cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1154004
title: Rat CNS Interactome (TF and coTFs)

description: To construct the CNS Interactome, ARACNe was applied to the Cleaner-normalized expression profile obtained from 8 brain regions believed to be relevant in alcohol’s reinforcing properties using the Affymetrix RN230.2 platform. Specifically, the following brain regions were microdissected and analyzed from nondependent and dependent alcohol self-administering rats as well as age-matched alcohol naive rats: (a) medial prefrontal cortex (MPF), (b) shell and (c) core NAc sub-regions, (d) central nucleus (CeA) and (e) basolateral nucleus of the amygdala (BLA), (f) dorsolateral and (g) ventral bed nucleus of the stria terminalis (BNST), and (h) ventral tegmental area (VTA). Transcription factors (TFs) were defined as rat genes annotated as “transcription factor activity” in Gene Ontology and the list of TFs from TRANSFAC. This produced a final list of 898 TFs, from which 898 were present on the Cleaner-mapped expression profile. ARACNe was run using the adaptive partitioning algorithm, which selects the optimal kernel width for calculating the MI threshold of a specified p-value. The MI threshold used by ARACNe (MI &gt;= 0.44068) corresponded to the p-value threshold of 10-8 after 100 bootstrap runs. The resulting CNS Interactome contained 244,276 statistically significant MIs between the 6,716 genes.
DOI: 10.6084/m9.figshare.1153969
title: Genetic Reprogramming of Human Amniotic cells

description: Genomic DNA from selected lines was treated with bisulfite and purified. The promoter of Oct4 was amplified by PCR and cloned into TOPO vectors. Inserts were sequenced by commercial services and shown here.
DOI: 10.6084/m9.figshare.1154006.v1
title: Rat CNS Interactome (Signalling Molecules)

description: To construct the CNS Signaling Molecule Interactome, ARACNe was applied to the Cleaner-normalized expression profile obtained from 8 brain regions believed to be relevant in alcohol’s reinforcing properties using the Affymetrix RN230.2 platform. Specifically, the following brain regions were microdissected and analyzed from nondependent and dependent alcohol self-administering rats as well as age-matched alcohol naive rats: (a) medial prefrontal cortex (MPF), (b) shell and (c) core NAc sub-regions, (d) central nucleus (CeA) and (e) basolateral nucleus of the amygdala (BLA), (f) dorsolateral and (g) ventral bed nucleus of the stria terminalis (BNST), and (h) ventral tegmental area (VTA). Signaling Molecules (Sigs), were defined as rat genes annotated in the GO Biological Process database as: ‘signal transduction’ and in the GO Cellular Component database as GO:0005622 – ‘intracellular’ or GO:0005886 – ‘plasma membrane’. This produced a final list of 2,842 genes from which 1,100 were present on the Cleaner-mapped expression profile. ARACNe was run using the adaptive partitioning algorithm, which selects the optimal kernel width for calculating the MI threshold of a specified p-value. The MI threshold used by the adaptive partitioning algorithm (MI ≥ 0.454302) corresponded to the p-value threshold of 10-8 after 100 bootstrap runs, and the resulting CNS signaling molecule interactome contained 93,946 statistically significant MIs between 7,018 genes.
DOI: 10.6084/m9.figshare.1153969.v1
title: Genetic Reprogramming of Human Amniotic cells

description: Genomic DNA from selected lines was treated with bisulfite and purified. The promoter of Oct4 was amplified by PCR and cloned into TOPO vectors. Inserts were sequenced by commercial services and shown here.
DOI: 10.6084/m9.figshare.1154004.v1
title: Rat CNS Interactome (TF and coTFs)

description: To construct the CNS Interactome, ARACNe was applied to the Cleaner-normalized expression profile obtained from 8 brain regions believed to be relevant in alcohol’s reinforcing properties using the Affymetrix RN230.2 platform. Specifically, the following brain regions were microdissected and analyzed from nondependent and dependent alcohol self-administering rats as well as age-matched alcohol naive rats: (a) medial prefrontal cortex (MPF), (b) shell and (c) core NAc sub-regions, (d) central nucleus (CeA) and (e) basolateral nucleus of the amygdala (BLA), (f) dorsolateral and (g) ventral bed nucleus of the stria terminalis (BNST), and (h) ventral tegmental area (VTA). Transcription factors (TFs) were defined as rat genes annotated as “transcription factor activity” in Gene Ontology and the list of TFs from TRANSFAC. This produced a final list of 898 TFs, from which 664 were present on the Cleaner-mapped expression profile. ARACNe was run using the adaptive partitioning algorithm, which selects the optimal kernel width for calculating the MI threshold of a specified p-value. The MI threshold used by ARACNe (MI &gt;= 0.44068) corresponded to the p-value threshold of 10-8 after 100 bootstrap runs. The resulting CNS Interactome contained 244,276 statistically significant MIs between the 6,716 genes..
DOI: 10.6084/m9.figshare.1154006.v2
title: Rat CNS Interactome (Signalling Molecules)

