cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4907066.v3
title: 3 - Agrogenom rooted gene phylogenies

description: 10774 rooted gene family trees.Obtained from unrooted gene trees (see project item #2) by two different means:- if the gene trees were multicopy, i.e. had several tips assigned to the same species: using TPMS combo rooting criterion minimizing species multiplicity (gene copy number) of clades and taxonomic depth of the anccesral node;<br>- if the gene tree was unicopy, i.e. had tips assigned at most one species: using Prunier reconciliation and rooting according to the most parsimonious transfer scenario.
DOI: 10.6084/m9.figshare.4906934
title: Supplementary material to BEH 3432

description: Data describing the associations in pilot whale groups by means of tables and sociograms.<br>
DOI: 10.6084/m9.figshare.4906934.v1
title: Supplementary material to BEH 3432

description: Data describing the associations in pilot whale groups by means of tables and sociograms.<br>
DOI: 10.6084/m9.figshare.4907009.v3
title: Ex vivo turtle cortex with visual stimulation [Shew Lab & Wessel Lab]

description: This data set was generated and analyzed for our paper, titled, "Adaptation towards scale-free dynamics improves cortical stimulus discrimination at the cost of reduced detection", published in PLOS Computational Biology.
DOI: 10.6084/m9.figshare.4906865
title: Multi-organ RNAseq Data

description: Raw and process multi-organ RNAseq datasets for use in a Genomics Data Carpentry workshop. Raw data was collected from the NCBI SRA, corresponding to the study conducted by Ruiz-Orera et al. (2015). Data was processed to create logical intermediate files to aid in keeping students on track.<br>The 'reference' directory contains the reference transcriptome of all RefSeq transcripts for the NCBI human genome.<br>The 'untrimmed_fastq' contains the raw FASTQ data for the human samples from this study, which are significantly subsetted to make them efficient for analysis during a workshop.<br>There is also a hidden '.backup' directory containing quality-trimmed and mapped files for each sample so they are available to aid student learning.
DOI: 10.6084/m9.figshare.4906817
title: Supplementary Material for: The Epigenetic Regulation of GATA4-Dependent Brain Natriuretic Peptide Expression during Alcohol Withdrawal

description: <b><i>Objective:</i></b> Natriuretic peptides participate in the collection of metabolic effects during alcohol withdrawal. Having witnessed modulation of other natriuretic peptides in alcohol-dependent patients during alcohol withdrawal, we were interested in the relation of brain natriuretic peptide (BNP) methylation with protein expression and craving in this longitudinal study. <b><i>Methods:</i></b> Ninety-nine male patients were compared to 101 healthy controls concerning epigenetic regulation and protein expression during detoxification treatment. <b><i>Results:</i></b> With BNP expression being GATA4 dependent, we observed a correlation of GATA4 binding site methylation and protein expression. BNP serum levels and Obsessive Compulsive Drinking Scale scores are significantly decreased during withdrawal. Focusing on the two CpGs that are between GATA transcription factor binding sites, statistical analysis revealed a reversely proportional methylation pattern, significantly increasing with ongoing detoxification and thereby supporting the observed serum level changes. <b><i>Conclusion:</i></b> Without the functional knowledge about regulation of BNP expression via the GATA transcription factor, it would have been easy to take the mean results of the global CpG data and propose a direct relationship between methylation and expression. Thus, these findings are a voice for functionally and mechanistically approved results. There was no causal relationship between protein expression levels and epigenetic changes. Further research is needed which includes protein expression and other approaches.
DOI: 10.6084/m9.figshare.4906805
title: I.0 - 47 Rhizobiaceae genome flat files

description: 47 EMBL formated genome sequence and annotation flat files; the dataset underlying Agrogenom phylogenomic database.<br>These sequences, their annotation and subsequences (e.g. CDSs) can be queried using fro them ACNUC sequence database 'agrogenom', which is freely accessible through the client tool Query; the name of the database ‘agrogenom’ must be typed in the top box, and the relevant password ‘LCSA’ must then be typed in the prompted box. <br>
DOI: 10.6084/m9.figshare.4906802
title: Supplementary Material for: Home-Based Physical Behavior in Late Stage Parkinson Disease Dementia: Differences between Cognitive Subtypes

