cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5786988
title: On the Protective Function of Y-SNPS/Y-STRS, and some Ancient Male Lineages

description: It is generally taken for granted that we inherit about half of our genes from each parent and so that, roughly speaking, a person's similarity to previous generations drops of at the rate 1/2 ^ g, where g is the number of generations separating that person from their ancestors. On this view it doesn't take many generations before the number of unique similarities between someone and their ancestors begins to dwindle to 0. Here this idea is disputed on the basis that non-recombined, rather than recombined DNA, determines identity, and the rate of decay of non-recombined DNA is very slow. It particular, it is suggested that the function of Y-SNPS/Y-STRS is the regulative function of protecting identity over a large number of regenerations.
DOI: 10.6084/m9.figshare.5786988.v9
title: On the Protective Function of Y-SNPS/Y-STRS, and some Ancient Male Lineages

description: It is generally taken for granted that we inherit about half of our genes from each parent and so that, roughly speaking, a person's similarity to previous generations drops of at the rate 1/2 ^ g, where g is the number of generations separating that person from their ancestors. On this view it doesn't take many generations before the number of unique similarities between someone and their ancestors begins to dwindle to 0. Here this idea is disputed on the basis that non-recombined, rather than recombined DNA, determines identity, and the rate of decay of non-recombined DNA is very slow. It particular, it is suggested that the function of Y-SNPS/Y-STRS is the regulative function of protecting identity over a large number of regenerations.
DOI: 10.6084/m9.figshare.5786931
title: TPMP_Open Loop vs Closed Loop

description: Behavioral Data of Drosophila melanogaster in stationary flight with transparently moving panorama patterns. Flies are in control of one of the two patterns, the other one is moving at a constant angular velocity.<br>
DOI: 10.6084/m9.figshare.5786931.v1
title: TPMP_Open Loop vs Closed Loop

description: Behavioral Data of Drosophila melanogaster in stationary flight with transparently moving panorama patterns. Flies are in control of one of the two patterns, the other one is moving at a constant angular velocity.<br>
DOI: 10.6084/m9.figshare.5786928
title: Peripheral neuropathy in patients with multiple sclerosis.xlsx

description: Patients with multiple sclerosis have evidence of sudomotor dysfunction and elevated vibration perception, which were associated with neurological disability from MS.
DOI: 10.6084/m9.figshare.5786928.v1
title: Peripheral neuropathy in patients with multiple sclerosis.xlsx

description: Patients with multiple sclerosis have evidence of sudomotor dysfunction and elevated vibration perception, which were associated with neurological disability from MS.
DOI: 10.6084/m9.figshare.5786925
title: Fig.1A2 (THP1 infection with HIV)

description: Infection assay, with increasing dose of HIV-NL4.3, of THP-1 cells stably expressing huTRIM5alpha R332G-R335G
DOI: 10.6084/m9.figshare.5786925.v2
title: Fig.1A2 (THP1 infection with HIV)

description: Infection assay, with increasing dose of HIV-NL4.3, of THP-1 cells stably expressing huTRIM5alpha R332G-R335G
DOI: 10.6084/m9.figshare.5786925.v1
title: Fig.4 A2 (THP1 infection with HIV)

description: Infection assay, with increasing dose of HIV-NL4.3, of THP-1 cells stably expressing huTRIM5alpha R332G-R335G
DOI: 10.6084/m9.figshare.5786922
title: TPMP_Coupling Coefficient and Relative Angular Velocity

description: Flight simulator data of Drosophila with transparently moving panorama patterns with different coupling coefficients and relative angular velocities.<br>
DOI: 10.6084/m9.figshare.5786838
title: P-values extracted from 11 scientific journals across two years

