cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6575438.v1
title: Models and trajectories of GLUTAMINE SYNTHETASE with palmitoyl-coenzyme A

description: These are the models and molecular dynamics trajectories obtained for the paper Role of glutamine synthetase in angiogenesis beyond glutamine synthesis [G. Eelen et al. Nature 2018 vol. 561 (7721) pp. 63-69].<br>The PDB files (human.pdb and bacterial.pdb) contain representative structures extracted from the molecular dynamics simulations of the S. Typhimurium (bacterial.pdb) and Human Glutamine Synthetase (human.pdb). For the latter, models of the two most relevant binding modes of Palmitoyl-CoA are included in the file.<br><br>The trajectories included are the FINAL 450 ns of 2 fully atomistic molecular dynamics simulations of Glutamine Synthetase (GS) performed with GROMACS and the Amber ff14SB force field. The Human_GS.x is the trajectory of human GS (reference PDB 2OJW) with Palmitoyl-CoA. In this trajecory the palmitate tail points upwards (which was the most interesting orientation found). "Bacterial_GS" is the bacterial GS trajectory (reference starting PDB 1FPY) with Palmitoyl-CoA - palmitate tail points downwards. The trajectories are in GROMACS trr format and have been saved every 200ps.<b> </b>Water molecules and the initial 50 ns (relaxation) are not included in the files.
DOI: 10.6084/m9.figshare.6572117
title: Species tree files

description: Files used to reconstruct the Agaricales species tree, includes RAxML resulting files.
DOI: 10.6084/m9.figshare.6571781
title: Plan of Christchurch Harbour, 1671

description: William Wilkinson's plan of Christchurch Harbour, showing 'the New Cutt through the barr, Intended', 13 Jul 1671<br>'This Drawet, or Figuer was taken on the 13th daie of July in 1671 From Christ-Church dowen in to the sea'. It shows the rivers Avon and Stour, noting that 'as great a quantety of wator maie bee commanded, and added unto these two Rivors; which yf united would raize the wator From the barr unto Christchurch bridge, which would prevent the depineng of the Channell thear'. Also mentions or shows Christchurch, the Church, the Mill, the Quay, the Bar, and the Salthouse.<br><b><i>Images courtesy of Dorset History Centre, reference: D-934 - NOT TO BE REPRODUCED</i></b><br>
DOI: 10.6084/m9.figshare.6571781.v1
title: Plan of Christchurch Harbour, 1671

description: William Wilkinson's plan of Christchurch Harbour, showing 'the New Cutt through the barr, Intended', 13 Jul 1671<br>'This Drawet, or Figuer was taken on the 13th daie of July in 1671 From Christ-Church dowen in to the sea'. It shows the rivers Avon and Stour, noting that 'as great a quantety of wator maie bee commanded, and added unto these two Rivors; which yf united would raize the wator From the barr unto Christchurch bridge, which would prevent the depineng of the Channell thear'. Also mentions or shows Christchurch, the Church, the Mill, the Quay, the Bar, and the Salthouse.<br><b><i>Images courtesy of Dorset History Centre, reference: D-934 - NOT TO BE REPRODUCED</i></b><br>
DOI: 10.6084/m9.figshare.6571730
title: Result of Data analysis of RNA-Seq

description: FASTQ files for RCC4-EV cells (DRR100656) and RCC4-VHL cells (DRR100657) were obtained from the Sequence Read Archive (https://trace.ddbj.nig.ac.jp/dra/index_e.html). The quality of sequence data was evaluated by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) after the trimming process by fastx_toolkit v 0.0.14 (http://hannonlab.cshl.edu/fastx_toolkit/). The human reference sequence file (hs37d5.fa) was downloaded from the 1000 genome ftp site (ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/), and the annotated general feature format (gff) file was downloaded from the Illumina iGenome ftp site (ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Homo_sapiens/NCBI/build37.2/). The human genome index was constructed with bowtie-build in Bowtie v.2.2.9. The fastq files were aligned to the reference genomic sequence by TopHat v.2.1.1 with default parameters. Bowtie2 v2.2.9 and Samtools v.1.3.1 was used with the TopHat program47. Estimation of transcript abundance was calculated, and the count values were normalized to the upper quartile of the fragments per kilobase of transcript per million fragments mapped reads (FPKM) using Cufflinks (cuffdiff) v2.1.1. cuffdiff output (gene_exp. diff) was presentated (gene_exp.diff.txt).
DOI: 10.6084/m9.figshare.6571454
title: The communicative life of a social carnivore: acoustic repertoire of the ring-tailed coati (<i>Nasua nasua</i>)

