cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5278102.v1
title: MacMillan.et.al.2017.Sci.Rep.Supplementary.Datasets.zip

description: This .zip file contains supplementary data and images accompanying MacMillan et al. (2017) <b>Thermal acclimation mitigates paracellular leak from the <i>Drosophila</i> gut. </b>Published in Scientific Reports.<br>For detailed descriptions of methods and analyses performed please see the main manuscript.<br><b>This archive contains:</b>1) An excel file containing supplementary datasets that is organized into tabs by experiment.2) A set of TEM images.3) A set of immunoblot images.4) A set of tissue damage images (Live/Dead cell staining).
DOI: 10.6084/m9.figshare.5278111.v1
title: MiSeq Analysis of on-target editing in vivo and in vitro

description: Next-generation sequencing (NGS; MiSeq) analysis of on-target editing evaluating deletions and insertions (indels) in the CRISPR-HTT group in vitro and in vivo.The files give for each read, the CIGAR string and whether indels were detected closed to expected cleavage site or not.
DOI: 10.6084/m9.figshare.5278069
title: Sample Size Estimation for On-Site Creel Surveys

description: Conducting sample size analysis is important to ensure that sample sizes are adequate to meet objectives for precision but not so large that valuable resources are wasted. When simple survey designs are used, sample size analysis is straightforward. However, creel surveys often follow complex designs that can make sample size estimation difficult. The objectives of this study were to provide sample size estimators for commonly used creel survey designs and investigate sample size requirements to achieve varying levels of precision. For estimates of angling effort, the average sample size among fisheries required to achieve relative 95% confidence intervals of 40% (i.e., coefficient of variation of approximately 0.2) was 16 d (range = 7–40 d). To estimate mean catch rate with the same level of precision, 43 survey days (range = 8–95 d) were required when the daily catch rate estimator was used, and 11 d (range = 3–30 d) were required when the multi-day estimator was used. Fifty-five days (range = 14–89 d) and 57 d (range = 19–140 d) were required to estimate total catch with relative 95% confidence intervals of 40% when the daily and multi-day estimators were used, respectively. Although absolute precision will vary among fisheries, our results suggest that approximately 30 d of surveying may serve as a reasonable starting point for planning creel surveys when no prior information is available on expected sample variance, as relatively large increases in sample size beyond 30 d were needed to achieve relatively small increases in precision. Received February 14, 2017; accepted June 9, 2017 Published online August 4, 2017
DOI: 10.6084/m9.figshare.5278069.v1
title: Sample Size Estimation for On-Site Creel Surveys

description: Conducting sample size analysis is important to ensure that sample sizes are adequate to meet objectives for precision but not so large that valuable resources are wasted. When simple survey designs are used, sample size analysis is straightforward. However, creel surveys often follow complex designs that can make sample size estimation difficult. The objectives of this study were to provide sample size estimators for commonly used creel survey designs and investigate sample size requirements to achieve varying levels of precision. For estimates of angling effort, the average sample size among fisheries required to achieve relative 95% confidence intervals of 40% (i.e., coefficient of variation of approximately 0.2) was 16 d (range = 7–40 d). To estimate mean catch rate with the same level of precision, 43 survey days (range = 8–95 d) were required when the daily catch rate estimator was used, and 11 d (range = 3–30 d) were required when the multi-day estimator was used. Fifty-five days (range = 14–89 d) and 57 d (range = 19–140 d) were required to estimate total catch with relative 95% confidence intervals of 40% when the daily and multi-day estimators were used, respectively. Although absolute precision will vary among fisheries, our results suggest that approximately 30 d of surveying may serve as a reasonable starting point for planning creel surveys when no prior information is available on expected sample variance, as relatively large increases in sample size beyond 30 d were needed to achieve relatively small increases in precision. Received February 14, 2017; accepted June 9, 2017 Published online August 4, 2017
DOI: 10.6084/m9.figshare.5277967.v1
title: Perturbations in the A<sup>1</sup>Π, <i>v</i> = 0 state of <sup>12</sup>C<sup>18</sup>O investigated via complementary spectroscopic techniques

