cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3181525
title: Rosh_HaNikra_MCA_DATA.gdb.zip

description: The two main files are: 1) the results of the pairwise comparison for each of the survey respondents indicating preferences for each of the four high-level criteria. This is an Excel File. 2) a geodatabase file containing all the relevant GIS files for use with ArcGIS or an applicable GIS software package.
DOI: 10.6084/m9.figshare.3181561
title: High resolution figures manuscript NATECOLEVOL-16040002

description: High resolution figures for the reviewing process of manuscript " <i>The developmental basis for the recurrent evolution of deuterostomy and protostomy"</i>
DOI: 10.6084/m9.figshare.3181555
title: OSSData.zip

description: This data set is about work and talk activities (time series) of hundreds of developers in 31 Open Source Software (OSS) projects collected from Apache Software Foundation on March 24th, 2012. The data set can be used to analyze the human online behaviors and the evolution patterns of social and collaboration networks between developers. <br>
DOI: 10.6084/m9.figshare.3181504
title: Data and Script for Genome Biology paper "Mapping the landscape of metabolic goals of a cell"

description: This directory contains all Matlab data (.mat) and scripts (.m) used to generate the results for the manuscript "Mapping the landscape of metabolic goals of a cell", by Qi Zhao, Arion Stettner, Ed Reznik, Ioannis Ch. Paschalidis and Daniel Segrè.<br>
DOI: 10.6084/m9.figshare.3181525.v1
title: Rosh_HaNikra_MCA_DATA.gdb.zip

description: The two main files are: 1) the results of the pairwise comparison for each of the survey respondents indicating preferences for each of the four high-level criteria. This is an Excel File. 2) a geodatabase file containing all the relevant GIS files for use with ArcGIS or an applicable GIS software package.
DOI: 10.6084/m9.figshare.3181492
title: Semantic-Based Profile Management System: A Case Study on VIVO

description: The article describe about the semantic technologies and open source profile management called VIVO
DOI: 10.6084/m9.figshare.3181495
title: Academic Identity: An Overview

description: The article describe about the academic identity and its important in the scholarly communication
DOI: 10.6084/m9.figshare.3181561.v2
title: High resolution figures manuscript NATECOLEVOL-16040002

description: High resolution figures for the reviewing process of manuscript " <i>The developmental basis for the recurrent evolution of deuterostomy and protostomy"</i>
DOI: 10.6084/m9.figshare.3181480
title: Macroscopic, microscopic and transcriptomal analysis of the heart.

description: Figure 5H.
DOI: 10.6084/m9.figshare.3181480.v1
title: Macroscopic, microscopic and transcriptomal analysis of the heart.

description: Figure 5H.
DOI: 10.6084/m9.figshare.3181555.v1
title: OSSData.zip

description: This data set is about work and talk activities of hundreds of developers in 31 Open Source Software (OSS) projects collected from Apache Software Foundation on March 24th, 2012. This data set can be used to analyze the developer online behaviors and the evolution patterns of social and collaboration networks between developers. <br>
DOI: 10.6084/m9.figshare.3181492.v2
title: Semantic-Based Profile Management System: A Case Study on VIVO

description: The article describe about the semantic technologies and open source profile management called VIVO
DOI: 10.6084/m9.figshare.3181555.v2
title: OSSData.zip

description: This data set is about work and talk activities of hundreds of developers in 31 Open Source Software (OSS) projects collected from Apache Software Foundation on March 24th, 2012. This data set can be used to analyze the developer online behaviors and the evolution patterns of social and collaboration networks between developers. <br>
DOI: 10.6084/m9.figshare.3181438
title: Reactivity of isolated thoracic aorta.

description: Figure 3.
DOI: 10.6084/m9.figshare.3181417
title: Hemodynamic parameters.

description: Figure 2.
DOI: 10.6084/m9.figshare.3181438.v1
title: Reactivity of isolated thoracic aorta.

description: Figure 3.
DOI: 10.6084/m9.figshare.3181495.v2
title: Academic Identity: An Overview

description: The article describe about the academic identity and its important in the scholarly communication
DOI: 10.6084/m9.figshare.3181369
title: An Introduction To Cement-Based Concrete

description: This paper was an introduction written to illustrate the background research needed before research was conducted to discover if recycled asphalt shingles can be used as a aggregate in cement based concrete.
DOI: 10.6084/m9.figshare.3181555.v3
title: OSSData.zip

description: This data set is about work and talk activities of hundreds of developers in 31 Open Source Software (OSS) projects collected from Apache Software Foundation on March 24th, 2012. This data set can be used to analyze the developer online behaviors and the evolution patterns of social and collaboration networks between developers. <br>
DOI: 10.6084/m9.figshare.3181369.v1
title: An Introduction To Cement-Based Concrete

description: This paper was an introduction written to illustrate the background research needed before research was conducted to discover if recycled asphalt shingles can be used as a aggregate in cement based concrete.
DOI: 10.6084/m9.figshare.3181417.v1
title: Hemodynamic parameters.