description: The coati is a highly social mammal that features sophisticated cognitive and social abilities. We hypothesized that the ring-tailed coati, <i>Nasua nasua</i>, uses an extensive acoustic repertoire that correlates to their diverse range of social interactions. We tested this hypothesis by observing and recording a free-ranging managed population of <i>N. nasua</i> in Tietê Ecological Park (PET), in the municipality of São Paulo, State of São Paulo, Brazil. Of 404 h of sampling, 47 h of coati vocalizations were recorded over 3 years. Additional records were obtained opportunistically on other free-living populations at PET by using passive acoustic monitoring. We describe here an acoustic repertoire composed of 15 calls (12 basic calls, 2 rhythmic calls and the non-random complex calls composed of three or four different units). This diverse repertoire of signals was used in contact/cohesion regulation, foraging activities, alert or potential threat situations, playing and fighting interactions and during social isolation and acute distress. The contact call (chirp) is produced through biphonation, and other non-linear phenomena are present. Our study found a complex vocal repertoire that encourages further studies to describe the evolution of the cognitive characteristics and social abilities of ring-tailed coatis.
DOI: 10.6084/m9.figshare.6571454.v2
title: The communicative life of a social carnivore: acoustic repertoire of the ring-tailed coati (<i>Nasua nasua</i>)

description: The coati is a highly social mammal that features sophisticated cognitive and social abilities. We hypothesized that the ring-tailed coati, <i>Nasua nasua</i>, uses an extensive acoustic repertoire that correlates to their diverse range of social interactions. We tested this hypothesis by observing and recording a free-ranging managed population of <i>N. nasua</i> in Tietê Ecological Park (PET), in the municipality of São Paulo, State of São Paulo, Brazil. Of 404 h of sampling, 47 h of coati vocalizations were recorded over 3 years. Additional records were obtained opportunistically on other free-living populations at PET by using passive acoustic monitoring. We describe here an acoustic repertoire composed of 15 calls (12 basic calls, 2 rhythmic calls and the non-random complex calls composed of three or four different units). This diverse repertoire of signals was used in contact/cohesion regulation, foraging activities, alert or potential threat situations, playing and fighting interactions and during social isolation and acute distress. The contact call (chirp) is produced through biphonation, and other non-linear phenomena are present. Our study found a complex vocal repertoire that encourages further studies to describe the evolution of the cognitive characteristics and social abilities of ring-tailed coatis.
DOI: 10.6084/m9.figshare.6571454.v1
title: The communicative life of a social carnivore: acoustic repertoire of the ring-tailed coati (<i>Nasua nasua</i>)

description: The coati is a highly social mammal that features sophisticated cognitive and social abilities. We hypothesized that the ring-tailed coati, <i>Nasua nasua</i>, uses an extensive acoustic repertoire that correlates to their diverse range of social interactions. We tested this hypothesis by observing and recording a free-ranging managed population of <i>N. nasua</i> in Tietê Ecological Park (PET), in the municipality of São Paulo, State of São Paulo, Brazil. Of 404 h of sampling, 47 h of coati vocalizations were recorded over 3 years. Additional records were obtained opportunistically on other free-living populations at PET by using passive acoustic monitoring. We describe here an acoustic repertoire composed of 15 calls (12 basic calls, 2 rhythmic calls and the non-random complex calls composed of three or four different units). This diverse repertoire of signals was used in contact/cohesion regulation, foraging activities, alert or potential threat situations, playing and fighting interactions and during social isolation and acute distress. The contact call (chirp) is produced through biphonation, and other non-linear phenomena are present. Our study found a complex vocal repertoire that encourages further studies to describe the evolution of the cognitive characteristics and social abilities of ring-tailed coatis.
DOI: 10.6084/m9.figshare.6571439
title: DNA barcoding and faunistic criteria for a revised taxonomy of Italian Ephemeroptera

