cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.652980.v1
title: The Application of Empirical Methods of 13C NMR Chemical Shift Prediction as a Filter for Determining Possible Relative Stereochemistry.

description: SUPPORTING MATERIALS associated with article. The reliable determination of stereocenters contained within chemical structures usually requires utilization of NMR data, chemical derivatization, molecular modeling, quantum-mechanical (QM) calculations and, if available, X-ray analysis. In this article, we show that the number of stereoisomers which need to be thoroughly verified, can be significantly reduced by the application of NMR chemical shift calculation to the full stereoisomer set of possibilities using a fragmental approach based on HOSE codes. The applicability of this suggested method is illustrated using experimental data published for a series of complex chemical structures
DOI: 10.6084/m9.figshare.652972
title: Why Open Drug Discovery Needs Four Simple Rules for Licensing Data and Models

description: When we look at the rapid growth of scientific databases on the Internet in the past decade, we tend to take the accessibility and provenance of the data for granted. As we see a future of increased database integration, the licensing of the data may be a hurdle that hampers progress and usability. We have formulated four rules for licensing data for open drug discovery, which we propose as a starting point for consideration by databases and for their ultimate adoption. This work could also be extended to the computational models derived from such data. We suggest that scientists in the future will need to consider data licensing before they embark upon re-using such content in databases they construct themselves.
DOI: 10.6084/m9.figshare.652964
title: DNA methylation coverage in two tissues of the Pacific Oyster

description: This work aims at characterizing and comparing DNA methylation in two tissues in the Pacific oyster using the methylKit R package. Bisulfite sequencing was used to examine genome-wide DNA methylation in the oyster gonad tissue and MBD-Seq was used to examine methylation in the gill tissue. The R script used for these analyses has been provided along with some visualization outputs comparing gill and gonad tissue from the Pacific oyster.
DOI: 10.6084/m9.figshare.652972.v1
title: Why Open Drug Discovery Needs Four Simple Rules for Licensing Data and Models

description: When we look at the rapid growth of scientific databases on the Internet in the past decade, we tend to take the accessibility and provenance of the data for granted. As we see a future of increased database integration, the licensing of the data may be a hurdle that hampers progress and usability. We have formulated four rules for licensing data for open drug discovery, which we propose as a starting point for consideration by databases and for their ultimate adoption. This work could also be extended to the computational models derived from such data. We suggest that scientists in the future will need to consider data licensing before they embark upon re-using such content in databases they construct themselves.
DOI: 10.6084/m9.figshare.652203
title: BioNames design document

description: Design document for BioNames project
DOI: 10.6084/m9.figshare.652964.v1
title: DNA methylation coverage in two tissues of the Pacific Oyster

description: This work aims at characterizing and comparing DNA methylation in two tissues in the Pacific oyster using the methylKit R package. Bisulfite sequencing was used to examine genome-wide DNA methylation in the oyster gonad tissue and MBD-Seq was used to examine methylation in the gill tissue. The R script used for these analyses has been provided along with some visualization outputs comparing gill and gonad tissue from the Pacific oyster.
DOI: 10.6084/m9.figshare.652203.v1
title: BioNames design document

description: Design document for BioNames project
DOI: 10.6084/m9.figshare.652964.v3
title: DNA methylation coverage in two tissues of the Pacific Oyster

description: This work aims at characterizing and comparing DNA methylation in two tissues in the Pacific oyster using the methylKit R package. Bisulfite sequencing was used to examine genome-wide DNA methylation in the oyster gonad tissue and MBD-Seq was used to examine methylation in the gill tissue. The R script used for these analyses has been provided along with some visualization outputs comparing gill and gonad tissue from the Pacific oyster.
DOI: 10.6084/m9.figshare.652964.v2
title: DNA methylation coverage in two tissues of the Pacific Oyster

description: This work aims at characterizing and comparing DNA methylation in two tissues in the Pacific oyster using the methylKit R package. Bisulfite sequencing was used to examine genome-wide DNA methylation in the oyster gonad tissue and MBD-Seq was used to examine methylation in the gill tissue. The R script used for these analyses has been provided along with some visualization outputs comparing gill and gonad tissue from the Pacific oyster.
DOI: 10.6084/m9.figshare.652220.v1
title: Biota graph

