cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4530866.v1
title: Chloroplast DNA variation in <i>Epipactis atrorubens</i> populations from northern Greece

description: <i>Epipactis</i> Zinn. is a highly diverse genus, with numerous taxa naturally occurring throughout Europe. While their morphological variability has resulted in contradictory opinions about their taxonomy, the knowledge of the genetic variation of many of its species is limited. Such an example is <i>E. atrorubens</i> in the Balkan Peninsula. In this work, the cpDNA variation of seven <i>E. atrorubens</i> populations from northern Greece and of one population from Germany has been investigated by means of PCR-RFLP markers. Two regions of the cpDNA were studied (<i>trn</i>H-<i>psb</i>A, <i>trn</i>L intron) and four PCR-RFLP markers were employed (<i>trn</i>H-<i>psb</i>A/<i>Hae</i>III, <i>trn</i>H-<i>psb</i>A/<i>Hinf</i>I, <i>trn</i>H-<i>psb</i>A/<i>Vsp</i>I, <i>trn</i>L/<i>Mbo</i>I), which have revealed variation in other <i>Epipactis</i> species. The results demonstrate limited genetic variability in the studied populations, as only one haplotype was present in all the populations (both Greek and German), with the exception of Mt. Menikion (Greece) where a second haplotype was also recorded. This limited variation may be attributed to the properties of the genetic markers involved, to the conserved status of the two cpDNA regions in this species or to factors related to the biology and evolutionary history of <i>E. atrorubens</i>. The presence of a second haplotype only in Mt. Menikion could be attributed to a hybridisation event in the past and/or to the potential existence of a glacial refugium on this mountain.
DOI: 10.6084/m9.figshare.4530863
title: Title

description: a description
DOI: 10.6084/m9.figshare.4530860
title: Antibiotic treatment patterns, costs, and resource utilization among patients with community acquired pneumonia: a US cohort study

description: <b>Objectives</b>: The current treatment options for patients with community-acquired pneumonia (CAP) often present a trade-off between the potential for treatment failure and safety concerns. We set out to investigate real-world outcomes associated with the use of currently available antimicrobial treatment options for CAP in both the outpatient and inpatient (non-intensive care unit [ICU]) settings. <b>Methods</b>: This claims-based retrospective study included adult patients diagnosed with CAP and treated with antibiotic therapies, including any oral fluoroquinolone, macrolide, or beta-lactam monotherapy in the outpatient setting, and intravenous (IV) levofloxacin or IV azithromycin/ceftriaxone in the inpatient setting. Generalized linear model (GLM) regression was used to determine total charges for inpatient stay, the length of stay, and days of inpatient therapy. For outpatients, rates of adverse events (AEs), treatment failure, and hospitalization were compared by type of initial antibiotic therapy using logistic regression multivariate models that controlled for baseline characteristics. <b>Results</b>: A total of 441,820 outpatients and 33,287 inpatients treated for CAP between 2007 and 2012 were included in this analysis. In the outpatient setting, fluoroquinolone therapy led to a higher rate of documented AEs (adjusted odds ratio [OR]: 1.23; 95% confidence interval [CI]: 1.20–1.25; p <b>Conclusion</b>: In both the inpatient and outpatient settings, the development of additional efficacious treatment options that have a reduced AE burden for patients with CAP may be warranted.
DOI: 10.6084/m9.figshare.4530863.v1
title: Title

description: a description
DOI: 10.6084/m9.figshare.4530857
title: Myeloperoxidase expression in human colonic mucosa is related to systemic oxidative balance in healthy subjects

