cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6434144
title: Dataset for Browne et al. - The relative contributions of seed and pollen dispersal to gene flow and genetic diversity in seedlings of a tropical palm

description: Data set from:The relative contributions of seed and pollen dispersal to gene flow and genetic diversity in seedlings of a tropical palm by Luke Browne, Kym Ottewell, Victoria Sork, and Jordan Karubian.<br>AbstractSeed and pollen dispersal shape patterns of gene flow and genetic diversity in plants. Pollen is generally thought to travel longer distances than seeds, but seeds determine the ultimate location of gametes. Resolving how interactions between these two dispersal processes shape micro-evolutionary processes is a long-standing research priority. We unambiguously isolated the separate and combined contributions of these two dispersal processes in seedlings of the animal-dispersed palm Oenocarpus bataua to address two questions. First, what is the spatial extent of pollen vs. seed movement in a system characterized by long distance seed dispersal? Second, how does seed dispersal mediate seedling genetic diversity? Despite evidence of frequent long distance seed dispersal, we found that pollen moves much further than seeds. Nonetheless, seed dispersal ultimately mediates genetic diversity and fine-scale spatial genetic structure. Compared to undispersed seedlings, seedlings dispersed by vertebrates were characterized by higher female gametic and diploid seedling diversity and weaker fine-scale spatial genetic structure for female gametes, male gametes, and diploid seedlings. Interestingly, the diversity of maternal seed sources at seed deposition sites (Nem) was associated with higher effective number of pollen sources (Nep), higher effective number of parents (Ne), and weaker spatial genetic structure, whereas seed dispersal distance had little impact on these or other parameters we measured. These findings highlight the importance of frugivore-mediated diversity of maternal seed sources (Nem) at deposition sites in driving emergent patterns of fine scale genetic diversity and structure.<br>
DOI: 10.6084/m9.figshare.6434144.v1
title: Dataset for Browne et al. - The relative contributions of seed and pollen dispersal to gene flow and genetic diversity in seedlings of a tropical palm

description: Data set from:The relative contributions of seed and pollen dispersal to gene flow and genetic diversity in seedlings of a tropical palm by Luke Browne, Kym Ottewell, Victoria Sork, and Jordan Karubian.<br>AbstractSeed and pollen dispersal shape patterns of gene flow and genetic diversity in plants. Pollen is generally thought to travel longer distances than seeds, but seeds determine the ultimate location of gametes. Resolving how interactions between these two dispersal processes shape micro-evolutionary processes is a long-standing research priority. We unambiguously isolated the separate and combined contributions of these two dispersal processes in seedlings of the animal-dispersed palm Oenocarpus bataua to address two questions. First, what is the spatial extent of pollen vs. seed movement in a system characterized by long distance seed dispersal? Second, how does seed dispersal mediate seedling genetic diversity? Despite evidence of frequent long distance seed dispersal, we found that pollen moves much further than seeds. Nonetheless, seed dispersal ultimately mediates genetic diversity and fine-scale spatial genetic structure. Compared to undispersed seedlings, seedlings dispersed by vertebrates were characterized by higher female gametic and diploid seedling diversity and weaker fine-scale spatial genetic structure for female gametes, male gametes, and diploid seedlings. Interestingly, the diversity of maternal seed sources at seed deposition sites (Nem) was associated with higher effective number of pollen sources (Nep), higher effective number of parents (Ne), and weaker spatial genetic structure, whereas seed dispersal distance had little impact on these or other parameters we measured. These findings highlight the importance of frugivore-mediated diversity of maternal seed sources (Nem) at deposition sites in driving emergent patterns of fine scale genetic diversity and structure.<br>
DOI: 10.6084/m9.figshare.6431549
title: Cauchoix, Chow, van Horik et al.