description: Graph of some biota, incorporating phylogenetic systematics/cladistics as well as obsoleted and informal classification and taxa. This version is without chronostratigraphy timeline data. Graph made using Graphiz. The graph is compiled from a number of subgraphs each for one of the most well known classes. Most but not all images are CC licensed. Image credits and permissions to be updated.
DOI: 10.6084/m9.figshare.651742
title: Corn Microbiome

description: Scripts used in the corn microbiome studies
DOI: 10.6084/m9.figshare.651726
title: Child Abuse Prevention in Public Libraries

description: MLIS Portfolio Project based on a survey of public library staff and their role in child abuse prevention. Poster presented at California Library Association Conference (November 2012).
DOI: 10.6084/m9.figshare.651742.v2
title: Corn Microbiome

description: Scripts used in the corn microbiome studies
DOI: 10.6084/m9.figshare.651718
title: Inverse PCR sequences

description: AACA4F-AACA4RI (REACTION AACA4F): An inverse PCR reaction was performed with primers AACAF and AACA4RI and the sequencing reaction was performed with primer AACA4F. This sequencing revealed the excised, circular form with the configuration “aacA4-gcu14” AACA4F-AACA4RI (REACTION AACA4RI): An inverse PCR reaction was performed with primers AACAF and AACA4RI and the sequencing reaction was performed with primer AACA4RI. This sequencing revealed the excised, circular form with the configuration “aacA4-gcu14” GESFSQ-GESR (REACTION GESFSQ): An inverse PCR reaction was performed with primers GESFSQ and GESR and the sequencing reaction was performed with primer GESFSQ. This sequencing revealed the excised, circular form with the full length configuration “gcu14-GES-1/aacA4”.<br>GESFSQ-GESR (REACTION GESR): An inverse PCR reaction was performed with primers GESFSQ and GESR and the sequencing reaction was performed with primer GESR. This sequencing revealed the excised, circular form with the full length configuration “gcu14-GES-1/aacA4”.<br>GESFSQ-GESR (REACTION AACA4F): An inverse PCR reaction was performed with primers GESFSQ and GESR and the sequencing reaction was performed with primer AACA4F. This sequencing revealed the excised, circular form with the full length configuration “gcu14-GES-1/aacA4”.<br>GESFSQ-GESR (REACTION AACA4FI): An inverse PCR reaction was performed with primers GESFSQ and GESR and the sequencing reaction was performed with primer AACA4FI. This sequencing revealed the excised, circular form with the full length configuration “gcu14-GES-1/aacA4”.<br>GESFSQ-GESR (REACTION AACA4R): An inverse PCR reaction was performed with primers GESFSQ and GESR and the sequencing reaction was performed with primer AACA4R. This sequencing revealed the excised, circular form with the full length configuration “gcu14-GES-1/aacA4”.<br>Orf126 menor: An inverse PCR reaction was performed with primers GCU FSQ and GCU RSQ and the sequencing reaction was performed with primer GCU FSQ. This sequencing revealed the excised, circular form with the configuration “gcu14”.
DOI: 10.6084/m9.figshare.651742.v1
title: Corn Microbiome

description: Scripts used in the corn microbiome studies
DOI: 10.6084/m9.figshare.651717
title: RQ fused cassette raw data for Pseudomonas aeruginosa isolates PS1 and PS26

description: The first column describes the P. aeruginosa isolates (PS1 and PS26) and the gene targeted in the quantitative PCR for measuring their transcription (gcu14; GES-1; aacA4; and the fusion GES-1-aacA4 and rpsL), which was performed in triplicate. Also in this column are the negative controls for each PCR reaction (NTC). The second column displays the cycle threshold (CT), i.e., the PCR cycle in which the fluorescence was detected by the machine. The third and the fourth columns refer to the standard deviation and the average of CT values, respectively, between triplicates. The fifth column refers to the to the normalization of the target gene transcript amount relative to that of endogenous gene (rpsL). The sixth column corresponds to the results of relative quantification. For example, the gcu14 gene and GES gene in PS1 had RQ values of 15,88 and 7,80. It means that gcu14 is 2-fold more transcribed than GES in PS1 isolate.
DOI: 10.6084/m9.figshare.650869
title: PhyloSift: phylogenetic analysis of genomes and metagenomes (supplementary manuscript data)

