cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.92090.v1
title: Three-dimensional (3D) temporal and spatial reconstructions of adult zebrafish swim paths rapidly expose overall affective phenotype.

description: After indicated experimental manipulations (Fig. 3), zebrafish novel tank behavior was manually observed and video-tracked using EthoVision XT7 program. Raw track and behavioral endpoints were processed, formatted, and visualized in a 3D scatter plot using RapidMiner 5.0 software; traditional computer-generated two-dimensional (2D) swim path traces were placed at t = 0.0 s (top left part of each panel) for reference. Representative 3D reconstructions were selected by comparing swim paths of all subjects within a cohort, ranking them from 1 to n based on similarity to each other (low/no to high activity) and choosing the middle for the illustrations. For better visuality and consistency, fish used for spatial 3D imaging were the same as those used for the respective temporal 3D reconstructions. For a more detailed analysis of 3D reconstructions, the average velocity (m/s) of each fish was reflected by changes in color from blue to green, yellow and red, as the velocity increases. Note that any other computer-generated behavioral indices (Table S1 of Supporting Information) may be expressed in color on 3D reconstructions of zebrafish locomotion paths. Overall, these 3D traces reveal striking differences between zebrafish high- and low-anxiety behaviors, thereby enabling a rapid visualization and interpretation of the observed phenotypes.
DOI: 10.6084/m9.figshare.92054
title: Arduino_project_voltages.xls

description: This data contains the input and output voltages in a circuit consisting of : an arduino 9V battery 4 x LEDs 4 x 220 Ohm resistors 1 x Push button switch 1 x 220kOhm resistor
DOI: 10.6084/m9.figshare.92089.v2
title: Dialectical Model of Human Nature

description: The DMoHN is a graphical representation of my current understanding and conceptualization of human nature, in addition to embodying the guiding ethos of social neuroscience. The dialectic is a logic, or way of thinking that joins opposite elements together in a uniting fashion to create emergent attributes not present in the elements alone. The dialectical structure of this model explicitly links Culture and Biology within the human brain in order to convey the symbiotic and dynamic interaction between these two realms of scientific thought and the natural world. It is always under revision, so check back for updates.
DOI: 10.6084/m9.figshare.92053
title: Cumulative data packages in the Knowledge Network for Biocomplexity data repository through October, 2011

description: Figure and data table of the cumulative number of data packages archived in the Knowledge Network for Biocomplexity data repository (http://knb.ecoinformatics.org/) from inception to October, 2011. Each count represents a data package, which may consist of one or more data files and other data objects.
DOI: 10.6084/m9.figshare.92053.v1
title: Cumulative data packages in the Knowledge Network for Biocomplexity data repository through October, 2011

description: Figure and data table of the cumulative number of data packages archived in the Knowledge Network for Biocomplexity data repository (http://knb.ecoinformatics.org/) from inception to October, 2011. Each count represents a data package, which may consist of one or more data files and other data objects.
DOI: 10.6084/m9.figshare.92054.v1
title: Arduino_project_voltages.xls

description: This data contains the input and output voltages in a circuit consisting of : an arduino 9V battery 4 x LEDs 4 x 220 Ohm resistors 1 x Push button switch 1 x 220kOhm resistor
DOI: 10.6084/m9.figshare.92051
title: Data table of cumulative data packages in the Knowledge Network for Biocomplexity data repository through October, 2011

description: Data table of the cumulative number of data packages archived in the Knowledge Network for Biocomplexity data repository (http://knb.ecoinformatics.org/) from inception to October, 2011. Each count represents a data package, which may consist of one or more data files and other data objects.
DOI: 10.6084/m9.figshare.92045
title: Arduino 3x3 LED cube Project Data

description: Data used in the building process of my LED 3x3 cube. The pin output voltage was taken to see the consistencies of the voltage between pins. This also confirmed the Arduino Uno was working properly. The potential difference between the cathode and ground can be used to make a rough calculation of the current going though the LEDs using Ohm's Law.
DOI: 10.6084/m9.figshare.92047
title: Final Project Current Readings