description: <b><i>Background:</i></b> For the early diagnosis of Parkinson disease dementia (PDD), objective home-based tools are needed to quantify even mild stages of dysfunction of the activities of daily living (ADL). <b><i>Objectives:</i></b> In this pilot study, home-based physical behavior was assessed to examine whether it is possible to distinguish mild cognitive impairment (PD-MCI) from PDD. <b><i>Methods:</i></b> Fifty-five patients with mild to severe Parkinson disease (PD) participated in this cross-sectional study. Based on comprehensive neuropsychological testing, PD patients were classified as cognitively nonimpaired (PD-NC), PD-MCI or PDD. For physical behavior assessments, patients wore the accelerometer DynaPort® (McRoberts) for 3 days. Ordinal logistic regression models with continuous Y were applied to correct results for motor impairment and depressive symptoms. <b><i>Results:</i></b> After excluding 7 patients due to insufficient wearing time, 48 patients with a mean of 2 recorded days were analyzed (17 PD-NC, 22 PD-MCI, 9 PDD). ADL-impaired PDD patients showed fewer sedentary bouts than non-ADL-impaired PD-MCI (<i>p</i> = 0.01, odds ratio [OR] = 8.9, 95% confidence interval [CI] = 1.8-45.2) and PD-NC (<i>p</i> = 0.01, OR = 10.3, CI = 1.6-67.3) patients, as well as a longer sedentary bout length (PD-NC: <i>p = </i>0.02, OR = 0.1, CI = 0.02-0.65; PD-MCI: <i>p</i> = 0.02, OR = 0.14, CI = 0.03-0.69). These differences were mainly caused by fewer (PD-NC: <i>p</i> = 0.02, OR = 9.6, CI = 1.5-62.4; PD-MCI: <i>p</i> = 0.01, OR = 8.5, CI = 1.5-37.3) but longer sitting bouts (PD-NC: <i>p</i> = 0.03, OR = 0.12, CI = 0.02-0.80; PD-MCI: <i>p</i> = 0.04, OR = 0.19, CI = 0.04-0.93). Tests assessing executive function, visuoconstruction and attention correlated significantly with specific activity parameters (ρ ≥ 0.3; <i>p</i> &lt; 0.05). <b><i>Conclusion:</i></b> Objective assessment of physical behavior, in particular the detection of sedentary bouts, is a promising contributor to the discrimination between PD-MCI and PDD.
DOI: 10.6084/m9.figshare.4906817.v1
title: Supplementary Material for: The Epigenetic Regulation of GATA4-Dependent Brain Natriuretic Peptide Expression during Alcohol Withdrawal

description: <b><i>Objective:</i></b> Natriuretic peptides participate in the collection of metabolic effects during alcohol withdrawal. Having witnessed modulation of other natriuretic peptides in alcohol-dependent patients during alcohol withdrawal, we were interested in the relation of brain natriuretic peptide (BNP) methylation with protein expression and craving in this longitudinal study. <b><i>Methods:</i></b> Ninety-nine male patients were compared to 101 healthy controls concerning epigenetic regulation and protein expression during detoxification treatment. <b><i>Results:</i></b> With BNP expression being GATA4 dependent, we observed a correlation of GATA4 binding site methylation and protein expression. BNP serum levels and Obsessive Compulsive Drinking Scale scores are significantly decreased during withdrawal. Focusing on the two CpGs that are between GATA transcription factor binding sites, statistical analysis revealed a reversely proportional methylation pattern, significantly increasing with ongoing detoxification and thereby supporting the observed serum level changes. <b><i>Conclusion:</i></b> Without the functional knowledge about regulation of BNP expression via the GATA transcription factor, it would have been easy to take the mean results of the global CpG data and propose a direct relationship between methylation and expression. Thus, these findings are a voice for functionally and mechanistically approved results. There was no causal relationship between protein expression levels and epigenetic changes. Further research is needed which includes protein expression and other approaches.
DOI: 10.6084/m9.figshare.4906865.v1
title: Multi-organ RNAseq Data

