cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1400550.v2
title: Data and code from Higuera et al. 2015, The changing strength and nature of fire-climate relationships in the northern Rocky Mountains, U.S.A., 1902-2008. PLoS ONE. DOI: 10.1371/journal.pone.0127563

description: This archive includes data and scripts needed to reproduce the analyses in Higuera et al. 2015; it includes 43 (including readMe.md and readMe.pdf) files and is 26 MB when downloaded as a .zip archive. After extracting the .zip archive, there are three folders: Code, Data, and Figures. The **Code** folder contains all the scripts and functions used in the analyses and figure creation. Scripts and functions are written for MATLAB software (.m file type; www.mathworks.com), and each is file fully commented, including dependencies. For some scripts or functions, the MATLAB statistics or curve fitting toolbox is required; all other functions required are provided in this archive. The **Data** folder contains all data used in the paper, stored in .mat (Matlab) or .xlsx (Excel) format. The **Figures** folder contains all figures from the publication, in .jpg, .TIF, and .fig (Matlab) formats. **Contact:** Philip Higuera, [University of Idaho, PaleoEcology and Fire Ecology Lab](http://www.uidaho.edu/cnr/paleoecologylab "PaleoEcology Lab"), phiguera@uidaho.edu #### Citation Information ###### Original Reference - *please cite if you use data, code, or figures in your own work* Higuera, P. E., J. T. Abatzoglou, J. S. Littell, and P. Morgan. 2015. The changing nature of fire-climate relationships in the U.S. Northern Rockies, 1902-2008. _PLoS ONE_ doi: 10.1371/journal.pone.0127563
DOI: 10.6084/m9.figshare.1400541
title: New WhiteText Corpus

description: <strong><br></strong> The WhiteText project aims to extract neuroanatomical information from the biomedical literature. We are specifically focused on the extraction of brain regions and connections between them. The corpus from our most recent article are provided above (descriptions below). More information at http://www.chibi.ubc.ca/whitetext <strong>WhiteTextUnseenEval.xml:</strong> AirolaXML file for the new evaluated corpus that was extracted from the large classification run on the Journal of Comparative Neurology abstracts. <strong>WhiteTextMerged2013.xml:</strong> Merged AirolaXML file that has both the old and new manually annotated corpus of connectivity statements.<br><br>
DOI: 10.17632/cryc28v3hx.2
title: Data for: Seizure description accuracy and seizure classification results from patient histories

description: Our results in the article were based on the data showed in these three supplementary tables.
DOI: 10.6084/m9.figshare.1400544.v1
title: The role of RNA conformation in RNA-protein recognition

description: Interactions between protein and RNA play a key role in many biological processes in the gene expression pathway. Those interactions are mediated through a variety of RNA-binding protein domains, among them the highly abundant RNA recognition motif (RRM). Here we studied protein-RNA complexes from different RNA binding domain families solved by NMR and x-ray crystallography. Characterizing the structural properties of the RNA at the binding interfaces revealed an unexpected number of nucleotides with unusual RNA conformations, specifically found in RNA-RRM complexes. Moreover, we observed that the RNA nucleotides that are directly involved in interactions with the RRM domains, via hydrogen bonds and hydrophobic contacts, are significantly enriched with unique RNA conformations. Further examination of the sequences binding the RRM domain showed a preference for G nucleotides in <i>syn</i> conformation to precede or to follow U nucleotides in the <i>anti</i>-conformation, and U nucleotides in C2' endo conformation to precede U and G nucleotides possessing the more common C3' endo conformation. These findings imply a possible mode of RNA recognition by the RRM domains which enables the recognition of a wide variety of different RNA sequences and shapes. Overall, this study suggests an additional way by which the RRM domain recognizes its RNA target, involving a conformational readout.
DOI: 10.6084/m9.figshare.1409398.v209
title: ABO phenotype protected reproduction as it is based on fucosylations.