description: This is the current readings taken from my 'Rita Shaker'.
DOI: 10.6084/m9.figshare.92051.v4
title: Data table of cumulative data packages in the Knowledge Network for Biocomplexity data repository through October, 2011

description: Data table of the cumulative number of data packages archived in the Knowledge Network for Biocomplexity data repository (http://knb.ecoinformatics.org/) from inception to October, 2011. Each count represents a data package, which may consist of one or more data files and other data objects.
DOI: 10.6084/m9.figshare.92047.v1
title: Final Project Current Readings

description: This is the current readings taken from my 'Rita Shaker'.
DOI: 10.6084/m9.figshare.92051.v3
title: Data table of cumulative data packages in the Knowledge Network for Biocomplexity data repository through Octiber, 2011

description: Data table of the cumulative number of data packages archived in the Knowledge Network for Biocomplexity data repository (http://knb.ecoinformatics.org/) from inception to October, 2011. Each count represents a data package, which may consist of one or more data files and other data objects.
DOI: 10.6084/m9.figshare.92045.v1
title: Arduino Project Data

description: Data used in the building process of my LED 3x3 cube. The pin output voltage was taken to see the consistencies of the voltage between pins. This also confirmed the Arduino Uno was working properly. The potential difference between the cathode and ground can be used to make a rough calculation of the current going though the LEDs using Ohm's Law.
DOI: 10.6084/m9.figshare.92031
title: CIL XV.1 Instrumentum Domesticum (a working copy)

description: This table is a rough and necessarily incomplete transcription of the information contained in the Corpus Inscriptionum Latinarum XV.1 Instrumentum domesticum, edited by H. Dressel, 1891. I make no guarantee that it is error free. I produced this during the course of my PhD research to have readily to hand my own copy of CIL XV.1, and it naturally reflects my own concerns during that work. It should not be used to identify stamped bricks (one should use instead Steinby's 'Indici complementari ai bolli doliari urbani (CIL XV.1) Acta Instituti Romani Finlandiae 11). Its utility lies in being able to be searched quickly, to narrow down the range of possibilities. I offer it in that spirit. It took me approximately 50 hours to produce.
DOI: 10.6084/m9.figshare.91975
title: Is the use of gold nanoparticles for photothermal ablation a better alternative to chemotherapy to treat cancer.docx

description: Nanoparticles
DOI: 10.6084/m9.figshare.91976
title: Travellersim Agent Based Model

description: This is the Netlogo4.1 code for the Travellersim model. An online implementation of the model may be found here. This version contains optimizations & cleaned up code produced by Andrew Bevan, to whom I am grateful. The model is a re-implementation of the Rihll & Wilson gravity settlement model: Rihll, T. and Wilson, A., Modelling settlement structures in ancient greece:<br>new approaches to the polis, in City and country in the ancient world, eds.<br>Rich, J. and Wallace-Hadrill, A., chapter 3 (1991). Our model & our interpretation of the results was published in 2008 (with J. Steiner) “Travellersim: Growing Settlement Structures and Territories with Agent-Based Modelling” in Jeffrey T. Clark and Emily M. Hagemeister (eds) <em>Digital Discovery: Exploring New Frontiers in Human Heritage. CAA 2006. Computer Applications and Quantitative Methods in Archaeology. Proceedings of the 34th Conference, Fargo, United States, April 2006</em>. Budapest: Archaeolingua. [<strong>PDF</strong>]
DOI: 10.6084/m9.figshare.91976.v1
title: Travellersim Agent Based Model

description: This is the Netlogo4.1 code for the Travellersim model. An online implementation of the model may be found here. This version contains optimizations & cleaned up code produced by Andrew Bevan, to whom I am grateful. The model is a re-implementation of the Rihll & Wilson gravity settlement model: Rihll, T. and Wilson, A., Modelling settlement structures in ancient greece:<br>new approaches to the polis, in City and country in the ancient world, eds.<br>Rich, J. and Wallace-Hadrill, A., chapter 3 (1991). Our model & our interpretation of the results was published in 2008 (with J. Steiner) “Travellersim: Growing Settlement Structures and Territories with Agent-Based Modelling” in Jeffrey T. Clark and Emily M. Hagemeister (eds) <em>Digital Discovery: Exploring New Frontiers in Human Heritage. CAA 2006. Computer Applications and Quantitative Methods in Archaeology. Proceedings of the 34th Conference, Fargo, United States, April 2006</em>. Budapest: Archaeolingua. [<strong>PDF</strong>]
DOI: 10.6084/m9.figshare.91953
title: E. Coli Growth in DI, DDW, D2O, 30% D2O, and 60% D2O

