cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5325313
title: p53 binding sites in normal and cancer cells are characterized by distinct chromatin context

description: The tumor suppressor protein p53 interacts with DNA in a sequence-dependent manner. Thousands of p53 binding sites have been mapped genome-wide in normal and cancer cells. However, the way p53 selectively binds its cognate sites in different types of cells is not fully understood. Here, we performed a comprehensive analysis of 25 published p53 cistromes and identified 3,551 and 6,039 ‘high-confidence’ binding sites in normal and cancer cells, respectively. Our analysis revealed 2 distinct epigenetic features underlying p53-DNA interactions <i>in vivo</i>. First, p53 binding sites are associated with transcriptionally active histone marks (H3K4me3 and H3K36me3) in normal-cell chromatin, but with repressive histone marks (H3K27me3) in cancer-cell chromatin. Second, p53 binding sites in cancer cells are characterized by a lower level of DNA methylation than their counterparts in normal cells, probably related to global hypomethylation in cancers. Intriguingly, regardless of the cell type, p53 sites are highly enriched in the endogenous retroviral elements of the ERV1 family, highlighting the importance of this repeat family in shaping the transcriptional network of p53. Moreover, the p53 sites exhibit an unusual combination of chromatin patterns: high nucleosome occupancy and, at the same time, high sensitivity to DNase I. Our results suggest that p53 can access its target sites in a chromatin environment that is non-permissive to most DNA-binding transcription factors, which may allow p53 to act as a pioneer transcription factor in the context of chromatin.
DOI: 10.6084/m9.figshare.5325313.v1
title: p53 binding sites in normal and cancer cells are characterized by distinct chromatin context

description: The tumor suppressor protein p53 interacts with DNA in a sequence-dependent manner. Thousands of p53 binding sites have been mapped genome-wide in normal and cancer cells. However, the way p53 selectively binds its cognate sites in different types of cells is not fully understood. Here, we performed a comprehensive analysis of 25 published p53 cistromes and identified 3,551 and 6,039 ‘high-confidence’ binding sites in normal and cancer cells, respectively. Our analysis revealed 2 distinct epigenetic features underlying p53-DNA interactions <i>in vivo</i>. First, p53 binding sites are associated with transcriptionally active histone marks (H3K4me3 and H3K36me3) in normal-cell chromatin, but with repressive histone marks (H3K27me3) in cancer-cell chromatin. Second, p53 binding sites in cancer cells are characterized by a lower level of DNA methylation than their counterparts in normal cells, probably related to global hypomethylation in cancers. Intriguingly, regardless of the cell type, p53 sites are highly enriched in the endogenous retroviral elements of the ERV1 family, highlighting the importance of this repeat family in shaping the transcriptional network of p53. Moreover, the p53 sites exhibit an unusual combination of chromatin patterns: high nucleosome occupancy and, at the same time, high sensitivity to DNase I. Our results suggest that p53 can access its target sites in a chromatin environment that is non-permissive to most DNA-binding transcription factors, which may allow p53 to act as a pioneer transcription factor in the context of chromatin.
DOI: 10.6084/m9.figshare.5325292
title: Citations for articles analyzed in a study of qualitative methodology in library and information science

description: Citations for articles analyzed in Dempsey, Paula R. 2018. “How LIS Scholars Conceptualize Rigor in Qualitative Data.” <i>portal: Libraries and the Academy</i> 18(2):363–90.<br>
DOI: 10.6084/m9.figshare.5325310.v1
title: Optogenetic Masking of olfactory system

description: Behavioral dataset for optogenetic during an odor concentration task.<br>The data can be loaded using Python software found at https://github.com/c-wilson/behavior_tools.<br>
DOI: 10.6084/m9.figshare.5325295
title: Fluctuations in the abundance of ammonia oxidizers and the contents of inorganic nitrogen in solarized soil