description: We examined how the proportion of reported significant results, expressed as p-values, changed with increasing impact factor (IF) We divided the range of IF into three intervals: low (IF&lt;4), medium (4≤IF&lt;8), and high (IF≥8) to ensure that our model was applicable to a broad range of impact factors. We then randomly selected at least two journals for each IF interval for both 2012 and 2014 from journals listed in the Science Citation Index Expanded (http://mjl.clarivate.com/cgi-bin/jrnlst/jloptions.cgi?PC=D) under four subject categories: biodiversity conservation, biology, ecology, and evolutionary biology. We examined 11 journals (lowest IF 0.36 to highest IF 17.95), six journals for both years, whilst we examined three for 2014 and two for 2012 alone. We collected p-values reported in all articles using the free trial version of Examine32 Text Search from Aquila Software. We extracted exact p-values and inexact p-values (e.g. p&lt;0.05). All the inexact p-values were reassigned to six intervals in order to calculate the proportion of significant results (Table A in S1 Text). Due to the ubiquitous use of 0.05 as the alpha level in ecology, we considered p-values below this level as significant. <br>
DOI: 10.6084/m9.figshare.5786838.v1
title: P-values extracted from 11 scientific journals across two years

description: We examined how the proportion of reported significant results, expressed as p-values, changed with increasing impact factor (IF) We divided the range of IF into three intervals: low (IF&lt;4), medium (4≤IF&lt;8), and high (IF≥8) to ensure that our model was applicable to a broad range of impact factors. We then randomly selected at least two journals for each IF interval for both 2012 and 2014 from journals listed in the Science Citation Index Expanded (http://mjl.clarivate.com/cgi-bin/jrnlst/jloptions.cgi?PC=D) under four subject categories: biodiversity conservation, biology, ecology, and evolutionary biology. We examined 11 journals (lowest IF 0.36 to highest IF 17.95), six journals for both years, whilst we examined three for 2014 and two for 2012 alone. We collected p-values reported in all articles using the free trial version of Examine32 Text Search from Aquila Software. We extracted exact p-values and inexact p-values (e.g. p&lt;0.05). All the inexact p-values were reassigned to six intervals in order to calculate the proportion of significant results (Table A in S1 Text). Due to the ubiquitous use of 0.05 as the alpha level in ecology, we considered p-values below this level as significant. <br>
DOI: 10.6084/m9.figshare.12616766
title: Supplementary Tables

description: Supplementary Tables
DOI: 10.6084/m9.figshare.12616766.v3
title: Supplementary Tables

description: Supplementary Tables
DOI: 10.6084/m9.figshare.12616766.v2
title: Supplementary Tables

description: Supplementary Tables
DOI: 10.6084/m9.figshare.5786796
title: Boreholes_Shafts

description: No additional description
DOI: 10.6084/m9.figshare.5786796.v1
title: Boreholes_Shafts

description: No additional description
DOI: 10.6084/m9.figshare.5786730
title: Progressive Variable Focal Lens Example

description: This is a Zemax OpticStudio lens file associated with the technical note "Progressive lens approach to variable focus without moving parts in electronic imaging systems," by Ronian Siew (see reference below). To use this file, you must use the Zemax OpticStudio optical design program (at least version 16 and above). The lens is a simple aspheric element whose surface provides variable focal length. As the aperture stop is shifted vertically from Y = 0 mm to Y = 12 mm above the optic axis, the lens accommodates for an object at 250 mm to infinity. To shift the aperture stop, vary the "Decenter Y" parameter on Surface 4. To read the paper associated with this file, click the following link: https://dx.doi.org/10.6084/m9.figshare.5786733<br>
DOI: 10.6084/m9.figshare.5786727
title: Timelapse 5b - raw confocal files

description: See accompanying word documents<br><br>
DOI: 10.6084/m9.figshare.5786727.v2
title: Timelapse 5b - raw confocal files

description: See accompanying word documents<br><br>
DOI: 10.6084/m9.figshare.5786727.v1
title: Timelapse 5b - raw confocal files