description: Raw and process multi-organ RNAseq datasets for use in a Genomics Data Carpentry workshop. Raw data was collected from the NCBI SRA, corresponding to the study conducted by Ruiz-Orera et al. (2015). Data was processed to create logical intermediate files to aid in keeping students on track.
DOI: 10.6084/m9.figshare.4906802.v1
title: Supplementary Material for: Home-Based Physical Behavior in Late Stage Parkinson Disease Dementia: Differences between Cognitive Subtypes

description: <b><i>Background:</i></b> For the early diagnosis of Parkinson disease dementia (PDD), objective home-based tools are needed to quantify even mild stages of dysfunction of the activities of daily living (ADL). <b><i>Objectives:</i></b> In this pilot study, home-based physical behavior was assessed to examine whether it is possible to distinguish mild cognitive impairment (PD-MCI) from PDD. <b><i>Methods:</i></b> Fifty-five patients with mild to severe Parkinson disease (PD) participated in this cross-sectional study. Based on comprehensive neuropsychological testing, PD patients were classified as cognitively nonimpaired (PD-NC), PD-MCI or PDD. For physical behavior assessments, patients wore the accelerometer DynaPort® (McRoberts) for 3 days. Ordinal logistic regression models with continuous Y were applied to correct results for motor impairment and depressive symptoms. <b><i>Results:</i></b> After excluding 7 patients due to insufficient wearing time, 48 patients with a mean of 2 recorded days were analyzed (17 PD-NC, 22 PD-MCI, 9 PDD). ADL-impaired PDD patients showed fewer sedentary bouts than non-ADL-impaired PD-MCI (<i>p</i> = 0.01, odds ratio [OR] = 8.9, 95% confidence interval [CI] = 1.8-45.2) and PD-NC (<i>p</i> = 0.01, OR = 10.3, CI = 1.6-67.3) patients, as well as a longer sedentary bout length (PD-NC: <i>p = </i>0.02, OR = 0.1, CI = 0.02-0.65; PD-MCI: <i>p</i> = 0.02, OR = 0.14, CI = 0.03-0.69). These differences were mainly caused by fewer (PD-NC: <i>p</i> = 0.02, OR = 9.6, CI = 1.5-62.4; PD-MCI: <i>p</i> = 0.01, OR = 8.5, CI = 1.5-37.3) but longer sitting bouts (PD-NC: <i>p</i> = 0.03, OR = 0.12, CI = 0.02-0.80; PD-MCI: <i>p</i> = 0.04, OR = 0.19, CI = 0.04-0.93). Tests assessing executive function, visuoconstruction and attention correlated significantly with specific activity parameters (ρ ≥ 0.3; <i>p</i> &lt; 0.05). <b><i>Conclusion:</i></b> Objective assessment of physical behavior, in particular the detection of sedentary bouts, is a promising contributor to the discrimination between PD-MCI and PDD.
DOI: 10.6084/m9.figshare.4906805.v1
title: 47 Rhizobiaceae genome flat files

description: 47 EMBL formated genome sequence and annotation flat files; the dataset underlying Agrogenom phylogenomic database.
DOI: 10.6084/m9.figshare.4906865.v3
title: Multi-organ RNAseq Data

description: Raw and process multi-organ RNAseq datasets for use in a Genomics Data Carpentry workshop. Raw data was collected from the NCBI SRA, corresponding to the study conducted by Ruiz-Orera et al. (2015). Data was processed to create logical intermediate files to aid in keeping students on track.<br>The 'reference' directory contains the reference transcriptome of all RefSeq transcripts for the NCBI human genome.<br>The 'untrimmed_fastq' contains the raw FASTQ data for the human samples from this study, which are significantly subsetted to make them efficient for analysis during a workshop.<br>There is also a hidden '.backup' directory containing quality-trimmed and mapped files for each sample so they are available to aid student learning.
DOI: 10.6084/m9.figshare.4906757
title: Effort-Oriented Methods and Tools for Software Development and Maintenance for Mobile Apps