description: <b>Objectives:</b> To improve understanding of the preclinical stage of colonic inflammation by exploring the existence of a link between early inflammatory changes in the colonic mucosa and the systemic redox balance. <b>Methods:</b> Clinical characteristics, a fasting blood draw, and mucosal biopsies from the right, left, and sigmoid-rectum colonic tracts collected from 28 healthy individuals (14/14 males/females) who underwent colonoscopy. Myeloperoxidase (MPO) positive cells infiltrating colonic mucosa specimens were assessed by immunohistochemistry, and patients divided into high or low MPO expressing cells/optical field groups (MPO<sup>high</sup> or MPO<sup>low</sup>, respectively).The systemic oxidative balance has been studied through derived-Reactive Oxygen Metabolites (d-ROMs), Biological Antioxidant Potential (BAP), and Lipoperoxide-cholesterol Oxidizing (LP-CHOLOX) tests on serum. <b>Results:</b> MPO<sup>high</sup> patients demonstrated an increased systemic oxidative stress compared to MPO<sup>low</sup> individuals (<i>P</i> = 0.035), especially when MPO is referred to the left-sided colonic mucosa (<i>P</i> = 0.007). MPO<sup>low</sup> subjects in the sigmoid-rectum showed a significant higher antioxidant capacity in the serum (<i>P</i> P = 0.044), and a decreasing gradient in MPO expression moving from the cecum to the rectum (ascendant, descendant, and sigmoid-rectum: 3.7 ± 2.8, 3.1 ± 1.7, and 1.4 ± 0.5, respectively, <i>P</i> = 0.012) were also found and discussed. <b>Discussion:</b> The study is the first demonstrating a connection between systemic redox balance and MPO expression in the colonic mucosa, according to the colonic tract and patient gender. Further research evaluating the MPO expression in the human colon and its relationship with pathological conditions could benefit from these results.
DOI: 10.6084/m9.figshare.4530860.v2
title: Antibiotic treatment patterns, costs, and resource utilization among patients with community acquired pneumonia: a US cohort study

description: <b>Objectives</b>: The current treatment options for patients with community-acquired pneumonia (CAP) often present a trade-off between the potential for treatment failure and safety concerns. We set out to investigate real-world outcomes associated with the use of currently available antimicrobial treatment options for CAP in both the outpatient and inpatient (non-intensive care unit [ICU]) settings. <b>Methods</b>: This claims-based retrospective study included adult patients diagnosed with CAP and treated with antibiotic therapies, including any oral fluoroquinolone, macrolide, or beta-lactam monotherapy in the outpatient setting, and intravenous (IV) levofloxacin or IV azithromycin/ceftriaxone in the inpatient setting. Generalized linear model (GLM) regression was used to determine total charges for inpatient stay, the length of stay, and days of inpatient therapy. For outpatients, rates of adverse events (AEs), treatment failure, and hospitalization were compared by type of initial antibiotic therapy using logistic regression multivariate models that controlled for baseline characteristics. <b>Results</b>: A total of 441,820 outpatients and 33,287 inpatients treated for CAP between 2007 and 2012 were included in this analysis. In the outpatient setting, fluoroquinolone therapy led to a higher rate of documented AEs (adjusted odds ratio [OR]: 1.23; 95% confidence interval [CI]: 1.20–1.25; p <b>Conclusion</b>: In both the inpatient and outpatient settings, the development of additional efficacious treatment options that have a reduced AE burden for patients with CAP may be warranted.
DOI: 10.6084/m9.figshare.4530857.v1
title: Myeloperoxidase expression in human colonic mucosa is related to systemic oxidative balance in healthy subjects

description: <b>Objectives:</b> To improve understanding of the preclinical stage of colonic inflammation by exploring the existence of a link between early inflammatory changes in the colonic mucosa and the systemic redox balance. <b>Methods:</b> Clinical characteristics, a fasting blood draw, and mucosal biopsies from the right, left, and sigmoid-rectum colonic tracts collected from 28 healthy individuals (14/14 males/females) who underwent colonoscopy. Myeloperoxidase (MPO) positive cells infiltrating colonic mucosa specimens were assessed by immunohistochemistry, and patients divided into high or low MPO expressing cells/optical field groups (MPO<sup>high</sup> or MPO<sup>low</sup>, respectively).The systemic oxidative balance has been studied through derived-Reactive Oxygen Metabolites (d-ROMs), Biological Antioxidant Potential (BAP), and Lipoperoxide-cholesterol Oxidizing (LP-CHOLOX) tests on serum. <b>Results:</b> MPO<sup>high</sup> patients demonstrated an increased systemic oxidative stress compared to MPO<sup>low</sup> individuals (<i>P</i> = 0.035), especially when MPO is referred to the left-sided colonic mucosa (<i>P</i> = 0.007). MPO<sup>low</sup> subjects in the sigmoid-rectum showed a significant higher antioxidant capacity in the serum (<i>P</i> P = 0.044), and a decreasing gradient in MPO expression moving from the cecum to the rectum (ascendant, descendant, and sigmoid-rectum: 3.7 ± 2.8, 3.1 ± 1.7, and 1.4 ± 0.5, respectively, <i>P</i> = 0.012) were also found and discussed. <b>Discussion:</b> The study is the first demonstrating a connection between systemic redox balance and MPO expression in the colonic mucosa, according to the colonic tract and patient gender. Further research evaluating the MPO expression in the human colon and its relationship with pathological conditions could benefit from these results.
DOI: 10.6084/m9.figshare.4530851
title: Files in the National Archives of Australia withheld from public access in 2016