description: The molecular biological relationship between human fertility and ABO(H) blood group phenotype formation becomes evident with the rare (Oh) or <i>Bombay</i> blood type, which based on the history of his own family, Charles Darwin would have interpreted as resulting from reduced fertility in consanguinities. In its native form, the <i>Bombay</i> type occurs in individuals with an extremely rare genotype (h/h;se/se), by which the fucosyltransferases FUT1 and FUT2 are not produced due to point mutations. These enzymes, encoded on chromosome 19, are epistatically connected with the A and B allelic glycotransferase functions encoded on chromosome 9, while the fucosyl residues provide the functional-structural basis for the formation of any ABO(H) phenotype on the cell surface or in secretions and plasma proteins. Immunoglobulins are also heavily fucosylated, and via developmental variation of the positions between the cell surfaces and the heavy chains of immunoglobulins, fucosyl residues appear to augment or reduce antibody-mediated cellular cytotoxicity involving physiological anti-self-reactivity; moreover, by regulating the assembly and intracellular signaling of precursor B cell receptors, the core fucosylation of immunoglobulin heavy chains represents a key mechanism in clonal selection. In fact, the seminal plasma of leucospermic infertile men has been reported to exert high levels of poorly core-fucosylated IgG. Consequently, in <i>Bombay </i>type individuals, the non-somatic glycosylation processes of embryogenic stem cell-to-germ cell transformation, which involve the modification and <i>O</i>-fucosylation of epidermal growth factor (EGF), are most likely exposed to metabolic competition with multiple glycosidic sites of poorly fucosylated, glycan-depleted immunoglobulins that might promote increased anti-self-reactive cytotoxicity.
DOI: 10.6084/m9.figshare.1400544.v3
title: The role of RNA conformation in RNA-protein recognition

description: Interactions between protein and RNA play a key role in many biological processes in the gene expression pathway. Those interactions are mediated through a variety of RNA-binding protein domains, among them the highly abundant RNA recognition motif (RRM). Here we studied protein-RNA complexes from different RNA binding domain families solved by NMR and x-ray crystallography. Characterizing the structural properties of the RNA at the binding interfaces revealed an unexpected number of nucleotides with unusual RNA conformations, specifically found in RNA-RRM complexes. Moreover, we observed that the RNA nucleotides that are directly involved in interactions with the RRM domains, via hydrogen bonds and hydrophobic contacts, are significantly enriched with unique RNA conformations. Further examination of the sequences binding the RRM domain showed a preference for G nucleotides in <i>syn</i> conformation to precede or to follow U nucleotides in the <i>anti</i>-conformation, and U nucleotides in C2' endo conformation to precede U and G nucleotides possessing the more common C3' endo conformation. These findings imply a possible mode of RNA recognition by the RRM domains which enables the recognition of a wide variety of different RNA sequences and shapes. Overall, this study suggests an additional way by which the RRM domain recognizes its RNA target, involving a conformational readout.
DOI: 10.6084/m9.figshare.1400544.v2
title: The role of RNA conformation in RNA-protein recognition

description: Interactions between protein and RNA play a key role in many biological processes in the gene expression pathway. Those interactions are mediated through a variety of RNA-binding protein domains, among them the highly abundant RNA recognition motif (RRM). Here we studied protein-RNA complexes from different RNA binding domain families solved by NMR and x-ray crystallography. Characterizing the structural properties of the RNA at the binding interfaces revealed an unexpected number of nucleotides with unusual RNA conformations, specifically found in RNA-RRM complexes. Moreover, we observed that the RNA nucleotides that are directly involved in interactions with the RRM domains, via hydrogen bonds and hydrophobic contacts, are significantly enriched with unique RNA conformations. Further examination of the sequences binding the RRM domain showed a preference for G nucleotides in <i>syn</i> conformation to precede or to follow U nucleotides in the <i>anti</i>-conformation, and U nucleotides in C2' endo conformation to precede U and G nucleotides possessing the more common C3' endo conformation. These findings imply a possible mode of RNA recognition by the RRM domains which enables the recognition of a wide variety of different RNA sequences and shapes. Overall, this study suggests an additional way by which the RRM domain recognizes its RNA target, involving a conformational readout.
DOI: 10.6084/m9.figshare.1409398.v210
title: ABO phenotype protected reproduction as it is based on fucosylations.

