cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3181165.v1
title: Heterodimerization of the <i>Entamoeba histolytica</i> EhCPADH virulence complex through molecular dynamics and protein–protein docking

description: EhCPADH is a protein complex involved in the virulence of <i>Entamoeba histolytica</i>, the protozoan responsible for human amebiasis. It is formed by the EhCP112 cysteine protease and the EhADH adhesin. To explore the molecular basis of the complex formation, three-dimensional models were built for both proteins and molecular dynamics simulations (MDS) and docking calculations were performed. Results predicted that the pEhCP112 proenzyme and the mEhCP112 mature enzyme were globular and peripheral membrane proteins. Interestingly, in pEhCP112, the propeptide appeared hiding the catalytic site (C167, H329, N348); while in mEhCP112, this site was exposed and its residues were found structurally closer than in pEhCP112. EhADH emerged as an extended peripheral membrane protein with high fluctuation in Bro1 and V shape domains. 500 ns-long MDS and protein–protein docking predictions evidenced different heterodimeric complexes with the lowest free energy. pEhCP112 interacted with EhADH by the propeptide and C-terminal regions and mEhCP112 by the C-terminal through hydrogen bonds. In contrast, EhADH bound to mEhCP112 by 442–479 residues, adjacent to the target cell-adherence region (480–600 residues), and by the Bro1 domain (9–349 residues). Calculations of the effective binding free energy and per residue free energy decomposition showed that EhADH binds to mEhCP112 with a higher binding energy than to pEhCP112, mainly through van der Waals interactions and the nonpolar part of solvation energy. The EhADH and EhCP112 structural relationship was validated in trophozoites by immunofluorescence, TEM, and immunoprecipitation assays. Experimental findings fair agreed with <i>in silico</i> results.
DOI: 10.6084/m9.figshare.3181132
title: Avoiding Missing Data Biases in Phylogenomic Inference: An Empirical Study in the Landfowl (Aves: Galliformes) - Concatenated DNA sequence alignments

description: Phylip format concatenated alignments for each missing data threshold<br>
DOI: 10.6084/m9.figshare.3181141.v1
title: Lumbar artery perforator (LAP) flap: a salvage tool for extended lumbo-sacral necrosis after bilateral internal iliac arteries embolization

description: We report the case of a 52-year-old man presenting an extensive lumbosacral necrosis after bilateral internal iliac arteries embolization following unstable pelvic fracture. Coverage of the defect was performed using two extended lumbar artery perforator flaps in a propeller fashion. Good functional and esthetic result was achieved at one-year follow-up.
DOI: 10.6084/m9.figshare.3181108
title: Phenotypes of gene disruptants in relation to a putative mitochondrial malate–citrate shuttle protein in citric acid-producing <i>Aspergillus niger</i>

description: The mitochondrial citrate transport protein (CTP) functions as a malate–citrate shuttle catalyzing the exchange of citrate plus a proton for malate between mitochondria and cytosol across the inner mitochondrial membrane in higher eukaryotic organisms. In this study, for functional analysis, we cloned the gene encoding putative CTP (<i>ctpA</i>) of citric acid-producing <i>Aspergillus niger</i> WU-2223L. The gene <i>ctpA</i> encodes a polypeptide consisting 296 amino acids conserved active residues required for citrate transport function. Only in early-log phase, the <i>ctpA</i> disruptant DCTPA-1 showed growth delay, and the amount of citric acid produced by strain DCTPA-1 was smaller than that by parental strain WU-2223L. These results indicate that the CTPA affects growth and thereby citric acid metabolism of <i>A. niger</i> changes, especially in early-log phase, but not citric acid-producing period. This is the first report showing that disruption of <i>ctpA</i> causes changes of phenotypes in relation to citric acid production in <i>A. niger</i>. Disruption of the gene encoding the citrate transport protein (CTPA, i.e., malate–citrate shuttle protein) affects the phenotype of <i>Aspergillus niger</i>.
DOI: 10.6084/m9.figshare.3181069
title: Impacts of cross-phase modulation on modulation instability of Airy pulses