description: To construct the CNS Signaling Molecule Interactome, ARACNe was applied to the Cleaner-normalized expression profile obtained from 8 brain regions believed to be relevant in alcohol’s reinforcing properties using the Affymetrix RN230.2 platform. Specifically, the following brain regions were microdissected and analyzed from nondependent and dependent alcohol self-administering rats as well as age-matched alcohol naive rats: (a) medial prefrontal cortex (MPF), (b) shell and (c) core NAc sub-regions, (d) central nucleus (CeA) and (e) basolateral nucleus of the amygdala (BLA), (f) dorsolateral and (g) ventral bed nucleus of the stria terminalis (BNST), and (h) ventral tegmental area (VTA). Signaling Molecules (Sigs), were defined as rat genes annotated in the GO Biological Process database as: ‘signal transduction’ and in the GO Cellular Component database as GO:0005622 – ‘intracellular’ or GO:0005886 – ‘plasma membrane’. This produced a final list of 2,842 genes from which 1,100 were present on the Cleaner-mapped expression profile. ARACNe was run using the adaptive partitioning algorithm, which selects the optimal kernel width for calculating the MI threshold of a specified p-value. The MI threshold used by the adaptive partitioning algorithm (MI ≥ 0.454302) corresponded to the p-value threshold of 10-8 after 100 bootstrap runs, and the resulting CNS signaling molecule interactome contained 93,946 statistically significant MIs between 7,018 genes.
DOI: 10.6084/m9.figshare.1153966
title: Modeling for Fidelity: Virtual mentorship by scientists fosters teacher self-efficacy and promotes implementation of novel high school biomedical curricula

description: Primary data from a small scale comparison case study to compare virtual professional development with face-to-face-professional development in the teaching of neuroscience in biology classes to 10th-12th grade high school students.
DOI: 10.6084/m9.figshare.1154004.v2
title: Rat CNS Interactome (TF and coTFs)

description: To construct the CNS Interactome, ARACNe was applied to the Cleaner-normalized expression profile obtained from 8 brain regions believed to be relevant in alcohol’s reinforcing properties using the Affymetrix RN230.2 platform. Specifically, the following brain regions were microdissected and analyzed from nondependent and dependent alcohol self-administering rats as well as age-matched alcohol naive rats: (a) medial prefrontal cortex (MPF), (b) shell and (c) core NAc sub-regions, (d) central nucleus (CeA) and (e) basolateral nucleus of the amygdala (BLA), (f) dorsolateral and (g) ventral bed nucleus of the stria terminalis (BNST), and (h) ventral tegmental area (VTA). Transcription factors (TFs) were defined as rat genes annotated as “transcription factor activity” in Gene Ontology and the list of TFs from TRANSFAC. This produced a final list of 898 TFs, from which 886 were present on the Cleaner-mapped expression profile. ARACNe was run using the adaptive partitioning algorithm, which selects the optimal kernel width for calculating the MI threshold of a specified p-value. The MI threshold used by ARACNe (MI &gt;= 0.46108) corresponded to the p-value threshold of 10-8 after 100 bootstrap runs. The resulting CNS Interactome contained 78,090 statistically significant MIs between the 6,716 genes.
DOI: 10.6084/m9.figshare.1153961
title: Dataset for A systematic review and conceptual framework for the mechanistic pathways of nurse plants

