cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.154190
title: Data from Temporal ordering deficits in female CGG KI mice heterozygous for the fragile X premutation

description: Raw data for Hunsaker, M. R., Goodrich-Hunsaker, N. J., Willemsen, R., & Berman, R. F. (2010). Temporal ordering deficits in female CGG KI mice heterozygous for the fragile X premutation. Behavioral Brain Research, 213(2), 263-268.
DOI: 10.6084/m9.figshare.154346.v4
title: Open access journal impacts & statistics

description: Graphics and data accompany blog post about the impact of open science journals relative to non-OA.
DOI: 10.6084/m9.figshare.154193
title: Accurate and robust genomic prediction of celiac disease using statistical learning

description: Practical application of genomic-based risk stratification to clinical diagnosis is appealing yet performance varies widely depending on the disease and genomic risk score (GRS) method. Celiac disease (CD), a common immune-mediated illness, is strongly genetically determined and requires specific HLA haplotypes. HLA testing can exclude diagnosis but has low specificity, providing little information suitable for clinical risk stratification. Using six European CD cohorts, we provide a proof-of-concept that statistical learning approaches which simultaneously model all SNPs can generate robust and highly accurate predictive models based on genome-wide SNP profiles. The high predictive capacity replicated both in cross-validation within each cohort (AUC of 0.87—0.89) and in independent replication across cohorts (AUC of 0.86—0.9), despite differences in ethnicity. The models explained 30—35% of disease variance and up to ~43% of heritability. The GRS’s utility was assessed in different clinically relevant settings. Comparable to HLA typing, the GRS can be used to identify individuals without CD with ≥99.6% negative predictive value however, unlike HLA typing, patients can also be stratified into categories of higher-risk for CD who would benefit from more invasive and costly definitive testing. The GRS is flexible and its performance can be adapted to the clinical situation by adjusting the threshold cut-off. Despite explaining a minority of disease heritability, our findings indicate a predictive GRS provides clinically relevant information to improve upon current diagnostic pathways for CD, and support further studies evaluating the clinical utility of this approach in CD and other complex diseases.
DOI: 10.6084/m9.figshare.154330.v1
title: README Quantitative Biology Practical

description: Some notes to accompany the Quantitative Biology Practical handout
DOI: 10.6084/m9.figshare.154361.v7
title: Downloadable data for fungal meningitis outbreak

description: Data are case counts and morbidities from the CDC website, for the fungal meningitis outbreak. Updated weekly(ish). Newest data from 3/11/13. Fungalmeningitiscasecounts.csv is a time series of case counts by state. Morbidities_cdc.csv is a breakdown of morbidities by state, using most recent data (3/11/13). This file does not include historical data. There is a column with exposures by state; those data are from: Updated analysis available via iPython notebook (see first link), more comprehensive but older analysis on my blog (see third link). Smith, R. M., Schaefer, M. K., Kainer, M. a, Wise, M., Finks, J., Duwve, J., Fontaine, E., et al. (2012). Fungal Infections Associated with Contaminated Methylprednisolone Injections - Preliminary Report. The New England Journal of Medicine, 1–11. doi:10.1056/NEJMoa1213978
DOI: 10.6084/m9.figshare.154190.v1
title: Data from Temporal ordering deficits in female CGG KI mice heterozygous for the fragile X premutation

description: Raw data for Hunsaker, M. R., Goodrich-Hunsaker, N. J., Willemsen, R., & Berman, R. F. (2010). Temporal ordering deficits in female CGG KI mice heterozygous for the fragile X premutation. Behavioral Brain Research, 213(2), 263-268.
DOI: 10.6084/m9.figshare.154330.v3
title: Quantitative Biology Practical

description: Some notes to accompany the Quantitative Biology Practical handout, and the handout itself.
DOI: 10.6084/m9.figshare.154361.v8
title: Downloadable data for fungal meningitis outbreak