description: See accompanying word documents<br><br>
DOI: 10.6084/m9.figshare.5786694
title: Supporting Data for Fig. 4 of "In vitro and in vivo phasor analysis of stoichiometry and pharmacokinetics using short lifetime near-infrared dyes and time-gated imaging"

description: This data is part of the manuscript "<i>In vitro </i>and<i> in vivo</i> phasor analysis of stoichiometry and pharmacokinetics using short lifetime near-infrared dyes and time-gated imaging" by Sez-Jade Chen, Nattawut Sinsuebphon, Alena Rudkouskaya, Margarida Barroso, Xavier Intes and Xavier Michalet<br>
DOI: 10.6084/m9.figshare.5786694.v2
title: Supporting Data for Fig. 4 of "In vitro and in vivo phasor analysis of stoichiometry and pharmacokinetics using short lifetime near-infrared dyes and time-gated imaging"

description: This data is part of the manuscript "<i>In vitro </i>and<i> in vivo</i> phasor analysis of stoichiometry and pharmacokinetics using short lifetime near-infrared dyes and time-gated imaging" by Sez-Jade Chen, Nattawut Sinsuebphon, Alena Rudkouskaya, Margarida Barroso, Xavier Intes and Xavier Michalet<br>
DOI: 10.6084/m9.figshare.5786694.v1
title: Supporting Data for Fig. 4 of "In vitro and in vivo phasor analysis of stoichiometry and pharmacokinetics using near-infrared dyes"

description: This data is part of the manuscript "In vitro and in vivo phasor analysis of stoichiometry and pharmacokinetics using near-infrared dyes" by Sez-Jade Chen, Nattawut Sinsuebphon, Alena Rudkouskaya, Margarida Barroso, Xavier Intes and Xavier Michalet<br>
DOI: 10.6084/m9.figshare.5786670
title: Simulated data and experimental data.xls

description: The spectra of the SF6 which measured by FTIR spectrometer with real background spectra.And the ruslts of the baseline correction methods for the simulated and experimental data are showed in the dataset.
DOI: 10.6084/m9.figshare.5786670.v1
title: Simulated data and experimental data.xls

description: The spectra of the SF6 which measured by FTIR spectrometer with real background spectra.And the ruslts of the baseline correction methods for the simulated and experimental data are showed in the dataset.
DOI: 10.6084/m9.figshare.5786667
title: Simulated data and experimental data.xls

description: The spectra of the SF6 which measured by FTIR spectrometer with real background spectra.And the ruslts of the baseline correction methods for the simulated and experimental data are showed in the dataset.
DOI: 10.6084/m9.figshare.5786634
title: New Analysis results

description: <br>X转录组证据<br>
DOI: 10.6084/m9.figshare.5786634.v1
title: New Analysis results

description: <br>X转录组证据<br>
DOI: 10.6084/m9.figshare.5786631
title: Detecting Code Smells using Machine Learning Techniques: Are We There Yet?

description: Code smells are symptoms of poor design and im- plementation choices weighing heavily on the quality of produced source code. During the last decades several code smell detection tools have been proposed. However, the literature shows that the results of these tools can be subjective and are intrinsically tied to the nature and approach of the detection. In a recent work the use of Machine-Learning (ML) techniques for code smell detection has been proposed, possibly solving the issue of tool subjectivity giving to a learner the ability to discern between smelly and non-smelly source code elements. While this work opened a new perspective for code smell detection, it only considered the case where instances affected by a single type smell are contained in each dataset used to train and test the machine learners. In this work we replicate the study with a different dataset configuration containing instances of more than one type of smell. The results reveal that with this configuration the machine learning techniques reveal critical limitations in the state of the art which deserve further research.<br>
DOI: 10.6084/m9.figshare.5786631.v1
title: Detecting Code Smells using Machine Learning Techniques: Are We There Yet?