description: This CSV file contains details of records held by the National Archives of Australia that were examined for release but withheld from public access in 2016. These files have an access status of 'Closed' in the NAA's online database.<br>The data of all files with an access status of 'Closed' was harvested from the NAA database on 9 January 2017. This was then filtered down to those with an access decision recorded sometime in 2016.<br>Similar datasets will be made available on an annual basis.<br>The fields in the CSV file are: barcode, control symbol, title, series, series title, contents dates, contents start year, contents end year, access status, access decision reasons (multiple values), access decision date (iso formatted).<br>The contents start year and end year have been parsed out of the original date string.<br>The access decision reasons are a list of the grounds on which access was withheld. These have been normalised to some extent to separate out references to multiple clauses of the Archives Act.
DOI: 10.6084/m9.figshare.4530839
title: Bird monitoring using the smartphone (iOS) application <i>Videography</i> for motion detection

description: <b>Capsule:</b> Automated monitoring of daily activity in birds can be facilitated by the use of a smartphone with video analysis software. <b>Aims:</b> To test the application of an iPhone 5 smartphone with video motion detection for monitoring birds remotely, transferring the data over a mobile network and extracting the data automatically. <b>Methods:</b> A customized bird feeder was used at an established feeding site where high visitor frequency provided a rigorous test of procedures. The application <i>Videography</i> was used to detect birds visiting the feeder. This runs advanced algorithms on the camera input to detect motion and trigger automated video recordings. <b>Results:</b> Recorded video was stored immediately in a cloud service or locally on the smartphone. The data were automatically processed using R-scripts, obviating the need for manual data entry prior to analysis. Bird visits to the feeder were distributed throughout the day, increasing rapidly after sunrise and ceasing before dusk. <b>Conclusions:</b> The system offered a novel and efficient means of automatically monitoring birds visiting a central place, and it would be suitable for close-up monitoring of birds that regularly visit the entrances of cavities, nests or feeding places.
DOI: 10.6084/m9.figshare.4530851.v1
title: Files in the National Archives of Australia withheld from public access in 2016

description: This CSV file contains details of records held by the National Archives of Australia that were examined for release but withheld from public access in 2016. These files have an access status of 'Closed' in the NAA's online database.<br>The data of all files with an access status of 'Closed' was harvested from the NAA database on 9 January 2017. This was then filtered down to those with an access decision recorded sometime in 2016.<br>Similar datasets will be made available on an annual basis.<br>The fields in the CSV file are: barcode, control symbol, title, series, series title, contents dates, contents start year, contents end year, access status, access decision reasons (multiple values), access decision date (iso formatted).<br>The contents start year and end year have been parsed out of the original date string.<br>The access decision reasons are a list of the grounds on which access was withheld. These have been normalised to some extent to separate out references to multiple clauses of the Archives Act.
DOI: 10.6084/m9.figshare.4530839.v1
title: Bird monitoring using the smartphone (iOS) application <i>Videography</i> for motion detection