description: Aim To conceptualize the mechanistic pathways of the nurse-plant syndrome by life-form and to identify the implications of positive plant–plant interactions for landscape and evolutionary ecology. Location Global. Methods We conducted a quantitative review examining 298 articles to catego- rize the literature on nurse-plant interactions based on geographic region, mecha- nism of facilitation, ecological hypothesis and nurse life-form. Results A total of nine different nurse mechanisms were identified and two were classified as meta-mechanisms. We found that shrubs were the dominant nurse life-form (46% of total studies) and that studies of positive plant interactions were most frequent in areas of high abiotic stress. Nurse-plant studies were also distrib- uted unevenly around the globe with nearly a quarter in the South American Andes and Spain. Studies testing the direct nurse–protégé interactions were the most frequently performed, including the ecophysiological responses of protégé species (32.2%). Research gaps identified in the nurse-plant literature included indirect interactions and seed trapping as well as the large-scale implications for landscape ecology and evolution. Main conclusions Nurse plants are often considered keystone species because they commonly structure plant communities. This is an important confirmatory finding in many respects, but it is also novel in that it challenges traditional plant ecology theory and has important implications for landscape-level dynamics over time. The categorization of mechanisms proposed provides a conceptual frame- work useful for organizing the research to date and can accelerate linkages with theory and application by identifying important connections. It is becoming increasingly apparent that future studies of the nurse-plant syndrome must decouple and consider multiple mechanisms of interaction to explain the processes that influence community structure, particularly in high-stress conditions, given a changing climate and potential shifts in biodiversity.
DOI: 10.6084/m9.figshare.1153961.v1
title: Dataset for A systematic review and conceptual framework for the mechanistic pathways of nurse plants

description: Aim To conceptualize the mechanistic pathways of the nurse-plant syndrome by life-form and to identify the implications of positive plant–plant interactions for landscape and evolutionary ecology. Location Global. Methods We conducted a quantitative review examining 298 articles to catego- rize the literature on nurse-plant interactions based on geographic region, mecha- nism of facilitation, ecological hypothesis and nurse life-form. Results A total of nine different nurse mechanisms were identified and two were classified as meta-mechanisms. We found that shrubs were the dominant nurse life-form (46% of total studies) and that studies of positive plant interactions were most frequent in areas of high abiotic stress. Nurse-plant studies were also distrib- uted unevenly around the globe with nearly a quarter in the South American Andes and Spain. Studies testing the direct nurse–protégé interactions were the most frequently performed, including the ecophysiological responses of protégé species (32.2%). Research gaps identified in the nurse-plant literature included indirect interactions and seed trapping as well as the large-scale implications for landscape ecology and evolution. Main conclusions Nurse plants are often considered keystone species because they commonly structure plant communities. This is an important confirmatory finding in many respects, but it is also novel in that it challenges traditional plant ecology theory and has important implications for landscape-level dynamics over time. The categorization of mechanisms proposed provides a conceptual frame- work useful for organizing the research to date and can accelerate linkages with theory and application by identifying important connections. It is becoming increasingly apparent that future studies of the nurse-plant syndrome must decouple and consider multiple mechanisms of interaction to explain the processes that influence community structure, particularly in high-stress conditions, given a changing climate and potential shifts in biodiversity.
DOI: 10.6084/m9.figshare.1153947
title: Royal Holloway RCUK Gold Open Access APCs 2013 - 2014

description: This file contains data regarding the article processing charges of the RCUK-funded gold open access publications from Royal Holloway, University of London, for the year 2013 - 2014.
DOI: 10.6084/m9.figshare.1153948
title: Excel file with PCR-RFLP patterns for identification of nursery Phytophthora spp.

description: Contains restriction fragement length polymorphism data and GenBank Accession numbers for common nursery <em>Phytophthora</em> species found in Oregon.
DOI: 10.6084/m9.figshare.1153934
title: Wall shear stress at the initiation site of cerebral aneurysms: Distribution on flattened branches

description: Animation of the wall shear stress field during the cardiac cycle. Data was created as part of the following study:Geers AJ, Morales HG, Larrabide I, Butakoff C, Bijlenga P, Frangi AF. Wall shear stress at the aneurysm initiation site. Biomechanics and Modeling in Mechanobiology, 16(1):97-115, 2017.Cases were anterior cerebral arteries (ACAs) harboring an aneurysm that had been virtually removed to approximate the pre-aneurysm geometry. Controls were ACAs that had never formed an aneurysm. ACA branches were flattened using the Vascular Modeling Toolkit (VMTK) to be able to view the whole branch surface at once.wss_normalized_ps.gif uses a fixed color range from 0 to 2 times the average WSS on the branch at peak systole.wss_normalized.gif uses a variable color range from 0 to 2 times the average WSS on the branch at the current timestep. This way of normalizing the color range emphasizes changes in distribution rather than magnitude.Contact: ajgeers@gmail.com
DOI: 10.6084/m9.figshare.1153947.v1
title: Royal Holloway RCUK Gold Open Access APCs 2013 - 2014