description: Methods for data collection and setup are linked below. Included in this fileset is: *The excel plot of the A600 readings over time. *The excel data edited from the nanodrop *The raw data as a .xml file from the nanodrop *an image of the absorbance spectrum of every reading. UPDATE: I added an Illustrator created version of the data to the dataset. Check it out.
DOI: 10.6084/m9.figshare.91975.v2
title: Is the use of gold nanoparticles for photothermal ablation a better alternative to chemotherapy to treat cancer.docx

description: Nanoparticles
DOI: 10.6084/m9.figshare.91952
title: XRD Results of analysis of selected Roman stamped bricks held at the British School at Rome

description: XRD results of selected stamped Roman bricks kept at the British School at Rome. The majority of these brick stamps were collected during the South Etruria Survey. The catalogue was published in Graham, S. 2006 EX FIGLINIS: The Network Dynamics of the Tiber Valley Brick Industry in the Hinterland of Rome BAR International Series 1468. John Hedges Ltd. [full text]
DOI: 10.6084/m9.figshare.91975.v1
title: Is the use of gold nanoparticles for photothermal ablation a better alternative to chemotherapy to treat cancer.docx

description: Nanoparticles
DOI: 10.6084/m9.figshare.91953.v2
title: E. Coli Growth in DI, DDW, D2O, 30% D2O, and 60% D2O

description: Methods for data collection and setup are linked below. Included in this fileset is: *The excel plot of the A600 readings over time. *The excel data edited from the nanodrop *The raw data as a .xml file from the nanodrop *an image of the absorbance spectrum of every reading. UPDATE: I added an Illustrator created version of the data to the dataset. Check it out.
DOI: 10.6084/m9.figshare.91949
title: Catalogue of Roman Stamped Bricks held at the British School at Rome

description: This is the epigraphic catalogue of stamped Roman bricks kept at the British School at Rome. The majority of these brick stamps were collected during the South Etruria Survey. The catalogue was published in Graham, S. 2006 <em>EX FIGLINIS: The Network Dynamics of the </em><em>Tiber</em><em> </em><em>Valley</em><em> Brick Industry in the Hinterland of Rome </em>BAR International Series 1468. John Hedges Ltd. [full text]
DOI: 10.6084/m9.figshare.91950
title: XRF results (traces) of analysis of selected Roman stamped bricks from the British School at Rome

description: XRF results (traces) of selected stamped Roman bricks kept at the British School at Rome. The majority of these brick stamps were collected during the South Etruria Survey. The catalogue was published in Graham, S. 2006 <em>EX FIGLINIS: The Network Dynamics of the </em><em>Tiber</em><em> </em><em>Valley</em><em> Brick Industry in the Hinterland of Rome </em>BAR International Series 1468. John Hedges Ltd. [full text]
DOI: 10.6084/m9.figshare.91951
title: XRF Results (majors) of analysis of selected Roman stamped bricks held at the British School at Rome

description: XRF results (majors) of selected stamped Roman bricks kept at the British School at Rome. The majority of these brick stamps were collected during the South Etruria Survey. The catalogue was published in Graham, S. 2006 EX FIGLINIS: The Network Dynamics of the Tiber Valley Brick Industry in the Hinterland of Rome BAR International Series 1468. John Hedges Ltd. [full text]
DOI: 10.6084/m9.figshare.91953.v1
title: E. Coli Growth in DI, DDW, D2O, 30% D2O, and 60% D2O

