cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4903145.v1
title: Characterisation of data resources for <i>in silico</i> modelling: benchmark datasets for ADME properties

description: <b>Introduction</b>: The cost of <i>in vivo</i> and <i>in vitro</i> screening of ADME properties of compounds has motivated efforts to develop a range of in silico models. At the heart of the development of any computational model are the data; high quality data are essential for developing robust and accurate models. The characteristics of a dataset, such as its availability, size, format and type of chemical identifiers used, influence the modelability of the data. <b>Areas covered</b>: This review explores the usefulness of publicly available ADME datasets for researchers to use in the development of predictive models. More than 140 ADME datasets were collated from publicly available resources and the modelability of 31 selected datasets were assessed using specific criteria derived in this study. <b>Expert opinion</b>: Publicly available datasets differ significantly in information content and presentation. From a modelling perspective, datasets should be of adequate size, available in a user-friendly format with all chemical structures associated with one or more chemical identifiers suitable for automated processing (e.g. CAS number, SMILES string or InChIKey). Recommendations for assessing dataset suitability for modelling and publishing data in an appropriate format are discussed.
DOI: 10.6084/m9.figshare.4903115
title: Differential demographic filtering by surface fires: how fuel type and fuel load affect sapling mortality of an obligate seeder savanna tree

description: Shows the effects of fuel type, fuel load and their associated flammability attributes on growth and survival of Callitris intratropica saplings in a tropical savanna.<br><br>A small scale field experiment was used to compare the effect of three fuel types (grass, eucalypt litter and Callitris litter), and a mix of grass and eucalypt litter, by varying fuel loads within their naturally occurring bounds.<br>
DOI: 10.6084/m9.figshare.4903115.v1
title: Differential demographic filtering by surface fires: how fuel type and fuel load affect sapling mortality of an obligate seeder savanna tree

description: Shows the effects of fuel type, fuel load and their associated flammability attributes on growth and survival of Callitris intratropica saplings in a tropical savanna.<br><br>A small scale field experiment was used to compare the effect of three fuel types (grass, eucalypt litter and Callitris litter), and a mix of grass and eucalypt litter, by varying fuel loads within their naturally occurring bounds.<br>
DOI: 10.6084/m9.figshare.4903091
title: SERS and Raman spectra of WT and mutant cytochromes c

description: Example Raman and SERS spectra of WT cytochrome c and three different mutants: p { margin-bottom: 0.1in; direction: ltr; color: rgb(0, 0, 0); line-height: 120%; }p.western { font-family: "NanumGothic","Times New Roman"; font-size: 10pt; }p.cjk { font-family: "Times New Roman",serif; font-size: 10pt; }p.ctl { font-family: "NanumGothic","Times New Roman"; font-size: 10pt; }a.western:link { }a.ctl:link { } <b>Mutant 1</b> T78N/K79Y/M80I/I81M/F82N<br> p { margin-bottom: 0.1in; direction: ltr; color: rgb(0, 0, 0); line-height: 120%; }p.western { font-family: "NanumGothic","Times New Roman"; font-size: 10pt; }p.cjk { font-family: "Times New Roman",serif; font-size: 10pt; }p.ctl { font-family: "NanumGothic","Times New Roman"; font-size: 10pt; }a.western:link { }a.ctl:link { } <b>Mutant 2</b> T78S/K79P<br> p { margin-bottom: 0.1in; direction: ltr; color: rgb(0, 0, 0); line-height: 120%; }p.western { font-family: "NanumGothic","Times New Roman"; font-size: 10pt; }p.cjk { font-family: "Times New Roman",serif; font-size: 10pt; }p.ctl { font-family: "NanumGothic","Times New Roman"; font-size: 10pt; }a.western:link { }a.ctl:link { } <b>Mutant 3</b> I81Y/A83Y/G84N"2ag_3mutant...." in the file name means that this is SERS spectrum of the mutant (1,2 or 3 or WT) cytochrome.<br>"mutant..sdt..." or "WT.._sdt.." in the file name means that this is Raman spectrum of the mutant or WT cytochrome c treated with sodium dithionite<br>
DOI: 10.6084/m9.figshare.4903076
title: ASR of family living and cooperation in birds