description: Solarization makes a great impact on the abundance of ammonia oxidizers and nitrifying activity in soil. To elucidate fluctuations in the abundance of ammonia oxidizers and nitrification in solarized soil, copy numbers of <i>amoA</i> gene of ammonia-oxidizing bacteria (AOB) and archaea (AOA), viable number of ammonia oxidizers and inorganic nitrogen contents were investigated in greenhouse experiments. The copy number of <i>amoA</i> gene and the viable number of ammonia oxidizers were determined by the quantitative polymerase chain reaction and most probable number methods, respectively. Abundance of AOB based on the estimation of <i>amoA</i> gene copy numbers and viable counts of ammonia oxidizers was decreased by the solarization treatment and increased during the tomato (<i>Solanum lycopersicum</i> L.) cultivation period following the solarization. Effect of solarization on the copy number of <i>amoA</i> gene of AOA was less evident than that on AOB. The proportion of nitrate in inorganic nitrogen contents was declined by the solarization and increased during the tomato cultivation period following the solarization. Positive correlations were found between the proportion of nitrate in inorganic nitrogen content and the copy number of bacterial or archaeal <i>amoA</i> gene or the viable number of ammonia oxidizers; the copy number of bacterial <i>amoA</i> gene showed a strong correlation with the viable number of ammonia oxidizers. The present study revealed influences of solarization on the fluctuation in the abundance of ammonia oxidizers and dynamics of inorganic nitrogen contents in soil and the results indicate that the determination of <i>amoA</i> gene of AOB is possibly a quick and useful diagnostic technique for evaluating suppression and restoration of nitrification following solarization.
DOI: 10.6084/m9.figshare.5325295.v1
title: Fluctuations in the abundance of ammonia oxidizers and the contents of inorganic nitrogen in solarized soil

description: Solarization makes a great impact on the abundance of ammonia oxidizers and nitrifying activity in soil. To elucidate fluctuations in the abundance of ammonia oxidizers and nitrification in solarized soil, copy numbers of <i>amoA</i> gene of ammonia-oxidizing bacteria (AOB) and archaea (AOA), viable number of ammonia oxidizers and inorganic nitrogen contents were investigated in greenhouse experiments. The copy number of <i>amoA</i> gene and the viable number of ammonia oxidizers were determined by the quantitative polymerase chain reaction and most probable number methods, respectively. Abundance of AOB based on the estimation of <i>amoA</i> gene copy numbers and viable counts of ammonia oxidizers was decreased by the solarization treatment and increased during the tomato (<i>Solanum lycopersicum</i> L.) cultivation period following the solarization. Effect of solarization on the copy number of <i>amoA</i> gene of AOA was less evident than that on AOB. The proportion of nitrate in inorganic nitrogen contents was declined by the solarization and increased during the tomato cultivation period following the solarization. Positive correlations were found between the proportion of nitrate in inorganic nitrogen content and the copy number of bacterial or archaeal <i>amoA</i> gene or the viable number of ammonia oxidizers; the copy number of bacterial <i>amoA</i> gene showed a strong correlation with the viable number of ammonia oxidizers. The present study revealed influences of solarization on the fluctuation in the abundance of ammonia oxidizers and dynamics of inorganic nitrogen contents in soil and the results indicate that the determination of <i>amoA</i> gene of AOB is possibly a quick and useful diagnostic technique for evaluating suppression and restoration of nitrification following solarization.
DOI: 10.6084/m9.figshare.5325292.v2
title: Citations for articles analyzed in a study of qualitative methodology in library and information science

description: Citations for articles analyzed in Dempsey, Paula R. 2018. “How LIS Scholars Conceptualize Rigor in Qualitative Data.” <i>portal: Libraries and the Academy</i> 18(2):363–90.<br>
DOI: 10.6084/m9.figshare.5325292.v1
title: Citations for articles analyzed in a study of qualitative methodology in library and information sciences

description: Citations for articles analyzed in Dempsey, Paula R. "How LIS Scholars Conceptualize Rigor with Qualitative Data." <i>portal: Libraries and the Academy</i>. Forthcoming April 2018.<br>
DOI: 10.6084/m9.figshare.5325277
title: Clinical radiobiology of proton therapy: modeling of RBE

