cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4258307
title: Non-invasive acoustic detection of wolves

description: Monitoring wolves (<i>Canis lupus</i>) is a difficult and often expensive task due to high mobility, pack dynamic, shyness and nocturnal activity of this species. Wolves communicate acoustically through howling, within pack and with packs of the neighbourhood. A wolf howl is a low-frequency vocalization that can be transmitted over long distances and thus it can be used for monitoring. Elicited howling survey is a current method to monitor wolves in different areas all over the world. Elicited howling, however, may be invasive to residential wolf packs and could create possible negative reactions from the human population. Here we show that it is possible to detect wolves by recording spontaneous howling events. We measured the sound pressure level of wolf howls by captive individuals and we further found that elicited howling may be recorded and clearly identified up to a distance of 3 km. We finally conducted a non-invasive acoustic detection of wolves in a free-ranging population. The use of passive sound recorders may provide a powerful non-invasive tool for future wolf monitoring and could help to establish sustainable management plans for this species.
DOI: 10.6084/m9.figshare.4258307.v1
title: Non-invasive acoustic detection of wolves

description: Monitoring wolves (<i>Canis lupus</i>) is a difficult and often expensive task due to high mobility, pack dynamic, shyness and nocturnal activity of this species. Wolves communicate acoustically through howling, within pack and with packs of the neighbourhood. A wolf howl is a low-frequency vocalization that can be transmitted over long distances and thus it can be used for monitoring. Elicited howling survey is a current method to monitor wolves in different areas all over the world. Elicited howling, however, may be invasive to residential wolf packs and could create possible negative reactions from the human population. Here we show that it is possible to detect wolves by recording spontaneous howling events. We measured the sound pressure level of wolf howls by captive individuals and we further found that elicited howling may be recorded and clearly identified up to a distance of 3 km. We finally conducted a non-invasive acoustic detection of wolves in a free-ranging population. The use of passive sound recorders may provide a powerful non-invasive tool for future wolf monitoring and could help to establish sustainable management plans for this species.
DOI: 10.6084/m9.figshare.4258313.v1
title: Continuous prophylaxis with recombinant factor IX Fc fusion protein and conventional recombinant factor IX products: comparisons of efficacy and weekly factor consumption

description: <b>Background:</b> Continuous prophylaxis for patients with hemophilia B requires frequent injections that are burdensome and that may lead to suboptimal adherence and outcomes. Hence, therapies requiring less-frequent injections are needed. In the absence of head-to-head comparisons, this study compared the first extended-half-life-recombinant factor IX (rFIX) product—recombinant factor IX Fc fusion protein (rFIXFc)—with conventional rFIX products based on annualized bleed rates (ABRs) and factor consumption reported in studies of continuous prophylaxis. <b>Methods:</b> This study compared ABRs and weekly factor consumption rates in clinical studies of continuous prophylaxis treatment with rFIXFc and conventional rFIX products (identified by systematic literature review) in previously-treated adolescents and adults with moderate-to-severe hemophilia B. Meta-analysis was used to pool ABRs reported for conventional rFIX products for comparison. Comparisons of weekly factor consumption were based on the mean, reported or estimated from the mean dose per injection. <b>Results:</b> Five conventional rFIX studies (injections 1 to &gt;3 times/week) met the criteria for comparison with once-weekly rFIXFc reported by the B-LONG study. The pooled mean ABR for conventional rFIX was slightly higher than but comparable to rFIXFc (difference=0.71; <i>p</i> = 0.210). Weekly factor consumption was significantly lower with rFIXFc than in conventional rFIX studies (difference in means = 42.8–74.5 IU/kg/week [93–161%], <i>p</i> <b>Conclusion:</b> Comparisons of clinical study results suggest weekly injections with rFIXFc result in similar bleeding rates and significantly lower weekly factor consumption compared with more-frequently-injected conventional rFIX products. The real-world effectiveness of rFIXFc may be higher based on results from a model of the impact of simulated differences in adherence.
DOI: 10.6084/m9.figshare.4258184
title: Table2.xlsx