description: Ancestral state reconstruction used in Griesser et al. "Family living sets the stage for cooperative breeding and ecological resilience in birds", PLoS Biology 2017.
DOI: 10.6084/m9.figshare.4903076.v1
title: ASR of family living and cooperation in birds

description: Ancestral state reconstruction used in Griesser et al. "Family living sets the stage for cooperative breeding and ecological resilience in birds", PLoS Biology 2017.
DOI: 10.6084/m9.figshare.4903043
title: Establishing and validating the fluorescent amyloid ligand h-FTAA (heptamer formyl thiophene acetic acid) to identify transthyretin amyloid deposits in carpal tunnel syndrome

description: Transthyretin-derived (ATTR) amyloidosis is a frequent finding in carpal tunnel syndrome. We tested the following hypotheses: the novel fluorescent amyloid ligand heptameric formic thiophene acetic acid (h-FTAA) has a superior sensitivity for the detection of amyloid compared with Congo red-staining; Amyloid load correlates with patient gender and/or patient age. We retrieved 208 resection specimens obtained from 184 patients with ATTR amyloid in the carpal tunnel. Serial sections were stained with Congo red, h-FTAA and an antibody directed against transthyretin (TTR). Stained sections were digitalized and forwarded to computational analyses. The amount of amyloid was correlated with patient demographics. Amyloid stained intensely with h-FTAA and an anti-TTR-antibody. Congo red-staining combined with fluorescence microscopy was significantly less sensitive than h-FTAA-fluorescence and TTR-immunostaining: the highest percentage area was found in TTR-immunostained sections, followed by h-FTAA and Congo red. The Pearson correlation coefficient was .8 (Congo red vs. h-FTAA) and .9 (TTR vs. h-FTAA). Amyloid load correlated with patient gender, anatomical site and patient age. h-FTAA is a highly sensitive method to detect even small amounts of ATTR amyloid in the carpal tunnel. The staining protocol is easy and h-FTAA may be a much more sensitive procedure to detect amyloid at an earlier stage.
DOI: 10.6084/m9.figshare.4903040
title: Enantioselective reduction of aryl and hetero aryl methyl ketones using plant cell suspension cultures of <i>Vigna radiata</i>

description: <i>Vigna radiata</i> was investigated as whole cell catalyst for the bioreduction of aryl and heteroaryl prochiral ketones into optically active alcohols. The study indicates selective bioreduction of different substituted aryl and heteroaryl ketones (<b>1a–12a</b>) to their respective (<i>S</i>) – chiral alcohols (<b>1b–12b</b>) in good to high enantioselectivity (77.7–97.5%) with very good yields (73–82%). The results obtained confirm that the keto reductase has broad substrate specificity and selectivity in catalyzing both six and five-membered heteroaryl methyl ketones. The current methodology substantiates a promising and alternative green approach for the synthesis of secondary chiral alcohols of biological importance in a mild, cheap and environmentally benign process.
DOI: 10.6084/m9.figshare.4903031
title: Table S5

description: Raw Data for Figure 9. <b>Monte Carlo simulations of two species competition when the habitat is probabilistically populated by individuals on initial iteration.</b><b><br></b><b></b>Cellular automata field was probabilistically populated by 22500 individuals of each of two competing species on initial iteration. The habitat consists of 300x300 microhabitats where 25% of the territory is occupied by individuals of the species 1, 25% of the territory is occupied by individuals of the species 2 and 50% of the territory is free. The number of Monte Carlo simulations equals 200. Parameter P<sub>1</sub> reflects fitness of Species 1 and parameter P<sub>2</sub> reflects fitness of Species 2. Raw data are presented in Table S5. (A) There were 197 cases of competitive exclusion and 3 cases of competitive coexistence. Species difference in fitness equals 100%. (B) There were 195 cases of competitive exclusion and 5 cases of competitive coexistence. Species difference in fitness equals 23%. (C-F) Stable coexistence of competing species was observed in all cases. Species differences in fitness equal 22% (C), 21% (D), 10% (E) and 0% (F).
DOI: 10.6084/m9.figshare.4903040.v1
title: Enantioselective reduction of aryl and hetero aryl methyl ketones using plant cell suspension cultures of <i>Vigna radiata</i>

