cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1120631.v4
title: Quantitative analysis of fluorescent image – from descriptive to computational microscopy

description: Application of fluorescence in microscopy led to a considerable breakthrough in biochemical sciences by facilitating a new way of observing complex biological processes, structures and interactions and locating them in particular parts of the cell. Today, fluorescent imaging is widely applied in published literature to confirm research hypotheses. However, about only one of ten publications provides supporting information for the observations based on fluorescence through a computational analysis of the acquired images. “One picture is worth ten thousand words” was once stated by Frederic R. Bernard, however, images alone may not be enough to provide reliable information. For example, given population diversity, it is very likely that a selected cell ( ‘the cell’ ) will be found that confirms a particular theory, while most others will refute it. In addition the validity of observations conducted on cell cultures may be disputable, as these are usually cancer or immortalized cells and therefore differ significantly from the original tissue. It is known, for example that cultured cancer cells easily evolve into a variety of clones that may not differ morphologically, but when stimulated to undergo differentiation or cell death they tend to react differently to normal cells at the biomolecular level. While cellular analysis requires a great deal of caution, descriptive tissue analysis is even more subjective and interpretations are highly dependent on personal experience of the observer. Baak, in his article [Baak 2002] addressed difficulties in qualitative assessment of microscopic samples in pathology. The reliability was acceptable when an observation was assessed by at least three specialists, but consistency was low especially in more complex analysis. Comparison of the data between different laboratories is also difficult considering the simplicity of observations made and the complexity of the pathological processes.<br>Modern imaging methods which use charged-coupled devices (CCDs) or photomultipliers (PMTs) provide a possibility to capture the visual observations in a numerical, digitalized form. In this format reliable quantitative data can be extracted which open new ways of understanding and supporting an observation process. In this chapter, various methods of quantitative analysis will be presented and discussed, applicable to studies of a single cell as well as whole populations and tissues.
DOI: 10.6084/m9.figshare.1120663.v7
title: deboever-sf3b1-2014

description: Files for replicating SF3B1 study.
DOI: 10.6084/m9.figshare.1120631.v3
title: Quantitative analysis of fluorescent image – from descriptive to computational microscopy

description: Application of fluorescence in microscopy led to a considerable breakthrough in biochemical sciences by facilitating a new way of observing complex biological processes, structures and interactions and locating them in particular parts of the cell. Today, fluorescent imaging is widely applied in published literature to confirm research hypotheses. However, about only one of ten publications provides supporting information for the observations based on fluorescence through a computational analysis of the acquired images. “One picture is worth ten thousand words” was once stated by Frederic R. Bernard, however, images alone may not be enough to provide reliable information. For example, given population diversity, it is very likely that a selected cell ( ‘the cell’ ) will be found that confirms a particular theory, while most others will refute it. In addition the validity of observations conducted on cell cultures may be disputable, as these are usually cancer or immortalized cells and therefore differ significantly from the original tissue. It is known, for example that cultured cancer cells easily evolve into a variety of clones that may not differ morphologically, but when stimulated to undergo differentiation or cell death they tend to react differently to normal cells at the biomolecular level. While cellular analysis requires a great deal of caution, descriptive tissue analysis is even more subjective and interpretations are highly dependent on personal experience of the observer. Baak, in his article [Baak 2002] addressed difficulties in qualitative assessment of microscopic samples in pathology. The reliability was acceptable when an observation was assessed by at least three specialists, but consistency was low especially in more complex analysis. Comparison of the data between different laboratories is also difficult considering the simplicity of observations made and the complexity of the pathological processes.<br>Modern imaging methods which use charged-coupled devices (CCDs) or photomultipliers (PMTs) provide a possibility to capture the visual observations in a numerical, digitalized form. In this format reliable quantitative data can be extracted which open new ways of understanding and supporting an observation process. In this chapter, various methods of quantitative analysis will be presented and discussed, applicable to studies of a single cell as well as whole populations and tissues.
DOI: 10.6084/m9.figshare.1120663.v8
title: deboever-sf3b1-2014