description: The molecular biological relationship between human fertility and ABO(H) blood group phenotype formation becomes evident with the rare (Oh) or <i>Bombay</i> blood type, which based on the history of his own family, Charles Darwin would have interpreted as resulting from reduced fertility in consanguinities. In its native form, the <i>Bombay</i> type occurs in individuals with an extremely rare genotype (h/h;se/se), by which the fucosyltransferases FUT1 and FUT2 are not produced due to point mutations. These enzymes, encoded on chromosome 19, are epistatically connected with the A and B allelic glycotransferase functions encoded on chromosome 9, while the fucosyl residues provide the functional-structural basis for the formation of any ABO(H) phenotype on the cell surface or in secretions and plasma proteins. Immunoglobulins are also heavily fucosylated, and via developmental variation of the positions between the cell surfaces and the heavy chains of immunoglobulins, fucosyl residues appear to augment or reduce antibody-mediated cellular cytotoxicity involving physiological anti-self-reactivity; moreover, by regulating the assembly and intracellular signaling of precursor B cell receptors, the core fucosylation of immunoglobulin heavy chains represents a key mechanism in clonal selection. In fact, the seminal plasma of leucospermic infertile men has been reported to exert high levels of poorly core-fucosylated IgG. Consequently, in <i>Bombay </i>type individuals, the non-somatic glycosylation processes of embryogenic stem cell-to-germ cell transformation, which involve the modification and <i>O</i>-fucosylation of epidermal growth factor (EGF), are most likely exposed to metabolic competition with multiple glycosidic sites of poorly fucosylated, glycan-depleted immunoglobulins that might promote increased anti-self-reactive cytotoxicity.
DOI: 10.6084/m9.figshare.1400514
title: Atom Condensed Fukui Functions Calculated for 2973 Organic Molecules

description: Data set Fukui_2973 ================== Atomic NBO charges for non-hydrogen atoms in 2973 small organic molecules at the B3LYP/6-31G*//DFTB level of theory. Related publication: * Qingyou Zhang, Fangfang Zheng, Tanfeng Zhao, Xiaohui Qu, João Aires-de-Sousa: Machine Learning Estimation of Atom Condensed Fukui Functions. Molecular Informatics (2015) DOI: 10.1002/minf.201500113 This data set is publicly available at http://dx.doi.org/10.6084/m9.figshare.1400514 Files ----- Fukui_2973_sdf.tar.gz - 2973 molecules in the MDL SDFile format charges_Fukui_2973.xlsx - NBO atomic charges for the non-hydrogen atoms in neutral and charged species Molecules --------- For a subset of the fragment-like ZINC database [1] consisting of 2973 neutral organic molecules composed from elements H,C,N,O,S, molecular geometries were relaxed by DFTB+ [2] and atomic charges were calculated by the NBO 5.9 program [3] from a natural population analysis on the B3LYP/6-31G* wavefunction. Charged species (+1:cation and -1:anion) were calculated with the geometry obtained for the corresponding neutral species. Format ------ Each molecule is stored in its own file, ending in ".sdf". The format is the standard MDL SDFile generated with the Marvin/JChem 5.8.2, 2012, software [5]. Atomic charges are stored in the charges_Fukui_2973.xlsx file. Three different sheets are used for the neutral, cation and anion species respectively. Column Content ------ ------- 1 Molecule ID (as appears in the corresponding .sdf file name and in the ZINC database) 2,... Atomic charge (in elementary charge units) for atoms in the same sequence as in the corresponding .sdf file References ---------- [1] Irwin JJ, Sterling T, Mysinger MM, Bolstad ES, Coleman RG: ZINC: a free tool to discover chemistry for biology. J Chem Inf Model 2012, 52: 1757-1768. [2] Aradi B, Hourahine B, Frauenheim T: DFTB+, a sparse matrix-based implementation of the DFTB method. J Phys Chem A 2007, 111:2678-5684. [3] NBO 5.9. Glendening ED, Badenhoop JK, Reed AE, JCarpenter JE, Bohmann JA, Morales CM, Weinhold F: Theoretical Chemistry Institute, University of Wisconsin, Madison, WI, 2011; [http://www.chem.wisc.edu/~nbo5]. [4] Schmidt MW, Baldridge KK, Boatz JA, Elbert ST, Gordon MS, Jensen JJ, Koseki S, Matsunaga N, Nguyen KA, Su S, Windus TL, Dupuis M, Montgomery JA: General atomic and molecular electronic structure system. J Comput Chem 1993, 14:1347-1363. GAMESS Version 11 Aug 2011 (R1) [5] ChemAxon [http://www.chemaxon.com/]
DOI: 10.6084/m9.figshare.1400514.v1
title: Atom Condensed Fukui Functions Calculated for 2973 Organic Molecules