description: Mayfly (Ephemeroptera) systematics has considerably changed over the years, but many questions have yet to be answered. The synergistic connection between traditional knowledge and new data sources, producing increasingly complex information, has become a compelling issue for modern taxonomy. Molecular tests and the use of reliable reference sequence libraries may constitute effective complements to the traditional method in guiding recognition of species and giving information about taxonomic incongruences which require further examination. In the present study, we sought to verify the current Italian mayfly nomenclatural system through DNA barcoding and relevant points to reliably manage the available amount of morpho-ecological and molecular data are discussed. We investigated COI (Cytochrome oxidase I) sequence variation in 163 individuals of Italian mayflies, 126 of which were previously assigned to 24 morphologically recognised species, and 37 could be attributed only to generic taxonomic entities (“sp.”, “cf.” or “gr.”). DNA barcoding statistical tests for species delimitation hypotheses based on genetic distances and inferred gene trees were integrated with GenBank searches and surveys of the historical literature to better understand the knowledge acquired on the status and diversity of the investigated taxa. Combined criteria to define three categories of reliability were then assessed. Concurrent data allowing unambiguous identification were attained for only eight species. High intraspecific genetic distances (&gt; 3%) and a lack of reliable reference material or convincing taxonomic information evidenced 29 critical states, deserving further investigation. Solid species names, potential cryptic species and entities about which little is known are pointed out for a future upgrade/reorganisation of the taxonomy of Italian Ephemeroptera.
DOI: 10.6084/m9.figshare.6571439.v1
title: DNA barcoding and faunistic criteria for a revised taxonomy of Italian Ephemeroptera

description: Mayfly (Ephemeroptera) systematics has considerably changed over the years, but many questions have yet to be answered. The synergistic connection between traditional knowledge and new data sources, producing increasingly complex information, has become a compelling issue for modern taxonomy. Molecular tests and the use of reliable reference sequence libraries may constitute effective complements to the traditional method in guiding recognition of species and giving information about taxonomic incongruences which require further examination. In the present study, we sought to verify the current Italian mayfly nomenclatural system through DNA barcoding and relevant points to reliably manage the available amount of morpho-ecological and molecular data are discussed. We investigated COI (Cytochrome oxidase I) sequence variation in 163 individuals of Italian mayflies, 126 of which were previously assigned to 24 morphologically recognised species, and 37 could be attributed only to generic taxonomic entities (“sp.”, “cf.” or “gr.”). DNA barcoding statistical tests for species delimitation hypotheses based on genetic distances and inferred gene trees were integrated with GenBank searches and surveys of the historical literature to better understand the knowledge acquired on the status and diversity of the investigated taxa. Combined criteria to define three categories of reliability were then assessed. Concurrent data allowing unambiguous identification were attained for only eight species. High intraspecific genetic distances (&gt; 3%) and a lack of reliable reference material or convincing taxonomic information evidenced 29 critical states, deserving further investigation. Solid species names, potential cryptic species and entities about which little is known are pointed out for a future upgrade/reorganisation of the taxonomy of Italian Ephemeroptera.
DOI: 10.6084/m9.figshare.6571367
title: A randomized, double-blind study of SHP465 mixed amphetamine salts extended-release in adults with ADHD using a simulated adult workplace design