description: <b>Purpose:</b> To better estimate relative biological effectiveness (RBE) in therapeutic proton beams by using a modeled approach, in order to improve their clinical safety and effectiveness. <b>Introduction:</b> Concerns exist about the 1.1 RBE used in proton therapy, since it may lead to unintentional over- and under-dosage in patients and so lead to unexpected clinical outcomes. Late reacting normal tissues (with low α/β values), might be overdosed if RBE &gt;1.1; very radiosensitive tumors (with high α/β), might be under-dosed if RBE &lt;1.1. Some physicists recommend ignoring RBE in favor of a LET × dose product to predict effects. <b>Material and methods:</b> Extensive linear-quadratic based modeling is scaled between a standard hospital megavoltage photon reference radiation (low LET of 0.22 keV μm<sup>−1</sup>) α and β values and their values at higher LETs, representative of the middle and end of the SOBPs. A previously published energy-efficiency model provide RBE estimates for different α/β (2–27 Gy). The concept of using a LET × dose product is assessed by comparing it with surviving fraction and the equivalent dose in 2 Gy fractions (EQD-2). <b>Results:</b> Low α/β value biosystems have the widest RBE ranges with dose per fraction changes and increasing LET, often above 1.1 even within the SOBP LET range, with lower values at higher dose per fraction. Highly radiosensitive tumors (α/β 10–27 Gy) have the lowest RBEs, often below 1.1, and are not fraction-sensitive. RBE’s generally increase with LET, so curtailment of LET in normal tissues is important. The LET × dose product is insufficiently discriminating when compared with surviving fraction and biological effective dose (BED) or EQD-2. <b>Conclusions:</b> An overall research framework is suggested. Proton therapy advantages will only be fully realized if reasonably correct RBE values are used.
DOI: 10.6084/m9.figshare.5325280.v2
title: Comparison of PET and CT radiomics for prediction of local tumor control in head and neck squamous cell carcinoma

description: <b>Purpose:</b> An association between radiomic features extracted from CT and local tumor control in the head and neck squamous cell carcinoma (HNSCC) has been shown. This study investigated the value of pretreatment functional imaging (18F-FDG PET) radiomics for modeling of local tumor control. <b>Material and Methods:</b> Data from HNSCC patients (<i>n</i> = 121) treated with definitive radiochemotherapy were used for model training. In total, 569 radiomic features were extracted from both contrast-enhanced CT and 18F-FDG PET images in the primary tumor region. CT, PET and combined PET/CT radiomic models to assess local tumor control were trained separately. Five feature selection and three classification methods were implemented. The performance of the models was quantified using concordance index (CI) in 5-fold cross validation in the training cohort. The best models, per image modality, were compared and verified in the independent validation cohort (<i>n</i> = 51). The difference in CI was investigated using bootstrapping. Additionally, the observed and radiomics-based estimated probabilities of local tumor control were compared between two risk groups. <b>Results:</b> The feature selection using principal component analysis and the classification based on the multivariabale Cox regression with backward selection of the variables resulted in the best models for all image modalities (CI<sub>CT</sub> = 0.72, CI<sub>PET</sub> = 0.74, CI<sub>PET/CT</sub> = 0.77). Tumors more homogenous in CT density (decreased GLSZM<sub>size_zone_entropy</sub>) and with a focused region of high FDG uptake (higher GLSZM<sub>SZLGE</sub>) indicated better prognosis. No significant difference in the performance of the models in the validation cohort was observed (CI<sub>CT</sub> = 0.73, CI<sub>PET</sub> = 0.71, CI<sub>PET/CT</sub> = 0.73). However, the CT radiomics-based model overestimated the probability of tumor control in the poor prognostic group (predicted = 68%, observed = 56%). <b>Conclusions:</b> Both CT and PET radiomics showed equally good discriminative power for local tumor control modeling in HNSCC. However, CT-based predictions overestimated the local control rate in the poor prognostic validation cohort, and thus, we recommend to base the local control modeling on the 18F-FDG PET.
DOI: 10.6084/m9.figshare.5325070
title: Supplementary material S5 from The morphology of the inner ear of squamate reptiles and its bearing on the origin of snakes

description: Scripts used to run the analyses in R.
DOI: 10.6084/m9.figshare.5325277.v1
title: Clinical radiobiology of proton therapy: modeling of RBE

description: <b>Purpose:</b> To better estimate relative biological effectiveness (RBE) in therapeutic proton beams by using a modeled approach, in order to improve their clinical safety and effectiveness. <b>Introduction:</b> Concerns exist about the 1.1 RBE used in proton therapy, since it may lead to unintentional over- and under-dosage in patients and so lead to unexpected clinical outcomes. Late reacting normal tissues (with low α/β values), might be overdosed if RBE &gt;1.1; very radiosensitive tumors (with high α/β), might be under-dosed if RBE &lt;1.1. Some physicists recommend ignoring RBE in favor of a LET × dose product to predict effects. <b>Material and methods:</b> Extensive linear-quadratic based modeling is scaled between a standard hospital megavoltage photon reference radiation (low LET of 0.22 keV μm<sup>−1</sup>) α and β values and their values at higher LETs, representative of the middle and end of the SOBPs. A previously published energy-efficiency model provide RBE estimates for different α/β (2–27 Gy). The concept of using a LET × dose product is assessed by comparing it with surviving fraction and the equivalent dose in 2 Gy fractions (EQD-2). <b>Results:</b> Low α/β value biosystems have the widest RBE ranges with dose per fraction changes and increasing LET, often above 1.1 even within the SOBP LET range, with lower values at higher dose per fraction. Highly radiosensitive tumors (α/β 10–27 Gy) have the lowest RBEs, often below 1.1, and are not fraction-sensitive. RBE’s generally increase with LET, so curtailment of LET in normal tissues is important. The LET × dose product is insufficiently discriminating when compared with surviving fraction and biological effective dose (BED) or EQD-2. <b>Conclusions:</b> An overall research framework is suggested. Proton therapy advantages will only be fully realized if reasonably correct RBE values are used.
DOI: 10.6084/m9.figshare.5325277.v3
title: Clinical radiobiology of proton therapy: modeling of RBE

