cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3502445.v13
title: The Infant Gut Data

description: The archive file contains the merged anvi'o profile, and the contigs database for the Infant Gut data from Sharon et al. that is suitable to analyze with anvi'o v3 or later.<br>Please see http://merenlab.org/tutorials/infant-gut/ for details.
DOI: 10.6084/m9.figshare.3502445.v14
title: The Infant Gut Data

description: The archive file contains the merged anvi'o profile, and the contigs database for the Infant Gut data from Sharon et al. that is suitable to analyze with anvi'o v4 or later.<br>Please see http://merenlab.org/tutorials/infant-gut/ for details.
DOI: 10.6084/m9.figshare.3502445.v15
title: The Infant Gut Data

description: The archive file contains the merged anvi'o profile, and the contigs database for the Infant Gut data from Sharon et al. that is suitable to analyze with anvi'o v5.1 or later.<br>Please see http://merenlab.org/tutorials/infant-gut/ for details.
DOI: 10.6084/m9.figshare.3502445.v16
title: The Infant Gut Data

description: The archive file contains the merged anvi'o profile, and the contigs database for the Infant Gut data from Sharon et al. that is suitable to analyze with anvi'o v5.1 or later.<br>Please see http://merenlab.org/tutorials/infant-gut/ for details.
DOI: 10.6084/m9.figshare.3502445.v17
title: The Infant Gut Data

description: The archive file contains the merged anvi'o profile, and the contigs database for the Infant Gut data from Sharon et al. that is suitable to analyze with anvi'o v5.1 or later.<br>Please see http://merenlab.org/tutorials/infant-gut/ for details.
DOI: 10.6084/m9.figshare.3502445.v18
title: The Infant Gut Dataset

description: The archive file contains the merged anvi'o profile, and the contigs database for the Infant Gut data from Sharon et al. that is suitable to analyze with anvi'o v6 or later.<br>Please see http://merenlab.org/tutorials/infant-gut/ for details.
DOI: 10.6084/m9.figshare.3502373
title: binarydata.xlsx

description: Four binary data sets are contained in the File S1, an Excel file, for the four phases of winemaking: Harvest field, Juice, Wine at bottling (Prewine) and bottled Wine.
DOI: 10.6084/m9.figshare.3502286
title: DA meter - readings and chlorophyll content on the blushed and unblushed sides of nine apple cultivars final.pdf

description: conference paper
DOI: 10.6084/m9.figshare.3502286.v1
title: DA meter - readings and chlorophyll content on the blushed and unblushed sides of nine apple cultivars final.pdf

description: conference paper
DOI: 10.6084/m9.figshare.3502268
title: Datasets for a paper on Metazoan parasites of African annual killifish (Nothobranchiidae): abundance, diversity and their environmental correlates, Biotropica, 2016

description: The file (_envi) contains source files for calculations of association between parasite fauna of annual killifish and environment of the hosts. Second file (_similarity) contains data on similarity between parasite communities.
DOI: 10.6084/m9.figshare.3502268.v2
title: Datasets for a paper on Metazoan parasites of African annual killifish (Nothobranchiidae): abundance, diversity and their environmental correlates, Biotropica, 2016

description: The file (_envi) contains source files for calculations of association between parasite fauna of annual killifish and environment of the hosts. Second file (_similarity) contains data on similarity between parasite communities.
DOI: 10.6084/m9.figshare.3502268.v1
title: killi_para_similarity.txt

description: The file (_envi) contains source files for calculations of association between parasite fauna of annual killifish and environment of the hosts. Second file (_similarity) contains data on similarity between parasite communities.
DOI: 10.6084/m9.figshare.3502262
title: Non-destructive maturity assessment of ‘Empire’ apples treated with preharvest inhibitors of ethylene perception and production with a delta absorbance (DA) meter

description: Article <br>
DOI: 10.6084/m9.figshare.3502238
title: MNI T1 6thGen NLIN to MNI 2009b NLIN ANTs transform

description: This nonlinear transform warps between two different MNI templates.<br>Specifically, it warps from• MNI 152 6th generation atlas (used within SPM and FSL) that can be found here: http://nist.mni.mcgill.ca/?p=858<br>to the• MNI 152 2009b NLIN template (used within Lead-DBS) that can be found here: http://nist.mni.mcgill.ca/?p=904<br>The 2009b version (as opposed to the 2009a and c versions) is the only one available in 0.5mm resolution.<br>The transform has been applied to several atlases distributed within Lead-DBS from version 1.4.9.4 on.<br>More detailed information on this matter may be found here: http://www.lead-dbs.org/?p=1241<br><br><br>
DOI: 10.6084/m9.figshare.3502166
title: Identifying the Riemann Zeta function as a smoothed version of the Riemann Siegel function off the critical line