description: This file contains data regarding the article processing charges of the RCUK-funded gold open access publications from Royal Holloway, University of London, for the year 2013 - 2014.
DOI: 10.6084/m9.figshare.1153921
title: Human TCRs and CDR3s sequenced from healthy volunteers and HIV-infected patients, before and after 14 weeks of therapy

description: We have employed an error-correcting, high-throughput transcript sequencing protocol to profile impact of HIV infection upon the T-cell receptor repertoire. We have sequences both alpha and beta chain TCR repertoires from 2.5ml of peripheral blood for 16 antiretroviral (ART)-naive HIV patients (de-identified reference numbers prefixed 'P0'). Two samples per patient were processed: one immediately before starting therapy ('v1') and another shortly after starting ('v2', after an average 14 weeks). We additionally sequenced the repertoires of ten healthy volunteers ('HV'), taking two blood samples three months apart for four of those donors (HV01 to HV04) in order to compare TCR dynamics over a comparable time frame. One of these healthy donors (HV01) and a further healthy donor (HVD1) also gave a larger blood sample, which was separated into CD4+ and CD8+ T-cell populations by FACS, and their TCR repertoires were seqeunced. Having amplified and sequenced the TCR repertoires of these 100 samples, we identified their VJ recombinations using a modified version of Decombinator (called vDCR), TCR analysis software designed in our lab. We then made use of random barcode sequences introduced before amplification to error- and frequency-correct our Decombinator assignations (DCRs), before translating them and extracting their complementarity determining region 3 (CDR3) sequences. Here we present the results of these analyses. The .dcrcdr3 files in this fileset consist of a unique DCR assignation per line, the CDR3 sequence it encodes, and the frequency with which that TCR appeared in the data following error-correction. Each line follows the format: 'V, J, Vdel, Jdel, insert: CDR3, freq' (V = V gene, J = J gene, Vdel = number of deletions from V, Jdel = number of deletions from J, insert = string of nucleotides from the end of the deleted V to the start of the deleted J, CDR3 = translation CDR3 sequence, from the second conserved cysteine residue in the V to the conserved phenylalanine of the FGXG motif of the J, freq = error-corrected frequency of that assignation.) The raw sequence data fastq files from which these TCRs were extracted is available in the Sequence Read Archive (SRA) under the Study accession number SRP045430. The AccessionKey.xls spreadsheet cross-references all filenames with their appropriate SRA individual accession numbers. The Python scripts which were used to generate this data from that raw fastq data are also available on figshare (see links below).
DOI: 10.6084/m9.figshare.1153934.v2
title: WSS distribution on flattened anterior cerebral artery branches

description: Animation of the wall shear stress field during the cardiac cycle. Data belongs to a study aimed at characterizing the WSS at the aneurysm initiation site. Cases were anterior cerebral arteries (ACAs) harboring an aneurysm that had been virtually removed to approximate the pre-aneurysm geometry. Controls were ACAs that had never formed an aneurysm. ACA branches were flattened using the Vascular Modeling Toolkit (VMTK) to be able to view the whole branch surface at once. wss_normalized_ps.gif uses a fixed color range from 0 to 2 times the average WSS on the branch at peak systole. wss_normalized.gif uses a variable color range from 0 to 2 times the average WSS on the branch at the current timestep. This way of normalizing the color range emphasizes changes in distribution rather than magnitude. Contact: ajgeers@gmail.com
DOI: 10.6084/m9.figshare.1153817
title: Known specificity human TCR CDR3 sequences

description: The hypervariable complementarity determining region 3 (CDR3) of T-cell receptors (TCRs) forms the major contacts with the peptide-MHC molecule, and thus is the key site of determining antigen specificity. In this dataset I have gathered CDR3 sequences from the literature, in order so that we may use these to search our high-throughput TCR repertoire DNA-sequencing data. The CDR3s gathered fall into one of two categories. The first category consists of CDR3s from TCRs reported to be reactive against known viral epitopes. This category includes CDR3s specific for human immunodeficiency virus (HIV), cytomegalovirus (CMV) and Epstein-Barr virus (EBV) (the latter two virus' CDR3 lists being collated and kindly contributed by Ilgar Mamedov, see Zvyagin et al, 2014). The second category consists of CDR3s of TCRs belonging to particular subsets of T-cells that are known to make use of partially invariant TCRs, namely (invariant) natural killer T-cells (i/NKT cells), mucosal associated invariant T (MAIT) cells and germline-encoded mycolyl-lipid reactive (GEM) cells. CDR3s are presented in lists in a format to be read into Python scripts. All CDR3 papers are referenced in the file.
DOI: 10.6084/m9.figshare.1153948.v2
title: Excel file with PCR-RFLP patterns for identification of nursery Phytophthora spp.

