cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.10047221.v1
title: Supplementary Material for: Aged Osteoporotic Bone Marrow Stromal Cells Demonstrate Defective Recruitment, Mechanosensitivity, and Matrix Deposition

description: Bone formation requires the replenishment of the osteoblast from a progenitor or stem cell population, which must be recruited, expanded, and differentiated to ensure continued anabolism. How this occurs and whether it is altered in the osteoporotic environment is poorly understood. Furthermore, given that emerging treatments for osteoporosis are targeting this progenitor population, it is critical to determine the regenerative capacity of this cell type in the setting of osteoporosis. Human bone marrow stromal cells (hMSCs) from a cohort of aged osteoporotic patients were compared to MSCs isolated from healthy donors in terms of the ability to undergo recruitment and proliferation, and also respond to both the biophysical and biochemical cues that drive osteogenic matrix deposition. hMSCs isolated from healthy donors demonstrate good recruitment, mechanosensitivity, proliferation, and differentiation capacity. Contrastingly, hMSCs isolated from aged osteoporotic patients had significantly diminished regenerative potential. Interestingly, we demonstrated that osteoporotic hMSCs no longer responded to chemokine-directing recruitment and became desensitised to mechanical stimulation. The osteoporotic MSCs had a reduced proliferative potential and, importantly, they demonstrated an attenuated differentiation capability with reduced mineral and lipid formation. Moreover, during osteogenesis, despite minimal differences in the quantity of deposited collagen, the distribution of collagen was dramatically altered in osteoporosis, suggesting a potential defect in matrix quality. Taken together, this study has demonstrated that hMSCs isolated from aged osteoporotic patients demonstrate defective cell behaviour on multiple fronts, resulting in a significantly reduced regenerative potential, which must be considered during the development of new anabolic therapies that target this cell population.
DOI: 10.6084/m9.figshare.10047041
title: ANI-1x Dataset Release

description: The data file requires special tools for extracting. These tools are available at our support GitHub repository: https://github.com/aiqm/ANI1x_datasets
DOI: 10.21227/j39v-2v65
title: New circuit for the electronics choke for tu

description: One best circuit for the electronics choke for tube light
DOI: 10.6084/m9.figshare.10047089
title: A novel doubly labelled <sup>13</sup>C, <sup>15</sup>N amino acid method for measuring energy and protein metabolism in man

description: A novel doubly [1-<sup>13</sup>C, α-<sup>15</sup>NH<sub>2</sub>]-labelled amino acid method (DLAAM) is presented for the determination of the CO<sub>2</sub> production (RCO<sub>2</sub>) and energy expenditure in humans. This method is based on the simultaneous administration of [1-<sup>13</sup>C]glycine and [<sup>15</sup>N]glycine followed by the measurement of excretion kinetics of breath <sup>13</sup>CO<sub>2</sub> and urinary <sup>15</sup>N. The basic idea of the DLAAM is that the unknown <sup>13</sup>C recovery RF(<sup>13</sup>C) of the 1-<sup>13</sup>C amino acid, essential for the calculation of the net CO<sub>2</sub> production, can be approximated by the easily measureable <sup>15</sup>N recovery RF(<sup>15</sup>N) of the α-<sup>15</sup>NH<sub>2</sub> labelled amino acid. In four healthy adult men (76–97 kg) the DLAAM was tested parallel to the IC and in one man (74 kg) parallel to the DLWM. Using the approximation RF(<sup>13</sup>C) ≈ RF(<sup>15</sup>N) the RCO<sub>2</sub> (in l CO<sub>2</sub> d<sup>–1</sup>) was calculated to 387.0 ± 30.3 (DLAAM) vs. 382.8 ± 22.6. (IC). The Bland–Altman plot shows that the difference between the DLAAM and IC of individual RCO<sub>2</sub> is within the 95 % confidence interval (mean ± 2 SD): +4.3 ± 37.5 l CO<sub>2</sub> d<sup>–1</sup>. We conclude that the DLAAM and IC may be used interchangeably. The physical activity level (PAL) was calculated based on the DLAAM vs. DLWM to about 1.5.
DOI: 10.6084/m9.figshare.10047089.v1
title: A novel doubly labelled <sup>13</sup>C, <sup>15</sup>N amino acid method for measuring energy and protein metabolism in man