description: Code smells are symptoms of poor design and implementation choices weighing heavily on the quality of produced source code. During the last decades several code smell detection tools have been proposed. However, literature shows that results of these tools can be subjective and are intrinsically tied to the nature and approach of the detection. In a recent work Arcelli Fontana et al. showed how Machine-Learning (ML) techniques can be effectively adopted for detecting and acting upon code smells, possibly solving the issue of tool subjectivity giving to a learner the ability to discern between smelly and non-smelly source code elements. While this work opened a new perspective for code smell detection, in the context of our research we found a number of possible limitations that might threaten the results of the study by Arcelli Fontana et al., namely: (i) the metric distribution of smelly elements, which strongly differs from the the one of non-smelly instances; (ii) the balance between smelly and non-smelly elements; (iii) the validation methodology, and (iv) the reliance on threshold metrics used to interpret the performance of the models. In this work, we start addressing these limitations by focusing on the first issue, i.e., trying to understanding whether the results of the study by Arcelli Fontana et al. are actually due to the distribution of the metrics of smelly and non-smelly source code elements in the dataset exploited by the reference study. Our findings show that the high performance achieved in the study by Arcelli Fontana et al. was in fact due to the specific dataset employed rather than the actual capabilities of machine-learning techniques for code smell detection.
DOI: 10.6084/m9.figshare.5786619
title: Class1

description: Image analysis using Fiji
DOI: 10.6084/m9.figshare.5786619.v1
title: Class1

description: Image analysis using Fiji
DOI: 10.6084/m9.figshare.5786586
title: DEGs qRT-PCR

description: DEGs qRT-PCR
DOI: 10.6084/m9.figshare.5786586.v1
title: DEGs qRT-PCR

description: DEGs qRT-PCR
DOI: 10.6084/m9.figshare.5786583
title: DEGs

description: DEGs
DOI: 10.6084/m9.figshare.5786583.v1
title: DEGs

description: DEGs
DOI: 10.6084/m9.figshare.5786577
title: subcluster

description: 8 <strong>subcluster</strong>
DOI: 10.6084/m9.figshare.5786577.v1
title: subcluster

description: 8 <strong>subcluster</strong>
DOI: 10.6084/m9.figshare.5786574
title: kegg

description: DEG_KEGG_pathway_enrichment
DOI: 10.6084/m9.figshare.5786574.v1
title: kegg

description: DEG_KEGG_pathway_enrichment
DOI: 10.6084/m9.figshare.5786538
title: Desarrollo cartografía detallada Angola.pdf

description: En la mayor parte del territorio angolano no existe cartografía detallada, lo que dificulta la gestión ciudades y áreas protegidas. Se presenta una metodología de bajo costo para desarrollar cartografía urbana y de áreas protegidas a escalas detallada con el fin de mejorara la gestión de estos territorios<br><br>
DOI: 10.6084/m9.figshare.5786538.v1
title: Desarrollo cartografía detallada Angola.pdf

description: En la mayor parte del territorio angolano no existe cartografía detallada, lo que dificulta la gestión ciudades y áreas protegidas. Se presenta una metodología de bajo costo para desarrollar cartografía urbana y de áreas protegidas a escalas detallada con el fin de mejorara la gestión de estos territorios<br><br>
DOI: 10.6084/m9.figshare.5786535
title: RWF9SvsRWF9SI.DEG_GO_enrichment_result_up.xls

description: GO_enrichment
DOI: 10.6084/m9.figshare.5786535.v1
title: RWF9SvsRWF9SI.DEG_GO_enrichment_result_up.xls

description: GO_enrichment
DOI: 10.6084/m9.figshare.5786532
title: RWF9SvsRWF9SI.DEG_GO_enrichment_result_down.xls

description: GO_enrichment
DOI: 10.6084/m9.figshare.5786532.v1
title: RWF9SvsRWF9SI.DEG_GO_enrichment_result_down.xls