description: Contains restriction fragement length polymorphism data and GenBank Accession numbers for common nursery <em>Phytophthora</em> species found in Oregon.
DOI: 10.6084/m9.figshare.1153817.v1
title: Known specificity human TCR CDR3 sequences

description: The hypervariable complementarity determining region 3 (CDR3) of T-cell receptors (TCRs) forms the major contacts with the peptide-MHC molecule, and thus is the key site of determining antigen specificity. In this dataset I have gathered CDR3 sequences from the literature, in order so that we may use these to search our high-throughput TCR repertoire DNA-sequencing data. The CDR3s gathered fall into one of two categories. The first category consists of CDR3s from TCRs reported to be reactive against known viral epitopes. This category includes CDR3s specific for human immunodeficiency virus (HIV), cytomegalovirus (CMV) and Epstein-Barr virus (EBV) (the latter two virus' CDR3 lists being collated and kindly contributed by Ilgar Mamedov, see Zvyagin et al, 2014). The second category consists of CDR3s of TCRs belonging to particular subsets of T-cells that are known to make use of partially invariant TCRs, namely (invariant) natural killer T-cells (i/NKT cells), mucosal associated invariant T (MAIT) cells and germline-encoded mycolyl-lipid reactive (GEM) cells. CDR3s are presented in lists in a format to be read into Python scripts. All CDR3 papers are referenced in the file.
DOI: 10.6084/m9.figshare.1153934.v3
title: WSS distribution on flattened anterior cerebral arteries

description: Animation of the wall shear stress field during the cardiac cycle. Data belongs to a study aimed at characterizing the WSS at the aneurysm initiation site. Cases were anterior cerebral arteries (ACAs) harboring an aneurysm that had been virtually removed to approximate the pre-aneurysm geometry. Controls were ACAs that had never formed an aneurysm. ACA branches were flattened using the Vascular Modeling Toolkit (VMTK) to be able to view the whole branch surface at once. wss_normalized_ps.gif uses a fixed color range from 0 to 2 times the average WSS on the branch at peak systole. wss_normalized.gif uses a variable color range from 0 to 2 times the average WSS on the branch at the current timestep. This way of normalizing the color range emphasizes changes in distribution rather than magnitude. Contact: ajgeers@gmail.com
DOI: 10.6084/m9.figshare.1153786
title: Shear Data

description: From manuscript: Development of emulsification resistant heavier-than-water tamponade using high molecular weight silicone oil polymers
DOI: 10.6084/m9.figshare.1153792
title: Statistical data of subareas of the dorsolateral frontal cortex in socially relevant decisions based on masked affect expressions

description: Subject<br>Age<br>EduYears - years of education<br>Sex<br>TAS20 - sum score of TAS-20<br>BDI - sum score of BDI<br>SPFfantasy - SPF scale fantasy<br>SPFperspect - SPF scale perspective-taking<br>SPFempathy - SPF scale empathy<br>Edingburgh - Handedness<br>CriticalLifeEvents - presence of critical life events<br>PANAS_moment - mood actually<br>PANAS_today - mood today<br>PANAS_generally - mood generally<br>RTimHappy - reaction time subliminal happiness<br>RTimSad - reaction time subliminal sadness<br>RTimAnger - reaction time subliminal anger<br>RTimFace - reaction time all subliminal<br>HITimHappy - hits subliminal happpiness<br>HITimSad - hits subliminal sadness<br>HITimAnger - hits subliminal anger<br>HITimFace - hits subliminal all<br>rpDLFC_PreDec - posterior dorsolateral frontal cortex pre-decision<br>rpDLFC_Dec - posterior dorsolateral frontal cortex decision<br>raDLFC_PreDec - anterior dorsolateral frontal cortex pre-decision<br>raDLFC_Dec - anterior dorsolateral frontal cortex decision