description: The A<sup>1</sup>Π(<i>v</i> = 0) level of <sup>12</sup>C<sup>18</sup>O has been reinvestigated using three different high-resolution spectroscopic methods: (1) 2 + 1′ resonance-enhanced multiphoton ionisation of the A<sup>1</sup>Π − X<sup>1</sup>Σ<sup>+</sup>(0, 0) band using narrowband lasers in a Doppler-free geometry; (2) Fourier-transform emission spectroscopy in the visible range probing the B<sup>1</sup>Σ<sup>+</sup> − A<sup>1</sup>Π(0, 0) band in a discharge; (3) Fourier-transform absorption spectroscopy in the vacuum-ultraviolet range measuring the A<sup>1</sup>Π − X<sup>1</sup>Σ<sup>+</sup>(0, 0) and B<sup>1</sup>Σ<sup>+</sup> − X<sup>1</sup>Σ<sup>+</sup>(0, 0) bands at multiple temperatures ranging from 90 to 900 K. An effective-Hamiltonian analysis of A<sup>1</sup>Π, <i>v</i> = 0 levels was performed up to <i>J</i> = 44 which quantitatively addresses perturbations by the e <sup>3</sup>Σ<sup>−</sup>(<i>v</i> = 1), d<sup>3</sup>Δ(<i>v</i> = 4), a′<sup>3</sup>Σ<sup>+</sup>(<i>v</i> = 9), D <sup>1</sup>Δ(<i>v</i> = 0), and I <sup>1</sup>Σ<sup>−</sup>(<i>v</i> = 0, 1) levels.
DOI: 10.6084/m9.figshare.5277907
title: Medical expulsive therapy in urolithiasis: a mixed treatment comparison network meta-analysis of randomized controlled clinical trials

description: <b>Background</b>: Medical expulsive therapy (MET) using alpha blockers, calcium channel blockers (CCB), phosphodiesterase inhibitors (PDEI) and spasmolytics have been shown to be effective in clinical trials on urolithiasis. The present study is a network meta-analysis comparing the above mentioned drug classes. <b>Research design and methods</b>: Electronic databases were searched for randomized controlled trials comparing the above mentioned drug classes in patients with urolithiasis using appropriate search strategy. Inverse variance heterogeneity model was used for the mixed treatment comparisons. Stone expulsion rate (SER) was the primary and stone expulsion time (SET) was the main secondary outcome measure. <b>Results</b>: We included a total of 114 studies for systematic review and 108 studies for the network meta-analysis. Alpha blockers, PDEI, and combined alpha blockers and corticosteroids had significantly increased SER and shorter SET than placebo or standard of care. Alpha blockers have the highest probability of being the ‘best’ in the pool with regard to SER. This effect persisted in patients with stones ≥ 5 mm, children, after shockwave lithotripsy, proximal ureteric stones and distal ureteric stones. <b>Conclusion</b>: To conclude, we observed a statistically significant increase in the expulsion rate and shorter expulsion time with alpha blockers, PDEI and combined alpha blockers with corticosteroids. Of these interventions, alpha blockers have the high probability of being the ‘best’.
DOI: 10.6084/m9.figshare.5277907.v1
title: Medical expulsive therapy in urolithiasis: a mixed treatment comparison network meta-analysis of randomized controlled clinical trials