description: Data set Fukui_2973 ================== Atomic NBO charges for non-hydrogen atoms in 2973 small organic molecules at the B3LYP/6-31G*//DFTB level of theory. Related publication: * Qingyou Zhang, Fangfang Zheng, Tanfeng Zhao, Xiaohui Qu, João Aires-de-Sousa: Machine Learning Estimation of Atom Condensed Fukui Functions. Molecular Informatics (2015) DOI: 10.1002/minf.201500113 This data set is publicly available at http://dx.doi.org/10.6084/m9.figshare.1400514 Files ----- Fukui_2973_sdf.tar.gz - 2973 molecules in the MDL SDFile format charges_Fukui_2973.xlsx - NBO atomic charges for the non-hydrogen atoms in neutral and charged species Molecules --------- For a subset of the fragment-like ZINC database [1] consisting of 2973 neutral organic molecules composed from elements H,C,N,O,S, molecular geometries were relaxed by DFTB+ [2] and atomic charges were calculated by the NBO 5.9 program [3] from a natural population analysis on the B3LYP/6-31G* wavefunction. Charged species (+1:cation and -1:anion) were calculated with the geometry obtained for the corresponding neutral species. Format ------ Each molecule is stored in its own file, ending in ".sdf". The format is the standard MDL SDFile generated with the Marvin/JChem 5.8.2, 2012, software [5]. Atomic charges are stored in the charges_Fukui_2973.xlsx file. Three different sheets are used for the neutral, cation and anion species respectively. Column Content ------ ------- 1 Molecule ID (as appears in the corresponding .sdf file name and in the ZINC database) 2,... Atomic charge (in elementary charge units) for atoms in the same sequence as in the corresponding .sdf file References ---------- [1] Irwin JJ, Sterling T, Mysinger MM, Bolstad ES, Coleman RG: ZINC: a free tool to discover chemistry for biology. J Chem Inf Model 2012, 52: 1757-1768. [2] Aradi B, Hourahine B, Frauenheim T: DFTB+, a sparse matrix-based implementation of the DFTB method. J Phys Chem A 2007, 111:2678-5684. [3] NBO 5.9. Glendening ED, Badenhoop JK, Reed AE, JCarpenter JE, Bohmann JA, Morales CM, Weinhold F: Theoretical Chemistry Institute, University of Wisconsin, Madison, WI, 2011; [http://www.chem.wisc.edu/~nbo5]. [4] Schmidt MW, Baldridge KK, Boatz JA, Elbert ST, Gordon MS, Jensen JJ, Koseki S, Matsunaga N, Nguyen KA, Su S, Windus TL, Dupuis M, Montgomery JA: General atomic and molecular electronic structure system. J Comput Chem 1993, 14:1347-1363. GAMESS Version 11 Aug 2011 (R1) [5] ChemAxon [http://www.chemaxon.com/]
DOI: 10.6084/m9.figshare.1400496
title: Revegetation Mapping file information and metadata

description: Mapping file and metadata associated with the study: "Fire severity shapes plant colonization effects on bacterial community structure, microbial biomass, and soil enzyme activity in secondary succession of a burned forest" Knelman et al.
DOI: 10.6084/m9.figshare.1409398.v211
title: ABO phenotype protected reproduction as it is based on fucosylations.

description: The molecular biological relationship between human fertility and ABO(H) blood group phenotype formation becomes evident with the rare (Oh) or <i>Bombay</i> blood type, which based on the history of his own family, Charles Darwin would have interpreted as resulting from reduced fertility in consanguinities. In its native form, the <i>Bombay</i> type occurs in individuals with an extremely rare genotype (h/h;se/se), by which the fucosyltransferases FUT1 and FUT2 are not produced due to point mutations. These enzymes, encoded on chromosome 19, are epistatically connected with the A and B allelic glycotransferase functions encoded on chromosome 9, while the fucosyl residues provide the functional-structural basis for the formation of any ABO(H) phenotype on the cell surface or in secretions and plasma proteins. Immunoglobulins are also heavily fucosylated, and via developmental variation of the positions between the cell surfaces and the heavy chains of immunoglobulins, fucosyl residues appear to augment or reduce antibody-mediated cellular cytotoxicity involving physiological anti-self-reactivity; moreover, by regulating the assembly and intracellular signaling of precursor B cell receptors, the core fucosylation of immunoglobulin heavy chains represents a key mechanism in clonal selection. In fact, the seminal plasma of leucospermic infertile men has been reported to exert high levels of poorly core-fucosylated IgG. Consequently, in <i>Bombay </i>type individuals, the non-somatic glycosylation processes of embryogenic stem cell-to-germ cell transformation, which involve the modification and <i>O</i>-fucosylation of epidermal growth factor (EGF), are most likely exposed to metabolic competition with multiple glycosidic sites of poorly fucosylated, glycan-depleted immunoglobulins that might promote increased anti-self-reactive cytotoxicity.
DOI: 10.6084/m9.figshare.1400494
title: Gaussian Job Archive for C6H5Br