description: The modulation instability (MI) of Airy pulses with the influence of cross-phase modulation is studied based on the coupled nonlinear Schrödinger equations in nonlinear media. The main lobe of Airy pulses can be manifested as breakup of MI under interaction with higher power pumped solitons, although the power of Airy pulses is small. By comparing the main lobe’s gain spectrum of MI, the gain spectrum has gradually improved with the increase of power of pumped solitons. The gain spectrum of MI of the main lobe is inversely proportional to the truncation coefficient, and then it gradually approaches to that of Gauss pulses with the truncation coefficient increasing to 1. For the side lobes of Airy pulses, there are similar MI but smaller gain spectrum than the main lobe when the pumped solitons is overlapping with corresponding ones of Airy pulses.
DOI: 10.6084/m9.figshare.3181108.v1
title: Phenotypes of gene disruptants in relation to a putative mitochondrial malate–citrate shuttle protein in citric acid-producing <i>Aspergillus niger</i>

description: The mitochondrial citrate transport protein (CTP) functions as a malate–citrate shuttle catalyzing the exchange of citrate plus a proton for malate between mitochondria and cytosol across the inner mitochondrial membrane in higher eukaryotic organisms. In this study, for functional analysis, we cloned the gene encoding putative CTP (<i>ctpA</i>) of citric acid-producing <i>Aspergillus niger</i> WU-2223L. The gene <i>ctpA</i> encodes a polypeptide consisting 296 amino acids conserved active residues required for citrate transport function. Only in early-log phase, the <i>ctpA</i> disruptant DCTPA-1 showed growth delay, and the amount of citric acid produced by strain DCTPA-1 was smaller than that by parental strain WU-2223L. These results indicate that the CTPA affects growth and thereby citric acid metabolism of <i>A. niger</i> changes, especially in early-log phase, but not citric acid-producing period. This is the first report showing that disruption of <i>ctpA</i> causes changes of phenotypes in relation to citric acid production in <i>A. niger</i>. Disruption of the gene encoding the citrate transport protein (CTPA, i.e., malate–citrate shuttle protein) affects the phenotype of <i>Aspergillus niger</i>.
DOI: 10.6084/m9.figshare.3181150.v1
title: Avoiding missing data biases in phylogenomic inference: An empirical study in the landfowl (Aves: Galliformes) - single UCE locus alignments

description: Single locus alignments for each UCE in nexus format<br>
DOI: 10.6084/m9.figshare.3181015
title: Assessment of cortical dysfunction in intermittent exotropia: an fMRI study

description: Primary data of an article entitled "Assessment of Cortical Dysfunction in Intermittent Exotropia: an fMRI Study"
DOI: 10.6084/m9.figshare.3181069.v1
title: Impacts of cross-phase modulation on modulation instability of Airy pulses

description: The modulation instability (MI) of Airy pulses with the influence of cross-phase modulation is studied based on the coupled nonlinear Schrödinger equations in nonlinear media. The main lobe of Airy pulses can be manifested as breakup of MI under interaction with higher power pumped solitons, although the power of Airy pulses is small. By comparing the main lobe’s gain spectrum of MI, the gain spectrum has gradually improved with the increase of power of pumped solitons. The gain spectrum of MI of the main lobe is inversely proportional to the truncation coefficient, and then it gradually approaches to that of Gauss pulses with the truncation coefficient increasing to 1. For the side lobes of Airy pulses, there are similar MI but smaller gain spectrum than the main lobe when the pumped solitons is overlapping with corresponding ones of Airy pulses.
DOI: 10.6084/m9.figshare.3181003
title: Supplemental Information Table S4 Compositional similarity

description: <b>Table S4. C</b><b>ompositional similarity </b><b>(<i>CS</i>) </b><b>of richness</b><b> (<i><sup>0</sup>D</i>) and dominant species (<i><sup>2</sup>D</i>) of woody and aquatic plants.</b>
DOI: 10.6084/m9.figshare.3181015.v1
title: Assessment of cortical dysfunction in intermittent exotropia: an fMRI study

description: Primary data of an article entitled "Assessment of Cortical Dysfunction in Intermittent Exotropia: an fMRI Study"
DOI: 10.6084/m9.figshare.3181132.v1
title: Avoiding missing data biases in phylogenomic inference: an empirical study in the landfowl (Aves: Galliformes)

description: Phylip format concatenated alignments for each missing data threshold<br>
DOI: 10.6084/m9.figshare.3180985
title: Supplemental Information Table S2 Local alpha diversity

description: <b>Table S2.</b><b> Local alpha diversity of wetlands (<i>α<sub>w</sub></i>) corresponding to the sum of richness of species of woody (W) and aquatic (Aq) plants in each wetland (Species: Ty, typical of Piedmont; IE, </b><b>introduced exotic</b><b>; NE,</b><b> native exotic</b><b>).</b>
DOI: 10.6084/m9.figshare.3181003.v1
title: Supplemental Information Table S4 Compositional similarity