description: <b>Background</b>: Medical expulsive therapy (MET) using alpha blockers, calcium channel blockers (CCB), phosphodiesterase inhibitors (PDEI) and spasmolytics have been shown to be effective in clinical trials on urolithiasis. The present study is a network meta-analysis comparing the above mentioned drug classes. <b>Research design and methods</b>: Electronic databases were searched for randomized controlled trials comparing the above mentioned drug classes in patients with urolithiasis using appropriate search strategy. Inverse variance heterogeneity model was used for the mixed treatment comparisons. Stone expulsion rate (SER) was the primary and stone expulsion time (SET) was the main secondary outcome measure. <b>Results</b>: We included a total of 114 studies for systematic review and 108 studies for the network meta-analysis. Alpha blockers, PDEI, and combined alpha blockers and corticosteroids had significantly increased SER and shorter SET than placebo or standard of care. Alpha blockers have the highest probability of being the ‘best’ in the pool with regard to SER. This effect persisted in patients with stones ≥ 5 mm, children, after shockwave lithotripsy, proximal ureteric stones and distal ureteric stones. <b>Conclusion</b>: To conclude, we observed a statistically significant increase in the expulsion rate and shorter expulsion time with alpha blockers, PDEI and combined alpha blockers with corticosteroids. Of these interventions, alpha blockers have the high probability of being the ‘best’.
DOI: 10.6084/m9.figshare.5277763
title: Data_IronMeteorites.zipData set for the publication "Multi-stage core formation in planetesimals revealed by numerical modeling and Hf-W chronometry of iron meteorites" by Neumann et al.

description: Data sets for the reproduction of the figures from Neumann et al. (2017).<br>
DOI: 10.6084/m9.figshare.5277763.v1
title: Data_IronMeteorites.zipData set for the publication "Multi-stage core formation in planetesimals revealed by numerical modeling and Hf-W chronometry of iron meteorites" by Neumann et al.

description: Data sets for the reproduction of the figures from Neumann et al. (2017).<br>
DOI: 10.6084/m9.figshare.5277745
title: Supplementary Material for: Effectiveness of Florbetapir PET Imaging in Changing Patient Management

description: <b><i>Aims:</i></b> To evaluate the impact of amyloid PET imaging on diagnosis and patient management in a multicenter, randomized, controlled study. <b><i>Methods:</i></b> Physicians identified patients seeking a diagnosis for mild cognitive impairment or dementia, possibly due to Alzheimer disease (AD), and recorded a working diagnosis and a management plan. The patients underwent florbetapir PET scanning and were randomized to either immediate or delayed (1-year) feedback regarding amyloid status. At the 3-month visit, the physician updated the diagnosis and recorded a summary of the actual patient management since the post-scan visit. The study examined the impact of immediate versus delayed feedback on patient diagnosis/management at 3 and 12 months. <b><i>Results:</i></b> A total of 618 subjects were randomized (1:1) to immediate or delayed feedback arms, and 602 subjects completed the 3-month primary endpoint visit. A higher proportion of patients in the immediate feedback arm showed a change in diagnosis compared to the controls (32.6 vs. 6.4%; <i>p</i> = 0.0001). Similarly, a higher proportion of patients receiving immediate feedback had a change in management plan (68 vs. 55.5%; <i>p</i> &lt; 0.002), mainly driven by changes in AD medication. Specifically, acetylcholinesterase inhibitors were prescribed to 67% of the amyloid-positive and 27% of the amyloid-negative subjects in the information group compared with 56 and 43%, respectively, in the control group (<i>p</i> &lt; 0.0001). These between-group differences persisted until the 12-month visit. <b><i>Conclusion:</i></b> Knowledge of the amyloid status affects the diagnosis and alters patient management.
DOI: 10.6084/m9.figshare.5277751
title: Effects of short-term flooding on aquatic and terrestrial micro-eukaryotic communities – a mesocosm approach