description: Data are case counts and morbidities from the CDC website, for the fungal meningitis outbreak. Case counts are now updated monthly. Newest data from 5/6/13. Fungalmeningitiscasecounts.csv is a time series of case counts by state. Morbidities_cdc.csv is a breakdown of morbidities by state, using most recent data (3/11/13). This file does not include historical data. There is a column with exposures by state; those data are from [1]. Updated analysis available via iPython notebook (see first link), more comprehensive but older analysis on my blog (see third link). [1] Smith, R. M., Schaefer, M. K., Kainer, M. a, Wise, M., Finks, J., Duwve, J., Fontaine, E., et al. (2012). Fungal Infections Associated with Contaminated Methylprednisolone Injections - Preliminary Report. The New England Journal of Medicine, 1–11. doi:10.1056/NEJMoa1213978
DOI: 10.6084/m9.figshare.154330.v2
title: Quantitative Biology Practical

description: Some notes to accompany the Quantitative Biology Practical handout, and the handout itself.
DOI: 10.6084/m9.figshare.154361.v10
title: Downloadable data for fungal meningitis outbreak

description: Data are case counts and morbidities from the CDC website, for the fungal meningitis outbreak. Case counts are now updated infrequently. Newest data from 10/23/13. Fungalmeningitiscasecounts.csv is a time series of case counts by state. Morbidities_cdc.csv is a breakdown of morbidities by state, using most recent data (10/23/13). This file does not include historical data. There is a column with exposures by state; those data are from [1]. Some basic analyses are available on my blog (see link below) [1] Smith, R. M., Schaefer, M. K., Kainer, M. a, Wise, M., Finks, J., Duwve, J., Fontaine, E., et al. (2012). Fungal Infections Associated with Contaminated Methylprednisolone Injections - Preliminary Report. The New England Journal of Medicine, 1–11. doi:10.1056/NEJMoa1213978
DOI: 10.6084/m9.figshare.154189
title: Data from Motor deficits on a ladder rung task in male and female adolescent CGG knock-in mice. Behavioural Brain Research,

description: Raw data for Hunsaker, M. R., von Leden, R. E., Ta, B. T, Goodrich-Hunsaker, N. J., Arque, G., Kim, K. M., … Berman, R. F. (2011). Motor deficits on a ladder rung task in male and female adolescent CGG knock-in mice. Behavioural Brain Research, 222, 117-121.
DOI: 10.6084/m9.figshare.154188
title: Data from Progressive spatial processing deficits in a mouse model of the fragile X premutation.

description: Raw data for Hunsaker, M. R., Wenzel, H. J., Willemsen, R., & Berman, R. F. (2009). Progressive spatial processing deficits in a mouse model of the fragile X premutation. Behavioral Neuroscience. 123(6), 1315-1324.
DOI: 10.6084/m9.figshare.154189.v1
title: Data from Motor deficits on a ladder rung task in male and female adolescent CGG knock-in mice. Behavioural Brain Research,

description: Raw data for Hunsaker, M. R., von Leden, R. E., Ta, B. T, Goodrich-Hunsaker, N. J., Arque, G., Kim, K. M., … Berman, R. F. (2011). Motor deficits on a ladder rung task in male and female adolescent CGG knock-in mice. Behavioural Brain Research, 222, 117-121.
DOI: 10.6084/m9.figshare.154361.v9
title: Downloadable data for fungal meningitis outbreak

description: Data are case counts and morbidities from the CDC website, for the fungal meningitis outbreak. Case counts are now updated monthly. Newest data from 5/6/13. Fungalmeningitiscasecounts.csv is a time series of case counts by state. Morbidities_cdc.csv is a breakdown of morbidities by state, using most recent data (3/11/13). This file does not include historical data. There is a column with exposures by state; those data are from [1]. Updated analysis available via iPython notebook (see first link), more comprehensive but older analysis on my blog (see third link). [1] Smith, R. M., Schaefer, M. K., Kainer, M. a, Wise, M., Finks, J., Duwve, J., Fontaine, E., et al. (2012). Fungal Infections Associated with Contaminated Methylprednisolone Injections - Preliminary Report. The New England Journal of Medicine, 1–11. doi:10.1056/NEJMoa1213978
DOI: 10.6084/m9.figshare.154186
title: Data from Spatiotemporal processing deficits in female CGG KI mice modeling the fragile X premutation