description: <b>Table S4. C</b><b>ompositional similarity </b><b>(<i>CS</i>) </b><b>of richness</b><b> (<i><sup>0</sup>D</i>) and dominant species (<i><sup>2</sup>D</i>) of woody and aquatic plants.</b>
DOI: 10.6084/m9.figshare.3181000
title: Supplemental Information Table S3 Total mean alpha diversity

description: <b>Table S3. Total (α) and mean (ᾱ </b><b>± SD</b><b>) alpha diversity, and range values</b><b> of richness</b><b> (<i><sup>0</sup>D</i>) and dominant species (<i><sup>2</sup>D</i>) of woody and aquatics plants in wetland types and origins.</b>
DOI: 10.6084/m9.figshare.3180961
title: Supplemental Information Table S1 Sample coverage .docx

description: <b>Table S1. Sample coverage (<i>Ĉm</i>), species richness (<i><sup>0</sup>D</i>) and dominant species diversity (<i><sup>2</sup>D</i>), and relative logarithmic inequality of woody (W) and aquatic (A) plants. </b>(<i>Ĉm</i> is expressed as a percentage of completeness, values from 0 represent no completeness and values of 100 maximum completeness based on Chao & Jost (2012). *only one single individual was found in this wetland, and it was excluded from the RLI analysis; -: in this wetland no plants in this formation were found during sample).
DOI: 10.6084/m9.figshare.3181132.v2
title: Avoiding missing data biases in phylogenomic inference: an empirical study in the landfowl (Aves: Galliformes) - Concatenated DNA sequence alignments

description: Phylip format concatenated alignments for each missing data threshold<br>
DOI: 10.6084/m9.figshare.3180985.v1
title: Supplemental Information Table S2 Local alpha diversity

description: <b>Table S2.</b><b> Local alpha diversity of wetlands (<i>α<sub>w</sub></i>) corresponding to the sum of richness of species of woody (W) and aquatic (Aq) plants in each wetland (Species: Ty, typical of Piedmont; IE, </b><b>introduced exotic</b><b>; NE,</b><b> native exotic</b><b>).</b>
DOI: 10.6084/m9.figshare.3181000.v1
title: Supplemental Information Table S3 Total mean alpha diversity

description: <b>Table S3. Total (α) and mean (ᾱ </b><b>± SD</b><b>) alpha diversity, and range values</b><b> of richness</b><b> (<i><sup>0</sup>D</i>) and dominant species (<i><sup>2</sup>D</i>) of woody and aquatics plants in wetland types and origins.</b>
DOI: 10.6084/m9.figshare.3180961.v1
title: Supplemental Information Table S1 Sample coverage .docx

description: <b>Table S1. Sample coverage (<i>Ĉm</i>), species richness (<i><sup>0</sup>D</i>) and dominant species diversity (<i><sup>2</sup>D</i>), and relative logarithmic inequality of woody (W) and aquatic (A) plants. </b>(<i>Ĉm</i> is expressed as a percentage of completeness, values from 0 represent no completeness and values of 100 maximum completeness based on Chao & Jost (2012). *only one single individual was found in this wetland, and it was excluded from the RLI analysis; -: in this wetland no plants in this formation were found during sample).
DOI: 10.6084/m9.figshare.3180826
title: WAST CHNRI survey data v2.xlsx

description: The data show the results of a CHNRI survey of nutrition experts on priorities in research on the relationships between wasting and stunting. The survey was carried out online and respondents were asked to prioritise from a list of possible research questions.
DOI: 10.6084/m9.figshare.3180790
title: Frienship and Trust.docx

description: friendship and trus
DOI: 10.6084/m9.figshare.3181132.v3
title: Avoiding Missing Data Biases in Phylogenomic Inference: An Empirical Study in the Landfowl (Aves: Galliformes) - Concatenated DNA sequence alignments

description: Phylip format concatenated alignments for each missing data threshold<br>
DOI: 10.6084/m9.figshare.3180790.v1
title: Frienship and Trust.docx

description: friendship and trus
DOI: 10.6084/m9.figshare.3181132.v5
title: Avoiding Missing Data Biases in Phylogenomic Inference: An Empirical Study in the Landfowl (Aves: Galliformes) - Concatenated DNA sequence alignments

description: Phylip format concatenated alignments for each missing data threshold<br>
DOI: 10.6084/m9.figshare.3180895.v1
title: Assessment of cortical dysfunction in intermittent exotropia: an fMRI study