description: Multivariate Pearson’s correlations (<i>r<sub>mvr</sub></i>) obtained from all participants after 10-fold cross-validated working memory load prediction from HbR fNIRS data over all channels using multivariate regression analysis (p &lt; 0.01 for all participants).
DOI: 10.6084/m9.figshare.4258148
title: Table1.xlsx

description: Descriptive statistics (mean values and standard deviation) of the task-related, driving behavior and physiological parameters in the five n-back conditions.
DOI: 10.6084/m9.figshare.4258184.v1
title: Table2.xlsx

description: Multivariate Pearson’s correlations (<i>r<sub>mvr</sub></i>) obtained from all participants after 10-fold cross-validated working memory load prediction from HbR fNIRS data over all channels using multivariate regression analysis (p &lt; 0.01 for all participants).
DOI: 10.6084/m9.figshare.4257860
title: KMZ file of subaerial beach sand volume change due to the June 2016 east coast low storm in SE Australia

description: Google Earth KMZ file of subaerial beach sand volume change (above mean sea level) due to the east coast low that impacted the coastline of SE Australia in June 2016. Data is at 100 m alongshore resolution spanning 177 km of surveyed coastline between Sydney and Nambucca Heads (New South Wales). Topographic measurements used to calculate sand volume changes were collected using Airborne Lidar flown immediately prior to and following the storm event.
DOI: 10.6084/m9.figshare.4257683
title: Simulated data

description: ##################################################Introduction##################################################<br>The data was simulated with ms (Hudson, Bioinformatics, 2002). The command that invoked ms (including the seed) and the simulated data are provided. For each simulation, the ms output was parsed into two files that are directly used for the analysis.100 unlinked loci were simulated, where each of them contains 100 SNPs. For each of the 100 demes, 20 chromosomes are simulated.<br>##################################################Folders and parameters##################################################<br>- Secondary contact models -<br>Parameters and files:mu mu_B t_C d t_s bottleneck_intensity archivename0.005 0.005 0 0.125 19 0.1 seccon.sim0.tgz 0.005 0.005 1 0.125 19 0.1 seccon.sim1.tgz 0.005 0.005 2 0.125 19 0.1 seccon.sim2.tgz 0.005 0.005 3 0.125 19 0.1 seccon.sim3.tgz 0.005 0.005 4 0.125 19 0.1 seccon.sim4.tgz 0.005 0.005 5 0.125 19 0.1 seccon.sim5.tgz 0.005 0.0005 1 0.125 19 0.1 seccon.sim31.tgz 0.005 0.0005 2 0.125 19 0.1 seccon.sim32.tgz 0.005 0.0005 3 0.125 19 0.1 seccon.sim33.tgz 0.005 0.0005 4 0.125 19 0.1 seccon.sim34.tgz 0.005 0.0005 5 0.125 19 0.1 seccon.sim35.tgz 0.005 0.005 1 0.125 19 0.25 seccon.sim51.tgz 0.005 0.005 1 0.125 19 0.5 seccon.sim52.tgz 0.005 0.005 1 0.25 19 0.1 seccon.sim61.tgz 0.005 0.005 1 0.375 19 0.1 seccon.sim62.tgz 0.01 0.01 1 0.125 19 0.1 seccon.sim71.tgz 0.05 0.05 1 0.125 19 0.1 seccon.sim72.tgz <br>main text (fig 3): sim0-sim5SI:- bottleneck intensity (fig S3): sim1, sim51-52- expansion speed (fig S4): sim1, sim61-62- migration rate (fig S5): sim1, sim71-72- secondary contact model with barrier (fig S6): sim0, sim31-35<br><br>- Stepping stone models -<br>Parameters and files:mu mu_B archivename0.005 0.005 step.sim10.tgz0.005 0.0005 step.sim11.tgz0.005 0.00005 step.sim12.tgz0.005 0.001 step.sim13.tgz0.005 0.0001 step.sim14.tgz0.005 0.00001 step.sim15.tgz0.01 0.00002 step.sim71.tgz0.05 0.0001 step.sim72.tgz<br>main text (fig 3): sim10-sim15SI: - migration rate (fig S5): sim15, sim71-72<br><br>############################################Files: ############################################<br>- Filenames -<br>sim* (see archivename) + number of the replicate (1-100)<br>- Filetypes - <br>- *.mscmd: Command that invoked ms.- *.posout: Positions of the segregating sites. One line per unlinked locus. For each locus, the positions of the 100 SNPs on a scale of (0, 1) are given, separated by blanks. - *.parseout: Segregating sites. One line per chromosome. Each line consists of the number of the deme (1-100, i. e. there are 20 lines per deme) followed by a sequence of 0s, and 1s, 0 for the ancestral and 1 for the derived allele at each polymorphic site, separated by blanks.<br>
DOI: 10.6084/m9.figshare.4257596
title: [dataset] Accessibility and Update status of published software: Benefits and missed opportunities