description: The Riemann Zeta function off the critical line can be understood as a smoothed version of the Riemann Siegel function scaled by the average growth, for Re(s) &lt; 0.5, of the Riemann Zeta function. The smoothing behaviour off the critical line avoids the zeroes present in the rescaled Riemann Siegel function explaining the Riemann Hypothesis.
DOI: 10.6084/m9.figshare.3502166.v1
title: Identifying the Riemann Zeta function as a smoothed version of the Riemann Siegel function off the critical line

description: The Riemann Zeta function off the critical line can be understood as a smoothed version of the Riemann Siegel function scaled by the average growth, for Re(s) &lt; 0.5, of the Riemann Zeta function. The smoothing behaviour off the critical line avoids the zeroes present in the rescaled Riemann Siegel function explaining the Riemann Hypothesis.
DOI: 10.6084/m9.figshare.3502166.v2
title: Identifying the Riemann Zeta function as a smoothed version of the Riemann Siegel function off the critical line

description: The Riemann Zeta function off the critical line can be understood as a smoothed version of the Riemann Siegel function scaled by the average growth, for Re(s) &lt; 0.5, of the Riemann Zeta function. The smoothing behaviour off the critical line avoids the zeroes present in the rescaled Riemann Siegel function explaining the Riemann Hypothesis.
DOI: 10.6084/m9.figshare.3502064
title: Bayesian Local Kriging

description: We consider the problem of constructing metamodels for computationally expensive simulation codes; that is, we construct interpolators/predictors of functions values (responses) from a finite collection of evaluations (observations). We use Gaussian process (GP) modeling and kriging, and combine a Bayesian approach, based on a finite set GP models, with the use of localized covariances indexed by the point where the prediction is made. Our approach is not based on postulating a generative model for the unknown function, but by letting the covariance functions depend on the prediction site, it provides enough flexibility to accommodate arbitrary nonstationary observations. Contrary to kriging prediction with plug-in parameter estimates, the resulting Bayesian predictor is constructed explicitly, without requiring any numerical optimization, and locally adjusts the weights given to the different models according to the data variability in each neighborhood. The predictor inherits the smoothness properties of the covariance functions that are used and its superiority over plug-in kriging, sometimes also called empirical-best-linear-unbiased predictor, is illustrated on various examples, including the reconstruction of an oceanographic field over a large region from a small number of observations. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.3502064.v1
title: Bayesian Local Kriging

description: We consider the problem of constructing metamodels for computationally expensive simulation codes; that is, we construct interpolators/predictors of functions values (responses) from a finite collection of evaluations (observations). We use Gaussian process (GP) modeling and kriging, and combine a Bayesian approach, based on a finite set GP models, with the use of localized covariances indexed by the point where the prediction is made. Our approach is not based on postulating a generative model for the unknown function, but by letting the covariance functions depend on the prediction site, it provides enough flexibility to accommodate arbitrary nonstationary observations. Contrary to kriging prediction with plug-in parameter estimates, the resulting Bayesian predictor is constructed explicitly, without requiring any numerical optimization, and locally adjusts the weights given to the different models according to the data variability in each neighborhood. The predictor inherits the smoothness properties of the covariance functions that are used and its superiority over plug-in kriging, sometimes also called empirical-best-linear-unbiased predictor, is illustrated on various examples, including the reconstruction of an oceanographic field over a large region from a small number of observations. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.3502043
title: A new late Hemingfordian vertebrate fauna from Hawk Rim, Oregon, with implications for biostratigraphy and geochronology