description: <i>Vigna radiata</i> was investigated as whole cell catalyst for the bioreduction of aryl and heteroaryl prochiral ketones into optically active alcohols. The study indicates selective bioreduction of different substituted aryl and heteroaryl ketones (<b>1a–12a</b>) to their respective (<i>S</i>) – chiral alcohols (<b>1b–12b</b>) in good to high enantioselectivity (77.7–97.5%) with very good yields (73–82%). The results obtained confirm that the keto reductase has broad substrate specificity and selectivity in catalyzing both six and five-membered heteroaryl methyl ketones. The current methodology substantiates a promising and alternative green approach for the synthesis of secondary chiral alcohols of biological importance in a mild, cheap and environmentally benign process.
DOI: 10.6084/m9.figshare.4903028
title: Table S4

description: Raw Data for Figure 8. <b>Monte Carlo simulations of two species competition when the habitat is probabilistically populated by individuals on initial iteration. </b><b><br></b>Cellular automata field was probabilistically populated by 625 individuals of each of two competing species on initial iteration. The habitat consists of 50x50 microhabitats where 25% of the territory is occupied by individuals of the species 1, 25% of the territory is occupied by individuals of the species 2 and 50% of the territory is free. The number of Monte Carlo simulations equals 200. Parameter P<sub>1</sub> reflects fitness of Species 1 and parameter P<sub>2</sub> reflects fitness of Species 2. Raw data are presented in Table S4. (A) There were 198 cases of competitive exclusion and 2 cases of competitive coexistence. Species difference in fitness equals 100%. (B) Competitive exclusion was observed in all cases. Species difference in fitness equals 24%. (C) There were 2 cases of competitive exclusion and 198 cases of competitive coexistence. Species difference in fitness equals 19%. (D-F) Stable coexistence of competing species was observed in all cases. Species differences in fitness equal 18% (D), 10% (E) and 0% (F).
DOI: 10.6084/m9.figshare.4903031.v1
title: Table S5

description: Raw Data for Figure 9. <b>Monte Carlo simulations of two species competition when the habitat is probabilistically populated by individuals on initial iteration.</b><b><br></b><b></b>Cellular automata field was probabilistically populated by 22500 individuals of each of two competing species on initial iteration. The habitat consists of 300x300 microhabitats where 25% of the territory is occupied by individuals of the species 1, 25% of the territory is occupied by individuals of the species 2 and 50% of the territory is free. The number of Monte Carlo simulations equals 200. Parameter P<sub>1</sub> reflects fitness of Species 1 and parameter P<sub>2</sub> reflects fitness of Species 2. Raw data are presented in Table S5. (A) There were 197 cases of competitive exclusion and 3 cases of competitive coexistence. Species difference in fitness equals 100%. (B) There were 195 cases of competitive exclusion and 5 cases of competitive coexistence. Species difference in fitness equals 23%. (C-F) Stable coexistence of competing species was observed in all cases. Species differences in fitness equal 22% (C), 21% (D), 10% (E) and 0% (F).
DOI: 10.6084/m9.figshare.4903043.v2
title: Establishing and validating the fluorescent amyloid ligand h-FTAA (heptamer formyl thiophene acetic acid) to identify transthyretin amyloid deposits in carpal tunnel syndrome

