vertebrae in an intact porcine spine were tracked and compared to the motions of high-contrast markers. To estimate precision under clinical conditions, motions of three human cervical spines were tracked independently ten times and vertebral and intervertebral motions associated with individual trials were compared to corresponding averages. Both tests produced errors in intervertebral angular and shear displacements no greater than 0.4° and 0.055 mm, respectively. When applied to two patient cases, aberrant intervertebral motions in the cervical spine were typically found to correlate with patient-specific anatomical features such as disc height loss and osteophytes. The case studies suggest that intervertebral kinematic time-course data could have value in clinical assessments, lead to broader understanding of how specific anatomical features influence joint motions, and in due course inform clinical treatments.
DOI: 10.6084/m9.figshare.4753975.v2
title: AFM Experimental Data

description: Here included are data sets of AFM images, corresponding cell height profiles for all time points, time stamp, and text describing experimental conditions.
DOI: 10.7910/dvn/pkjufn/yxq2gb
title: FCC2003.153.ran

description: :unav
DOI: 10.6084/m9.figshare.4753708
title: Zymoseptoria tritici IPO323 gene annotation RRes v4.0

description: Annotation of Zymoseptoria tritici merging JGI and custom annotations at Rothamsted.