description: A novel doubly [1-<sup>13</sup>C, α-<sup>15</sup>NH<sub>2</sub>]-labelled amino acid method (DLAAM) is presented for the determination of the CO<sub>2</sub> production (RCO<sub>2</sub>) and energy expenditure in humans. This method is based on the simultaneous administration of [1-<sup>13</sup>C]glycine and [<sup>15</sup>N]glycine followed by the measurement of excretion kinetics of breath <sup>13</sup>CO<sub>2</sub> and urinary <sup>15</sup>N. The basic idea of the DLAAM is that the unknown <sup>13</sup>C recovery RF(<sup>13</sup>C) of the 1-<sup>13</sup>C amino acid, essential for the calculation of the net CO<sub>2</sub> production, can be approximated by the easily measureable <sup>15</sup>N recovery RF(<sup>15</sup>N) of the α-<sup>15</sup>NH<sub>2</sub> labelled amino acid. In four healthy adult men (76–97 kg) the DLAAM was tested parallel to the IC and in one man (74 kg) parallel to the DLWM. Using the approximation RF(<sup>13</sup>C) ≈ RF(<sup>15</sup>N) the RCO<sub>2</sub> (in l CO<sub>2</sub> d<sup>–1</sup>) was calculated to 387.0 ± 30.3 (DLAAM) vs. 382.8 ± 22.6. (IC). The Bland–Altman plot shows that the difference between the DLAAM and IC of individual RCO<sub>2</sub> is within the 95 % confidence interval (mean ± 2 SD): +4.3 ± 37.5 l CO<sub>2</sub> d<sup>–1</sup>. We conclude that the DLAAM and IC may be used interchangeably. The physical activity level (PAL) was calculated based on the DLAAM vs. DLWM to about 1.5.
DOI: 10.21227/032a-a191
title: New circuit for the electronics choke for tu

description: One best circuit for the electronics choke for tube light
DOI: 10.6084/m9.figshare.10046618
title: Data Carpentry data

description: Data for 10/24 data carpentry<br>
DOI: 10.6084/m9.figshare.10046618.v1
title: Data Carpentry data

description: Data for 10/24 data carpentry<br>
DOI: 10.6084/m9.figshare.10046558
title: Actinidia chinensis genome data

description: Actinidia chinensis genome fasta and gff3 files
DOI: 10.26180/5db26bbd7ff51
title: Singh_etal_2019

description: Data and code archive for the paper:<br>Singh, M.S., Warren, R.A., & Jakob, C. (2019): A steady-state model for the relationship between humidity, instability, and precipitation in the tropics, Journal of Advances in Modeling Earth Systems (in review).<br><br>Version 4 corresponds to the exact code and figures used in the paper.<br>See the readme.txt for further details.
DOI: 10.6084/m9.figshare.10046570.v1
title: 0821-origin里面数据整理.xlsx

description: database
DOI: 10.6084/m9.figshare.10046570.v2
title: 0821-origin里面数据整理.xlsx

description: database
DOI: 10.6084/m9.figshare.10046570.v3
title: sap flow

description: database
DOI: 10.6084/m9.figshare.10046105
title: Figures_raw_data.xlsx

description: The small fiber neuropathy NaV1.7 I228M mutation: impaired neurite integrity <em>via</em> bioenergetic and mitotoxic mechanisms, and protection by dexpramipexole
DOI: 10.6084/m9.figshare.10046024
title: Social and cultural factors perpetuating early marriage in rural Gambia: an exploratory mixed methods study

description: Focus group discussion guide
DOI: 10.6084/m9.figshare.10046105.v1
title: Figures_raw_data.xlsx

description: The small fiber neuropathy NaV1.7 I228M mutation: impaired neurite integrity <em>via</em> bioenergetic and mitotoxic mechanisms, and protection by dexpramipexole
DOI: 10.6084/m9.figshare.10046024.v1
title: Social and cultural factors perpetuating early marriage in rural Gambia: an exploratory mixed methods study

description: Focus group discussion guide
DOI: 10.6084/m9.figshare.10045976
title: Time series of long-term experimental predator-prey cycles

description: Tine series from a set of ten chemostat experiments with a planktonic predator-prey system. The data contain measured population densities of the prey (unicellular algae) and the predator (rotifer) and predator life stage characteristics for a total of about 2,000 measurement days - exhibiting predator-prey cycles of unprecedented length.<br>Reference:Blasius B, Rudolf L, Weithoff G, Gaedke U, Fussmann G.F. Long-term cyclic persistence in an experimental predator-prey system. Nature (2019).<br><br>The ten data files correspond to the 10 experiments, explained in the Extended Data Table 1 of this publication.<br>Please acknowledge the use of this data by citing the above reference.<br><br>
DOI: 10.6084/m9.figshare.10045979
title: Social and cultural factors perpetuating early marriage in rural Gambia: an exploratory mixed methods study