description: Transthyretin-derived (ATTR) amyloidosis is a frequent finding in carpal tunnel syndrome. We tested the following hypotheses: the novel fluorescent amyloid ligand heptameric formic thiophene acetic acid (h-FTAA) has a superior sensitivity for the detection of amyloid compared with Congo red-staining; Amyloid load correlates with patient gender and/or patient age. We retrieved 208 resection specimens obtained from 184 patients with ATTR amyloid in the carpal tunnel. Serial sections were stained with Congo red, h-FTAA and an antibody directed against transthyretin (TTR). Stained sections were digitalized and forwarded to computational analyses. The amount of amyloid was correlated with patient demographics. Amyloid stained intensely with h-FTAA and an anti-TTR-antibody. Congo red-staining combined with fluorescence microscopy was significantly less sensitive than h-FTAA-fluorescence and TTR-immunostaining: the highest percentage area was found in TTR-immunostained sections, followed by h-FTAA and Congo red. The Pearson correlation coefficient was .8 (Congo red vs. h-FTAA) and .9 (TTR vs. h-FTAA). Amyloid load correlated with patient gender, anatomical site and patient age. h-FTAA is a highly sensitive method to detect even small amounts of ATTR amyloid in the carpal tunnel. The staining protocol is easy and h-FTAA may be a much more sensitive procedure to detect amyloid at an earlier stage.
DOI: 10.6084/m9.figshare.4903013
title: Table S1

description: Raw Data for Figure 5. <b>Influence of the habitat size in contribution of stochastic fluctuations on coexistence of two identical resource competitors</b>.<br> Colonization of free habitat started from single individuals of each species. Parameter P<sub>1</sub> = 0.5 reflects fitness of Species 1 and parameter P<sub>2</sub> = 0.5 reflects fitness of Species 2. Raw data are presented in Table S1. (A) Species 1 excludes Species 2. The lattice consists of 5x5 sites. (B) Species 2 excludes Species 1. The lattice consists of 6x6 sites. (C) Species 2 excludes Species 1. The lattice consists of 7x7 sites. (D) Species 1 and Species 2 stably coexist. The lattice consists of 8x8 sites.
DOI: 10.6084/m9.figshare.4903016
title: Table S3

description: Raw Data for Figure 7. <b>Monte Carlo simulations of two species competition with colonization of free habitat consisted of 300x300 sites. </b><b><br></b>Colonization of free habitat started from single individuals of each species.<b> </b>The number of Monte Carlo simulations equals 200. Parameter P<sub>1</sub> reflects fitness of Species 1 and parameter P<sub>2</sub> reflects fitness of Species 2. Raw data are presented in Table S3. (A, B) Competitive exclusion of the recessive Species 2 was observed in all cases. Species differences in fitness equal 100% (A) and 32% (B). (C-F) Stable coexistence of competing species was observed in all cases. Species differences in fitness equal 31% (C), 20% (D), 10% (E) and 0% (F).
DOI: 10.6084/m9.figshare.4903043.v1
title: Establishing and validating the fluorescent amyloid ligand h-FTAA (heptamer formyl thiophene acetic acid) to identify transthyretin amyloid deposits in carpal tunnel syndrome

description: Transthyretin-derived (ATTR) amyloidosis is a frequent finding in carpal tunnel syndrome. We tested the following hypotheses: the novel fluorescent amyloid ligand heptameric formic thiophene acetic acid (h-FTAA) has a superior sensitivity for the detection of amyloid compared with Congo red-staining; Amyloid load correlates with patient gender and/or patient age. We retrieved 208 resection specimens obtained from 184 patients with ATTR amyloid in the carpal tunnel. Serial sections were stained with Congo red, h-FTAA and an antibody directed against transthyretin (TTR). Stained sections were digitalized and forwarded to computational analyses. The amount of amyloid was correlated with patient demographics. Amyloid stained intensely with h-FTAA and an anti-TTR-antibody. Congo red-staining combined with fluorescence microscopy was significantly less sensitive than h-FTAA-fluorescence and TTR-immunostaining: the highest percentage area was found in TTR-immunostained sections, followed by h-FTAA and Congo red. The Pearson correlation coefficient was .8 (Congo red vs. h-FTAA) and .9 (TTR vs. h-FTAA). Amyloid load correlated with patient gender, anatomical site and patient age. h-FTAA is a highly sensitive method to detect even small amounts of ATTR amyloid in the carpal tunnel. The staining protocol is easy and h-FTAA may be a much more sensitive procedure to detect amyloid at an earlier stage.
DOI: 10.6084/m9.figshare.4903028.v1
title: Table S4