description: Gemma Catolino - Doctorial Symposium ICSE 2018
DOI: 10.6084/m9.figshare.4906760
title: Supplementary Material for: Cutaneous Complications Related to Tattoos: 31 Cases from Finland

description: <b><i>Background:</i></b> Cutaneous complications related to permanent tattoos affect 2-30% of those patients who have tattooed their skin. Little is known about the cases of tattoo complications in Finland. <b><i>Objective:</i></b> The aim of this study was to conduct a retrospective review of a series of Finnish patients with cutaneous tattoo reactions. <b><i>Methods:</i></b> We collected cases of tattoo reactions from the Department of Dermatology at Helsinki University Central Hospital, from members of the Finnish dermatological society and from various other sources (author's private practice, tattooists, professional internet forum). We analysed the demographics, clinical presentation, diagnosis, and microscopic findings on the skin biopsies, and evaluated the therapeutic outcome. <b><i>Results:</i></b> Thirty-one patients (16 men and 15 women, mean age 37.8) were included from 9 cities, mainly from Helsinki. Fifty-two percent (16/31) presented with an allergic tattoo reaction mainly against the red colour (75%, 12/16). Reactions were clinically polymorph ranging from scattered papules or nodules to complete infiltration of a colour. Lesions were itchy and sometimes painful. The reactions were lichenoid, granulomatous, pseudolymphomatous or less specific with a dermal lympho-histiocytic or plasmocytic infiltrate. Other diagnoses included tattoo blow-out (13%), melanoma within a tattoo, naevi within a tattoo (10% each), lichen planus (6%), granulomatous reaction with uveitis, sarcoidosis and dermatofibroma (3% each). Allergic tattoo reactions were mainly treated with local corticosteroid (CS) ointments, CS infiltration or surgical removal. <b><i>Conclusion:</i></b> This review is the largest series of tattoo complications in the Baltic area. It illustrates the wide spectrum of complications. Prospective, controlled therapeutic studies are necessary to assess the best treatment protocols for tattoo allergies and tattoo reaction management in general.
DOI: 10.6084/m9.figshare.4906805.v3
title: I.0 - 47 Rhizobiaceae genome flat files

description: 47 EMBL formated genome sequence and annotation flat files; the dataset underlying Agrogenom phylogenomic database.<br>These sequences, their annotation and subsequences (e.g. CDSs) can be queried using fro them ACNUC sequence database 'agrogenom', which is freely accessible through the client tool Query; the name of the database ‘agrogenom’ must be typed in the top box, and the relevant password ‘LCSA’ must then be typed in the prompted box. <br>
DOI: 10.6084/m9.figshare.4906865.v2
title: Multi-organ RNAseq Data

description: Raw and process multi-organ RNAseq datasets for use in a Genomics Data Carpentry workshop. Raw data was collected from the NCBI SRA, corresponding to the study conducted by Ruiz-Orera et al. (2015). Data was processed to create logical intermediate files to aid in keeping students on track.<br>The 'reference' directory contains the reference transcriptome of all RefSeq transcripts for the NCBI human genome.<br>The 'untrimmed_fastq' contains the raw FASTQ data for the human samples from this study, which are significantly subsetted to make them efficient for analysis during a workshop.<br>There is also a hidden '.backup' directory containing quality-trimmed and mapped files for each sample so they are available to aid student learning.
DOI: 10.6084/m9.figshare.4906745
title: Reproducible results for: Evidence for widespread dysregulation of circadian clock progression in human cancer

description: The zip file contains all code, data, results, and figures.<br>The tar file is a docker image that was generated from "Dockerfile" (see the log file) and contains the entire computing environment to reproduce the analysis. Load the image and start the container using the following commands:$ docker load &lt; circadian_clock_cancer.tar$ docker run -it circadian_clock_cancer
DOI: 10.6084/m9.figshare.4906760.v1
title: Supplementary Material for: Cutaneous Complications Related to Tattoos: 31 Cases from Finland