description: To further our understanding of the evolution of cognition we gathered 44 datasets of 26 species and used meta-analysis to evaluate whether cognitive performance is repeatable across taxa. We assessed individual repeatability in performance on the same task presented at different time intervals (Temporal Repeatability), and on different tasks that measure the same putative cognitive ability (Contextual Repeatability). We found support for both temporal and contextual repeatability of individual variation in cognitive performance, with significant mean R estimates ranging between 0.15 and 0.28. Our overall findings highlight the widespread occurrence of consistent inter-individual variation in cognition.
DOI: 10.6084/m9.figshare.6431489
title: denovo-genes.fna.tar.gz

description: Sequences of the genes predicted <i>de novo</i> by prodigal in the co-assembled metagenomic data
DOI: 10.6084/m9.figshare.6431489.v1
title: denovo-genes.fna.tar.gz

description: Sequences of the genes predicted <i>de novo</i> by prodigal in the co-assembled metagenomic data
DOI: 10.6084/m9.figshare.6431441
title: denovo_DESeq.zip

description: The differentially abundant genes in each pairwise comparison of treatments
DOI: 10.6084/m9.figshare.6431441.v1
title: denovo_DESeq.zip

description: The differentially abundant genes in each pairwise comparison of treatments
DOI: 10.6084/m9.figshare.6431435
title: Humann2-AllSamples.genefamilies.biom.zip

description: The gene family abundance table (in biom format) calculated by humann2 using uniref50 reference database.
DOI: 10.6084/m9.figshare.6431435.v1
title: Humann2-AllSamples.genefamilies.biom.zip

description: The gene family abundance table (in biom format) calculated by humann2 using uniref50 reference database.
DOI: 10.6084/m9.figshare.6431432
title: Taxonomy.zip

description: The taxonomy files including genus level an family level taxonomy
DOI: 10.6084/m9.figshare.6431432.v1
title: Taxonomy.zip

description: The taxonomy files including genus level an family level taxonomy
DOI: 10.6084/m9.figshare.6431108
title: Cane Toad

description: Raw data for potential Func Ecol paper
DOI: 10.6084/m9.figshare.6430982
title: FishTrees

description: Here is the fish trees used in our paper "Prioritizing phylogenetic diversity captures functional diversity unreliably"( in Nature Communications (https://www.nature.com/articles/s41467-018-05126-3).<br><br>
DOI: 10.6084/m9.figshare.6430982.v1
title: FishTrees

description: Here is the fish trees used in our paper "Prioritizing phylogenetic diversity captures functional diversity unreliably"( in Nature Communications (https://www.nature.com/articles/s41467-018-05126-3).<br><br>
DOI: 10.6084/m9.figshare.6429635
title: CAD Drawing of Centrifugal Pump with Gearbox.step

description: This CAD drawing is of a centrifugal pump and gearbox. The pump and gearbox package are designed to be attached to the top tube of a bicycle. My goal for this product is to make a low-cost and mass producible pump for small-scale farmers to use for irrigation. Considerably more detail is available about the project, drawing, and design decisions in my thesis, which is linked below. In particular, look for the “Design Iteration” section and the “Design Decisions” Appendix. The drawing was made on a cloud-based software called Onshape. The drawing is public ally available at the following link: https://cad.onshape.com/documents/b0f8c16ed722823e0c0c7eea/w/b30c7aed828691fffe065eaf/e/b205bec239811c42af7d37fdThe pump is intended to be made and distributed by World Bicycle Relief’s Buffalo Bikes program. I made the drawing in conjunction with a drawing of a Buffalo Bike frame. However, to preserve the trade secrets of the Buffalo Bike, I have removed the bicycle from the public version of the pump drawing. The pump impeller, the pump volute, and the various threads are for illustration purposes only. The shape of centrifugal pump impellers and volute are complex and beyond my immediate scope to design. For more details on their design, see Centrifugal Pumps Design & Application by Lobanoff and Ross. ISBN 0-87201-200-X <br>I built the pump housing off of another onshape drawing; the “Centrifugal Pump” by tony_soares459. About his drawing, Tony said “The pump was a pet project that I did for some documentation work. I didn't have a good illustration of a centrifugal pump and decided to create one using Onshape. So no grand purpose for it—I tried only to make it seem realistic. Sadly, it probably wouldn't work too well if manufactured.” Because I was working from Tony’s drawing, in the pump tab of my drawing there are lots of suppressed elements and at one point I scale down the whole drawing by around a factor of 3. I field tested an earlier prototype of a centrifugal bike pump, but I have not made or tested the design in this drawing. I hope you find the drawing useful, and I hope that as a community, we can improve the lives of small-scale farmers.
DOI: 10.6084/m9.figshare.6429629
title: real ice accumulation