description: Primary Data of an article entitled with Assessment of cortical dysfunction in intermittent exotropia: an fMRI study
DOI: 10.6084/m9.figshare.3180679
title: Ungulate behavioral responses to the heterogeneous road network of a touristic protected area in Africa

description: Data describing impala behavioral responses to roads and traffic in an African protected area (Kruger National Park). The data were analyzed in “Mulero-Pázmány, M., D'Amico, M. and González-Suárez, M. (2016), Ungulate behavioral responses to the heterogeneous road-network of a touristic protected area in Africa. J Zool, 298: 233–240. doi:10.1111/jzo.12310”Additional details are available on the metadata and the paper copy uploaded here
DOI: 10.6084/m9.figshare.3180679.v1
title: Impala_road_response_KrugerNP_data.csv

description: Data describing impala behavioral responses to roads and traffic in an African protected area (Kruger National Park). The data were analyzed in “Mulero-Pázmány, M., D'Amico, M. and González-Suárez, M. (2016), Ungulate behavioral responses to the heterogeneous road-network of a touristic protected area in Africa. J Zool, 298: 233–240. doi:10.1111/jzo.12310”Additional details are available on the metadata and the paper copy uploaded here
DOI: 10.6084/m9.figshare.3180679.v3
title: Ungulate behavioral responses to the heterogeneous road network of a touristic protected area in Africa

description: Data describing impala behavioral responses to roads and traffic in an African protected area (Kruger National Park). The data were analyzed in “Mulero-Pázmány, M., D'Amico, M. and González-Suárez, M. (2016), Ungulate behavioral responses to the heterogeneous road-network of a touristic protected area in Africa. J Zool, 298: 233–240. doi:10.1111/jzo.12310”Additional details are available on the metadata and the paper copy uploaded here
DOI: 10.6084/m9.figshare.3180679.v2
title: Ungulate behavioral responses to the heterogeneous road network of a touristic protected area in Africa

description: Data describing impala behavioral responses to roads and traffic in an African protected area (Kruger National Park). The data were analyzed in “Mulero-Pázmány, M., D'Amico, M. and González-Suárez, M. (2016), Ungulate behavioral responses to the heterogeneous road-network of a touristic protected area in Africa. J Zool, 298: 233–240. doi:10.1111/jzo.12310”Additional details are available on the metadata and the paper copy uploaded here
DOI: 10.6084/m9.figshare.3180487
title: Hazard Database

description: Hazard database
DOI: 10.6084/m9.figshare.3180478
title: Model Changes Data

description: Model changes detection data (EMSE paper)
DOI: 10.6084/m9.figshare.3180478.v1
title: Model Changes Data

description: Model changes detection data (EMSE paper)
DOI: 10.6084/m9.figshare.3180487.v1
title: Hazard Database

description: Hazard database
DOI: 10.6084/m9.figshare.3180487.v2
title: Hazard Database

description: Hazard database
DOI: 10.6084/m9.figshare.3180418.v1
title: 19 June 2014 VID00010 Zoom on Animal(s) Eating Deer

description: This video does not display adequately using the online viewer.<br>VID00010 processed to zoom in on the anomalous large primate(s) feeding on one or more whitetail deer. The original VID00010 is processed using GoPro Studio with Zoom set to 3X and play speed reduced to 9%. The format is converted during the processing.<br><br>
DOI: 10.6084/m9.figshare.3180418.v2
title: 19 June 2014 VID00010 Zoom

description: This video does not display adequately using the online viewer.<br>VID00010 processed to zoom in on the areas with large frame to frame change. The original VID00010 is processed using GoPro Studio with Zoom set to 3X and play speed reduced to 9%. The format is converted during the processing.<br><br>
DOI: 10.6084/m9.figshare.3180367
title: Exploring the meaning of altmetrics

description: Haustein, S. (2016). Exploring the meaning of altmetrics. Presentation at FORCE2016 panel "Altmetrics and my career: real barriers or limitations of our minds?"<br>https://www.force11.org/meetings/force2016/program/agenda/concurrent-session-altmetrics-and-my-career-real-barriers-or<br>The acts on which various altmetrics are based are quite heterogeneous: likes on Facebook, mentions on Twitter, saves on Mendeley, and expert recommendations on F1000 are acts that differ in terms of user community, engagement, motivation and audience. While the act of citing has been an essential part of the scholarly communication process since the beginning of modern science, it is unclear whether the acts leading to online events used for altmetrics are relevant in scholarly communication. While empirical studies have shown that most altmetrics correlate weakly with citations, conceptual discussions about their meaning are rare. For most of these new metrics it thus remains quite unclear what exactly they measure. This presentation aims to discuss the heterogeneity of altmetrics, potential biases and their effects on their use in the scientific evaluation and reward system.<br>#FORCE2016 #realaltmetrics
DOI: 10.6084/m9.figshare.3180352
title: Randomized Isoflurane and Sevoflurane Comparison in Cardiac Surgery (RISCCS) trial