description: <b><i>Background:</i></b> Cutaneous complications related to permanent tattoos affect 2-30% of those patients who have tattooed their skin. Little is known about the cases of tattoo complications in Finland. <b><i>Objective:</i></b> The aim of this study was to conduct a retrospective review of a series of Finnish patients with cutaneous tattoo reactions. <b><i>Methods:</i></b> We collected cases of tattoo reactions from the Department of Dermatology at Helsinki University Central Hospital, from members of the Finnish dermatological society and from various other sources (author's private practice, tattooists, professional internet forum). We analysed the demographics, clinical presentation, diagnosis, and microscopic findings on the skin biopsies, and evaluated the therapeutic outcome. <b><i>Results:</i></b> Thirty-one patients (16 men and 15 women, mean age 37.8) were included from 9 cities, mainly from Helsinki. Fifty-two percent (16/31) presented with an allergic tattoo reaction mainly against the red colour (75%, 12/16). Reactions were clinically polymorph ranging from scattered papules or nodules to complete infiltration of a colour. Lesions were itchy and sometimes painful. The reactions were lichenoid, granulomatous, pseudolymphomatous or less specific with a dermal lympho-histiocytic or plasmocytic infiltrate. Other diagnoses included tattoo blow-out (13%), melanoma within a tattoo, naevi within a tattoo (10% each), lichen planus (6%), granulomatous reaction with uveitis, sarcoidosis and dermatofibroma (3% each). Allergic tattoo reactions were mainly treated with local corticosteroid (CS) ointments, CS infiltration or surgical removal. <b><i>Conclusion:</i></b> This review is the largest series of tattoo complications in the Baltic area. It illustrates the wide spectrum of complications. Prospective, controlled therapeutic studies are necessary to assess the best treatment protocols for tattoo allergies and tattoo reaction management in general.
DOI: 10.6084/m9.figshare.4906805.v2
title: 0 - 47 Rhizobiaceae genome flat files

description: 47 EMBL formated genome sequence and annotation flat files; the dataset underlying Agrogenom phylogenomic database.
DOI: 10.6084/m9.figshare.4906727
title: Spitschan_2017_PNAS

description: Complete raw dataset for the referenced paper
DOI: 10.6084/m9.figshare.4906736
title: Electromagnetic optimization of corrugated metallic sheets for maximum power focusing

description: We present full-wave electromagnetic optimization of corrugated metallic sheets to achieve maximum power focusing at desired locations when illuminated by plane waves. The corrugations are freely applied by moving the discretization nodes, leading to huge optimization spaces that are scanned by employing genetic algorithms. The required simulations are performed accurately and efficiently via the method of moments or the multilevel fast multipole algorithm. Hundreds of thousands of simulations are performed to demonstrate the feasibility of strong optical focusing, even with relatively small sheets in terms of wavelength. The corrugated sheets can be useful in various applications, such as energy harvesting, solar cells, imaging, and optical sensing.
DOI: 10.6084/m9.figshare.4906757.v3
title: Effort-Oriented Methods and Tools for Software Development and Maintenance for Mobile Apps

description: Gemma Catolino - Doctorial Symposium ICSE 2018
DOI: 10.6084/m9.figshare.4906757.v2
title: Better safe than sorry! A Set of Metrics for Early Effort Estimation of Mobile Apps

description: We present a study carried out to identify a set of metrics to early estimate the development effort of mobile apps
DOI: 10.6084/m9.figshare.12906485
title: Data Giroux 2020.xlsx

description: Embodiment and kinaesthesia scores (speed, duration) from two experiments (Giroux et al)
DOI: 10.6084/m9.figshare.4906727.v1
title: Spitschan_2017_NatureNeuro_fMRIMelanopsin

description: Complete raw dataset for the referenced paper
DOI: 10.6084/m9.figshare.4906634
title: Local genes for local bacteria: evidence of allopatry in the genomes of transatlantic Campylobacter populations