description: This dataset comprise the detailed sample descripton, OTU sequences and abundance matrix of the study:<br><br>Graupner, N., Röhl, O., Jensen, M., Beisser, D., Begerow, D., Boenigk, J. Effects of short-term flooding on aquatic and terrestrial micro-eukaryotic communities – a mesocosm approach. Aquatic Microbial Ecology (submitted).<br><br>The study aimed on on identifying the effects of short-term flooding on the micro-eukaryotic communities of both habitat types, freshwater and soil. As flooding provide one possible route for the organismic exchange, we focused besides the general community patters on the immigration of allochtonous taxa.<br><br>Experiments were conducted in mesocosms called AquaFlows for a duration of 14 days. In three of six AquaFlow systems we simulated at the beginning of the experiment a 24 hour flooding. The other three AquaFlow systems were not flooded throughout the whole experiment. Investigations of the micro-eukaryotic communities are based on amplicon diversity (v9 region of 18S SSU and ITS1). <br>
DOI: 10.6084/m9.figshare.5277742
title: ORDINAMENTO TOPOGRAFICO DELLA LIBRERIA DI GABRIELLO RICCARDI, di Guglielmo Bartoletti

description: Ordinamento topografico della Libreria di Gabriello Riccardi<br>(Appendice all'interno del volume: <b>Guglielmo Bartoletti, <i>La Libreria privata del Marchese Suddecano Gabriello Riccardi. Il fondo manoscritti</i>, Firenze, Firenze University Press, 2017</b>)<br><i><b>Legenda dell’inventario topografico</b></i><b>Collocazione</b>: si tratta di due numeri romani indicanti rispettivamente lo scaffale e il palchetto della segnatura della Libreria di Gabriello.<b>Numero: </b>è il terzo elemento della segnatura della Libreria di Gabriello, costituito da un numero arabo a correre dal 1 a 1239; seguono ad esso dei numeri convenzionali che indicano le successive tappe di incremento di tale Libreria.<b>bis</b>: si tratta dell’indicazione di una singola parte del manoscritto, nel caso in cui manoscritti di provenienza diversa fossero stati rilegati in unico volume da Gabriello.<b>Titolo</b>: è l’espressione che troviamo sul dorso originale per indicare il contenuto del volume; nel caso frequente in cui sia andato perduto, lo abbiamo sostituito, riadattandolo in parte, con l’espressione usata dall’Inventario e stima del 1810 per descrivere il medesimo manoscritto.<b>O. D. R. T</b>: si tratta della segnalazione che l’ultimo numero della segnatura di Gabriello, quello arabo, è riportato anche sul manoscritto stesso in varia forma: O = in forma originale; D = sul dorso; R = riportato da mano successiva; T = vi è rimasta solo una traccia.<b>Indici</b>: si tratta della persona che eventualmente redatto l’indice sul manoscritto stesso. Gabriello stesso o il Mehus.<b>Legatura</b>: è l’indicazione che si tratta di una legatura eseguita dal legatore di fiducia di Gabriello, Giuseppe Pagani; la sigla P indica che la legatura è attribuibile al Pagani per confronto, la sigla B significa che l’indicazione compare nella tesi di laurea di G. Bani.<b>Bullettone</b>: si indica quando il manoscritto è descritto nel catalogo alfabetico della Libreria di Gabriello, noto come “Bullettone”.<b>Mehus</b>: indica la presenza di quel manoscritto negli spogli del Mehus.<b>F/R</b>: indica che la segnatura di Gabriello è riportata, accanto alla nuova nelle illustrazioni di codici rispettivamente del Fontani e del Rigoli.<b>Provenienza</b>: sono riportate, quando individuate, le provenienze da cui Gabriello ha attinto per la costruzione della sua raccolta.<b>Ricc.</b>: è la segnatura attuale del manoscritto.<b>bis:</b> è l’indicazione della sezione cui ci si riferisce, nel caso di manoscritti compositi.<b>Osservazioni</b>: si tratta di espressioni molto concise con le quali si ritiene utile dare ulteriori informazioni o chiarimenti.
DOI: 10.6084/m9.figshare.5277751.v1
title: Effects of short-term flooding on aquatic and terrestrial micro-eukaryotic communities – a mesocosm approach