description: Methods for data collection and setup are linked below. Included in this fileset is: *The excel plot of the A600 readings over time. *The excel data edited from the nanodrop *The raw data as a .xml file from the nanodrop *an image of the absorbance spectrum of every reading.
DOI: 10.6084/m9.figshare.91944
title: 24h Growth of E. coli in D2O, DDW, DI, 30% D2O, and 60% D2O

description: Experimental setup and methods are described in the 2 links below. This is data from an overnight e. coli incubation at 37C. LB media was dissolved in DI water, deuterium depleted water (DDW), heavy water (D2O), and 30% and 60% D2O to DDW mixtures respectively (ie 30% D2O, 70% DDW by volume). Results acquired via Thermo NanoDrop 2000c.
DOI: 10.6084/m9.figshare.91951.v1
title: Xrf Results (majors) of analysis of selected Roman stamped bricks held at the British School at Rome

description: XRF results (traces) of selected stamped Roman bricks kept at the British School at Rome. The majority of these brick stamps were collected during the South Etruria Survey. The catalogue was published in Graham, S. 2006 EX FIGLINIS: The Network Dynamics of the Tiber Valley Brick Industry in the Hinterland of Rome BAR International Series 1468. John Hedges Ltd. [full text]
DOI: 10.6084/m9.figshare.91951.v2
title: XRF Results (majors) of analysis of selected Roman stamped bricks held at the British School at Rome

description: XRF results (majors) of selected stamped Roman bricks kept at the British School at Rome. The majority of these brick stamps were collected during the South Etruria Survey. The catalogue was published in Graham, S. 2006 EX FIGLINIS: The Network Dynamics of the Tiber Valley Brick Industry in the Hinterland of Rome BAR International Series 1468. John Hedges Ltd. [full text]
DOI: 10.6084/m9.figshare.91940
title: All-optic control and readout of membrane potential - analysis

description: VoltageRhodopsin is a mutant bacterial proton pump conjugated with a long Stokes shift FP in its terminal . The retinal core in the pump shifts its absorbance according to membrane voltage shifts or cross-membrane pH ratio changes. The FRET efficiency from FP to retinal core, thus, covaries with membrane voltage changes, given pH is stable. We control the N2A cell membrane voltage with red-light responsive VChR1, and readout the membrane voltage using blue fluorescence emission from a Cerulean-tagged VoltageRhodopsin. The experiment starts from a period of silence, then 10 pulses of red laser are delivered to stimulate the cell. As membrane voltage shifts, one could notice the bright fluorescence burst.
DOI: 10.6084/m9.figshare.91944.v1
title: 24h Growth of E. coli in D2O, DDW, DI, 30% D2O, and 60% D2O

description: Experimental setup and methods are described in the 2 links below. This is data from an overnight e. coli incubation at 37C. LB media was dissolved in DI water, deuterium depleted water (DDW), heavy water (D2O), and 30% and 60% D2O to DDW mixtures respectively (ie 30% D2O, 70% DDW by volume). Results acquired via Thermo NanoDrop 2000c.
DOI: 10.6084/m9.figshare.91934
title: 24 hour growth of e. coli in DDW and D2O

description: Here is some growth data. The cells were incubated at 37C for 24 hours in two batches. One sample was incubated in LB broth dissolved in deuterium depleted water, the other sample was incubated in LB broth dissolved in deuterium oxide (heavy water, D2O). Measurements were recorded via a Thermo Nanodrop. The setup is linked below. The data file includes a bunch of different readings, and the measurements that should be analyzed are in the A600 column. I did an initial blank reading with LB media in DI water. I then measured "blanks" of LB in DDW, 99% D2O, 30% D2O, and 60% D2O. The absorption readings for 30% D2O and DDW were pretty comparable (but less than the initial reading for DI water, hence the negative numbers). Next I blanked the machine with DDW LB media, and measured the absorption. Finally I blanked the machine again with 30% D2O LB media, and measured the 30% D2O culture growth. It is interesting to note that the absorption at 600nm in the D2O sample is a little more than 50% of the absorption in the DDW sample. The data from yesterday (linked below) shows that over 5 hours cells grown in 30% D2O reach a peak at around 0.750 (arbitrary units) and actually decline. I'm not sure if this is the case here but the results of this experiment after 24 hours seems to be consistent with those results.
DOI: 10.6084/m9.figshare.91940.v1
title: All-optic control and readout of membrane potential - analysis