description: <b>Capsule:</b> Automated monitoring of daily activity in birds can be facilitated by the use of a smartphone with video analysis software. <b>Aims:</b> To test the application of an iPhone 5 smartphone with video motion detection for monitoring birds remotely, transferring the data over a mobile network and extracting the data automatically. <b>Methods:</b> A customized bird feeder was used at an established feeding site where high visitor frequency provided a rigorous test of procedures. The application <i>Videography</i> was used to detect birds visiting the feeder. This runs advanced algorithms on the camera input to detect motion and trigger automated video recordings. <b>Results:</b> Recorded video was stored immediately in a cloud service or locally on the smartphone. The data were automatically processed using R-scripts, obviating the need for manual data entry prior to analysis. Bird visits to the feeder were distributed throughout the day, increasing rapidly after sunrise and ceasing before dusk. <b>Conclusions:</b> The system offered a novel and efficient means of automatically monitoring birds visiting a central place, and it would be suitable for close-up monitoring of birds that regularly visit the entrances of cavities, nests or feeding places.
DOI: 10.6084/m9.figshare.4530797
title: Supplementary Material for the paper "Learning Discriminative Features from Electroencephalography Recordings by Encoding Similarity Constraints" (ICASSP 2017)

description: Supplementary Material for the paper: Sebastian Stober: <i>"Learning Discriminative Features from Electroencephalography Recordings by Encoding Similarity Constraints."</i> In: Proceedings of the 42nd IEEE International Conference on Acoustics, Speech and Signal Processing<br>(ICASSP'17), 2017.<br>
DOI: 10.6084/m9.figshare.4530746
title: Reference used for the alignment

description: Sequence reference used to align the bisulfite sequencing.
DOI: 10.6084/m9.figshare.4530746.v1
title: Reference used for the alignment

description: Sequence reference used to align the bisulfite sequencing.
DOI: 10.6084/m9.figshare.4530740
title: Information on files

description: Information on the samples
DOI: 10.6084/m9.figshare.4530740.v1
title: Information on files

description: Information on the samples
DOI: 10.6084/m9.figshare.4530707
title: BAM and BAI files

description: Massively parallel deep sequencing of plasma cfDNA methylation in HCC and controls.
DOI: 10.6084/m9.figshare.4530683
title: FigShare (OLD/OUTDATED)

description: <br> Selective outcome reporting is a significant methodological concern in medicine leading to bias in clinical trial results. Comparisons between the outcomes reported in clinical trial registrations and those later published allow investigators to understand the extent to which selective reporting bias occurs among trialists. The purpose of this study is to examine the possibility of selective outcome reporting in randomized controlled trials (RCTs) published in high impact factor hematology journals. A PubMed search was conducted to identify randomized controlled trials (RCT) published in five hematology journals from 2010-2015. After screening, primary and secondary outcomes were recorded for each trial and then compared with outcomes prespecified in the trial’s registration. Comparisons were made to determine if pre-specified trial registry outcomes were changed in the published reports. Of 113 RCTs, 56 (49.6%) demonstrated major outcome discrepancies between registry and publication, totaling 119 major discrepant outcomes, the majority of which favored a statistically significant result. We found a high rate of discordance between registered and published outcomes in high impact factor hematology journals. In addition, a high proportion of outcome discrepancies favored publication of a statistically significant result, suggesting selective outcome reporting bias.
DOI: 10.6084/m9.figshare.4530683.v1
title: New draft item

description: <br> Selective outcome reporting is a significant methodological concern in medicine leading to bias in clinical trial results. Comparisons between the outcomes reported in clinical trial registrations and those later published allow investigators to understand the extent to which selective reporting bias occurs among trialists. The purpose of this study is to examine the possibility of selective outcome reporting in randomized controlled trials (RCTs) published in high impact factor hematology journals. A PubMed search was conducted to identify randomized controlled trials (RCT) published in five hematology journals from 2010-2015. After screening, primary and secondary outcomes were recorded for each trial and then compared with outcomes prespecified in the trial’s registration. Comparisons were made to determine if pre-specified trial registry outcomes were changed in the published reports. Of 113 RCTs, 56 (49.6%) demonstrated major outcome discrepancies between registry and publication, totaling 119 major discrepant outcomes, the majority of which favored a statistically significant result. We found a high rate of discordance between registered and published outcomes in high impact factor hematology journals. In addition, a high proportion of outcome discrepancies favored publication of a statistically significant result, suggesting selective outcome reporting bias.
DOI: 10.6084/m9.figshare.4530683.v3
title: FigShare (OLD/OUTDATED)