description: Figure 2.
DOI: 10.6084/m9.figshare.3181555.v4
title: OSSData.zip

description: This data set is about work and talk activities of hundreds of developers in 31 Open Source Software (OSS) projects collected from Apache Software Foundation on March 24th, 2012. This data set can be used to analyze the developer online behaviors and the evolution patterns of social and collaboration networks between developers. <br>
DOI: 10.6084/m9.figshare.3181345.v3
title: Microwave-assisted catalyst-free synthesis of tetrasubstituted pyrroles using dialkyl acetylenedicarboxylates and monophenacylanilines

description: An efficient catalyst-free microwave-assisted synthesis of tetrasubstituted pyrroles using dialkyl acetylenedicarboxylates and substituted monophenacylanilines has been developed. Axial chirality has been noticed in some <i>N</i>-(α-naphthyl/2-isopropylphenyl)-2,3-dicarbethoxy-4-arylpyrroles, but not with <i>N</i>-aryl-2,3-dicarbethoxy-4-(α-naphthyl)pyrrole.
DOI: 10.6084/m9.figshare.3181555.v5
title: OSSData.zip

description: This data set is about work and talk activities of hundreds of developers in 31 Open Source Software (OSS) projects collected from Apache Software Foundation on March 24th, 2012. This data set can be used to analyze the developer online behaviors and the evolution patterns of social and collaboration networks between developers. <br>
DOI: 10.6084/m9.figshare.3181345
title: Microwave-assisted catalyst-free synthesis of tetrasubstituted pyrroles using dialkyl acetylenedicarboxylates and monophenacylanilines

description: An efficient catalyst-free microwave-assisted synthesis of tetrasubstituted pyrroles using dialkyl acetylenedicarboxylates and substituted monophenacylanilines has been developed. Axial chirality has been noticed in some <i>N</i>-(α-naphthyl/2-isopropylphenyl)-2,3-dicarbethoxy-4-arylpyrroles, but not with <i>N</i>-aryl-2,3-dicarbethoxy-4-(α-naphthyl)pyrrole.
DOI: 10.6084/m9.figshare.3181306
title: Arachidonic and oleic acid exert distinct effects on the DNA methylome

description: Abnormal fatty acid metabolism and availability are landmarks of metabolic diseases, which in turn are associated with aberrant DNA methylation profiles. To understand the role of fatty acids in disease epigenetics, we sought DNA methylation profiles specifically induced by arachidonic (AA) or oleic acid (OA) in cultured cells and compared those with published profiles of normal and diseased tissues. THP-1 monocytes were stimulated with AA or OA and analyzed using Infinium HumanMethylation450 BeadChip (Illumina) and Human Exon 1.0 ST array (Affymetrix). Data were corroborated in mouse embryonic fibroblasts. Comparisons with publicly available data were conducted by standard bioinformatics. AA and OA elicited a complex response marked by a general DNA hypermethylation and hypomethylation in the 1–200 μM range, respectively, with a maximal differential response at the 100 μM dose. The divergent response to AA and OA was prominent within the gene body of target genes, where it correlated positively with transcription. AA-induced DNA methylation profiles were similar to the corresponding profiles described for palmitic acid, atherosclerosis, diabetes, obesity, and autism, but relatively dissimilar from OA-induced profiles. Furthermore, human atherosclerosis grade-associated DNA methylation profiles were significantly enriched in AA-induced profiles. Biochemical evidence pointed to β-oxidation, PPAR-α, and sirtuin 1 as important mediators of AA-induced DNA methylation changes. In conclusion, AA and OA exert distinct effects on the DNA methylome. The observation that AA may contribute to shape the epigenome of important metabolic diseases, supports and expands current diet-based therapeutic and preventive efforts.
DOI: 10.6084/m9.figshare.3181294
title: Gaussian Job Archive for C44H64N8Si4Zn2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.3181555.v6
title: OSSData.zip

description: This data set is about work and talk activities of hundreds of developers in 31 Open Source Software (OSS) projects collected from Apache Software Foundation on March 24th, 2012. This data set can be used to analyze the developer online behaviors and the evolution patterns of social and collaboration networks between developers. <br>
DOI: 10.6084/m9.figshare.3181294.v1
title: Gaussian Job Archive for C44H64N8Si4Zn2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.3181306.v2
title: Arachidonic and oleic acid exert distinct effects on the DNA methylome