description: The two tables contain data of software packages published in <i>Molecular Ecology Resource </i>(MER) from 2001 to 2015, and in <i>BMC Bioinformatics</i> (2004). These data sets are part of an analysis under the title stated above.
DOI: 10.6084/m9.figshare.4257596.v1
title: [dataset] Accessibility and Update status of published software: Benefits and missed opportunities

description: The two tables contain data of software packages published in <i>Molecular Ecology Resource </i>(MER) from 2001 to 2015, and in <i>BMC Bioinformatics</i> (2004). These data sets are part of an analysis under the title stated above.
DOI: 10.6084/m9.figshare.4257683.v1
title: Simulated data

description: ##################################################Introduction##################################################<br>The data was simulated with ms (Hudson, Bioinformatics, 2002). The command that invoked ms (including the seed) and the simulated data are provided. For each simulation, the ms output was parsed into two files that are directly used for the analysis.100 unlinked loci were simulated, where each of them contains 100 SNPs. For each of the 100 demes, 20 chromosomes are simulated.<br>##################################################Folders and parameters##################################################<br>- Secondary contact models -<br>Parameters and files:mu mu_B t_C d t_s bottleneck_intensity archivename0.005 0.005 0 0.125 19 0.1 seccon.sim0.tgz 0.005 0.005 1 0.125 19 0.1 seccon.sim1.tgz 0.005 0.005 2 0.125 19 0.1 seccon.sim2.tgz 0.005 0.005 3 0.125 19 0.1 seccon.sim3.tgz 0.005 0.005 4 0.125 19 0.1 seccon.sim4.tgz 0.005 0.005 5 0.125 19 0.1 seccon.sim5.tgz 0.005 0.0005 1 0.125 19 0.1 seccon.sim31.tgz 0.005 0.0005 2 0.125 19 0.1 seccon.sim32.tgz 0.005 0.0005 3 0.125 19 0.1 seccon.sim33.tgz 0.005 0.0005 4 0.125 19 0.1 seccon.sim34.tgz 0.005 0.0005 5 0.125 19 0.1 seccon.sim35.tgz 0.005 0.005 1 0.125 19 0.25 seccon.sim51.tgz 0.005 0.005 1 0.125 19 0.5 seccon.sim52.tgz 0.005 0.005 1 0.25 19 0.1 seccon.sim61.tgz 0.005 0.005 1 0.375 19 0.1 seccon.sim62.tgz 0.01 0.01 1 0.125 19 0.1 seccon.sim71.tgz 0.05 0.05 1 0.125 19 0.1 seccon.sim72.tgz <br>main text (fig 3): sim0-sim5SI:- bottleneck intensity (fig S3): sim1, sim51-52- expansion speed (fig S4): sim1, sim61-62- migration rate (fig S5): sim1, sim71-72- secondary contact model with barrier (fig S6): sim0, sim31-35<br><br>- Stepping stone models -<br>Parameters and files:mu mu_B archivename0.005 0.005 step.sim10.tgz0.005 0.0005 step.sim11.tgz0.005 0.00005 step.sim12.tgz0.005 0.001 step.sim13.tgz0.005 0.0001 step.sim14.tgz0.005 0.00001 step.sim15.tgz0.01 0.00002 step.sim71.tgz0.05 0.0001 step.sim72.tgz<br>main text (fig 3): sim10-sim15SI: - migration rate (fig S5): sim15, sim71-72<br><br>############################################Files: ############################################<br>- Filenames -<br>sim* (see archivename) + number of the replicate (1-100)<br>- Filetypes - <br>- *.mscmd: Command that invoked ms.- *.posout: Positions of the segregating sites. One line per unlinked locus. For each locus, the positions of the 100 SNPs on a scale of (0, 1) are given, separated by blanks. - *.parseout: Segregating sites. One line per chromosome. Each line consists of the number of the deme (1-100, i. e. there are 20 lines per deme) followed by a sequence of 0s, and 1s, 0 for the ancestral and 1 for the derived allele at each polymorphic site, separated by blanks.<br>
DOI: 10.6084/m9.figshare.4257269
title: A protease/peptidase from culture medium of <i>Flammulina velutipes</i> that acts on arabinogalactan-protein