description: The Hemingfordian North American Land Mammal Age is not well sampled, especially in the Pacific Northwest. Here we present both a description of a new fauna and two radiometric dates, 16.26 Ma and 16.44 Ma, constraining the Hawk Rim locality of central Oregon. Hawk Rim represents the first diverse late Hemingfordian fauna in the Northwest and is one of the stratigraphically lowest fossiliferous outcrops of the Mascall Formation. Much of Oregon was blanketed by Columbia River Flood Basalts during late Hemingfordian time, limiting not only outcrops but places for organisms to have survived. The site yields a taxonomically rich fauna sharing strong faunal similarity with the type locality of the Mascall but also containing taxa new to the formation and region. We describe occurrences of five genera of Artiodactyla, four genera of Perissodactyla, three genera of Rodentia, and six genera of Carnivora, with all but three new occurrences for the Hemingfordian of the Pacific Northwest. In particular, the carnivore fauna extends the geographic and temporal range of several carnivorans, and we describe a new hypercarnivorous mustelid, <i>Watay tabutsigwii</i>.http://zoobank.org/urn:lsid:zoobank.org:pub:B415069F-8BE6-4629-A872-5A640A644210 SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP Citation for this article: McLaughlin, W. N. F., S. S. B. Hopkins, and M. D. Schmitz. 2016. A new late Hemingfordian vertebrate fauna from Hawk Rim, Oregon, with implications for biostratigraphy and geochronology. Journal of Vertebrate Paleontology. DOI: 10.1080/02724634.2016.1201095.
DOI: 10.6084/m9.figshare.3502043.v1
title: A new late Hemingfordian vertebrate fauna from Hawk Rim, Oregon, with implications for biostratigraphy and geochronology

description: The Hemingfordian North American Land Mammal Age is not well sampled, especially in the Pacific Northwest. Here we present both a description of a new fauna and two radiometric dates, 16.26 Ma and 16.44 Ma, constraining the Hawk Rim locality of central Oregon. Hawk Rim represents the first diverse late Hemingfordian fauna in the Northwest and is one of the stratigraphically lowest fossiliferous outcrops of the Mascall Formation. Much of Oregon was blanketed by Columbia River Flood Basalts during late Hemingfordian time, limiting not only outcrops but places for organisms to have survived. The site yields a taxonomically rich fauna sharing strong faunal similarity with the type locality of the Mascall but also containing taxa new to the formation and region. We describe occurrences of five genera of Artiodactyla, four genera of Perissodactyla, three genera of Rodentia, and six genera of Carnivora, with all but three new occurrences for the Hemingfordian of the Pacific Northwest. In particular, the carnivore fauna extends the geographic and temporal range of several carnivorans, and we describe a new hypercarnivorous mustelid, <i>Watay tabutsigwii</i>.http://zoobank.org/urn:lsid:zoobank.org:pub:B415069F-8BE6-4629-A872-5A640A644210 SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP Citation for this article: McLaughlin, W. N. F., S. S. B. Hopkins, and M. D. Schmitz. 2016. A new late Hemingfordian vertebrate fauna from Hawk Rim, Oregon, with implications for biostratigraphy and geochronology. Journal of Vertebrate Paleontology. DOI: 10.1080/02724634.2016.1201095.
DOI: 10.6084/m9.figshare.3502025
title: MicroRNA expression profiling of <i>Leishmania donovani</i>-infected host cells uncovers the regulatory role of MIR30A-3p in host autophagy

description: <i>Leishmania</i> is an obligate intracellular parasite that replicates inside phagolysosomes or parasitophorous vacuoles (PV) of the monocyte/macrophage lineage. It reprograms macrophages and produces a metabolic state conducive to successful infection and multiplication. MicroRNAs (miRNAs), a class of small 22 to 24 nucleotide noncoding regulatory RNAs alter the gene expression and consequently proteome output by targeting mRNAs, may play a regulatory role in modulating host cell functions. In the present study, we demonstrate the novel regulatory role of host microRNA, <i>MIR30A-3p</i> in modulation of host cell macroautophagy/autophagy after infection with <i>L. donovani</i>. Our in vitro studies showed that <i>MIR30A-3p</i> expression was significantly enhanced after <i>L. donovani</i> infection in a time-dependent manner. Transient transfection with a <i>MIR30A-3p</i> inhibitor followed by <i>L. donovani</i> infection promoted the autophagic response and decreased the intracellular parasite burden in both THP-1 cells and human monocyte-derived macrophages (HsMDM). BECN1/Beclin 1, the mammalian ortholog of yeast Vps30/Atg6, is a key autophagy-promoting protein that plays a key role in the regulation of cell death and survival. We report BECN1-dependent modulation of host cell autophagy in response to <i>L. donovani</i> infection. Pretreatment of <i>L. donovani</i>-infected macrophages with the <i>MIR30A-3p</i> mimic decreased and with antagomir increased the expression of BECN1 protein. We demonstrate that <i>BECN1</i> is a potential target of <i>MIR30A-3p</i> and this miRNA negatively regulates <i>BECN1</i> expression. Our present study reveals for the first time a novel role of <i>MIR30A-3p</i> in regulating autophagy-mediated <i>L. donovani</i> elimination by targeting <i>BECN1</i>. The present study has significant impact for the treatment of visceral leishmaniasis.
DOI: 10.6084/m9.figshare.3502025.v2
title: MicroRNA expression profiling of <i>Leishmania donovani</i>-infected host cells uncovers the regulatory role of MIR30A-3p in host autophagy