description: Raw data from Borthwell, R. M., Hunsaker, M. R., Willemsen, R., & Berman, R. F. (2012). Spatiotemporal processing deficits in female CGG KI mice modeling the fragile X premutation. Behavioural Brain Research, 233(1), 29-34.
DOI: 10.6084/m9.figshare.154187
title: Data from Female CGG knock-in mice modeling the fragile X premutation are impaired on a skilled forelimb reaching task

description: Raw data from Diep, A. A., Hunsaker, M. R., Kwock, R., Kim, K. M., Willemsen, R., & Berman, R. F. (2012). Female CGG knock-in mice modeling the fragile X premutation are impaired on a skilled forelimb reaching task. Neurobiology of Learning and Memory, 97, 229-234.
DOI: 10.6084/m9.figshare.154193.v1
title: Accurate and robust genomic prediction of celiac disease using statistical learning

description: Practical application of genomic-­‐based risk stratification to clinical diagnosis is appealing yet performance varies widely depending on the disease and genomic risk score (GRS) method. Celiac disease (CD), a common immune-­‐mediated illness, is strongly genetically determined and requires specific HLA haplotypes. HLA testing can exclude diagnosis but has low specificity, providing little information suitable for clinical risk stratification. Using six European CD cohorts, we provide a proof-­‐ of-­‐concept that statistical learning approaches which simultaneously model all SNPs can generate robust and highly accurate predictive models based on genome-­‐wide SNP profiles. The high predictive capacity replicated both in cross-­‐validation within each cohort (AUC of 0.87—0.89) and in independent replication across cohorts (AUC of 0.86—0.9), despite differences in ethnicity. The models explained 30—35% of disease variance and less than 50% of heritability. The GRS’s utility was assessed in different screening settings. For known family history (10% prevalence), the GRS captured 35% of cases with 1 misdiagnosis per correct diagnosis. In the population-­‐wide setting (1% prevalence), the GRS captured 10% of cases with 5 misdiagnoses per correct diagnosis. Comparable to HLA typing, the GRS can identify individuals without CD with &gt;99.6% negative predictive value and, unlike HLA typing, patients can be stratified for further more invasive and costly testing. Despite explaining a minority of disease heritability, our findings indicate a predictive GRS provides clinically relevant information to improve upon current diagnostic pathways for CD, and support further studies evaluating the clinical utility of this approach in CD and other complex diseases.
DOI: 10.6084/m9.figshare.154175
title: Data from CGG Trinucleotide repeat length modulates neural plasticity and spatiotemporal processing in a mouse model of the fragile X premutation

description: Raw data from Hunsaker, M. R., Kim, K. M., Willemsen, R., & Berman, R. F. (2012). CGG Trinucleotide repeat length modulates neural plasticity and spatiotemporal processing in a mouse model of the fragile X premutation. Hippocampus, 22(12), 2260-2275.
DOI: 10.6084/m9.figshare.154186.v1
title: Data from Spatiotemporal processing deficits in female CGG KI mice modeling the fragile X premutation

description: Raw data from Borthwell, R. M., Hunsaker, M. R., Willemsen, R., & Berman, R. F. (2012). Spatiotemporal processing deficits in female CGG KI mice modeling the fragile X premutation. Behavioural Brain Research, 233(1), 29-34.
DOI: 10.6084/m9.figshare.154193.v2
title: Accurate and robust genomic prediction of celiac disease using statistical learning