description: Raw Data for Figure 8. <b>Monte Carlo simulations of two species competition when the habitat is probabilistically populated by individuals on initial iteration. </b><b><br></b>Cellular automata field was probabilistically populated by 625 individuals of each of two competing species on initial iteration. The habitat consists of 50x50 microhabitats where 25% of the territory is occupied by individuals of the species 1, 25% of the territory is occupied by individuals of the species 2 and 50% of the territory is free. The number of Monte Carlo simulations equals 200. Parameter P<sub>1</sub> reflects fitness of Species 1 and parameter P<sub>2</sub> reflects fitness of Species 2. Raw data are presented in Table S4. (A) There were 198 cases of competitive exclusion and 2 cases of competitive coexistence. Species difference in fitness equals 100%. (B) Competitive exclusion was observed in all cases. Species difference in fitness equals 24%. (C) There were 2 cases of competitive exclusion and 198 cases of competitive coexistence. Species difference in fitness equals 19%. (D-F) Stable coexistence of competing species was observed in all cases. Species differences in fitness equal 18% (D), 10% (E) and 0% (F).
DOI: 10.6084/m9.figshare.4903013.v1
title: Table S1

description: Raw Data for Figure 5. <b>Influence of the habitat size in contribution of stochastic fluctuations on coexistence of two identical resource competitors</b>.<br> Colonization of free habitat started from single individuals of each species. Parameter P<sub>1</sub> = 0.5 reflects fitness of Species 1 and parameter P<sub>2</sub> = 0.5 reflects fitness of Species 2. Raw data are presented in Table S1. (A) Species 1 excludes Species 2. The lattice consists of 5x5 sites. (B) Species 2 excludes Species 1. The lattice consists of 6x6 sites. (C) Species 2 excludes Species 1. The lattice consists of 7x7 sites. (D) Species 1 and Species 2 stably coexist. The lattice consists of 8x8 sites.
DOI: 10.6084/m9.figshare.4903016.v1
title: Table S3

description: Raw Data for Figure 7. <b>Monte Carlo simulations of two species competition with colonization of free habitat consisted of 300x300 sites. </b><b><br></b>Colonization of free habitat started from single individuals of each species.<b> </b>The number of Monte Carlo simulations equals 200. Parameter P<sub>1</sub> reflects fitness of Species 1 and parameter P<sub>2</sub> reflects fitness of Species 2. Raw data are presented in Table S3. (A, B) Competitive exclusion of the recessive Species 2 was observed in all cases. Species differences in fitness equal 100% (A) and 32% (B). (C-F) Stable coexistence of competing species was observed in all cases. Species differences in fitness equal 31% (C), 20% (D), 10% (E) and 0% (F).
DOI: 10.17633/rd.brunel.4902977
title: Why rate when you could compare? Elo strength data

description: Data related to the manuscript, "Why rate when you could compare? Using the "EloChoice" package to assess pairwise comparisons of perceived physical strength", by Andrew P. Clark, Kate L. Howard, Andy T. Woods, Ian S. Penton-Voak and Christof Neumann.
DOI: 10.6084/m9.figshare.4902968
title: Credit Operations

description: Files indicates the value of each credit operation solicited per plaintiff, yearly.<br>Operations are aggregated at the Federated Unity level.<br>
DOI: 10.6084/m9.figshare.4902986
title: Table S2