description: Abnormal fatty acid metabolism and availability are landmarks of metabolic diseases, which in turn are associated with aberrant DNA methylation profiles. To understand the role of fatty acids in disease epigenetics, we sought DNA methylation profiles specifically induced by arachidonic (AA) or oleic acid (OA) in cultured cells and compared those with published profiles of normal and diseased tissues. THP-1 monocytes were stimulated with AA or OA and analyzed using Infinium HumanMethylation450 BeadChip (Illumina) and Human Exon 1.0 ST array (Affymetrix). Data were corroborated in mouse embryonic fibroblasts. Comparisons with publicly available data were conducted by standard bioinformatics. AA and OA elicited a complex response marked by a general DNA hypermethylation and hypomethylation in the 1–200 μM range, respectively, with a maximal differential response at the 100 μM dose. The divergent response to AA and OA was prominent within the gene body of target genes, where it correlated positively with transcription. AA-induced DNA methylation profiles were similar to the corresponding profiles described for palmitic acid, atherosclerosis, diabetes, obesity, and autism, but relatively dissimilar from OA-induced profiles. Furthermore, human atherosclerosis grade-associated DNA methylation profiles were significantly enriched in AA-induced profiles. Biochemical evidence pointed to β-oxidation, PPAR-α, and sirtuin 1 as important mediators of AA-induced DNA methylation changes. In conclusion, AA and OA exert distinct effects on the DNA methylome. The observation that AA may contribute to shape the epigenome of important metabolic diseases, supports and expands current diet-based therapeutic and preventive efforts.
DOI: 10.6084/m9.figshare.3181306.v1
title: Arachidonic and oleic acid exert distinct effects on the DNA methylome

description: Abnormal fatty acid metabolism and availability are landmarks of metabolic diseases, which in turn are associated with aberrant DNA methylation profiles. To understand the role of fatty acids in disease epigenetics, we sought DNA methylation profiles specifically induced by arachidonic (AA) or oleic acid (OA) in cultured cells and compared those with published profiles of normal and diseased tissues. THP-1 monocytes were stimulated with AA or OA and analyzed using Infinium HumanMethylation450 BeadChip (Illumina) and Human Exon 1.0 ST array (Affymetrix). Data were corroborated in mouse embryonic fibroblasts. Comparisons with publicly available data were conducted by standard bioinformatics. AA and OA elicited a complex response marked by a general DNA hypermethylation and hypomethylation in the 1–200 μM range, respectively, with a maximal differential response at the 100 μM dose. The divergent response to AA and OA was prominent within the gene body of target genes, where it correlated positively with transcription. AA-induced DNA methylation profiles were similar to the corresponding profiles described for palmitic acid, atherosclerosis, diabetes, obesity, and autism, but relatively dissimilar from OA-induced profiles. Furthermore, human atherosclerosis grade-associated DNA methylation profiles were significantly enriched in AA-induced profiles. Biochemical evidence pointed to β-oxidation, PPAR-alpha, and sirtuin 1 as important mediators of AA-induced DNA methylation changes. In conclusion, AA and OA exert distinct effects on the DNA methylome. The observation that AA may contribute to shape the epigenome of important metabolic diseases, supports and expands current diet-based therapeutic and preventive efforts.
DOI: 10.6084/m9.figshare.3181555.v7
title: OSSData.zip

description: This data set is about work and talk activities of hundreds of developers in 31 Open Source Software (OSS) projects collected from Apache Software Foundation on March 24th, 2012. This data set can be used to analyze the developer online behaviors and the evolution patterns of social and collaboration networks between developers. <br>
DOI: 10.6084/m9.figshare.3181276
title: Supplement Note

description: Supplement Note
DOI: 10.6084/m9.figshare.3181555.v8
title: OSSData.zip

description: This data set is about work and talk activities of hundreds of developers in 31 Open Source Software (OSS) projects collected from Apache Software Foundation on March 24th, 2012. This data set can be used to analyze the developer online behaviors and the evolution patterns of social and collaboration networks between developers. <br>
DOI: 10.6084/m9.figshare.3181276.v1
title: Supplement Note

description: Supplement Note
DOI: 10.6084/m9.figshare.3181555.v10
title: OSSData.zip