description: Practical application of genomic-­‐based risk stratification to clinical diagnosis is appealing yet performance varies widely depending on the disease and genomic risk score (GRS) method. Celiac disease (CD), a common immune-­‐mediated illness, is strongly genetically determined and requires specific HLA haplotypes. HLA testing can exclude diagnosis but has low specificity, providing little information suitable for clinical risk stratification. Using six European CD cohorts, we provide a proof-­‐ of-­‐concept that statistical learning approaches which simultaneously model all SNPs can generate robust and highly accurate predictive models based on genome-­‐wide SNP profiles. The high predictive capacity replicated both in cross-­‐validation within each cohort (AUC of 0.87—0.89) and in independent replication across cohorts (AUC of 0.86—0.9), despite differences in ethnicity. The models explained 30—35% of disease variance and less than 50% of heritability. The GRS’s utility was assessed in different screening settings. For known family history (10% prevalence), the GRS captured 35% of cases with 1 misdiagnosis per correct diagnosis. In the population-­‐wide setting (1% prevalence), the GRS captured 10% of cases with 5 misdiagnoses per correct diagnosis. Comparable to HLA typing, the GRS can identify individuals without CD with &gt;99.6% negative predictive value and, unlike HLA typing, patients can be stratified for further more invasive and costly testing. Despite explaining a minority of disease heritability, our findings indicate a predictive GRS provides clinically relevant information to improve upon current diagnostic pathways for CD, and support further studies evaluating the clinical utility of this approach in CD and other complex diseases.
DOI: 10.6084/m9.figshare.154042
title: Forebrain Specific ß-catenin KO shows deficits for hippocampus-dependent cognitive processing

description: A mouse lacking proper hippocampal development shows deficits for tasks shown to be hippocampus dependent, but not for tasks that require extrahippocampal substrates.
DOI: 10.6084/m9.figshare.154043
title: Using TB Mobile to Predict Potential Targets for TB hits from Phenotypic Screening

description: A poster describing how to use a free mobile app called TB Mobile to predict potential TB targets for new hits from phenotypic screening.
DOI: 10.6084/m9.figshare.154044
title: Gaussian Job Archive for C8H17ClO2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.154042.v1
title: Forebrain Specific ß-catenin KO shows deficits for hippocampus-dependent cognitive processing

description: A mouse lacking proper hippocampal development shows deficits for tasks shown to be hippocampus dependent, but not for tasks that require extrahippocampal substrates.
DOI: 10.6084/m9.figshare.153960
title: Gaussian Job Archive for C8H17ClO2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.154044.v1
title: Gaussian Job Archive for C8H17ClO2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.154043.v1
title: Using TB Mobile to Predict Potential Targets for TB hits from Phenotypic Screening

description: A poster describing how to use a free mobile app called TB Mobile to predict potential TB targets for new hits from phenotypic screening.
DOI: 10.6084/m9.figshare.153957
title: Gaussian Job Archive for C7H15ClO2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.153958
title: Gaussian Job Archive for C8H17ClO2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.153959
title: Gaussian Job Archive for C7H15ClO2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.153960.v1
title: Gaussian Job Archive for C8H17ClO2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.153956
title: Gaussian Job Archive for C7H15ClO2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.153957.v1
title: Gaussian Job Archive for C7H15ClO2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.153958.v1
title: Gaussian Job Archive for C8H17ClO2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.153959.v1
title: Gaussian Job Archive for C7H15ClO2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.153954
title: R code and data for: Models of maximum chlorophyll concentrations based on environmental data

description: This is the R markdown code and data for the section: Models of maximum chlorophyll concentrations based on environmental data inside the manuscript: On the phytoplankton bloom in coastal waters of southern King George Island (Antarctica) in January 2010: an exceptional feature? (2014) I.R. Schloss, A. Wasilowska, D. Dumont, G.O. Almandoz, M.P. Hernando, C.-A. Michaud-Tremblay, L. Saravia, M. Rzepecki, P. Monien, D. Monien, E.E. Kopczyńska, V. Bers, G.A. Ferreyra. Limnol Oceanogr 59: 195–210.
DOI: 10.6084/m9.figshare.153956.v1
title: Gaussian Job Archive for C7H15ClO2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.153955
title: Gaussian Job Archive for C7H15ClO2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.153940
title: trajectory experiment metadata

description: Experiment got their metadata: who, when, what was tested. This is a rough try to get information about the experiment itself, other elements should probably be included like a link to a proper material and method description. This would probably need to go to a RDF format: for one experiment can multiple authors and multiple changing variables be present (for instance genotype x treatment)...
DOI: 10.6084/m9.figshare.153939
title: trajectory metadata

description: Data to be found in the data fileset, metadata for each experiment will also be produced and posted, see links. This is intended to become a repository for all data analysed with CeTrAn, an open source centroid trajetory analysis tool written in R (third link). The data will be uploaded while analysed (automatically), making it open by default. I am looking for people interested in developing the tool and the database structure. I am no specialist, not in R, not in database structures, but I so far managed to find help in the R community. Come and comment, your feedback is needed !!
DOI: 10.6084/m9.figshare.153940.v2
title: trajectory experiment metadata