description: Assembled genomes used in Pascoe et al (2017) Local genes for local bacteria: evidence of allopatry in the genomes of transatlantic <i>Campylobacter </i>populations.
DOI: 10.6084/m9.figshare.4906727.v2
title: Spitschan_2017_NatureNeuro_fMRIMelanopsin

description: Complete raw dataset for the referenced paper
DOI: 10.6084/m9.figshare.4906634.v1
title: Local genes for local bacteria: evidence of allopatry in the genomes of transatlantic Campylobacter populations

description: Assembled genomes used in Pascoe et al (2017) Local genes for local bacteria: evidence of allopatry in the genomes of transatlantic <i>Campylobacter </i>populations.
DOI: 10.6084/m9.figshare.4906727.v4
title: Spitschan_2017_NatureNeuro_fMRIMelanopsin

description: Complete raw dataset for the referenced paper
DOI: 10.6084/m9.figshare.4906451
title: StrainSeeker database k=32

description: StrainSeeker database built with <i>k</i>-mer length 32. Contains 4,324 bacterial and archaeal refererence genomes from NCBI RefSeq.
DOI: 10.6084/m9.figshare.4906451.v1
title: StrainSeeker database k=32

description: StrainSeeker database built with <i>k</i>-mer length 32. Contains 4,324 bacterial and archaeal refererence genomes from NCBI RefSeq.
DOI: 10.6084/m9.figshare.4906727.v5
title: Spitschan_2017_NatureNeuro_fMRIMelanopsin

description: Complete raw dataset for the referenced paper
DOI: 10.6084/m9.figshare.4906427
title: Strainseeker database k=16

description: StrainSeeker database built with <i>k</i>-mer length 16. Contains 4,324 bacterial and archaeal refererence genomes from NCBI RefSeq.
DOI: 10.6084/m9.figshare.4906436
title: Peptide Lists for crude surface membrane, transverse tubules, triads and sarcolemma.

description: This file is supplementary to "Mass spectrometric identification of dystrophin, the protein product of the Duchenne muscular dystrophy gene, in distinct muscle surface membranes" which has been provisionally accepted by the International Journal of Molecular Medicine. The excel files show the peptide sequences for proteins identified from on-membrane digestion of crude surface membranes, triads, transverse tubules and purified sarcolemma (from rabbit skeletal muscle).
DOI: 10.6084/m9.figshare.4906727.v6
title: Spitschan_2017_NatureNeuro_fMRIMelanopsin

description: Complete raw dataset for the referenced paper
DOI: 10.6084/m9.figshare.4906427.v2
title: Strainseeker database k=16

description: StrainSeeker database built with <i>k</i>-mer length 16. Contains 4,324 bacterial and archaeal refererence genomes from NCBI RefSeq.
DOI: 10.6084/m9.figshare.4906436.v1
title: Peptide Lists for crude surface membrane, transverse tubules, triads and sarcolemma.

description: This file is supplementary to "Mass spectrometric identification of dystrophin, the protein product of the Duchenne muscular dystrophy gene, in distinct muscle surface membranes" which has been provisionally accepted by the International Journal of Molecular Medicine. The excel files show the peptide sequences for proteins identified from on-membrane digestion of crude surface membranes, triads, transverse tubules and purified sarcolemma (from rabbit skeletal muscle).
DOI: 10.6084/m9.figshare.4906727.v7
title: Spitschan_2017_NatureNeuro_fMRIMelanopsin

description: Complete raw dataset for the referenced paper
DOI: 10.6084/m9.figshare.4906427.v1
title: ss_db_w16.tar.gz

description: StrainSeeker database built with <i>k</i>-mer length 16. Contains 4,324 bacterial and archaeal refererence genomes from NCBI RefSeq.
DOI: 10.6084/m9.figshare.4906727.v8
title: Spitschan_2017_NatureNeuro_fMRIMelanopsin

description: Complete raw dataset for the referenced paper