description: The dataset deposited here is part of a larger study that was conducted to determine the factors that either perpetuate or lead to a decline in early marriage in 24 rural communities in Lower Baddibu District in the North Bank of the Gambia.
DOI: 10.6084/m9.figshare.10045979.v1
title: Social and cultural factors perpetuating early marriage in rural Gambia: an exploratory mixed methods study

description: The dataset deposited here is part of a larger study that was conducted to determine the factors that either perpetuate or lead to a decline in early marriage in 24 rural communities in Lower Baddibu District in the North Bank of the Gambia.
DOI: 10.6084/m9.figshare.10043216
title: Multilocus phylogeny of Acrospermaceae: New epibiotic species and placement of <i>Gonatophragmium, Pseudovirgaria</i>, and <i>Phaeodactylium</i> anamorphs

description: <i>Acrospermum</i> is a poorly known genus of epibiotic and saprophytic species with a subcosmopolitan distribution. Here, we investigate the intriguing relationship between <i>Acrospermum</i> and its host plants in the fern family Polypodiaceae, where it occurs upon approximately 45 neotropical species. We conducted phylogenetic analyses using an eight-marker comprehensive ascomycete data set comprising 719 species representing all major lineages along with 23 new <i>Acrospermum</i> specimens sampled from ferns. We ask whether fern-dwelling <i>Acrospermum</i> are monophyletic, whether epibiotic <i>Acrospermum</i> have evolved independently from saprophytic ancestors, and identify anamorphic phases by incorporating sequences for all suspected taxa. Our results corroborate the placement of Acrospermales within the Dothideomycetes with strong support. However, the order remains incertae sedis due to weak support along the branches subtending the clade that includes the Acrospermales plus Dyfrolomycetales. Our results show a strong phylogenetic pattern in lifestyles but do not clearly identify an ancestral life history state. The first divergence in Acrospermaceae splits fungicolous taxa from taxa that inhabit plants; saprophytes and anamorphic phases found on angiosperms occur in both clades. Fungicolous species are monophyletic, whereas species with an epibiotic or necrotic life history upon plants are nonmonophyletic due to the position of the saprophyte <i>A. longisporium</i>. Previously, all <i>Acrospermum</i> collected from ferns were identified as <i>A. maxonii</i>. Our results indicate that this is not monophyletic due to the inclusion of <i>Gonatophragmium triuniae</i>. Two species are described herein as <i>A. gorditum</i>, sp. nov., and <i>A. leucocephalum</i>, sp. nov. We find no instances of co-cladogenesis; however, our ability to detect this is limited by the lack of resolution in the <i>A. maxonii</i> clade. Rather, we see that that the distribution of epibiotic <i>Acrospermum</i> is explained by the overlap between the ecological niche of the <i>Acrospermum</i> species and its host.
DOI: 10.6084/m9.figshare.10043216.v1
title: Multilocus phylogeny of Acrospermaceae: New epibiotic species and placement of <i>Gonatophragmium, Pseudovirgaria</i>, and <i>Phaeodactylium</i> anamorphs

description: <i>Acrospermum</i> is a poorly known genus of epibiotic and saprophytic species with a subcosmopolitan distribution. Here, we investigate the intriguing relationship between <i>Acrospermum</i> and its host plants in the fern family Polypodiaceae, where it occurs upon approximately 45 neotropical species. We conducted phylogenetic analyses using an eight-marker comprehensive ascomycete data set comprising 719 species representing all major lineages along with 23 new <i>Acrospermum</i> specimens sampled from ferns. We ask whether fern-dwelling <i>Acrospermum</i> are monophyletic, whether epibiotic <i>Acrospermum</i> have evolved independently from saprophytic ancestors, and identify anamorphic phases by incorporating sequences for all suspected taxa. Our results corroborate the placement of Acrospermales within the Dothideomycetes with strong support. However, the order remains incertae sedis due to weak support along the branches subtending the clade that includes the Acrospermales plus Dyfrolomycetales. Our results show a strong phylogenetic pattern in lifestyles but do not clearly identify an ancestral life history state. The first divergence in Acrospermaceae splits fungicolous taxa from taxa that inhabit plants; saprophytes and anamorphic phases found on angiosperms occur in both clades. Fungicolous species are monophyletic, whereas species with an epibiotic or necrotic life history upon plants are nonmonophyletic due to the position of the saprophyte <i>A. longisporium</i>. Previously, all <i>Acrospermum</i> collected from ferns were identified as <i>A. maxonii</i>. Our results indicate that this is not monophyletic due to the inclusion of <i>Gonatophragmium triuniae</i>. Two species are described herein as <i>A. gorditum</i>, sp. nov., and <i>A. leucocephalum</i>, sp. nov. We find no instances of co-cladogenesis; however, our ability to detect this is limited by the lack of resolution in the <i>A. maxonii</i> clade. Rather, we see that that the distribution of epibiotic <i>Acrospermum</i> is explained by the overlap between the ecological niche of the <i>Acrospermum</i> species and its host.
DOI: 10.6084/m9.figshare.10043177
title: Effects of sterilization techniques on chemodenitrification and N2O production in tropical peat soil microcosms