description: Arabinogalactan-proteins (AGPs) are highly diverse plant proteoglycans found on the plant cell surface. AGPs have large arabinogalactan (AG) moieties attached to a core-protein rich in hydroxyproline (Hyp). The AG undergoes hydrolysis by various glycoside hydrolases, most of which have been identified, whereas the core-proteins is presumably degraded by unknown proteases/peptidases secreted from fungi and bacteria in nature. Although several enzymes hydrolyzing other Hyp-rich proteins are known, the enzymes acting on the core-proteins of AGPs remain to be identified. The present study describes the detection of protease/peptidase activity toward AGP core-proteins in the culture medium of winter mushroom (<i>Flammulina velutipes</i>) and partial purification of the enzyme by several conventional chromatography steps. The enzyme showed higher activity toward Hyp residues than toward proline and alanine residues and acted on core-proteins prepared from gum arabic. Since the activity was inhibited in the presence of Pefabloc SC, the enzyme is probably a serine protease. The degradation of the core-protein of AGPs by a protease/peptidase from winter mushroom.
DOI: 10.6084/m9.figshare.4257269.v1
title: A protease/peptidase from culture medium of <i>Flammulina velutipes</i> that acts on arabinogalactan-protein

description: Arabinogalactan-proteins (AGPs) are highly diverse plant proteoglycans found on the plant cell surface. AGPs have large arabinogalactan (AG) moieties attached to a core-protein rich in hydroxyproline (Hyp). The AG undergoes hydrolysis by various glycoside hydrolases, most of which have been identified, whereas the core-proteins is presumably degraded by unknown proteases/peptidases secreted from fungi and bacteria in nature. Although several enzymes hydrolyzing other Hyp-rich proteins are known, the enzymes acting on the core-proteins of AGPs remain to be identified. The present study describes the detection of protease/peptidase activity toward AGP core-proteins in the culture medium of winter mushroom (<i>Flammulina velutipes</i>) and partial purification of the enzyme by several conventional chromatography steps. The enzyme showed higher activity toward Hyp residues than toward proline and alanine residues and acted on core-proteins prepared from gum arabic. Since the activity was inhibited in the presence of Pefabloc SC, the enzyme is probably a serine protease. The degradation of the core-protein of AGPs by a protease/peptidase from winter mushroom.
DOI: 10.6084/m9.figshare.4257128
title: Lyon's BSS 2011

description: This dataset is composed of 2 files : One corresponds to the position (lat, long) of BSS stations in Lyon.The other correspond to the total number of journeys between all pairs of stations in 2011.This dataset was used to test space-corrected community detection. (article under review)
DOI: 10.6084/m9.figshare.4257044
title: KBay_MOKH1.mat

description: Wind, air temp, water temp, and rain data from the National Buoy Data Center buoy MOKH1, located within Kane'ohe Bay.
DOI: 10.6084/m9.figshare.4257128.v1
title: Lyon's BSS 2011

description: This dataset is composed of 2 files : One corresponds to the position (lat, long) of BSS stations in Lyon.The other correspond to the total number of journeys between all pairs of stations in 2011.This dataset was used to test space-corrected community detection. (article under review)
DOI: 10.6084/m9.figshare.4257044.v1
title: KBay_MOKH1.mat