description: <b>Objectives</b>: The objective of this paper was to evaluate the efficacy, duration of effect, and tolerability of SHP465 mixed amphetamine salts (MAS) extended-release versus placebo and immediate-release MAS (MAS IR) in adults with attention-deficit/hyperactivity disorder (ADHD). <b>Methods</b>: Adults with ADHD Rating Scale, Version IV (ADHD-RS-IV) scores ≥24 were randomized to SHP465 MAS (50 or 75 mg), placebo, or 25 mg MAS IR in a double-blind, three-period, crossover study using a simulated adult workplace environment. On the final day of each 7-day treatment period, efficacy was assessed for 16 h postdose. Primary efficacy analyses for Permanent Product Measure of Performance (PERMP) total score averaged across all postdose assessments and each postdose time point were conducted in the intent-to-treat population using a mixed linear model. Secondary end-points included PERMP problems attempted and answered correctly and ADHD-RS-IV scores based on clinician ratings of counselor observations using the Time Segment Rating System and participant self-report. Tolerability assessments included treatment-emergent adverse events (TEAEs) and vital signs. <b>Results</b>: Least squares mean (95% CI) treatment differences (combined 50/75 mg SHP465 MAS–placebo) significantly favored SHP465 MAS over placebo for PERMP total score averaged across all postdose assessments (18.38 [11.28, 25.47]; <i>P </i>P P = .0001); treatment differences between SHP465 MAS and MAS IR were not significant (nominal <i>P </i>= .2443). The two most frequently reported TEAEs associated with SHP465 MAS were insomnia (36.5%) and anorexia (21.2%). Mean increases in pulse and blood pressure with SHP465 MAS exceeded those of placebo. <b>Conclusions</b>: SHP465 MAS (combined 50/75 mg) significantly improved PERMP total score versus placebo, with superiority observed from 2 to 16 h postdose. The tolerability profile of SHP465 MAS was similar to previous reports of SHP465 MAS in adults with ADHD. <b>Clinical trial registration</b>: https://clinicaltrials.gov/ct2/show/NCT00928148 identifier is NCT00928148.
DOI: 10.6084/m9.figshare.6571367.v1
title: A randomized, double-blind study of SHP465 mixed amphetamine salts extended-release in adults with ADHD using a simulated adult workplace design

description: <b>Objectives</b>: The objective of this paper was to evaluate the efficacy, duration of effect, and tolerability of SHP465 mixed amphetamine salts (MAS) extended-release versus placebo and immediate-release MAS (MAS IR) in adults with attention-deficit/hyperactivity disorder (ADHD). <b>Methods</b>: Adults with ADHD Rating Scale, Version IV (ADHD-RS-IV) scores ≥24 were randomized to SHP465 MAS (50 or 75 mg), placebo, or 25 mg MAS IR in a double-blind, three-period, crossover study using a simulated adult workplace environment. On the final day of each 7-day treatment period, efficacy was assessed for 16 h postdose. Primary efficacy analyses for Permanent Product Measure of Performance (PERMP) total score averaged across all postdose assessments and each postdose time point were conducted in the intent-to-treat population using a mixed linear model. Secondary end-points included PERMP problems attempted and answered correctly and ADHD-RS-IV scores based on clinician ratings of counselor observations using the Time Segment Rating System and participant self-report. Tolerability assessments included treatment-emergent adverse events (TEAEs) and vital signs. <b>Results</b>: Least squares mean (95% CI) treatment differences (combined 50/75 mg SHP465 MAS–placebo) significantly favored SHP465 MAS over placebo for PERMP total score averaged across all postdose assessments (18.38 [11.28, 25.47]; <i>P </i>P P = .0001); treatment differences between SHP465 MAS and MAS IR were not significant (nominal <i>P </i>= .2443). The two most frequently reported TEAEs associated with SHP465 MAS were insomnia (36.5%) and anorexia (21.2%). Mean increases in pulse and blood pressure with SHP465 MAS exceeded those of placebo. <b>Conclusions</b>: SHP465 MAS (combined 50/75 mg) significantly improved PERMP total score versus placebo, with superiority observed from 2 to 16 h postdose. The tolerability profile of SHP465 MAS was similar to previous reports of SHP465 MAS in adults with ADHD. <b>Clinical trial registration</b>: https://clinicaltrials.gov/ct2/show/NCT00928148 identifier is NCT00928148.
DOI: 10.6084/m9.figshare.6571364
title: TrajectoryFiles.zip

description: These are raw 168hour forward trajectory files used in the paper titled "Mapping areas of the Southern Ocean where productivity likely depends on dust delivered iron"<br>The "Analyses.zip" contains results used in the paper.
DOI: 10.6084/m9.figshare.6571364.v2
title: TrajectoryFiles.zip

description: These are raw 168hour forward trajectory files used in the paper titled "Mapping areas of the Southern Ocean where productivity likely depends on dust delivered iron"<br>The "Analyses.zip" contains results used in the paper.
DOI: 10.6084/m9.figshare.6571364.v1
title: TrajectoryFiles.zip