description: Chemodenitrification – the non-enzymatic process of nitrite reduction – may be an important sink for fixed nitrogen in tropical peatlands with low oxygen, low pH, high organic matter, and variable ferrous iron concentrations. Assessing abiotic reaction pathways is difficult because sterilization/inhibition agents can alter the availability of reactants by changing iron speciation and organic matter composition. We compared six commonly used soil sterilization techniques – γ-irradiation, chloroform, autoclaving, and chemical inhibitors (mercury, zinc, and azide) – for their compatibility with chemodenitrification assays for tropical peatland soils (organic-rich low pH soil from the Eastern Amazon). Out of the six techniques, γ-irradiation resulted in soil treatments with lowest cell viability and denitrification activity, and least effect on pH, iron speciation, and organic matter composition. Nitrite depletion rates in γ-irradiated soils were highly similar to untreated/live soils, whereas other sterilization techniques showed deviations. Chemodenitrification was a dominant process in tropical peatland soils assayed in this study. Abiotic N2O production was low to moderate (3–16 % of converted nitrite), and different sterilization techniques lead to significant variations on production rates due to inherent processes or potential artifacts. Our work represents the first methodological basis for testing the abiotic denitrification and N2O production potential in tropical peatland soil.
DOI: 10.6084/m9.figshare.10043132
title: ProteomeTools - Prosit iRT - Data (update) // missing c + splitting

description: The original Prosit iRT dataset missed ProteomeTools sequences containing cysteine.<br>We applied now the same criteria as in the original publication<i>Data for learning was restricted to peptides identified with a minimum MaxQuant score of 70 and an iRT variance between different ProteomeTools runs of less than 1.<br></i><br>iRT values are the same as in the publication, the scaled values can differ as the normalization function is now applied on a different data range.<br>Please be aware that the original iRT model error can not be achieved as their was train/validation leakage. Therefore please don`t compare to the reported validation error of the weight file. The overall performance stays similar when using the new data.<b><br></b><b>Sry for the inconvenience.</b><br>The model trained on the original data will stay on the prosit website for fair comparison to the publication.
DOI: 10.6084/m9.figshare.10042934
title: Índice H.pdf

description: sdfsdfsdf
DOI: 10.6084/m9.figshare.10042934.v1
title: Índice H.pdf

description: sdfsdfsdf
DOI: 10.6084/m9.figshare.10042928
title: When policy meets the pedal: A reduction in motorcyclist fatalities following the implementation of a road traffic law in Lagos, Nigeria

description: <b>Objective:</b> The Lagos State Road Traffic Law of 2012 sought to curb reckless <i>okada</i> use and the objective of this study is to determine its impact on motorcyclist fatalities in Nigeria’s most densely populated state. This is the first study to date that analyzes the potential impact of the Law on motorcyclist fatalities across Lagos State. <b>Methods:</b> We retrospectively reviewed monthly motorcyclist fatalities in Lagos between January 2012 and December 2015. We analyzed the data using Geographic Information Systems (GIS) software, and used Quantum GIS ver. 2.16.2 to create maps illustrating the spatial-epidemiological distribution of motorcyclist fatalities across Lagos’ health facilities. The data was collated into three eight-month periods for analysis (pre-intervention, immediate post-intervention, and sustained post-intervention). Period 1 was January to August 2012, Period 2 was September 2012 to April 2013, and Period 3 was May to December 2013. The data were compared in SPSS using the Welch’s ANOVA and Tanhame (post-hoc) tests with a 5% significance level. <b>Results:</b> Motorcyclist fatalities in Lagos fell by an average of 76% over the study period. Over 55% of the fatalities were recorded in five health facilities, located in an area of high road network density. The number of newly registered motorcycles also declined by an average of 69%. The Welch’s ANOVA yielded a statistically significant difference between the Periods’ means (p <b>Conclusions:</b> This study shows a significant decline in motorcyclist fatalities following the implementation of the Lagos State Road Traffic Law of 2012. A more comprehensive approach to data collection along with an updated law could contribute towards a sustainable reduction of motorcyclist mortality.
DOI: 10.6084/m9.figshare.10042928.v1
title: When policy meets the pedal: A reduction in motorcyclist fatalities following the implementation of a road traffic law in Lagos, Nigeria