description: Raw Data for Figure 6. <b>Monte Carlo simulations of two species competition with colonization of free habitat consisted of 50x50 sites. </b><br>Colonization of free habitat started from single individuals of each species. The number of Monte Carlo simulations equals 200. Parameter P<sub>1</sub> reflects fitness of Species 1 and parameter P<sub>2</sub> reflects fitness of Species 2. Raw data are presented in Table S2. (A) Competitive exclusion of the recessive Species 2 was observed in all cases. Species difference in fitness equals 100%. (B) There were 78 cases of competitive exclusion and 122 cases of competitive coexistence. Species difference in fitness equals 30%. (C-F) Competing species stably coexisted in all cases. Species differences in fitness equal 29% (C), 20% (D), 10% (E) and 0% (F).
DOI: 10.6084/m9.figshare.4902965
title: Model Parameters

description: Parameters of the fit models of the paper "Is the Public Sector of Your Country a Diffusion Borrower?"<br>
DOI: 10.6084/m9.figshare.4902986.v1
title: Table S2

description: Raw Data for Figure 6. <b>Monte Carlo simulations of two species competition with colonization of free habitat consisted of 50x50 sites. </b><br>Colonization of free habitat started from single individuals of each species. The number of Monte Carlo simulations equals 200. Parameter P<sub>1</sub> reflects fitness of Species 1 and parameter P<sub>2</sub> reflects fitness of Species 2. Raw data are presented in Table S2. (A) Competitive exclusion of the recessive Species 2 was observed in all cases. Species difference in fitness equals 100%. (B) There were 78 cases of competitive exclusion and 122 cases of competitive coexistence. Species difference in fitness equals 30%. (C-F) Competing species stably coexisted in all cases. Species differences in fitness equal 29% (C), 20% (D), 10% (E) and 0% (F).
DOI: 10.6084/m9.figshare.4902941
title: TARA-NON-REDUNDANT-MAGs-SPLIT

description: Anvi'o profiles for each MAG in Delmont et al.<br>Each of which can be visualized using anvi'o version 2.3.0 or later.
DOI: 10.6084/m9.figshare.4902965.v1
title: Model Parameters

description: Parameters of the fit models of the paper "Is the Public Sector of Your Country a Diffusion Borrower?"<br>
DOI: 10.6084/m9.figshare.4902926
title: TARA-NON-REDUNDANT-MAGs-SUMMARY

description: The anvi'o summary output for 957 non-redundant metagenome-assembled genomes from the TARA Oceans metagenomes.
DOI: 10.6084/m9.figshare.4902929
title: Enhancing Ebola virus disease surveillance and prevention in counties without confirmed cases in rural Liberia: Experiences from Sinoe County during the flare-up in Monrovia, April to June, 2016 - Data

description: Data for the <b>manuscript</b>
DOI: 10.6084/m9.figshare.4902923
title: TARA-NON-REDUNDANT-MAGs

description: FASTA files for 957 non-redundant MAGs recovered from TARA Oceans metagenomes.
DOI: 10.6084/m9.figshare.4902920
title: TARA-RAW-ASSEMBLIES-1000nt

description: Raw assembly results for TARA Oceans metagenomic sets (&gt;1000nt). Assemblies were done using MEGAHIT.
DOI: 10.6084/m9.figshare.4902917
title: TARA-AA-SEQUENCE-DATABASE

description: Amino acid sequences occurring in all scaffolds &gt;1,000 in each co-assembly of TARA Oceans metagenomic sets.
DOI: 10.6084/m9.figshare.4902914
title: Datasets used in "Qualitative assessment of climate-driven ecological shifts in the Caspian Sea"

description: The datasets used in this study belong to three categories: regional fisheries-derived ecological datasets, large-scale climatic indices and local satellite-based environmental time series. Their properties were fully described in the paper, while their time scopes and data providers are shown in Table 1 in the paper.<br>