description: VoltageRhodopsin is a mutant bacterial proton pump conjugated with a long Stokes shift FP in its terminal . The retinal core in the pump shifts its absorbance according to membrane voltage shifts or cross-membrane pH ratio changes. The FRET efficiency from FP to retinal core, thus, covaries with membrane voltage changes, given pH is stable. We control the N2A cell membrane voltage with red-light responsive VChR1, and readout the membrane voltage using blue fluorescence emission from a Cerulean-tagged VoltageRhodopsin. The experiment starts from a period of silence, then 10 pulses of red laser are delivered to stimulate the cell. As membrane voltage shifts, one could notice the bright fluorescence burst.
DOI: 10.6084/m9.figshare.91931
title: GO terms bacterial virulence

description: Annotated sequences of<em> </em><em>V. tubiashii</em> strain RE22<em> de novo</em> assembly. Top gene hits from BLAST results filtered for e-values less than or equal to 1e-05.
DOI: 10.6084/m9.figshare.91933
title: Vibrio tubiashii ATCC19106 virulence associated contiguous sequences

description: <em>V. tubiashii</em> sequences matched to GO identifiers with putative bacterial virulence. Results limited to sequences with top BLAST hit e-values of less than or equal to 1e-05 and greater than 20x coverage.
DOI: 10.6084/m9.figshare.91932
title: E. coli growth in D2O, DDW, and DI

description: This data is the first experiment in a series that looks at the growth of E. coli in DI water, DDW, and D2O. This data is not optimal because of experimental conditions and setup issues, which you can read about in the links below. Interestingly the D2O sample declines in growth after a few hours. I have no understanding of why this would happen. Feel free to comment on the experiment in my notebook.
DOI: 10.6084/m9.figshare.91931.v1
title: GO terms bacterial virulence

description: Annotated sequences of<em> </em><em>V. tubiashii</em> strain RE22<em> de novo</em> assembly. Top gene hits from BLAST results filtered for e-values less than or equal to 1e-05.
DOI: 10.6084/m9.figshare.91932.v1
title: E. coli growth in D2O, DDW, and DI

description: This data is the first experiment in a series that looks at the growth of E. coli in DI water, DDW, and D2O. This data is not optimal because of experimental conditions and setup issues, which you can read about in the links below. Interestingly the D2O sample declines in growth after a few hours. I have no understanding of why this would happen. Feel free to comment on the experiment in my notebook.
DOI: 10.6084/m9.figshare.91933.v1
title: ATCC19106 sequences with putative virulence

description: <em>V. tubiashii</em> sequences matched to GO identifiers with putative bacterial virulence. Results limited to sequences with top BLAST hit e-values of less than or equal to 1e-05 and greater than 20x coverage.
DOI: 10.6084/m9.figshare.91933.v3
title: Vibrio tubiashii ATCC19106 virulence associated contiguous sequences

description: <em>V. tubiashii</em> sequences matched to GO identifiers with putative bacterial virulence. Results limited to sequences with top BLAST hit e-values of less than or equal to 1e-05 and greater than 20x coverage.
DOI: 10.6084/m9.figshare.91933.v2
title: Vibrio tubiashii ATCC19106 contiguous sequences with putative virulence

description: <em>V. tubiashii</em> sequences matched to GO identifiers with putative bacterial virulence. Results limited to sequences with top BLAST hit e-values of less than or equal to 1e-05 and greater than 20x coverage.
DOI: 10.6084/m9.figshare.91916
title: sparql3WP1531.csv