description: Wind, air temp, water temp, and rain data from the National Buoy Data Center buoy MOKH1, located within Kane'ohe Bay.
DOI: 10.6084/m9.figshare.4257038
title: KBay_met.mat

description: Wind, air temp, and rain data from the Kane'ohe Bay Marine Corps Base weather station.
DOI: 10.6084/m9.figshare.4257041
title: HFP_Stakes.mat

description: Pond temperature data from TidBit v2 sensors in Heʻeia fishpond.
DOI: 10.6084/m9.figshare.4257038.v1
title: KBay_met.mat

description: Wind, air temp, and rain data from the Kane'ohe Bay Marine Corps Base weather station.
DOI: 10.6084/m9.figshare.4257041.v1
title: HFP_Stakes.mat

description: Pond temperature data from TidBit v2 sensors in Heʻeia fishpond.
DOI: 10.6084/m9.figshare.4257032
title: HFP_flux.mat

description: Pond water volume flux data from current sensors placed at the base of each makaha (pond gate). Data is separated into flood and ebb tide time-series for each site.<br>
DOI: 10.6084/m9.figshare.4257032.v1
title: HFP_flux.mat

description: Pond water volume flux data from current sensors placed at the base of each makaha (pond gate). Data is separated into flood and ebb tide time-series for each site.<br>
DOI: 10.6084/m9.figshare.4257035
title: HFP_Hobos.mat

description: Pressure and temperature data from the HOBO water-level sensors placed on the seafloor within the makaha (pond gates).
DOI: 10.6084/m9.figshare.4257011
title: A list of all identified proteins determined from the hippocampal mitochondria of OT and Ctrl AD mice.

description: Mitochondrial repair effects of oxygen treatment on Alzheimer’s disease model mice revealed by quantitative proteomics Methodology 1. Animals Triple-transgenic AD mice [B6; 129-Psen1tm1Mpm Tg (APPSwe, tauP301L) 1Lfa/Mmjax] purchased from The Jackson Laboratory were divided into an oxygen-treated (OT) group (N = 12) and a control (Ctrl) group (N = 9). The oxygen treatment methods are described in detail elsewhere. 2. Mitochondrion isolation The hippocampus was homogenized with isolation buffer (225 mM sucrose, 75 mM mannitol, 1 mM EGTA, and 5 mM HEPES; pH 7.4) by Potter homogenization. Large cellular debris and nuclei were pelleted by centrifugation for 3 min at 1300 ×<i>g</i>. The resulting supernatant was centrifuged for 10 min at 21,000 ×<i>g</i> and the pellet was re-suspended in 1.5 mL of a 15% (v/v) Percoll (Sigma) solution. A stock Percoll solution was prepared as a mixture of Percoll and isolation buffer. A 1-mL aliquot of 40% Percoll solution was placed into a 4.0-mL polycarbonate tube and a neat layer of 1.5 mL of 24% Percoll was placed over the 40% Percoll solution aliquot. The re-suspended pellet was placed gently onto the Percoll gradient column. Separation was performed by centrifugation at 30,700 ×<i>g</i> for 50 min. After centrifugation, the upper band comprised of myelin and synaptosomes was removed carefully, and then the lower band containing mitochondria was collected. 3. Protein sample preparation and iTRAQ labeling To isolate mitochondria, we employed a method developed originally for use with lens tissues that was modified slightly for preparation of hippocampal mitochondria. Briefly, the mitochondria were lysed in ice-cold lysis buffer (KeyGEN, China) with an ultrasonic crusher (Branson Ultrasonics, USA). Subsequent protein digestion was performed by filter-aided sample preparation. After digestion, the tryptic peptides were labeled with iTRAQ reagents (AB SCIEX, USA) in accordance with the manufacturer’s protocol. Samples from the OT group were labeled with reagents 113 and 114; Ctrl group samples were labeled with reagents 115 and 116. 4. LC-MS/MS analysis LC-MS/MS analysis was performed with a nanoLC trap column (ChromXP C18) and a TripleTOF 5600 System (AB SCIEX, Concord, ON) fitted with a Nanospray III source (AB SCIEX, Concord, ON). Samples were loaded into a ChromXP C18 (3 μm, 120 Å) nanoLC trap column. Online chromatography separation was performed in a EksigentnanoLC-Ultra™ 2D System (AB SCIEX, Concord, ON). The scan scope (m/z) for TOF-MS is 350–1500 and that for MS/MS is 400–1250. The MS/MS data were analyzed for protein identification with ProteinPilot Software v.4.5 (AB Sciex Inc., USA). Gene Ontology (GO) categorization and protein-protein interaction were performed with the PANTHER and STRING databases, respectively.
DOI: 10.6084/m9.figshare.4257035.v1
title: HFP_Hobos.mat