description: Files for replicating SF3B1 study.
DOI: 10.6084/m9.figshare.1120570
title: Note to accompany the Research Information Network data

description: An independent statistical analysis of the articles published in Nature Communications, carried out by the Research Information Network (RIN) has found that open access (OA) articles are viewed three times more often than articles that are only available to subscribers. RIN also found that OA articles are cited more than subscription articles. This note accompanies the data used by RIN.
DOI: 10.6084/m9.figshare.1120663.v9
title: deboever-sf3b1-2014

description: Files for replicating SF3B1 study.
DOI: 10.6084/m9.figshare.1120663.v10
title: deboever-sf3b1-2014

description: Files for replicating SF3B1 study.
DOI: 10.6084/m9.figshare.1120663.v11
title: deboever-sf3b1-2014

description: Files for replicating SF3B1 study.
DOI: 10.6084/m9.figshare.1120558
title: Gaussian Job Archive for C13H26O4

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1120541
title: Gaussian Job Archive for C13H26O4

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1120663.v12
title: deboever-sf3b1-2014

description: Files for replicating SF3B1 study.
DOI: 10.6084/m9.figshare.1120558.v1
title: Gaussian Job Archive for C13H26O4

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1120541.v1
title: Gaussian Job Archive for C13H26O4

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1120663.v13
title: deboever-sf3b1-2014

description: Files for replicating SF3B1 study.
DOI: 10.6084/m9.figshare.1120663.v14
title: deboever-sf3b1-2014

description: Files for replicating SF3B1 study.
DOI: 10.6084/m9.figshare.1120505
title: A window of opportunity to control the bacterial pathogen Pseudomonas aeruginosa combining antibiotics and phages

description: Optical density measurements at different time points of replicate populations of P. aeruginosa treated with streptomycin and/or phages. Measurements of level of antibiotic resistance have been also recorded (MIC). And level of resistance (OD) to co-evolved phages.
DOI: 10.6084/m9.figshare.1120663.v15
title: deboever-sf3b1-2014

description: Files for replicating SF3B1 study.
DOI: 10.6084/m9.figshare.1120505.v1
title: A window of opportunity to control the bacterial pathogen Pseudomonas aeruginosa combining antibiotics and phages

description: Optical density measurements at different time points of replicate populations of P. aeruginosa treated with streptomycin and/or phages. Measurements of level of antibiotic resistance have been also recorded (MIC). And level of resistance (OD) to co-evolved phages.
DOI: 10.6084/m9.figshare.1120501
title: Comparing the effects of nocturnal sleep and daytime napping on declarative memory consolidation

description: Experiment 1: nocturnal sleep
DOI: 10.6084/m9.figshare.1120502
title: Comparing the effects of nocturnal sleep and daytime napping on declarative memory consolidation

description: Experiment 2: daytime nap
DOI: 10.6084/m9.figshare.1120663.v16
title: deboever-sf3b1-2014

description: Files for replicating SF3B1 study.
DOI: 10.6084/m9.figshare.1120500
title: HORTICULTURE LITERATURE CITED IN DOCTORAL DISSERTATIONS: AN OBSOLESCENCE STUDY, 1991-2010

description: Obsolescence study is useful for librarians and managers of information centers in identifying the use of periodical literature. The present study aims to examine the obsolescence literature in zhorticulture by citation analysis and reviewed<br>various studies and outlined the results. The study based on the 10,845 citations, cited in the 80 horticultural doctoral dissertations accepted and awarded at Bidhan Chandra Krishi Viswavidyalay (BCKV), Mohanpur, West Bengal and Uttar<br>Banga Krishi Viswavidyalay (UBKV), Cooch Bihar, West Bengal during the period of 1991-2010.
DOI: 10.6084/m9.figshare.1120486
title: Science blogging: An exploratory study of motives, styles, and audience reactions (supplementary data)