description: This data set is about work and talk activities (time series) of hundreds of developers in 31 Open Source Software (OSS) projects collected from Apache Software Foundation on March 24th, 2012. The data set can be used to analyze the human online behaviors and the evolution patterns of social and collaboration networks between developers. <br>
DOI: 10.6084/m9.figshare.3181231
title: Instructed fear learning, extinction, and recall: additive effects of cognitive information on emotional learning of fear

description: The effects of instruction on learning of fear and safety are rarely studied. We aimed to examine the effects of cognitive information and experience on fear learning. Fourty healthy participants, randomly assigned to three groups, went through fear conditioning, extinction learning, and extinction recall with two conditioned stimuli (CS+). Information was presented about the presence or absence of conditioned stimulus–unconditioned stimulus (CS–US) contingency at different stages of the experiment. Information about the CS–US contingency prior to fear conditioning enhanced fear response and reduced extinction recall. Information about the absence of CS–US contingency promoted extinction learning and recall, while omission of this information prior to recall resulted in fear renewal. These findings indicate that contingency information can facilitate fear expression during fear learning, and can facilitate extinction learning and recall. Information seems to function as an element of the larger context in which conditioning occurs.
DOI: 10.6084/m9.figshare.3181555.v9
title: OSSData.zip

description: This data set is about work and talk activities of hundreds of developers in 31 Open Source Software (OSS) projects collected from Apache Software Foundation on March 24th, 2012. The data set can be used to analyze the developer online behaviors and the evolution patterns of social and collaboration networks between developers. <br>
DOI: 10.6084/m9.figshare.3181174
title: Conformal prediction to define applicability domain – A case study on predicting ER and AR binding

description: A fundamental element when deriving a robust and predictive <i>in silico</i> model is not only the statistical quality of the model in question but, equally important, the estimate of its predictive boundaries. This work presents a new method, conformal prediction, for applicability domain estimation in the field of endocrine disruptors. The method is applied to binders and non-binders related to the oestrogen and androgen receptors. Ensembles of decision trees are used as statistical method and three different sets (dragon, rdkit and signature fingerprints) are investigated as chemical descriptors. The conformal prediction method results in valid models where there is an excellent balance in quality between the internally validated training set and the corresponding external test set, both in terms of validity and with respect to sensitivity and specificity. With this method the level of confidence can be readily altered by the user and the consequences thereof immediately inspected. Furthermore, the predictive boundaries for the derived models are rigorously defined by using the conformal prediction framework, thus no ambiguity exists as to the level of similarity needed for new compounds to be in or out of the predictive boundaries of the derived models where reliable predictions can be expected.
DOI: 10.6084/m9.figshare.3181231.v1
title: Instructed fear learning, extinction, and recall: additive effects of cognitive information on emotional learning of fear

description: The effects of instruction on learning of fear and safety are rarely studied. We aimed to examine the effects of cognitive information and experience on fear learning. Fourty healthy participants, randomly assigned to three groups, went through fear conditioning, extinction learning, and extinction recall with two conditioned stimuli (CS+). Information was presented about the presence or absence of conditioned stimulus–unconditioned stimulus (CS–US) contingency at different stages of the experiment. Information about the CS–US contingency prior to fear conditioning enhanced fear response and reduced extinction recall. Information about the absence of CS–US contingency promoted extinction learning and recall, while omission of this information prior to recall resulted in fear renewal. These findings indicate that contingency information can facilitate fear expression during fear learning, and can facilitate extinction learning and recall. Information seems to function as an element of the larger context in which conditioning occurs.
DOI: 10.6084/m9.figshare.3181174.v1
title: Conformal prediction to define applicability domain – A case study on predicting ER and AR binding

description: A fundamental element when deriving a robust and predictive <i>in silico</i> model is not only the statistical quality of the model in question but, equally important, the estimate of its predictive boundaries. This work presents a new method, conformal prediction, for applicability domain estimation in the field of endocrine disruptors. The method is applied to binders and non-binders related to the oestrogen and androgen receptors. Ensembles of decision trees are used as statistical method and three different sets (dragon, rdkit and signature fingerprints) are investigated as chemical descriptors. The conformal prediction method results in valid models where there is an excellent balance in quality between the internally validated training set and the corresponding external test set, both in terms of validity and with respect to sensitivity and specificity. With this method the level of confidence can be readily altered by the user and the consequences thereof immediately inspected. Furthermore, the predictive boundaries for the derived models are rigorously defined by using the conformal prediction framework, thus no ambiguity exists as to the level of similarity needed for new compounds to be in or out of the predictive boundaries of the derived models where reliable predictions can be expected.
DOI: 10.6084/m9.figshare.3181150
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.3181165
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.3181141
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.