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1400491
title: Bird dropping masquerading of the nest by the potter wasp <i>Minixi suffusum</i> (Fox, 1899) (Hymenoptera: Vespidae: Eumeninae)

description: The nest of <i>Minixi suffusum</i> offers a rare form of mimicry: bird dropping masquerading of the nest by the potter wasp was recorded in mid-western Brazil, in the municipality of Dourados MS. Nesting biology of <i>M. suffusum</i> and the material involved in the action of the camouflage were observed. Eleven nests were sampled, with a total of 38 cells. Use of uric acid for staining the cell was evident in all nests. The way that the wasp stains the cells was observed. Substrate nest site, seasonality, larvae biology, sex ratio, prey and parasitoids of <i>M</i>. <i>suffusum</i> were reported. Nest camouflage may be related to defense against natural enemies.
DOI: 10.6084/m9.figshare.1400494.v1
title: Gaussian Job Archive for C6H5Br

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1409398.v212
title: ABO phenotype protected reproduction as it is based on fucosylations.

description: The molecular biological relationship between human fertility and ABO(H) blood group phenotype formation becomes evident with the rare (Oh) or <i>Bombay</i> blood type, which based on the history of his own family, Charles Darwin would have interpreted as resulting from reduced fertility in consanguinities. In its native form, the <i>Bombay</i> type occurs in individuals with an extremely rare genotype (h/h;se/se), by which the fucosyltransferases FUT1 and FUT2 are not produced due to point mutations. These enzymes, encoded on chromosome 19, are epistatically connected with the A and B allelic glycotransferase functions encoded on chromosome 9, while the fucosyl residues provide the functional-structural basis for the formation of any ABO(H) phenotype on the cell surface or in secretions and plasma proteins. Immunoglobulins are also heavily fucosylated, and via developmental variation of the positions between the cell surfaces and the heavy chains of immunoglobulins, fucosyl residues appear to augment or reduce antibody-mediated cellular cytotoxicity involving physiological anti-self-reactivity; moreover, by regulating the assembly and intracellular signaling of precursor B cell receptors, the core fucosylation of immunoglobulin heavy chains represents a key mechanism in clonal selection. In fact, the seminal plasma of leucospermic infertile men has been reported to exert high levels of poorly core-fucosylated IgG. Consequently, in <i>Bombay </i>type individuals, the non-somatic glycosylation processes of embryogenic stem cell-to-germ cell transformation, which involve the modification and <i>O</i>-fucosylation of epidermal growth factor (EGF), are most likely exposed to metabolic competition with multiple glycosidic sites of poorly fucosylated, glycan-depleted immunoglobulins that might promote increased anti-self-reactive cytotoxicity.
DOI: 10.6084/m9.figshare.1400481
title: Hydroxymethylcytosine and demethylation of the <i>γ-globin</i> gene promoter during erythroid differentiation

description: The mechanism responsible for developmental stage-specific regulation of γ<i>-globin</i> gene expression involves DNA methylation. Previous results have shown that the γ<i>-globin</i> promoter is nearly fully demethylated during fetal liver erythroid differentiation and partially demethylated during adult bone marrow erythroid differentiation. The hypothesis that 5-hydroxymethylcytosine (5hmC), a known intermediate in DNA demethylation pathways, is involved in demethylation of the γ<i>-globin</i> gene promoter during erythroid differentiation was investigated by analyzing levels of 5-methylcytosine (5mC) and 5hmC at a CCGG site within the 5′ γ<i>-globin</i> gene promoter region in FACS-purified cells from baboon bone marrow and fetal liver enriched for different stages of erythroid differentiation. Our results show that 5mC and 5hmC levels at the γ<i>-globin</i> promoter are dynamically modulated during erythroid differentiation with peak levels of 5hmC preceding and/or coinciding with demethylation. The Tet2 and Tet3 dioxygenases that catalyze formation of 5hmC are expressed during early stages of erythroid differentiation and Tet3 expression increases as differentiation proceeds. In baboon CD34+ bone marrow-derived erythroid progenitor cell cultures, γ<i>-globin</i> expression was positively correlated with 5hmC and negatively correlated with 5mC at the γ<i>-globin</i> promoter. Supplementation of culture media with Vitamin C, a cofactor of the Tet dioxygenases, reduced γ<i>-globin</i> promoter DNA methylation and increased γ-globin expression when added alone and in an additive manner in combination with either DNA methyltransferase or LSD1 inhibitors. These results strongly support the hypothesis that the Tet-mediated 5hmC pathway is involved in developmental stage-specific regulation of γ-globin expression by mediating demethylation of the γ<i>-globin</i> promoter.