description: Pressure and temperature data from the HOBO water-level sensors placed on the seafloor within the makaha (pond gates).
DOI: 10.6084/m9.figshare.4257011.v2
title: A list of all identified proteins determined from the hippocampal mitochondria of OT and Ctrl AD mice.

description: Mitochondrial repair effects of oxygen treatment on Alzheimer’s disease model mice revealed by quantitative proteomics Methodology 1. Animals Triple-transgenic AD mice [B6; 129-Psen1tm1Mpm Tg (APPSwe, tauP301L) 1Lfa/Mmjax] purchased from The Jackson Laboratory were divided into an oxygen-treated (OT) group (N = 12) and a control (Ctrl) group (N = 9). The oxygen treatment methods are described in detail elsewhere. 2. Mitochondrion isolation The hippocampus was homogenized with isolation buffer (225 mM sucrose, 75 mM mannitol, 1 mM EGTA, and 5 mM HEPES; pH 7.4) by Potter homogenization. Large cellular debris and nuclei were pelleted by centrifugation for 3 min at 1300 ×<i>g</i>. The resulting supernatant was centrifuged for 10 min at 21,000 ×<i>g</i> and the pellet was re-suspended in 1.5 mL of a 15% (v/v) Percoll (Sigma) solution. A stock Percoll solution was prepared as a mixture of Percoll and isolation buffer. A 1-mL aliquot of 40% Percoll solution was placed into a 4.0-mL polycarbonate tube and a neat layer of 1.5 mL of 24% Percoll was placed over the 40% Percoll solution aliquot. The re-suspended pellet was placed gently onto the Percoll gradient column. Separation was performed by centrifugation at 30,700 ×<i>g</i> for 50 min. After centrifugation, the upper band comprised of myelin and synaptosomes was removed carefully, and then the lower band containing mitochondria was collected. 3. Protein sample preparation and iTRAQ labeling To isolate mitochondria, we employed a method developed originally for use with lens tissues that was modified slightly for preparation of hippocampal mitochondria. Briefly, the mitochondria were lysed in ice-cold lysis buffer (KeyGEN, China) with an ultrasonic crusher (Branson Ultrasonics, USA). Subsequent protein digestion was performed by filter-aided sample preparation. After digestion, the tryptic peptides were labeled with iTRAQ reagents (AB SCIEX, USA) in accordance with the manufacturer’s protocol. Samples from the OT group were labeled with reagents 113 and 114; Ctrl group samples were labeled with reagents 115 and 116. 4. LC-MS/MS analysis LC-MS/MS analysis was performed with a nanoLC trap column (ChromXP C18) and a TripleTOF 5600 System (AB SCIEX, Concord, ON) fitted with a Nanospray III source (AB SCIEX, Concord, ON). Samples were loaded into a ChromXP C18 (3 μm, 120 Å) nanoLC trap column. Online chromatography separation was performed in a EksigentnanoLC-Ultra™ 2D System (AB SCIEX, Concord, ON). The scan scope (m/z) for TOF-MS is 350–1500 and that for MS/MS is 400–1250. The MS/MS data were analyzed for protein identification with ProteinPilot Software v.4.5 (AB Sciex Inc., USA). Gene Ontology (GO) categorization and protein-protein interaction were performed with the PANTHER and STRING databases, respectively.