description: the excel for velocity and ice thickness analysis <br><br>
DOI: 10.6084/m9.figshare.6429629.v1
title: real ice accumulation

description: the excel for velocity and ice thickness analysis <br><br>
DOI: 10.6084/m9.figshare.6429509
title: Correlates to Shared Decision Making in Healthcare In Uganda

description: The Uganda Medical and Dental Practitioners Act, chapter 272, provides for the ‘right to treatment based on clinical need regardless of one’s ability to pay; participation in health care decisions; accessing information about Health care worker providing care, patients’ diseases and treatment; respect, dignity and privacy’. Additionally, The Uganda Patients’ Charter of 2009 describes a ‘set of rights, responsibilities and duties under which a person can seek and receive health care service and empowers patients to responsibly demand for quality health care and actively participate in their care at public facilities’
DOI: 10.6084/m9.figshare.6429509.v2
title: Correlates to Shared Decision Making in Healthcare In Uganda

description: The Uganda Medical and Dental Practitioners Act, chapter 272, provides for the ‘right to treatment based on clinical need regardless of one’s ability to pay; participation in health care decisions; accessing information about Health care worker providing care, patients’ diseases and treatment; respect, dignity and privacy’. Additionally, The Uganda Patients’ Charter of 2009 describes a ‘set of rights, responsibilities and duties under which a person can seek and receive health care service and empowers patients to responsibly demand for quality health care and actively participate in their care at public facilities’
DOI: 10.6084/m9.figshare.6429452
title: GUI for a historical database

description: In this research the characteristics of a <i>usable</i> Graphical User Interface (GUI) are determined in the context of a historical database. A GUI is an interface that enables users to directly interact with the content the GUI is build upon and the functionalities the GUI offers. The historical database is about former German citizens residing in the Netherlands, in the process of removing their <i>Enemy of the state </i>status. This status was given by the Dutch government in the aftermath of WWII, as a retribution for the German atrocities during WWII. The operation ended due to resistance amongst the Dutch citizens, after which the citizens could remove their <i>Enemy of the State</i> status. The mockup GUI incorporated the following <i>usable</i> characteristics; giving users the information they seek with justification, clear and useful functionalities of the GUI, simple in its use, and a structured layout. The mockup GUI was evaluated by average internet users, that tested the mockup GUI version interactively and reviewed their experience with usability statements. The mockup GUI was evaluated as good, so the given <i>usable</i> characteristics make the GUI usable.
DOI: 10.6084/m9.figshare.6429443
title: Gender-specific preference in online dating

description: This web page contains the dataset for the paper “Gender-specific preference in online dating” by Xixian Su and Haibo Hu. Please see the word document README.doc for detailed data description.
DOI: 10.6084/m9.figshare.6429386
title: Between-group encounters in Nicobar long-tailed macaque (<i>Macaca fascicularis umbrosus</i>)

description: Group living primates often participate in between-group encounters to defend monopolizable resources. Participation in an encounter is influenced by the density and abundance of resources and the relative fighting ability of groups. We studied between-group encounters in three groups of Nicobar long-tailed macaques (<i>Macaca fascicularis umbrosus</i>) in the Great Nicobar Island, with one group, TR, being the focal study group to measure the influence of these factors on between-group encounters. Encounters varied from mutual tolerance to aggressive fights, with females participating less aggressively than males. Sleeping site and vegetation cover were the primary influences on the nature of interaction in the areas where home range overlapped. The initiation and intensity of an encounter were influenced by relative group size. The focal group (TR) was the smallest of the three groups in the area and it actively avoided confrontation with the other two groups (MG and PI), resulting in a lower observed encounter rate than expected. Both the frequency and aggressiveness of encounters was influenced by the number of females cycling and the number of males present in the study group. Inasmuch as encounters were influenced by the number of females and the distribution of food, rather than geography, we conclude that encounters serve to defend food resources and mates rather than that they are examples of territoriality.
DOI: 10.6084/m9.figshare.6429386.v1
title: Between-group encounters in Nicobar long-tailed macaque (<i>Macaca fascicularis umbrosus</i>)