description: This dataset comprise the detailed sample descripton, OTU sequences and abundance matrix of the study:<br><br>Graupner, N., Röhl, O., Jensen, M., Beisser, D., Begerow, D., Boenigk, J. Effects of short-term flooding on aquatic and terrestrial micro-eukaryotic communities – a mesocosm approach. Aquatic Microbial Ecology (submitted).<br><br>The study aimed on on identifying the effects of short-term flooding on the micro-eukaryotic communities of both habitat types, freshwater and soil. As flooding provide one possible route for the organismic exchange, we focused besides the general community patters on the immigration of allochtonous taxa.<br><br>Experiments were conducted in mesocosms called AquaFlows for a duration of 14 days. In three of six AquaFlow systems we simulated at the beginning of the experiment a 24 hour flooding. The other three AquaFlow systems were not flooded throughout the whole experiment. Investigations of the micro-eukaryotic communities are based on amplicon diversity (v9 region of 18S SSU and ITS1). <br>
DOI: 10.6084/m9.figshare.5277742.v1
title: ORDINAMENTO TOPOGRAFICO DELLA LIBRERIA DI GABRIELLO RICCARDI, di Guglielmo Bartoletti

description: Ordinamento topografico della Libreria di Gabriello Riccardi<br>(Appendice all'interno del volume: <b>Guglielmo Bartoletti, <i>La Libreria privata del Marchese Suddecano Gabriello Riccardi. Il fondo manoscritti</i>, Firenze, Firenze University Press, 2017</b>)<br><i><b>Legenda dell’inventario topografico</b></i><b>Collocazione</b>: si tratta di due numeri romani indicanti rispettivamente lo scaffale e il palchetto della segnatura della Libreria di Gabriello.<b>Numero: </b>è il terzo elemento della segnatura della Libreria di Gabriello, costituito da un numero arabo a correre dal 1 a 1239; seguono ad esso dei numeri convenzionali che indicano le successive tappe di incremento di tale Libreria.<b>bis</b>: si tratta dell’indicazione di una singola parte del manoscritto, nel caso in cui manoscritti di provenienza diversa fossero stati rilegati in unico volume da Gabriello.<b>Titolo</b>: è l’espressione che troviamo sul dorso originale per indicare il contenuto del volume; nel caso frequente in cui sia andato perduto, lo abbiamo sostituito, riadattandolo in parte, con l’espressione usata dall’Inventario e stima del 1810 per descrivere il medesimo manoscritto.<b>O. D. R. T</b>: si tratta della segnalazione che l’ultimo numero della segnatura di Gabriello, quello arabo, è riportato anche sul manoscritto stesso in varia forma: O = in forma originale; D = sul dorso; R = riportato da mano successiva; T = vi è rimasta solo una traccia.<b>Indici</b>: si tratta della persona che eventualmente redatto l’indice sul manoscritto stesso. Gabriello stesso o il Mehus.<b>Legatura</b>: è l’indicazione che si tratta di una legatura eseguita dal legatore di fiducia di Gabriello, Giuseppe Pagani; la sigla P indica che la legatura è attribuibile al Pagani per confronto, la sigla B significa che l’indicazione compare nella tesi di laurea di G. Bani.<b>Bullettone</b>: si indica quando il manoscritto è descritto nel catalogo alfabetico della Libreria di Gabriello, noto come “Bullettone”.<b>Mehus</b>: indica la presenza di quel manoscritto negli spogli del Mehus.<b>F/R</b>: indica che la segnatura di Gabriello è riportata, accanto alla nuova nelle illustrazioni di codici rispettivamente del Fontani e del Rigoli.<b>Provenienza</b>: sono riportate, quando individuate, le provenienze da cui Gabriello ha attinto per la costruzione della sua raccolta.<b>Ricc.</b>: è la segnatura attuale del manoscritto.<b>bis:</b> è l’indicazione della sezione cui ci si riferisce, nel caso di manoscritti compositi.<b>Osservazioni</b>: si tratta di espressioni molto concise con le quali si ritiene utile dare ulteriori informazioni o chiarimenti.
DOI: 10.6084/m9.figshare.5277730
title: Supplementary Material for: Characterisation of “Positive” Behaviours in Primary Progressive Aphasias