description: <i>Leishmania</i> is an obligate intracellular parasite that replicates inside phagolysosomes or parasitophorous vacuoles (PV) of the monocyte/macrophage lineage. It reprograms macrophages and produces a metabolic state conducive to successful infection and multiplication. MicroRNAs (miRNAs), a class of small 22 to 24 nucleotide noncoding regulatory RNAs alter the gene expression and consequently proteome output by targeting mRNAs, may play a regulatory role in modulating host cell functions. In the present study, we demonstrate the novel regulatory role of host microRNA, <i>MIR30A-3p</i> in modulation of host cell macroautophagy/autophagy after infection with <i>L. donovani</i>. Our in vitro studies showed that <i>MIR30A-3p</i> expression was significantly enhanced after <i>L. donovani</i> infection in a time-dependent manner. Transient transfection with a <i>MIR30A-3p</i> inhibitor followed by <i>L. donovani</i> infection promoted the autophagic response and decreased the intracellular parasite burden in both THP-1 cells and human monocyte-derived macrophages (HsMDM). BECN1/Beclin 1, the mammalian ortholog of yeast Vps30/Atg6, is a key autophagy-promoting protein that plays a key role in the regulation of cell death and survival. We report BECN1-dependent modulation of host cell autophagy in response to <i>L. donovani</i> infection. Pretreatment of <i>L. donovani</i>-infected macrophages with the <i>MIR30A-3p</i> mimic decreased and with antagomir increased the expression of BECN1 protein. We demonstrate that <i>BECN1</i> is a potential target of <i>MIR30A-3p</i> and this miRNA negatively regulates <i>BECN1</i> expression. Our present study reveals for the first time a novel role of <i>MIR30A-3p</i> in regulating autophagy-mediated <i>L. donovani</i> elimination by targeting <i>BECN1</i>. The present study has significant impact for the treatment of visceral leishmaniasis.
DOI: 10.6084/m9.figshare.3502025.v1
title: MicroRNA expression profiling of <i>Leishmania donovani</i>-infected host cells uncovers the regulatory role of <i>MIR30A-3p</i> in host autophagy

description: <i>Leishmania</i> is an obligate intracellular parasite that replicates inside phagolysosomes or parasitophorous vacuole (PV) of the monocyte/macrophage lineage. It reprograms macrophages and produces a metabolic state conducive to successful infection and multiplication. MicroRNAs (miRNAs), a class of small 22 to 24 nucleotide noncoding regulatory RNAs alter the gene expression and consequently proteome output by targeting mRNAs, may play a regulatory role in modulating host cell functions. In the present study, we demonstrate the novel regulatory role of host microRNA, <i>MIR30A-3p</i> in modulation of host cell macroautophagy/autophagy after infection with <i>L. donovani</i>. Our <i>in vitro</i> studies showed that <i>MIR30A-3p</i> expression was significantly enhanced after <i>L. donovani</i> infection in a time-dependent manner. Transient transfection with a <i>MIR30A-3p</i> inhibitor followed by <i>L. donovani</i> infection promoted the autophagic response and decreased the intracellular parasite burden in both THP-1 cells and human monocyte-derived macrophages (HsMDM). BECN1/Beclin 1, the mammalian ortholog of yeast Vps30/Atg6, is a key autophagy-promoting protein that plays a key role in the regulation of cell death and survival. We report BECN1 dependent modulation of host cell autophagy in response to <i>L. donovani</i> infection. Pretreatment of <i>L. donovani</i>-infected macrophages with the <i>MIR30A-3p</i> mimic decreased and with antagomir increased the expression of BECN1 protein. We demonstrate that <i>BECN1</i> is a potential target of <i>MIR30A-3p</i> and this miRNA negatively regulates <i>BECN1</i> expression. Our present study for the first time reveals a novel role of <i>MIR30A-3p</i> in regulating autophagy-mediated <i>L. donovani</i> elimination by targeting <i>BECN1</i>. The present study has significant impact in the treatment of visceral leishmaniasis.
DOI: 10.6084/m9.figshare.3501911
title: HCP-MMP1.0 projected on MNI2009a GM (volumetric) in NIfTI format