description: Supplementary data from Mahrt, M., & Puschmann, C. (2014). Science blogging: An exploratory study of motives, styles, and audience reactions. Journal of Science Communication, 13(3), A05.
DOI: 10.6084/m9.figshare.1120500.v1
title: HORTICULTURE LITERATURE CITED IN DOCTORAL DISSERTATIONS: AN OBSOLESCENCE STUDY, 1991-2010

description: Obsolescence study is useful for librarians and managers of information centers in identifying the use of periodical literature. The present study aims to examine the obsolescence literature in zhorticulture by citation analysis and reviewed<br>various studies and outlined the results. The study based on the 10,845 citations, cited in the 80 horticultural doctoral dissertations accepted and awarded at Bidhan Chandra Krishi Viswavidyalay (BCKV), Mohanpur, West Bengal and Uttar<br>Banga Krishi Viswavidyalay (UBKV), Cooch Bihar, West Bengal during the period of 1991-2010.
DOI: 10.6084/m9.figshare.1120663.v17
title: deboever-sf3b1-2014

description: Files for replicating SF3B1 study.
DOI: 10.6084/m9.figshare.1120485
title: Rawdata used to calculate multiple stressor effects on multifunctionality

description: Rawdata used to calculate multiple stressor effects on multifunctionality
DOI: 10.6084/m9.figshare.1120485.v1
title: Rawdata used to calculate multiple stressor effects on multifunctionality

description: Rawdata used to calculate multiple stressor effects on multifunctionality
DOI: 10.6084/m9.figshare.1120663.v18
title: deboever-sf3b1-2014

description: Files for replicating SF3B1 study.
DOI: 10.6084/m9.figshare.1119788
title: Supplementary Figure 13, Dreadnoughtus sacrum - Lacovara et al., 2014, A Gigantic, Exceptionally Complete Titanosaurian Sauropod Dinosaur from Southern Patagonia, Argentina, Scientific Reports,

description: Supplementary Fig. 13. Digital 3D PDF of the sacrum of <em>Dreadnoughtus schrani</em> (MPM-PV 1156).
DOI: 10.6084/m9.figshare.1119789
title: Supplementary Figure 15, Dreadnoughtus shoulder girdle - Lacovara et al., 2014, A Gigantic, Exceptionally Complete Titanosaurian Sauropod Dinosaur from Southern Patagonia, Argentina, Scientific Reports,

description: Supplementary Fig. 15. Digital reconstruction of the left shoulder girdle of <em>Dreadnoughtus schrani</em> (MPM-PV 1156) in lateral view.
DOI: 10.6084/m9.figshare.1119789.v1
title: Supplementary Figure 15, Dreadnoughtus shoulder girdle - Lacovara et al., 2014, A Gigantic, Exceptionally Complete Titanosaurian Sauropod Dinosaur from Southern Patagonia, Argentina, Scientific Reports,

description: Supplementary Fig. 15. Digital reconstruction of the left shoulder girdle of <em>Dreadnoughtus schrani</em> (MPM-PV 1156) in lateral view.
DOI: 10.6084/m9.figshare.1119790
title: Supplementary Figure 9, Dreadnoughtus skeleton - Lacovara et al., 2014, A Gigantic, Exceptionally Complete Titanosaurian Sauropod Dinosaur from Southern Patagonia, Argentina, Scientific Reports,

description: Supplementary Fig. 9. Digital reconstruction of known skeletal elements of <em>Dreadnoughtus schrani</em> (MPM-PV 1156 and MPM-PV 3546) in left lateral view. In the reconstruction, two left and one right dorsal ribs were mirrored to yield a total of six representative ribs. Moreover, except for the sternal plate, the right pectoral girdle and forelimb were mirrored from the left. The right femur, fibula, and astragalus were also mirrored from the left side, whereas the left metatarsals and pedal ungual were mirrored from the right. <strong>Note:</strong> The placement of skeletal elements in this reconstruction is approximate. Taphonomic deformation within the axial skeleton prevented some bones from being property articulated. Thus, error has been introduced into the skeletal proportions represented here. Our most accurate estimates for the skeletal proportions of <em>Dreadnoughtus</em> can be found in the 2D reconstruction (Figure 2), published in Lacovara et al (2014). (See the link below)
DOI: 10.6084/m9.figshare.1119786
title: Supplementary Figure 16, Dreadnoughtus left forelimb - Lacovara et al., 2014, A Gigantic, Exceptionally Complete Titanosaurian Sauropod Dinosaur from Southern Patagonia, Argentina, Scientific Reports,