description: Group living primates often participate in between-group encounters to defend monopolizable resources. Participation in an encounter is influenced by the density and abundance of resources and the relative fighting ability of groups. We studied between-group encounters in three groups of Nicobar long-tailed macaques (<i>Macaca fascicularis umbrosus</i>) in the Great Nicobar Island, with one group, TR, being the focal study group to measure the influence of these factors on between-group encounters. Encounters varied from mutual tolerance to aggressive fights, with females participating less aggressively than males. Sleeping site and vegetation cover were the primary influences on the nature of interaction in the areas where home range overlapped. The initiation and intensity of an encounter were influenced by relative group size. The focal group (TR) was the smallest of the three groups in the area and it actively avoided confrontation with the other two groups (MG and PI), resulting in a lower observed encounter rate than expected. Both the frequency and aggressiveness of encounters was influenced by the number of females cycling and the number of males present in the study group. Inasmuch as encounters were influenced by the number of females and the distribution of food, rather than geography, we conclude that encounters serve to defend food resources and mates rather than that they are examples of territoriality.
DOI: 10.6084/m9.figshare.6429362
title: Gold Open Access Journals 2012-2017 (GOAJ3)

description: This dataset is identical to the misnamed GOAJ3: Gray Open Access Journals 2012-2017, added because I see no way to change the title of a dataset once it's been published. The dataset is, of course, GOLD open access journals, not gray ones.<br>
DOI: 10.6084/m9.figshare.6429362.v1
title: Gold Open Access Journals 2012-2017 (GOAJ3)

description: This dataset is identical to the misnamed GOAJ3: Gray Open Access Journals 2012-2017, added because I see no way to change the title of a dataset once it's been published. The dataset is, of course, GOLD open access journals, not gray ones.<br>
DOI: 10.17633/rd.brunel.6429200
title: Faces and voices in the brain dataset

description: The main compressed file contains data and scripts to conduct the main analyses in the manuscript. All scripts run in Matlab, and can run directly if you keep the original folder structure.<br>There is also a file with ROIs in MNI space.<br>Folder_contents.rtf lists all contents, names of data files, scripts, and outputs.<br><br><br>The preprint is available here:https://www.biorxiv.org/content/early/2018/07/13/338475<br><br>
DOI: 10.17028/rd.lboro.6429194
title: Fileset for "The role of residence time distribution in the continuous steady-state MSMPR crystallization of glycine"

description: These are the supporting data files for the article "The role of residence time distribution in the continuous steady-state MSMPR crystallization of glycine".<br>Abstract:In this work, a vacuum-driven intermittent transfer technique has been implemented to solve transfer line blockage issues and facilitate steady-state cooling crystallization studies of 𝛼-glycine in a single- and 2-stage MSMPR crystallizer. Experimental residence time distribution (RTD) analysis of the stirred tank MSMPR cascade is performed using an imperfect pulse method of the axial dispersion model to benchmark the mixing performance against that of tubular crystallizers and determine the influence of RTD on steady-state size distribution of 𝛼-glycine product. Process analytical technology (PAT) is used to monitor and understand crystallization process dynamics, and the effect of MSMPR operating temperature, mean residence time, and number of MSMPR stages on mean particle size, crystal size distribution, and yield is studied. Results show the significance of nucleation and growth mechanisms alongside RTD in determining steady-state size distribution, and the need for optimum control of supersaturation to benefit from improved RTDs provided by multistage MSMPR crystallizers.
DOI: 10.6084/m9.figshare.6429089
title: Hyponatremia associates with poor outcome in metastatic renal cell carcinoma patients treated with everolimus: prognostic impact