description: These are raw 168hour forward trajectory files used in the paper titled "Mapping areas of the Southern Ocean where productivity likely depends on dust delivered iron"
DOI: 10.6084/m9.figshare.6571340
title: Cognitive-behavioral longitudinal assessment in ALS: the Italian Edinburgh Cognitive and Behavioral ALS screen (ECAS)

description: <i>Objective</i>: The study presents data on the longitudinal administration of the Italian Edinburgh Cognitive and Behavioral ALS Screen (ECAS). We investigated cognitive-behavioral performance in a group of ALS patients over time and the feasibility of repeating the ECAS longitudinally compared with standard neuropsychological tests. Finally, correlations between clinical/genetic and cognitive/behavioral data were considered. <i>Methods</i>: One hundred and sixty-eight ALS patients were tested at baseline (T<sub>0</sub>). Among these, 48 patients performed the ECAS after 6 months (T<sub>1</sub>), 18 patients performed it at T<sub>2</sub> (12 months), and five patients were assessed after 24 months (T<sub>3</sub>). Participants were also administered two cognitive test (FAB; MoCA) and psychological questionnaires (BDI; STAI/Y). The FBI was carried out with caregivers. <i>Results</i>: No cognitive deterioration was found across follow-ups. In contrast, although scores did not change between T<sub>0</sub> and T<sub>1</sub>, scores improved significantly for ECAS Total/ALS Non-specific and Memory domains when the ECAS was repeated on three occasions (T<sub>0</sub>, T<sub>1</sub>, T<sub>2</sub>). Apathy/Inertia was the most common behavioral symptom, but no worsening of behavioral scores was detected over time. After 12–24 months, patients were still able to perform the ECAS in total, in contrast to FAB and MoCA, which were only partially administrable. <i>Conclusions</i>: The significant improvement of some ECAS scores over time supports the presence of possible practice effects, particularly in the memory domain, highlighting the need to accommodate for these in longitudinal assessments, through healthy controls groups or alternate versions. This work represents the first Italian ECAS follow-up study and confirms ECAS feasibility in patients with increasing physical disability.
DOI: 10.6084/m9.figshare.6571340.v1
title: Cognitive-behavioral longitudinal assessment in ALS: the Italian Edinburgh Cognitive and Behavioral ALS screen (ECAS)

description: <i>Objective</i>: The study presents data on the longitudinal administration of the Italian Edinburgh Cognitive and Behavioral ALS Screen (ECAS). We investigated cognitive-behavioral performance in a group of ALS patients over time and the feasibility of repeating the ECAS longitudinally compared with standard neuropsychological tests. Finally, correlations between clinical/genetic and cognitive/behavioral data were considered. <i>Methods</i>: One hundred and sixty-eight ALS patients were tested at baseline (T<sub>0</sub>). Among these, 48 patients performed the ECAS after 6 months (T<sub>1</sub>), 18 patients performed it at T<sub>2</sub> (12 months), and five patients were assessed after 24 months (T<sub>3</sub>). Participants were also administered two cognitive test (FAB; MoCA) and psychological questionnaires (BDI; STAI/Y). The FBI was carried out with caregivers. <i>Results</i>: No cognitive deterioration was found across follow-ups. In contrast, although scores did not change between T<sub>0</sub> and T<sub>1</sub>, scores improved significantly for ECAS Total/ALS Non-specific and Memory domains when the ECAS was repeated on three occasions (T<sub>0</sub>, T<sub>1</sub>, T<sub>2</sub>). Apathy/Inertia was the most common behavioral symptom, but no worsening of behavioral scores was detected over time. After 12–24 months, patients were still able to perform the ECAS in total, in contrast to FAB and MoCA, which were only partially administrable. <i>Conclusions</i>: The significant improvement of some ECAS scores over time supports the presence of possible practice effects, particularly in the memory domain, highlighting the need to accommodate for these in longitudinal assessments, through healthy controls groups or alternate versions. This work represents the first Italian ECAS follow-up study and confirms ECAS feasibility in patients with increasing physical disability.