description: This is the result of query: PREFIX dcterms: PREFIX dc: PREFIX skos: PREFIX str: PREFIX pao: SELECT DISTINCT ?pmid COUNT(DISTINCT ?concept) AS ?count WHERE { { SELECT DISTINCT ?concept WHERE { { SELECT ?wpLinkout WHERE { SERVICE { dcterms:hasVersion ?pwversion . ?pwNode dcterms:isPartOf ?pwversion . ?pwNode dc:identifier ?wpLinkout . } } } ?wpLinkout skos:exactMatch ?scaiLinkout . ?concept skos:exactMatch ?scaiLinkout . } } ?concept pao:incarnationOf ?hit . ?hit str:subString ?pmid . ?pmid rdf:type str:Document . OPTIONAL { { SELECT DISTINCT ?pmidOrigin WHERE { SERVICE { dcterms:hasVersion ?pwversion . ?pwNode dcterms:isPartOf ?pwversion . ?pwNode dcterms:bibliographicCitation ?pmidOrigin . } } } FILTER (?pmidOrigin = ?pmid) . } FILTER (!BOUND(?pmidOrigin)) . } ORDER BY DESC (?count)
DOI: 10.6084/m9.figshare.91917
title: sparql3WP716.csv

description: PREFIX dcterms: PREFIX dc: PREFIX skos: PREFIX str: PREFIX pao: SELECT DISTINCT ?pmid COUNT(DISTINCT ?concept) AS ?count WHERE { { SELECT DISTINCT ?concept WHERE { { SELECT ?wpLinkout WHERE { SERVICE { dcterms:hasVersion ?pwversion . ?pwNode dcterms:isPartOf ?pwversion . ?pwNode dc:identifier ?wpLinkout . } } } ?wpLinkout skos:exactMatch ?scaiLinkout . ?concept skos:exactMatch ?scaiLinkout . } } ?concept pao:incarnationOf ?hit . ?hit str:subString ?pmid . ?pmid rdf:type str:Document . OPTIONAL { { SELECT DISTINCT ?pmidOrigin WHERE { SERVICE { dcterms:hasVersion ?pwversion . ?pwNode dcterms:isPartOf ?pwversion . ?pwNode dcterms:bibliographicCitation ?pmidOrigin . } } } FILTER (?pmidOrigin = ?pmid) . } FILTER (!BOUND(?pmidOrigin)) . } ORDER BY DESC (?count)
DOI: 10.6084/m9.figshare.91912
title: SparqlQuery2.csv

description: This is the output file of the following federated sparql query: PREFIX dcterms: } PREFIX skos: PREFIX str: PREFIX pao: vocabular/pao\#&gt; PREFIX hmdbid: WikiPathways/HMDB/&gt; SELECT DISTINCT ?pmid ?title WHERE {{ SELECT DISTINCT ?pmid WHERE { hmdbid:HMDB03598 skos:exactMatch ?scaiLinkout . ?concept skos:exactMatch ?scaiLinkout . ?concept pao:incarnationOf ?hit . ?hit str:subString ?pmid . ?pmid rdf:type str:Document .}} hmdbid:HMDB00305&gt; skos:exactMatch ?scaiLinkout . ?concept skos:exactMatch ?scaiLinkout . ?concept pao:incarnationOf ?hit . ?hit str:subString ?pmid .
DOI: 10.6084/m9.figshare.91916.v1
title: sparql3WP1531.csv

description: This is the result of query: PREFIX dcterms: PREFIX dc: PREFIX skos: PREFIX str: PREFIX pao: SELECT DISTINCT ?pmid COUNT(DISTINCT ?concept) AS ?count WHERE { { SELECT DISTINCT ?concept WHERE { { SELECT ?wpLinkout WHERE { SERVICE { dcterms:hasVersion ?pwversion . ?pwNode dcterms:isPartOf ?pwversion . ?pwNode dc:identifier ?wpLinkout . } } } ?wpLinkout skos:exactMatch ?scaiLinkout . ?concept skos:exactMatch ?scaiLinkout . } } ?concept pao:incarnationOf ?hit . ?hit str:subString ?pmid . ?pmid rdf:type str:Document . OPTIONAL { { SELECT DISTINCT ?pmidOrigin WHERE { SERVICE { dcterms:hasVersion ?pwversion . ?pwNode dcterms:isPartOf ?pwversion . ?pwNode dcterms:bibliographicCitation ?pmidOrigin . } } } FILTER (?pmidOrigin = ?pmid) . } FILTER (!BOUND(?pmidOrigin)) . } ORDER BY DESC (?count)