description: Supplementary Fig. 16. Digital reconstruction of the left forelimb (minus the manus) of <em>Dreadnoughtus schrani</em> (MPM-PV 1156).
DOI: 10.6084/m9.figshare.1119788.v1
title: Supplementary Figure 13, Dreadnoughtus sacrum - Lacovara et al., 2014, A Gigantic, Exceptionally Complete Titanosaurian Sauropod Dinosaur from Southern Patagonia, Argentina, Scientific Reports,

description: Supplementary Fig. 13. Digital 3D PDF of the sacrum of <em>Dreadnoughtus schrani</em> (MPM-PV 1156).
DOI: 10.6084/m9.figshare.1120663.v19
title: deboever-sf3b1-2014

description: Files for replicating SF3B1 study.
DOI: 10.6084/m9.figshare.1119787
title: Supplementary Figure 17, Dreadnoughtus pelvic girdle - Lacovara et al., 2014, A Gigantic, Exceptionally Complete Titanosaurian Sauropod Dinosaur from Southern Patagonia, Argentina, Scientific Reports,

description: Supplementary Fig. 17. Digital reconstruction of the pelvic girdle of <em>Dreadnoughtus schrani</em> (MPM-PV 1156).
DOI: 10.6084/m9.figshare.1119785
title: Supplementary Figure 14, Dreadnoughtus caudal series - Lacovara et al., 2014, A Gigantic, Exceptionally Complete Titanosaurian Sauropod Dinosaur from Southern Patagonia, Argentina, Scientific Reports,

description: Supplementary Fig. 14. Digital reconstruction of the first 32 caudal vertebrae and associated haemal arches of the holotype of <em>Dreadnoughtus schrani</em> (MPM-PV 1156).
DOI: 10.6084/m9.figshare.1119786.v1
title: Supplementary Figure 16, Dreadnoughtus left forelimb - Lacovara et al., 2014, A Gigantic, Exceptionally Complete Titanosaurian Sauropod Dinosaur from Southern Patagonia, Argentina, Scientific Reports,

description: Supplementary Fig. 16. Digital reconstruction of the left forelimb (minus the manus) of <em>Dreadnoughtus schrani</em> (MPM-PV 1156).
DOI: 10.6084/m9.figshare.1119785.v1
title: Supplementary Figure 14, Dreadnoughtus caudal series - Lacovara et al., 2014, A Gigantic, Exceptionally Complete Titanosaurian Sauropod Dinosaur from Southern Patagonia, Argentina, Scientific Reports,

description: Supplementary Fig. 14. Digital reconstruction of the first 32 caudal vertebrae and associated haemal arches of the holotype of <em>Dreadnoughtus schrani</em> (MPM-PV 1156).
DOI: 10.6084/m9.figshare.1120663.v20
title: deboever-sf3b1-2014

description: Files for replicating SF3B1 study.
DOI: 10.6084/m9.figshare.1119781
title: Supplementary Figure 11, Dreadnoughtus (~4th) dorsal vertebra - Lacovara et al., 2014, A Gigantic, Exceptionally Complete Titanosaurian Sauropod Dinosaur from Southern Patagonia, Argentina, Scientific Reports,

description: Supplementary Fig. 11. Digital 3D PDF of an anterior (~4th) dorsal vertebra of <em>Dreadnoughtus schrani</em>.
DOI: 10.6084/m9.figshare.1119782
title: Supplementary Figure 10, Dreadnoughtus (~9th) cervical vertebra - Lacovara et al., 2014, A Gigantic, Exceptionally Complete Titanosaurian Sauropod Dinosaur from Southern Patagonia, Argentina, Scientific Reports,