description: <b>Background:</b> The prognostication of metastatic renal cell carcinoma (mRCC) is based on Memorial Sloan Kettering Cancer Center (MSKCC) and International Metastatic Renal Cell Carcinoma Database Consortium (IMDC) risk classifications. Research has shown that hyponatremia is associated with worse prognosis in cancer. We analyzed the association of hyponatremia and outcome in everolimus-treated mRCC patients. <b>Patients and methods:</b> Baseline and on-treatment (≤12 weeks) sodium in 233 mRCC patients was analyzed using Kaplan–Meier, Cox regression and logistic regression. Baseline sodium was correlated with baseline thrombocyte and neutrophil values. <b>Results:</b> 65 (28%) and 41 (18%) patients had sodium p &lt; .001) and progression-free survival (PFS) (2.8 vs. 3.5 months; <i>p =</i> .04). On-treatment sodium p &lt; .001) and PFS (2.8 vs. 4.0 months; <i>p &lt;</i> .001). In multivariate analyses adjusted for IMDC factors, baseline and on-treatment sodium p = .02; adjusted HR 1.80 (95% CI 1.23–2.61); <i>p =</i> .002<i>;</i> respectively). On-treatment sodium p = .001). A landmark analysis demonstrated that on-treatment hyponatremia was significantly associated with shorter OS and PFS (<i>p =</i> .01 and <i>p =</i> .03, respectively). On-treatment normalization of hyponatremia was associated with improved OS (unadjusted HR 0.61 (95% CI 0.35–0.98); <i>p =</i> .04), as compared to patients with sustained hyponatremia throughout follow-up. <b>Conclusions:</b> Hyponatremia associates with poor outcome in mRCC patients treated with everolimus. On-treatment normalization of hyponatremia to normal sodium values associates with favorable outcome.
DOI: 10.6084/m9.figshare.6429089.v1
title: Hyponatremia associates with poor outcome in metastatic renal cell carcinoma patients treated with everolimus: prognostic impact

description: <b>Background:</b> The prognostication of metastatic renal cell carcinoma (mRCC) is based on Memorial Sloan Kettering Cancer Center (MSKCC) and International Metastatic Renal Cell Carcinoma Database Consortium (IMDC) risk classifications. Research has shown that hyponatremia is associated with worse prognosis in cancer. We analyzed the association of hyponatremia and outcome in everolimus-treated mRCC patients. <b>Patients and methods:</b> Baseline and on-treatment (≤12 weeks) sodium in 233 mRCC patients was analyzed using Kaplan–Meier, Cox regression and logistic regression. Baseline sodium was correlated with baseline thrombocyte and neutrophil values. <b>Results:</b> 65 (28%) and 41 (18%) patients had sodium p &lt; .001) and progression-free survival (PFS) (2.8 vs. 3.5 months; <i>p =</i> .04). On-treatment sodium p &lt; .001) and PFS (2.8 vs. 4.0 months; <i>p &lt;</i> .001). In multivariate analyses adjusted for IMDC factors, baseline and on-treatment sodium p = .02; adjusted HR 1.80 (95% CI 1.23–2.61); <i>p =</i> .002<i>;</i> respectively). On-treatment sodium p = .001). A landmark analysis demonstrated that on-treatment hyponatremia was significantly associated with shorter OS and PFS (<i>p =</i> .01 and <i>p =</i> .03, respectively). On-treatment normalization of hyponatremia was associated with improved OS (unadjusted HR 0.61 (95% CI 0.35–0.98); <i>p =</i> .04), as compared to patients with sustained hyponatremia throughout follow-up. <b>Conclusions:</b> Hyponatremia associates with poor outcome in mRCC patients treated with everolimus. On-treatment normalization of hyponatremia to normal sodium values associates with favorable outcome.
DOI: 10.6084/m9.figshare.6429083
title: Decomposition of CH<sub>4</sub> hydrate: effects of temperature and salt from molecular simulations

description: We report a molecular simulation study to investigate the decomposition of CH<sub>4</sub> hydrate. The decomposition is revealed to be stepwise from the outer to inner layers. Upon decomposition, the number of 5<sup>12</sup>6<sup>2</sup> cages drops faster than that of 5<sup>12</sup> cages. CH<sub>4</sub> molecules are released, dissolved in water, then enter gas phase; meanwhile, CH<sub>4</sub> bubbles may form particularly at a high temperature. Based on the variations of potential energy, order parameter, cage number and density profile of CH<sub>4</sub> at different temperatures (300, 330, 345 and 360 K) and NaCl concentrations (0, 0.6 and 1.8 M), the effects of temperature and salt are comprehensively examined. With increasing temperature, the decomposition in pure water is accelerated, whereas two opposite effects are observed in NaCl solution. At 330 K, the decomposition is retarded at a higher NaCl concentration, as attributed to the reduced CH<sub>4</sub> solubility in NaCl solution and the participation of ions in cage formation; at 360 K, however, the decomposition is accelerated when NaCl concentration increases due to bubble formation. This simulation study provides microscopic insights into hydrate decomposition, which might be useful towards the optimisation of operating conditions for CH<sub>4</sub> production from CH<sub>4</sub> hydrate.