description: GO_enrichment
DOI: 10.6084/m9.figshare.5786529
title: RWF9SvsRWF9SI.DEG_GO_enrichment_result_all.xls

description: GO_enrichment
DOI: 10.6084/m9.figshare.5786529.v1
title: RWF9SvsRWF9SI.DEG_GO_enrichment_result_all.xls

description: GO_enrichment
DOI: 10.6084/m9.figshare.5786526
title: RWF9SvsRWF9M.DEG_GO_enrichment_result_down.xls

description: GO_enrichment
DOI: 10.6084/m9.figshare.5786523
title: RWF9SvsRWF9M.DEG_GO_enrichment_result_up.xls

description: GO_enrichment
DOI: 10.6084/m9.figshare.5786523.v1
title: RWF9SvsRWF9M.DEG_GO_enrichment_result_up.xls

description: GO_enrichment
DOI: 10.6084/m9.figshare.5786520
title: RWF9SvsRWF9M.DEG_GO_enrichment_result_all.xls

description: GO_enrichment
DOI: 10.6084/m9.figshare.5786520.v1
title: RWF9SvsRWF9M.DEG_GO_enrichment_result_all.xls

description: GO_enrichment
DOI: 10.6084/m9.figshare.5786517
title: RWF9SIvsRWF9M.DEG_GO_enrichment_result_up.xls

description: GO_enrichment
DOI: 10.6084/m9.figshare.5786517.v1
title: RWF9SIvsRWF9M.DEG_GO_enrichment_result_up.xls

description: GO_enrichment
DOI: 10.6084/m9.figshare.5786511
title: RWF9SIvsRWF9M.DEG_GO_enrichment_result_all.xls

description: DEG_GOList
DOI: 10.6084/m9.figshare.5786511.v1
title: RWF9SIvsRWF9M.DEG_GO_enrichment_result_all.xls

description: DEG_GOList
DOI: 10.6084/m9.figshare.5786496
title: Alignments from "Evolutionary conservation of a core fungal phosphate homeostasis pathway tied to development in Blastocladiella emersonii"

description: Alignments used in phylogenetic tree reconstructions. Homologues of PHO proteins were identified in predicted proteomes using BLASTp (Altschul et al., 1997) and HMMer (Finn et al., 2011) homology searching algorithms. Proteins from diverse fungal predicted proteomes were considered orthologous when retrieved as reciprocal best hits when using S. cerevisiae PHO proteins as search queries. In some cases, (e.g. Pho4, Pho7, and Pho2 transcription factors) manual examination of alignments was used to identify putative orthologues based on sequence similarity or presence of unique motifs. In cases where orthologues could not be identified in a predicted proteome, tBLASTn was used to identify possible orthologues in corresponding genomes not identified during original annotations. In order to identify putative conserved phosphorylation motifs present in Pho4 orthologues, putative Pho4 proteins were collected from diverse fungal predicted proteomes. Pho4 proteins from more closely related species were aligned using MUSCLE (Edgar, 2004). These clade-specific alignments were then aligned to one another using the profile-profile alignment option in MUSCLE.
DOI: 10.6084/m9.figshare.5786496.v1
title: Alignments from "Evolutionary conservation of a core fungal phosphate homeostasis pathway tied to development in Blastocladiella emersonii"

description: Alignments used in phylogenetic tree reconstructions. Homologues of PHO proteins were identified in predicted proteomes using BLASTp (Altschul et al., 1997) and HMMer (Finn et al., 2011) homology searching algorithms. Proteins from diverse fungal predicted proteomes were considered orthologous when retrieved as reciprocal best hits when using S. cerevisiae PHO proteins as search queries. In some cases, (e.g. Pho4, Pho7, and Pho2 transcription factors) manual examination of alignments was used to identify putative orthologues based on sequence similarity or presence of unique motifs. In cases where orthologues could not be identified in a predicted proteome, tBLASTn was used to identify possible orthologues in corresponding genomes not identified during original annotations. In order to identify putative conserved phosphorylation motifs present in Pho4 orthologues, putative Pho4 proteins were collected from diverse fungal predicted proteomes. Pho4 proteins from more closely related species were aligned using MUSCLE (Edgar, 2004). These clade-specific alignments were then aligned to one another using the profile-profile alignment option in MUSCLE.
DOI: 10.6084/m9.figshare.5786484
title: Timelapse 5a - raw confocal files