description: These files are supplementary data for the following manuscript: <strong>Darling AE, Jospin G, Lowe E, Matsen FA, Bik HM, Eisen JA. (submitted) PhyloSift: phylogenetic analysis of genomes and metagenomes. </strong> Please visit the PhyloSift website for software downloads and extensive user documentation.
DOI: 10.6084/m9.figshare.651068.v1
title: Gaussian Job Archive for C6H8LiNO

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.650868
title: Recruitment data for kittiwakes breeding in Middleton Island (Alaska)

description: Data from the experimental manipulation of food availability during early development and at recruitment for a long-lived seabird, the black-legged kittiwake Rissa tridactyla, breeding on Middleton Island, Alaska. Birds were born and raised in nests with supplemented food (“Fed”) or unsupplemented control nests (“Unfed”), and later recruited into either Fed or Unfed nests. ----------- Data have been collected by Scott Hatch. Data have been prepared and presented in the current form by Simone Vincenzi. ------------ Dataset: --------- The dataset reports the variables and descriptors explained below relative to both the nestling phase and recruitment phase ---------- For each individual (each row), we recorded: Feeding: feeding treatment (Fed/Unfed) at the nestling stage Rank: hatching order (A-chick, B-chick, C-chick, Singleton) Band: ID of bird Mean_growth: daily growth during the linear phase in g/day (between day 5 and day 20, from approximately 75 to 300 g) Peak_weight: maximum weight reached by the chick (g) Year_of_birth Sex Treatment_recruit: feeding treatment (Fed/Unfed) at breeding First_breeding: year at recruitment Recruit_age: age at recruitment Clutch_size: number of eggs laid by the female Chicks_fledged: number of chicks leaving the nest Repro_succ01_rel: Chicks fledged per nest (productivity) at first breeding relative to the mean productivity in that year for Fed or Unfed nests
DOI: 10.6084/m9.figshare.650868.v1
title: Recruitment data for kittiwakes breeding in Middleton Island (Alaska)

description: Data from the experimental manipulation of food availability during early development and at recruitment for a long-lived seabird, the black-legged kittiwake Rissa tridactyla, breeding on Middleton Island, Alaska. Birds were born and raised in nests with supplemented food (“Fed”) or unsupplemented control nests (“Unfed”), and later recruited into either Fed or Unfed nests. ----------- Data have been collected by Scott Hatch. Data have been prepared and presented in the current form by Simone Vincenzi. ------------ Dataset: --------- The dataset reports the variables and descriptors explained below relative to both the nestling phase and recruitment phase ---------- For each individual (each row), we recorded: Feeding: feeding treatment (Fed/Unfed) at the nestling stage Rank: hatching order (A-chick, B-chick, C-chick, Singleton) Band: ID of bird Mean_growth: daily growth during the linear phase in g/day (between day 5 and day 20, from approximately 75 to 300 g) Peak_weight: maximum weight reached by the chick (g) Year_of_birth Sex Treatment_recruit: feeding treatment (Fed/Unfed) at breeding First_breeding: year at recruitment Recruit_age: age at recruitment Clutch_size: number of eggs laid by the female Chicks_fledged: number of chicks leaving the nest Repro_succ01_rel: Chicks fledged per nest (productivity) at first breeding relative to the mean productivity in that year for Fed or Unfed nests
DOI: 10.6084/m9.figshare.650869.v2
title: PhyloSift: phylogenetic analysis of genomes and metagenomes (supplementary manuscript data)