description: <b>Purpose:</b> To better estimate relative biological effectiveness (RBE) in therapeutic proton beams by using a modeled approach, in order to improve their clinical safety and effectiveness. <b>Introduction:</b> Concerns exist about the 1.1 RBE used in proton therapy, since it may lead to unintentional over- and under-dosage in patients and so lead to unexpected clinical outcomes. Late reacting normal tissues (with low α/β values), might be overdosed if RBE &gt;1.1; very radiosensitive tumors (with high α/β), might be under-dosed if RBE &lt;1.1. Some physicists recommend ignoring RBE in favor of a LET × dose product to predict effects. <b>Material and methods:</b> Extensive linear-quadratic based modeling is scaled between a standard hospital megavoltage photon reference radiation (low LET of 0.22 keV μm<sup>−1</sup>) α and β values and their values at higher LETs, representative of the middle and end of the SOBPs. A previously published energy-efficiency model provide RBE estimates for different α/β (2–27 Gy). The concept of using a LET × dose product is assessed by comparing it with surviving fraction and the equivalent dose in 2 Gy fractions (EQD-2). <b>Results:</b> Low α/β value biosystems have the widest RBE ranges with dose per fraction changes and increasing LET, often above 1.1 even within the SOBP LET range, with lower values at higher dose per fraction. Highly radiosensitive tumors (α/β 10–27 Gy) have the lowest RBEs, often below 1.1, and are not fraction-sensitive. RBE’s generally increase with LET, so curtailment of LET in normal tissues is important. The LET × dose product is insufficiently discriminating when compared with surviving fraction and biological effective dose (BED) or EQD-2. <b>Conclusions:</b> An overall research framework is suggested. Proton therapy advantages will only be fully realized if reasonably correct RBE values are used.
DOI: 10.6084/m9.figshare.5325064
title: Supplementary material S7 from The morphology of the inner ear of squamate reptiles and its bearing on the origin of snakes

description: Three-dimensional ordinary PCA plot of PC1 vs PC2 vs PC3. Colour coding is the same as in Figure 2.
DOI: 10.6084/m9.figshare.5325067
title: Supplementary material S1 - Table S1 from The morphology of the inner ear of squamate reptiles and its bearing on the origin of snakes

description: Specimen numbers, taxonomic authorities, and institutional abbreviations.
DOI: 10.6084/m9.figshare.5325070.v1
title: Supplementary material S5 from The morphology of the inner ear of squamate reptiles and its bearing on the origin of snakes

description: Scripts used to run the analyses in R.
DOI: 10.6084/m9.figshare.5325061
title: Supplementary material S9 from The morphology of the inner ear of squamate reptiles and its bearing on the origin of snakes

description: Three-dimensional phylogenetic PCA plot of PC1 vs PC2 vs PC3 (based on phylogeny where <i>Dinilysia</i> is a stem alethinophidian). Colour coding is the same as in Figure 2.
DOI: 10.6084/m9.figshare.5325277.v2
title: Clinical radiobiology of proton therapy: modeling of RBE