description: Experiment got their metadata: who, when, what was tested. This is a rough try to get information about the experiment itself, other elements should probably be included like a link to a proper material and method description. This would probably need to go to a RDF format: for one experiment can multiple authors and multiple changing variables be present (for instance genotype x treatment)...
DOI: 10.6084/m9.figshare.153938
title: raw trajectory data

description: Still in a testing phase: need to deal with duplicates. format is time (in ms), x position (in mm), y position (in mm), burst (increase while the experiment is stopped and started again with the same animal). Information about the experiment is found in the metadata.
DOI: 10.6084/m9.figshare.153940.v1
title: trajectory experiment metadata

description: Experiment got their metadata: who, when, what was tested. This is a rough try to get information about the experiment itself, other elements should probably be included like a link to a proper material and method description. This would probably need to go to a RDF format: for one experiment can multiple authors and multiple changing variables be present (for instance genotype x treatment)...
DOI: 10.6084/m9.figshare.153954.v1
title: R code and data for: Models of maximum chlorophyll concentrations based on environmental data

description: This is the R markdown code and data for the section: Models of maximum chlorophyll concentrations based on environmental data inside the manuscript in review: On the phytoplankton bloom in coastal waters of southern King George Island (Antarctica) in January 2010: an exceptional feature? I.R. Schloss, A. Wasilowska, D. Dumont, G.O. Almandoz, M.P. Hernando, C.-A. Michaud-Tremblay, L. Saravia, M. Rzepecki, P. Monien, D. Monien, E.E. Kopczyńska, V. Bers, G.A. Ferreyra Submitted to Limnology & Oceanography
DOI: 10.6084/m9.figshare.153938.v1
title: raw trajectory data

description: Still in a testing phase: need to deal with duplicates. format is time (in ms), x position (in mm), y position (in mm), burst (increase while the experiment is stopped and started again with the same animal). Information about the experiment is found in the metadata.
DOI: 10.6084/m9.figshare.153907
title: Paleoclimate insolation calculation

description: R package to compute Incoming Solar Radiation (insolation) for paleoclimate studies. Features three solutions: BER78, BER90 and LA04. Computes daily-mean, season-averaged and annual means for all latitudes. Licenced under MIT licence. Refer to original papers when using specific insolation solutions.
DOI: 10.6084/m9.figshare.153837
title: Gaussian Job Archive for C7H15ClO2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.153907.v1
title: insol_0.91

description: R package to compute Incoming Solar Radiation (insolation) for paleoclimate studies. Features three solutions: BER78, BER90 and LA04. Computes daily-mean, season-averaged and annual means for all latitudes.
DOI: 10.6084/m9.figshare.153837.v1
title: Gaussian Job Archive for C7H15ClO2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.153874.v1
title: WATOC2011 poster

description: My poster for WATOC2011
DOI: 10.6084/m9.figshare.153836
title: Gaussian Job Archive for C8H17ClO2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.153880.v1
title: ICQC2012 poster

description: My poster for ICQC2012
DOI: 10.6084/m9.figshare.153836.v1
title: Gaussian Job Archive for C8H17ClO2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.153874.v2
title: Moecular Properties through Polarizable Embedding

description: My poster for WATOC2011
DOI: 10.6084/m9.figshare.153907.v2
title: insol_0.91

description: R package to compute Incoming Solar Radiation (insolation) for paleoclimate studies. Features three solutions: BER78, BER90 and LA04. Computes daily-mean, season-averaged and annual means for all latitudes. Licenced under MIT licence. Refer to original papers when using specific insolation solutions.
DOI: 10.6084/m9.figshare.153835
title: Rhesus Gastric Microbiome

description: This data is part of the projet to study the rhesus gastric microbiome and the effects of <em>Helicobacter pylori</em> on it.
DOI: 10.6084/m9.figshare.153828
title: Spatial Networks

description: Network datasets and meta data using in work which develops a new model of spatial network structure: http://arxiv.org/abs/1210.4246