description: Data and statistical analysis code for the RISCCS trial.
DOI: 10.6084/m9.figshare.3180370.v1
title: Demonstrating impact as a practitioner-researcher

description: This presentation was delivered at FORCE16 in Portland, OR. Librarians have a unique perspective on the scholarly ecosystem as authors, consumers, and stewards. This perspective, combined with our roles in collecting and curating information, enables librarians to identify changes in policy, practice, and technology that can improve the openness, transparency, and sustainability of the scholarly ecosystem. It also reveals opportunities for aligning institutional and professional incentives with these changes. I will share examples of evidence used in my promotion and tenure dossier to demonstrate how librarian practitioner-scholars can be both advocates and exemplars for the changes we want to see in open access, data, and educational resources.
DOI: 10.6084/m9.figshare.3180352.v1
title: Randomized Isoflurane and Sevoflurane Comparison in Cardiac Surgery (RISCCS) trial

description: Data and statistical analysis code for the RISCCS trial.
DOI: 10.6084/m9.figshare.3180376.v1
title: VanTuylWhitmire-Force2016-Poster.pdf

description: Poster for FORCE 2016 Conference on our project to define and assess data sharing at Oregon State University.
DOI: 10.6084/m9.figshare.3180325
title: 2014 09 20 VID00043 Enhanced Frames

description: Every frame of VID00043 taken on 20 September 2014. Frames are extracted using Cisco FlipShare software distributed with the Cisco Flip UltraHD 720p digital video recorder used to record the video. Frames are then enhanced using Adobe Photoshop Creative Cloud as follows:1) Image Size; Width 300%; Resolution: 300 per inch; With Scale Styles; With Constrain Proportions; Interpolation: preserve details; Noise: 100.2) Save; As: PNG Format; Interlace: None; Filter: Adaptive; Compression: 9.<br><br>Project order 45a<br>
DOI: 10.6084/m9.figshare.3180322
title: Oil migration and its influence in fracture-fill cementation (south-eastern Pyrenees, Spain): geochemistry and fluid inclusion evidence.

description: <br> <b>The presence of a large number of oil shows and the existence of a good source rock (i.e., Armàncies Formation) have attracted considerable interest from oil companies in the southeastern Pyrenees. However, no reservoirs have been discovered to date. </b>
DOI: 10.6084/m9.figshare.3180313
title: 2014 09 20 VID00043 Original Frames

description: Every frame of VID00043 taken on 20 September 2014. Frames are extracted using Cisco FlipShare software distributed with the Cisco Flip UltraHD 720p digital video recorder used to record the video.<br><br>Project order 44a<br>
DOI: 10.6084/m9.figshare.3180322.v1
title: Oil migration and its influence in fracture-fill cementation (south-eastern Pyrenees, Spain): geochemistry and fluid inclusion evidence.

description: <br> <b>The presence of a large number of oil shows and the existence of a good source rock (i.e., Armàncies Formation) have attracted considerable interest from oil companies in the southeastern Pyrenees. However, no reservoirs have been discovered to date. </b>
DOI: 10.6084/m9.figshare.3180325.v1
title: 20 September 2014 VID00040 Enhanced Frames

description: Every frame of VID00040 taken on 20 September 2014. Frames are extracted using Cisco FlipShare software distributed with the Cisco Flip UltraHD 720p digital video recorder used to record the video. Frames are then enhanced using Adobe Photoshop Creative Cloud as follows:1) Image Size; Width 300%; Resolution: 300 per inch; With Scale Styles; With Constrain Proportions; Interpolation: preserve details; Noise: 100.2) Save; As: PNG Format; Interlace: None; Filter: Adaptive; Compression: 9.<br>
DOI: 10.6084/m9.figshare.3180313.v1
title: 20 September 2014 VID00040 Original Frames

description: Every frame of VID00040 taken on 20 September 2014. Frames are extracted using Cisco FlipShare software distributed with the Cisco Flip UltraHD 720p digital video recorder used to record the video.<br>