description: <br> Selective outcome reporting is a significant methodological concern in medicine leading to bias in clinical trial results. Comparisons between the outcomes reported in clinical trial registrations and those later published allow investigators to understand the extent to which selective reporting bias occurs among trialists. The purpose of this study is to examine the possibility of selective outcome reporting in randomized controlled trials (RCTs) published in high impact factor hematology journals. A PubMed search was conducted to identify randomized controlled trials (RCT) published in five hematology journals from 2010-2015. After screening, primary and secondary outcomes were recorded for each trial and then compared with outcomes prespecified in the trial’s registration. Comparisons were made to determine if pre-specified trial registry outcomes were changed in the published reports. Of 113 RCTs, 56 (49.6%) demonstrated major outcome discrepancies between registry and publication, totaling 119 major discrepant outcomes, the majority of which favored a statistically significant result. We found a high rate of discordance between registered and published outcomes in high impact factor hematology journals. In addition, a high proportion of outcome discrepancies favored publication of a statistically significant result, suggesting selective outcome reporting bias.
DOI: 10.6084/m9.figshare.4530683.v2
title: Evidence of selective reporting bias in hematology journals: a methodological review.

description: <br> Selective outcome reporting is a significant methodological concern in medicine leading to bias in clinical trial results. Comparisons between the outcomes reported in clinical trial registrations and those later published allow investigators to understand the extent to which selective reporting bias occurs among trialists. The purpose of this study is to examine the possibility of selective outcome reporting in randomized controlled trials (RCTs) published in high impact factor hematology journals. A PubMed search was conducted to identify randomized controlled trials (RCT) published in five hematology journals from 2010-2015. After screening, primary and secondary outcomes were recorded for each trial and then compared with outcomes prespecified in the trial’s registration. Comparisons were made to determine if pre-specified trial registry outcomes were changed in the published reports. Of 113 RCTs, 56 (49.6%) demonstrated major outcome discrepancies between registry and publication, totaling 119 major discrepant outcomes, the majority of which favored a statistically significant result. We found a high rate of discordance between registered and published outcomes in high impact factor hematology journals. In addition, a high proportion of outcome discrepancies favored publication of a statistically significant result, suggesting selective outcome reporting bias.
DOI: 10.6084/m9.figshare.4530647
title: RMM results

description: Data set for the clinical trial paper: "Rhythm-centred Music Making in Community Living Elderly: A randomized pilot study"
DOI: 10.6084/m9.figshare.4530524
title: Raw Dataset - Water Consumption Volumes in Eastern Nairobi

description: Raw data gathered on water consumption volumes for households in different socio-economic groups and neighbourhoods in Eastern Nairobi.
DOI: 10.6084/m9.figshare.4530500
title: Avoiding missing data biases in phylogenomic inference: an empirical study in the landfowl (Aves: Galliformes) - RAxML genetree bootstraps inferred from all UCE alignments

description: 500 RAxML genetrees estimated from each UCE alignment, used for downstream analyses in ASTRAL and ASTRID.<br>
DOI: 10.6084/m9.figshare.4530500.v2
title: Avoiding missing data biases in phylogenomic inference: an empirical study in the landfowl (Aves: Galliformes) - RAxML genetree bootstraps inferred from all UCE alignments

description: 500 RAxML genetrees estimated from each UCE alignment, used for downstream analyses in ASTRAL and ASTRID.<br>
DOI: 10.6084/m9.figshare.4530500.v1
title: Avoiding missing data biases in phylogenomic inference: an empirical study in the landfowl (Aves: Galliformes)

description: 500 RAxML genetrees estimated from each UCE alignment, used for downstream analyses in ASTRAL and ASTRID.<br>
DOI: 10.6084/m9.figshare.4530359
title: Is your dog empathic? Developing a Dog Emotional Reactivity Survey

description: Owners from Hungary (N=591) and from Germany (N=2283) were asked to rate their level of agreement on a 1-5 Likert scale with statements about the reactivity of their dogs to their emotions and to other dogs’ behaviour. We created two scales with satisfactory internal reliability: reactivity to the owner’s emotion and reactivity to other dogs’ behaviour. In addition we also examined how anthropomorphism, contagious yawning, attitude toward the dog are related to emotional reactivity in dogs as perceived by the owner, we examined how owners rate dog pictures.