description: These files are supplementary data for the following manuscript: <strong>Darling AE, Jospin G, Lowe E, Matsen FA, Bik HM, Eisen JA. (submitted) PhyloSift: phylogenetic analysis of genomes and metagenomes. </strong> Please visit the PhyloSift website for software downloads and extensive user documentation.
DOI: 10.6084/m9.figshare.650869.v1
title: PhyloSift: phylogenetic analysis of genomes and metagenomes (supplementary manuscript data)

description: These files are supplementary data for the following manuscript: <strong>Darling AE, Jospin G, Lowe E, Matsen FA, Bik HM, Eisen JA. (submitted) PhyloSift: phylogenetic analysis of genomes and metagenomes. </strong> Please visit the PhyloSift website for software downloads and extensive user documentation.
DOI: 10.6084/m9.figshare.650851.v1
title: Retracing the evolution of Reddit through post data

description: Randy Olson explores how the Reddit community has changed over time since its inception in 2005 by analyzing posts that were submitted to the various subreddit communities.
DOI: 10.6084/m9.figshare.650798
title: Publication volumes for major OA publishers

description: CSV file containing publication volumes for major OA publishers from 2000-2012. Data collated by OASPA.
DOI: 10.6084/m9.figshare.650799
title: Growth of Open Access - Major Publishers

description: Data on publication volumes for major Open Access publishers. Included are PLOS, BMC, Hindawi, Springer Open Choice, OUP, Copernicus and Frontiers. Data collated by OASPA.
DOI: 10.6084/m9.figshare.650798.v1
title: Publication volumes for major OA publishers

description: CSV file containing publication volumes for major OA publishers from 2000-2012. Data collated by OASPA.
DOI: 10.6084/m9.figshare.650799.v1
title: Growth of Open Access - Major Publishers

description: Data on publication volumes for major Open Access publishers. Included are PLOS, BMC, Hindawi, Springer Open Choice, OUP, Copernicus and Frontiers. Data collated by OASPA.
DOI: 10.6084/m9.figshare.650553
title: Ouabain inhibition of Na/K-ATPase across the retina in chicks: ERG data

description: Electroretinography recordings from the eyes of chicks injected with ouabain, DMSO or PBS.
DOI: 10.6084/m9.figshare.650543
title: Ouabain inhibition of Na/K-ATPase across the retina in chicks: biometric data

description: Biometric measures for refractive state, axial length, vitreous chamber depth and anterior chamber depth.
DOI: 10.6084/m9.figshare.650553.v1
title: Ouabain inhibition of Na/K-ATPase across the retina in chicks: ERG data

description: Electroretinography recordings from the eyes of chicks injected with ouabain, DMSO or PBS.
DOI: 10.6084/m9.figshare.650228
title: Code and example data to calibrate the niche model of food webs based on allometric relationships

description: #### READ ME ################################### The code has the following structure # 1. Loading of an artificial dataset of i) predator-prey interactions, ii) body size distribution, iii) hypothetical species presence/absence lists # 2. Definition of functions run for the analysis # 3. Calculation of the observed parameters for the niche model # 4. Inferrence of the parameters for all species in the metaweb ## Name of the parameters of the niche model # n: niche position along the niche axis # c: centroid of the niche # r: range of the niche
DOI: 10.6084/m9.figshare.650543.v2
title: Ouabain inhibition of Na/K-ATPase across the retina in chicks: biometric data

description: Biometric measures for refractive state, axial length, vitreous chamber depth and anterior chamber depth.
DOI: 10.6084/m9.figshare.650602.v1
title: Haemolymph extraction

description: The figure shows the very simple protocol of how to extract haemolymph from adult <em>Drosophila melanogaster</em>.
DOI: 10.6084/m9.figshare.650543.v1
title: Ouabain inhibition of Na/K-ATPase across the retina in chicks: ERG data

description: Description to be changed
DOI: 10.6084/m9.figshare.650220
title: Natural Selection practical

description: This is a 1st year undergraduate practical on Natural Selection. See README for details.
DOI: 10.6084/m9.figshare.650216
title: Simple3D Java Source Code