description: Supplementary Fig. 10. Digital 3D PDF image of a posterior (~9th) cervical vertebra of <em>Dreadnoughtus schrani</em> (MPM-PV 1156).
DOI: 10.6084/m9.figshare.1119783
title: Supplementary Figure 12, Dreadnoughtus posterior (~8th) dorsal vertebra - Lacovara et al., 2014, A Gigantic, Exceptionally Complete Titanosaurian Sauropod Dinosaur from Southern Patagonia, Argentina, Scientific Reports,

description: Supplementary Fig. 12. Digital 3D PDF of a posterior (~8th) dorsal vertebra of <em>Dreadnoughtus schrani</em>.
DOI: 10.6084/m9.figshare.1119784
title: Supplementary Figure 18, Dreadnoughtus hind limb - Lacovara et al., 2014, A Gigantic, Exceptionally Complete Titanosaurian Sauropod Dinosaur from Southern Patagonia, Argentina, Scientific Reports,

description: Supplementary Fig. 18. Digital 3D PDF of all known skeletal elements of the hind limb of <em>Dreadnoughtus schrani</em> (MPM-PV 1156). Femur and fibula from left side; tibia, metatarsals, and ungual mirrored from right side.
DOI: 10.6084/m9.figshare.1119781.v1
title: Supplementary Figure 11, Dreadnoughtus (~4th) dorsal vertebra - Lacovara et al., 2014, A Gigantic, Exceptionally Complete Titanosaurian Sauropod Dinosaur from Southern Patagonia, Argentina, Scientific Reports,

description: Supplementary Fig. 11. Digital 3D PDF of an anterior (~4th) dorsal vertebra of <em>Dreadnoughtus schrani</em>.
DOI: 10.6084/m9.figshare.1119782.v1
title: Supplementary Figure 10, Dreadnoughtus (~9th) cervical vertebra - Lacovara et al., 2014, A Gigantic, Exceptionally Complete Titanosaurian Sauropod Dinosaur from Southern Patagonia, Argentina, Scientific Reports,

description: Supplementary Fig. 10. Digital 3D PDF image of a posterior (~9th) cervical vertebra of <em>Dreadnoughtus schrani</em> (MPM-PV 1156).
DOI: 10.6084/m9.figshare.1119783.v1
title: Supplementary Figure 12, Dreadnoughtus posterior (~8th) dorsal vertebra - Lacovara et al., 2014, A Gigantic, Exceptionally Complete Titanosaurian Sauropod Dinosaur from Southern Patagonia, Argentina, Scientific Reports,

description: Supplementary Fig. 12. Digital 3D PDF of a posterior (~8th) dorsal vertebra of <em>Dreadnoughtus schrani</em>.
DOI: 10.6084/m9.figshare.1120663.v21
title: deboever-sf3b1-2014

description: Files for replicating SF3B1 study.
DOI: 10.6084/m9.figshare.1120663.v22
title: deboever-sf3b1-2014

description: Files for replicating SF3B1 study.
DOI: 10.6084/m9.figshare.1120663.v23
title: deboever-sf3b1-2014

description: Files for replicating SF3B1 study.
DOI: 10.6084/m9.figshare.1120663.v24
title: deboever-sf3b1-2014

description: Files for replicating SF3B1 study.
DOI: 10.6084/m9.figshare.1119735
title: Flow cytometry data from iPS-derived macrophages.

description: This page contains raw flow cytometry data from macrophages derived from three different iPS cell lines<strong>. </strong>The data are part of the manuscript "Transcriptional profiling of macrophages derived from monocytes and iPS cells identifies a conserved response to LPS and novel alternative transcription" (http://dx.doi.org/10.1101/014209). <strong>iPS lines and dates of experiments</strong> 1. FSPS10C (05/12/13) 2. FSPS11B (17/12/13) 3. S7RE (05/11/13) Experimental procedures are described in the manuscript.
DOI: 10.6084/m9.figshare.1120663.v25
title: deboever-sf3b1-2014

description: Files for replicating SF3B1 study.
DOI: 10.6084/m9.figshare.1119711
title: DevoWorm Project Presentation, Summer 2014

description: Current iteration of the DevoWorm project, development and status report as of Summer, 2014.
DOI: 10.6084/m9.figshare.1119735.v5
title: Flow cytometry data from iPS-derived macrophages.