description: <b>Objective:</b> The Lagos State Road Traffic Law of 2012 sought to curb reckless <i>okada</i> use and the objective of this study is to determine its impact on motorcyclist fatalities in Nigeria’s most densely populated state. This is the first study to date that analyzes the potential impact of the Law on motorcyclist fatalities across Lagos State. <b>Methods:</b> We retrospectively reviewed monthly motorcyclist fatalities in Lagos between January 2012 and December 2015. We analyzed the data using Geographic Information Systems (GIS) software, and used Quantum GIS ver. 2.16.2 to create maps illustrating the spatial-epidemiological distribution of motorcyclist fatalities across Lagos’ health facilities. The data was collated into three eight-month periods for analysis (pre-intervention, immediate post-intervention, and sustained post-intervention). Period 1 was January to August 2012, Period 2 was September 2012 to April 2013, and Period 3 was May to December 2013. The data were compared in SPSS using the Welch’s ANOVA and Tanhame (post-hoc) tests with a 5% significance level. <b>Results:</b> Motorcyclist fatalities in Lagos fell by an average of 76% over the study period. Over 55% of the fatalities were recorded in five health facilities, located in an area of high road network density. The number of newly registered motorcycles also declined by an average of 69%. The Welch’s ANOVA yielded a statistically significant difference between the Periods’ means (p <b>Conclusions:</b> This study shows a significant decline in motorcyclist fatalities following the implementation of the Lagos State Road Traffic Law of 2012. A more comprehensive approach to data collection along with an updated law could contribute towards a sustainable reduction of motorcyclist mortality.
DOI: 10.6084/m9.figshare.10042808
title: LipidPWs20191024

description: All pathways related to lipids from WikiPathways and LipidMaps for species Homo sapiens (Human). These files are presented as GPML files, which can be used for pathway analysis in Pathvisio. Please use the latest mapping files from BridgeDb (https://www.bridgedb.org/mapping-databases/hmdb-metabolite-mappings/ ) when performing pathway analysis.
DOI: 10.6084/m9.figshare.10042808.v1
title: LipidPWs20191024

description: All pathways related to lipids from WikiPathways and LipidMaps for species Homo sapiens (Human). These files are presented as GPML files, which can be used for pathway analysis in Pathvisio. Please use the latest mapping files from BridgeDb (https://www.bridgedb.org/mapping-databases/hmdb-metabolite-mappings/ ) when performing pathway analysis.
DOI: 10.6084/m9.figshare.10042379
title: Voltage vs. Ligand I: Structural basis of the intrinsic flexibility of S3 segment and its significance in ion channel activation

description: We systematically predict the internal flexibility of the S3 segment, one of the most mobile elements in the voltage-sensor domain. By analyzing the primary amino acid sequences of V-sensor containing proteins, including Hv1, TPC channels and the voltage-sensing phosphatases, we established correlations between the local flexibility and modes of activation for different members of the VGIC superfamily. Taking advantage of the structural information available, we also assessed structural aspects to understand the role played by the flexibility of S3 during the gating of the pore. We found that S3 flexibility is mainly determined by two specific regions: (1) a short NxxD motif in the N-half portion of the helix (S3a), and (2) a short sequence at the beginning of the so-called <i>paddle</i> motif where the segment has a kink that, in some cases, divide S3 into two distinct helices (S3a and S3b). A good correlation between the flexibility of S3 and the reported sensitivity to temperature and mechanical stretch was found. Thus, if the channel exhibits high sensitivity to heat or membrane stretch, local S3 flexibility is low. On the other hand, high flexibility of S3 is preferentially associated to channels showing poor heat and mechanical sensitivities. In contrast, we did not find any apparent correlation between S3 flexibility and voltage or ligand dependence. Overall, our results provide valuable insights into the dynamics of channel-gating and its modulation.