description: <b>Purpose:</b> To better estimate relative biological effectiveness (RBE) in therapeutic proton beams by using a modeled approach, in order to improve their clinical safety and effectiveness. <b>Introduction:</b> Concerns exist about the 1.1 RBE used in proton therapy, since it may lead to unintentional over- and under-dosage in patients and so lead to unexpected clinical outcomes. Late reacting normal tissues (with low α/β values), might be overdosed if RBE &gt;1.1; very radiosensitive tumors (with high α/β), might be under-dosed if RBE &lt;1.1. Some physicists recommend ignoring RBE in favor of a LET × dose product to predict effects. <b>Material and methods:</b> Extensive linear-quadratic based modeling is scaled between a standard hospital megavoltage photon reference radiation (low LET of 0.22 keV μm<sup>−1</sup>) α and β values and their values at higher LETs, representative of the middle and end of the SOBPs. A previously published energy-efficiency model provide RBE estimates for different α/β (2–27 Gy). The concept of using a LET × dose product is assessed by comparing it with surviving fraction and the equivalent dose in 2 Gy fractions (EQD-2). <b>Results:</b> Low α/β value biosystems have the widest RBE ranges with dose per fraction changes and increasing LET, often above 1.1 even within the SOBP LET range, with lower values at higher dose per fraction. Highly radiosensitive tumors (α/β 10–27 Gy) have the lowest RBEs, often below 1.1, and are not fraction-sensitive. RBE’s generally increase with LET, so curtailment of LET in normal tissues is important. The LET × dose product is insufficiently discriminating when compared with surviving fraction and biological effective dose (BED) or EQD-2. <b>Conclusions:</b> An overall research framework is suggested. Proton therapy advantages will only be fully realized if reasonably correct RBE values are used.
DOI: 10.6084/m9.figshare.5325052
title: Supplementary material S8 - Table S4 from The morphology of the inner ear of squamate reptiles and its bearing on the origin of snakes

description: First 10 phylogenetic principal components (PPCs) for all taxa included in the study and for both phylogenentic PCA analyses (i.e. with <i>Dinilysia</i> as a stem alethinophidian and as a stem ophidian).
DOI: 10.6084/m9.figshare.5325055
title: Supplementary material S6 - Table S3 from The morphology of the inner ear of squamate reptiles and its bearing on the origin of snakes

description: First 10 ordinary principal components for all taxa included in the study.
DOI: 10.6084/m9.figshare.5325061.v1
title: Supplementary material S9 from The morphology of the inner ear of squamate reptiles and its bearing on the origin of snakes

description: Three-dimensional phylogenetic PCA plot of PC1 vs PC2 vs PC3 (based on phylogeny where <i>Dinilysia</i> is a stem alethinophidian). Colour coding is the same as in Figure 2.
DOI: 10.6084/m9.figshare.5325064.v1
title: Supplementary material S7 from The morphology of the inner ear of squamate reptiles and its bearing on the origin of snakes

description: Three-dimensional ordinary PCA plot of PC1 vs PC2 vs PC3. Colour coding is the same as in Figure 2.
DOI: 10.6084/m9.figshare.5325067.v1
title: Supplementary material S1 - Table S1 from The morphology of the inner ear of squamate reptiles and its bearing on the origin of snakes

description: Specimen numbers, taxonomic authorities, and institutional abbreviations.
DOI: 10.6084/m9.figshare.5325055.v1
title: Supplementary material S6 - Table S3 from The morphology of the inner ear of squamate reptiles and its bearing on the origin of snakes

description: First 10 ordinary principal components for all taxa included in the study.
DOI: 10.6084/m9.figshare.5325046
title: Supplementary material S4 - Table S2 from The morphology of the inner ear of squamate reptiles and its bearing on the origin of snakes

description: Ecology of all the taxa included in the study and literature sources.
DOI: 10.6084/m9.figshare.5325049
title: Supplementary material S2 from The morphology of the inner ear of squamate reptiles and its bearing on the origin of snakes

description: Landmark coordinates of all taxa included in the study (.nts format).
DOI: 10.6084/m9.figshare.5325052.v1
title: Supplementary material S8 - Table S4 from The morphology of the inner ear of squamate reptiles and its bearing on the origin of snakes

description: First 10 phylogenetic principal components (PPCs) for all taxa included in the study and for both phylogenentic PCA analyses (i.e. with <i>Dinilysia</i> as a stem alethinophidian and as a stem ophidian).
DOI: 10.6084/m9.figshare.5325046.v1
title: Supplementary material S4 - Table S2 from The morphology of the inner ear of squamate reptiles and its bearing on the origin of snakes

description: Ecology of all the taxa included in the study and literature sources.
DOI: 10.6084/m9.figshare.5325049.v1
title: Supplementary material S2 from The morphology of the inner ear of squamate reptiles and its bearing on the origin of snakes

description: Landmark coordinates of all taxa included in the study (.nts format).