description: This page contains raw flow cytometry data from macrophages derived from three different iPS cell lines<strong>. </strong>The data are part of the manuscript "Transcriptional profiling of macrophages derived from monocytes and iPS cells identifies a conserved response to LPS and novel alternative transcription" (http://dx.doi.org/10.1101/014209). <strong>iPS lines and dates of experiments</strong> 1. FSPS10C (05/12/13) 2. FSPS11B (17/12/13) 3. S7RE (05/11/13) Experimental procedures are described in the manuscript.
DOI: 10.6084/m9.figshare.1120663.v26
title: deboever-sf3b1-2014

description: Files for replicating SF3B1 study.
DOI: 10.6084/m9.figshare.1119735.v4
title: Flow cytometry results from iPS-derived macrophages.

description: <strong>iPS lines and dates of experiments</strong> 1. FSPS10C (05/12/13) 2. FSPS11B (17/12/13) 3. S7RE (05/11/13)
DOI: 10.6084/m9.figshare.1120663.v27
title: deboever-sf3b1-2014

description: Files for replicating SF3B1 study.
DOI: 10.6084/m9.figshare.1119711.v1
title: DevoWorm Project Presentation, Summer 2014

description: Current iteration of the DevoWorm project, development and status report as of Summer, 2014.
DOI: 10.6084/m9.figshare.1120663.v28
title: deboever-sf3b1-2014

description: Files for replicating SF3B1 study.
DOI: 10.6084/m9.figshare.1119711.v2
title: DevoWorm Project Presentation, Summer 2014

description: Current iteration of the DevoWorm project, development and status report as of Summer, 2014.
DOI: 10.6084/m9.figshare.1120663.v29
title: deboever-sf3b1-2014

description: Files for replicating SF3B1 study.
DOI: 10.6084/m9.figshare.1119711.v3
title: DevoWorm Project Presentation, Summer 2014

description: Current iteration of the DevoWorm project, development and status report as of Summer, 2014.
DOI: 10.6084/m9.figshare.1120663.v30
title: deboever-sf3b1-2014

description: Files for replicating SF3B1 study.
DOI: 10.6084/m9.figshare.1119711.v5
title: DevoWorm Project Presentation, Summer 2014

description: Current iteration of the DevoWorm project, development and status report as of Summer, 2014.
DOI: 10.6084/m9.figshare.1119711.v4
title: DevoWorm Project Presentation, Summer 2014

description: Current iteration of the DevoWorm project, development and status report as of Summer, 2014.
DOI: 10.6084/m9.figshare.1120663.v31
title: deboever-sf3b1-2014

description: Files for replicating SF3B1 study.
DOI: 10.6084/m9.figshare.1120663.v32
title: deboever-sf3b1-2014

description: Files for replicating SF3B1 study.
DOI: 10.6084/m9.figshare.1120663.v33
title: deboever-sf3b1-2014

description: Files for replicating SF3B1 study.
DOI: 10.6084/m9.figshare.1119638
title: Comment on sustainability and innovation in staple crop production in the US Midwest

description: This comment highlight issues when comparing genetically modified (GM) crops to non-GM ones across countries. Ignoring structural differences between agricultural sectors and assuming common yield trajectories before the time of introduction of GM crops results on misestimating the effect of GM varieties. Further data collection and analyses should guide policy-makers to encourage diverse approaches to agriculture, rather than excluding specific technologies (like GM crops) from the onset.
DOI: 10.6084/m9.figshare.1120663.v34
title: deboever-sf3b1-2014

description: Files for replicating SF3B1 study.
DOI: 10.6084/m9.figshare.1119635
title: Gaussian Job Archive for C21H23N3O3

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.