description: Based on the Freesurfer version of the HCP-MMP1.0 parcellation (https://figshare.com/articles/HCP-MMP1_0_projected_on_fsaverage/3498446), I created a volumetric version of the HCP-MMP1.0 parcellation that was published by Glasser et al. (Nature, 2016).<br>Please note that this volumetric version should be used and applied with great care – and under certain circumstances only. According to the authors of the original work, this fine parcellation could not have been achieved on a volumetric basis but was only realizable using a multimodal surface-based analysis (and co-registration).Thus, this volumetric version of their work is not ideally suited to be used for standard brain-mapping approaches that use (volumetric) nonlinear deformations. It is rather thought to be an accompanying volumetric version to the surface-based version. Also, it could be used for comparative purposes within MNI space (e.g. to compare it to other cortical parcellations available in this space such as the AAL, Hammersmith, AICHA, Mindboggle 101 atlases).<br>The conversion to volumetric space (projection to the ICBM 152 2009a NLIN version within MNI space) is based on the fsaverage version of the HCP-MMP1.0 available here (https://figshare.com/articles/HCP-MMP1_0_projected_on_fsaverage/3498446).<br>See Matlab code file for details and/or to project to different MNI templates.
DOI: 10.6084/m9.figshare.3501911.v2
title: HCP-MMP1.0 projected on MNI2009a GM (volumetric) in NIfTI format

description: Based on the Freesurfer version of the HCP-MMP1.0 parcellation (https://figshare.com/articles/HCP-MMP1_0_projected_on_fsaverage/3498446), I created a volumetric version of the HCP-MMP1.0 parcellation that was published by Glasser et al. (Nature, 2016).<br>Please note that this volumetric version should be used and applied with great care – and under certain circumstances only. According to the authors of the original work, the parcellation could not have been done on a volumetric basis but was only realizable using a multimodal surface-based analysis (and co-registration).Thus, this volumetric version of their work is not ideally suited to be used for standard brain-mapping approaches that use (volumetric) nonlinear deformations. It is rather thought to be an accompanying volumetric version to the surface-based version. Also, it could be used for comparative purposes within MNI space (e.g. to compare it to other cortical parcellations available in this space such as the AAL, Hammersmith, AICHA, Mindboggle 101 atlases).<br>The conversion to volumetric space (projection to the ICBM 152 2009a NLIN version within MNI space) is based on the fsaverage version of the HCP-MMP1.0 available here (https://figshare.com/articles/HCP-MMP1_0_projected_on_fsaverage/3498446).<br>See Matlab code file for details and/or to project to different MNI templates.
DOI: 10.6084/m9.figshare.3501911.v3
title: HCP-MMP1.0 projected on MNI2009a GM (volumetric) in NIfTI format

description: Based on the Freesurfer version of the HCP-MMP1.0 parcellation (https://figshare.com/articles/HCP-MMP1_0_projected_on_fsaverage/3498446), I created a volumetric version of the HCP-MMP1.0 parcellation that was published by Glasser et al. (Nature, 2016).<br>Please note that this volumetric version should be used and applied with great care – and under certain circumstances only. According to the authors of the original work, the parcellation could not have been done on a volumetric basis but was only realizable using a multimodal surface-based analysis (and co-registration).Thus, this volumetric version of their work is not ideally suited to be used for standard brain-mapping approaches that use (volumetric) nonlinear deformations. It is rather thought to be an accompanying volumetric version to the surface-based version. Also, it could be used for comparative purposes within MNI space (e.g. to compare it to other cortical parcellations available in this space such as the AAL, Hammersmith, AICHA, Mindboggle 101 atlases).<br>The conversion to volumetric space (projection to the ICBM 152 2009a NLIN version within MNI space) is based on the fsaverage version of the HCP-MMP1.0 available here (https://figshare.com/articles/HCP-MMP1_0_projected_on_fsaverage/3498446).<br>See Matlab code file for details and/or to project to different MNI templates.
DOI: 10.6084/m9.figshare.3501863
title: Africanized Honey Bee Pooled Sequence Variants

description: Variant Call File (VCF) for SNPs associated with upload to dbSNP (Data Citation 2; BioProject PRNJA324081). Because our data consist of pooled sequence for 30 colonies, we report the allele frequency at each site
DOI: 10.6084/m9.figshare.3501863.v1
title: Africanized Honey Bee Pooled Sequence Variants

description: Variant Call File (VCF) for SNPs associated with upload to dbSNP (Data Citation 2; BioProject PRNJA324081). Because our data consist of pooled sequence for 30 colonies, we report the allele frequency at each site