description: <b><i>Background/Aims:</i></b> Although some patients with primary progressive aphasia (PPA) exhibit novel or improved skills after the onset of dementia, these changes have yet to be quantified. Therefore, this study systematically explored and identified the emergence of positive behaviours after dementia onset. <b><i>Methods:</i></b> This study included 48 carers of patients with PPA: 12 nonfluent/agrammatic PPA (nfvPPA), 22 semantic variant PPA (svPPA), and 14 logopenic variant PPA (lvPPA). The presence and frequency of positive behaviour changes after dementia onset were established using the Hypersensory and Social/Emotional Scale (HSS). <b><i>Results:</i></b> Scores on Sensitivity to Details, Visuospatial Activities, and Music Activities differed significantly among the groups. More specifically, svPPA was associated with increased visuospatial activity, but only in the mild stage of the disease; nfvPPA was associated with increased visuospatial activity and decreased music activity, while lvPPA exhibited the reverse profile. <b><i>Conclusions:</i></b> The results demonstrate that subsets of PPA patients show novel or increased positive behaviours following dementia onset, and differences among subtypes may be helpful for improving diagnostic accuracy. Additionally, harnessing these skills may improve the quality of life of both patients and carers.
DOI: 10.6084/m9.figshare.5277724
title: Table S4 from Coevolution in the timing of GABAergic and pyramidal neuron maturation in primates

description: The cortex of primates is relatively expanded relative to many other mammals, yet little is known about what developmental processes account for the expansion of cortical subtype numbers in primates, including humans. We asked whether GABAergic and pyramidal neuron production occurs for longer than expected in primates than in mice in a sample of 86 developing primate and rodent brains. We use high-resolution structural, diffusion MR scans and histological material to compare the timing of the ganglionic eminences (GE) and cortical proliferative pool (CPP) maturation between humans, macaques, rats and mice. We also compare the timing of post-neurogenetic maturation of GABAergic and pyramidal neurons in primates (i.e. humans, macaques) relative to rats and mice to identify whether delays in neurogenesis are concomitant with delayed post-neurogenetic maturation. We found that the growth of the GE and CPP are both selectively delayed compared with other events in primates. By contrast, the timing of post-neurogenetic GABAergic and pyramidal events (e.g. synaptogenesis) are predictable from the timing of other events in primates and in studied rodents. The extended duration of GABAergic and pyramidal neuron production is associated with the amplification of GABAerigc and pyramidal neuron numbers in the human and non-human primate cortex.
DOI: 10.6084/m9.figshare.5277727
title: Tables of human adipose tissue cell type-specific genes

description: The data set includes:1) "Celltype_enriched.txt" files separated by ";" that contain genes significantly enriched in one cell type compared to other three analyzed hWAT cell types according to the analysis described in R markdown file:http://figshare.com/s/509ea9441af442a735acAdjusted p-value &lt;0.05 for all pairwise comparisons, moderated F-statistics p-value &lt;0.05 (from R package/bioconductor package Limma).<br>2) "Celltype_enriched_collected.txt" files separated by ";". These files contain tables that include mean expression of the gene in a fraction where it is enriched, log fold change (logFC) and adjusted P values (adj.P.val) compared to each of other fractions. Minimal logFC and maximal adj.P.Val against other fractions are included as separate columns to enable easy sorting of the data in search for best expressed, best enriched or most specific genes. <br>3) R-code used to generate "Celltype_enriched_collected.txt" tables is provided.<br>4) In addition, a table with 100 highest-ranked genes from each fraction (based on highest logFC_min and lowest adj.P.val_max) is also included ("Selected_enriched_genes_all_fractions" - separated by tab).