description: See accompanying word documents<br><br>
DOI: 10.6084/m9.figshare.5786481
title: Timelapse 5a - Maximum intensity projections - bleach corrected

description: See accompanying word documents<br><br>
DOI: 10.6084/m9.figshare.5786481.v1
title: Timelapse 5a - Maximum intensity projections - bleach corrected

description: See accompanying word documents<br><br>
DOI: 10.6084/m9.figshare.5786475
title: Timelapse 5a - Maximum intensity projections

description: See accompanying word documents<br><br>
DOI: 10.6084/m9.figshare.5786475.v1
title: Timelapse 5a - Maximum intensity projections

description: See accompanying word documents<br><br>
DOI: 10.6084/m9.figshare.5786463
title: Chemically defined and growth-factor-free culture system for the expansion and derivation of human pluripotent stem cells

description: High resolution figures of "Chemically defined and growth-factor-free culture system for the expansion and derivation of human pluripotent stem cells" Nature Biomedical Engineering.
DOI: 10.6084/m9.figshare.5786463.v1
title: Chemically defined and growth-factor-free culture system for the expansion and derivation of human pluripotent stem cells

description: High resolution figures of "Chemically defined and growth-factor-free culture system for the expansion and derivation of human pluripotent stem cells" Nature Biomedical Engineering.
DOI: 10.6084/m9.figshare.5786457
title: Longitudinal Study

description: We examined whether a short training (eight weeks) in second-language (L2-English) to university students has any facilitative effects on their executive functions. One group received English language training for two months and a control group matched on age and background did not receive any training. We administered objective language task (object-naming) and executive function tasks (Flanker, Stroop and colour-shape switching task) before and after the course. We found that the group that received the training improved significantly on the colour-shape switching task but no improvements were found on the Stroop or the Flanker tasks. Their object-naming latency on English also became faster compared to the control group after the training. The control group’s performance was not different at these two time points. We conclude that even a short training in second-language can enhance some components of executive functions beyond improving language skills in young adult students. We discuss the results with reference to similar other training studies and the effect of language learning on cognitive aspects of neuroplasticity.
DOI: 10.6084/m9.figshare.5786457.v1
title: Longitudinal Study

description: We examined whether a short training (eight weeks) in second-language (L2-English) to university students has any facilitative effects on their executive functions. One group received English language training for two months and a control group matched on age and background did not receive any training. We administered objective language task (object-naming) and executive function tasks (Flanker, Stroop and colour-shape switching task) before and after the course. We found that the group that received the training improved significantly on the colour-shape switching task but no improvements were found on the Stroop or the Flanker tasks. Their object-naming latency on English also became faster compared to the control group after the training. The control group’s performance was not different at these two time points. We conclude that even a short training in second-language can enhance some components of executive functions beyond improving language skills in young adult students. We discuss the results with reference to similar other training studies and the effect of language learning on cognitive aspects of neuroplasticity.
DOI: 10.6084/m9.figshare.5786439
title: RHI_dataset

description: Results of Rubber Hand Illusion in 21 people with Parkinson's disease and 20 healthy controls
DOI: 10.6084/m9.figshare.5786394
title: MOESM7 of Systematic quantitative analysis of H2A and H2B variants by targeted proteomics

description: Additional file 7. PRM transition results. List of transitions used to quantify each monitored peptide. Precursor charge, fragment ion, light precursor m/z ratio, light product m/z ratio, light retention time are indicated.