description: Java source code for rendering data points in 3-dimentional space.
DOI: 10.6084/m9.figshare.650220.v1
title: Natural Selection practical

description: This is a 1st year undergraduate practical on Natural Selection. See README for details.
DOI: 10.6084/m9.figshare.650602.v2
title: Haemolymph extraction of adult Drosophila

description: The figure shows the very simple protocol of how to extract haemolymph from adult <em>Drosophila melanogaster</em>.
DOI: 10.6084/m9.figshare.650215
title: Rotatable

description: Defines basic 3D rotations around each axis.
DOI: 10.6084/m9.figshare.650215.v1
title: Rotatable

description: Defines basic 3D rotations around each axis.
DOI: 10.6084/m9.figshare.650216.v1
title: Simple3D Java Source Code

description: Java source code for rendering data points in 3-dimentional space.
DOI: 10.6084/m9.figshare.650602.v3
title: Haemolymph extraction of adult Drosophila

description: The figure shows the very simple protocol of how to extract haemolymph from adult <em>Drosophila melanogaster</em>.
DOI: 10.6084/m9.figshare.650602.v4
title: Haemolymph extraction of adult Drosophila

description: The figure shows the very simple protocol of how to extract haemolymph from adult <em>Drosophila melanogaster</em>.
DOI: 10.6084/m9.figshare.649431
title: Gaussian Job Archive for C10H7F3N2O3

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.649431.v1
title: Gaussian Job Archive for C10H7F3N2O3

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.649433.v1
title: Supplementary material to “Estimating the nature and the horizontal and vertical positions of 3D magnetic sources using Euler deconvolution”

description: <strong>Abstract</strong> We have provided supplementary material to our article titled “Estimating the nature and the horizontal and vertical positions of 3D magnetic sources using Euler deconvolution” and whose authors are Felipe F. Melo, Valeria C. F. Barbosa, Leonardo Uieda, Vanderlei C. Oliveira Jr, and João B. C. Silva. In this material, we presented an extra synthetic test to illustrate the steps of our methodology didactically. Additionally, we illustrated with synthetic test the ability of our method to correctly estimate the source positions when it is applied to a reduced area that does not cover the anomalies entirely.
DOI: 10.6084/m9.figshare.649429
title: Presentation: Apparent-density mapping using entropic regularization

description: <strong>Slides for the oral presentation "Apparent-density mapping using entropic regularization" presented at AGU Joint Assembly 2007 Acapulco, Mexico.</strong> <strong>Abstract</strong> We present a new apparent-density mapping method on the horizontal plane that combines the minimization of the first-order entropy with the maximization of the zeroth-order entropy of the estimated density contrasts. The interpretation model consists of a grid of vertical, juxtaposed prisms in both horizontal directions.We assume that the top and the bottom of the gravity sources are flat and horizontal and estimate the prisms’ density contrasts. The minimization of the first-order entropy favors solutions presenting sharp borders, and the maximization of the zeroth-order entropy prevents the tendency of the source estimate to become a single prism. Thus, a judicious combination of both constraints may lead to solutions characterized by regions with virtually constant estimated density contrasts separated by sharp discontinuities. We apply our method to synthetic data from simulated intrusive bodies in sediments that present flat and horizontal tops. By comparing our results with those obtained with the smoothness constraint, we show that both methods produce good and equivalent locations of the sources’ central positions. However, the entropic regularization delineates the boundaries of the bodies with greater resolution, even in the case of 100-m-wide bodies separated by a distance as small as 50 m. Both the proposed and the global smoothness constraints are applied to real anomalies from the eastern Alps and from the Matsitama intrusive complex, northeastern Botswana. In the first case, the entropic regularization delineates two sources, with a horizontal and nearly flat top being consistent with the known geologic information. In the second case, both constraints produce virtually the same estimate, indicating, in agreement with results of synthetic tests, that the tops of the sources are neither flat nor horizontal.
DOI: 10.6084/m9.figshare.650602.v5
title: Haemolymph extraction of adult Drosophila

description: The figure shows the very simple protocol of how to extract haemolymph from adult <em>Drosophila melanogaster</em>.