cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1140439.v1
title: A simple extension to the CMASA method for the prediction of catalytic residues in the presence of single point mutations

description: The automatic identification of catalytic residues still remains an important challenge in<br>structural bioinformatics. Sequence-based methods are good alternatives when the<br>query shares a high percentage of identity with a well-annotated enzyme. However,<br>when the homology is not apparent, which occurs with many structures from the<br>structural genome initiative, structural information should be exploited. A local<br>structural comparison is preferred to a global structural comparison when predicting<br>functional residues. CMASA is a recently proposed method for predicting catalytic<br>residues based on a local structure comparison. The method achieves high accuracy<br>and a high value for the Matthews correlation coefficient. However, point substitutions<br>or a lack of relevant data strongly affect the performance of the method. In the present<br>study, we propose a simple extension to the CMASA method to overcome this<br>difficulty. Extensive computational experiments are shown as proof of concept<br>instances, as well as for a few real cases. The results show that the extension<br>performs well when the catalytic site contains mutated residues or when some<br>residues are missing. The proposed modification could correctly predict the catalytic<br>residues of a mutant transferase of the kinase family, 1EVF. It also successfully<br>predicted the catalytic residues for 3HRC despite the lack of information for a relevant<br>side chain atom in the PDB file.
DOI: 10.6084/m9.figshare.1140391
title: Quantum imagination leading to the "theory of everything"

description: Attempt to connect the dots and maybe prove that the theory of everything has been solved.
DOI: 10.6084/m9.figshare.1140439.v2
title: A simple extension to the CMASA method for the prediction of catalytic residues in the presence of single point mutations

description: The automatic identification of catalytic residues still remains an important challenge in<br>structural bioinformatics. Sequence-based methods are good alternatives when the<br>query shares a high percentage of identity with a well-annotated enzyme. However,<br>when the homology is not apparent, which occurs with many structures from the<br>structural genome initiative, structural information should be exploited. A local<br>structural comparison is preferred to a global structural comparison when predicting<br>functional residues. CMASA is a recently proposed method for predicting catalytic<br>residues based on a local structure comparison. The method achieves high accuracy<br>and a high value for the Matthews correlation coefficient. However, point substitutions<br>or a lack of relevant data strongly affect the performance of the method. In the present<br>study, we propose a simple extension to the CMASA method to overcome this<br>difficulty. Extensive computational experiments are shown as proof of concept<br>instances, as well as for a few real cases. The results show that the extension<br>performs well when the catalytic site contains mutated residues or when some<br>residues are missing. The proposed modification could correctly predict the catalytic<br>residues of a mutant transferase of the kinase family, 1EVF. It also successfully<br>predicted the catalytic residues for 3HRC despite the lack of information for a relevant<br>side chain atom in the PDB file.
DOI: 10.6084/m9.figshare.1140328
title: Models 360 dataset

description: This the molecular dataset in JSON format of the Models360 web resource (http://www.chemeddl.org/resources/models360). Models 360 enables users to investigate a collection of 3-D interactive models of organic and inorganic compounds, including extended-structure solids. Users can manipulate the models to examine structure and bonding and demonstrate molecular geometries, vibrations, symmetry, and orbitals. This resource has been built specifically to meet the needs of educators. The molecules and structures shown have been vetted as to their usefulness in teaching, and their accuracy. The structure of each molecule has been calculated using modern quantum mechanical software in order to obtain high-accuracy properties to be used in classrooms. Models 360 was initiated by Xavier Prat-Resina during his period as a postdoctoral fellow with the Chemical Education Digital Library. Major contributions to the project were made by David Pieper, Justin Shorb, Robert Anglin, Brandon Korf, Greg Sovinski, Zak Kastelik, Rachel Bain, Angela Jones, Ieva Reich, Adam Hahn, and John W. Moore, all working for the Chemical Education Digital Library (ChemEd DL).
DOI: 10.6084/m9.figshare.1140330
title: Lithium ionophore VIII as an extraordinarily strong receptor for the trivalent europium cation

description: On the basis of extraction experiments and γ-activity measurements, the extraction constant corresponding to the equilibrium Eu<sup>3+</sup>(aq) + 3A<sup>−</sup>(aq) + <b>1</b>(nb) ⇆ <b>1</b><b>·</b>Eu<sup>3+</sup>(nb) + 3A<sup>‑</sup>(nb) occurring in the two-phase water–nitrobenzene system (A<sup>−</sup> = CF<sub>3</sub>SO<sup>−</sup><sub>3</sub>; <b>1</b> = lithium ionophore VIII; aq = aqueous phase, nb = nitrobenzene phase) was determined as log <i>K</i><sub>ex</sub> (<b>1</b><b>·</b>Eu<sup>3+</sup>, 3A<sup>‑</sup>) = 2.5 ± 0.1. Furthermore, the extremely high stability constant of the <b>1</b><b>·</b>Eu<sup>3+</sup> complex in nitrobenzene saturated with water was calculated: log β<sub>nb</sub> (<b>1</b><b>·</b>Eu<sup>3+</sup>) = 15.6 ± 0.1. Finally, by using DFT calculations, the most probable structure of the cationic complex species <b>1</b><b>·</b>Eu<sup>3+</sup> was derived. In the resulting complex, the ‘central’ cation Eu<sup>3+</sup> is bound by six very strong bond interactions to the corresponding six oxygen atoms of the parent ligand <b>1</b>. It is evident that this exceptionally effective receptor <b>1</b> for the Eu<sup>3+</sup> cation could be considered as a potential extraction agent for nuclear waste treatment.
DOI: 10.6084/m9.figshare.1140391.v1
title: Quantum imagination leading to the "theory of everything"

description: Attempt to connect the dots and maybe prove that the theory of everything has been solved.
DOI: 10.6084/m9.figshare.1140330.v1
title: Lithium ionophore VIII as an extraordinarily strong receptor for the trivalent europium cation

description: On the basis of extraction experiments and γ-activity measurements, the extraction constant corresponding to the equilibrium Eu<sup>3+</sup>(aq) + 3A<sup>−</sup>(aq) + <b>1</b>(nb) ⇆ <b>1</b><b>·</b>Eu<sup>3+</sup>(nb) + 3A<sup>‑</sup>(nb) occurring in the two-phase water–nitrobenzene system (A<sup>−</sup> = CF<sub>3</sub>SO<sup>−</sup><sub>3</sub>; <b>1</b> = lithium ionophore VIII; aq = aqueous phase, nb = nitrobenzene phase) was determined as log <i>K</i><sub>ex</sub> (<b>1</b><b>·</b>Eu<sup>3+</sup>, 3A<sup>‑</sup>) = 2.5 ± 0.1. Furthermore, the extremely high stability constant of the <b>1</b><b>·</b>Eu<sup>3+</sup> complex in nitrobenzene saturated with water was calculated: log β<sub>nb</sub> (<b>1</b><b>·</b>Eu<sup>3+</sup>) = 15.6 ± 0.1. Finally, by using DFT calculations, the most probable structure of the cationic complex species <b>1</b><b>·</b>Eu<sup>3+</sup> was derived. In the resulting complex, the ‘central’ cation Eu<sup>3+</sup> is bound by six very strong bond interactions to the corresponding six oxygen atoms of the parent ligand <b>1</b>. It is evident that this exceptionally effective receptor <b>1</b> for the Eu<sup>3+</sup> cation could be considered as a potential extraction agent for nuclear waste treatment.
DOI: 10.6084/m9.figshare.1140330.v3
title: Lithium ionophore VIII as an extraordinarily strong receptor for the trivalent europium cation

description: On the basis of extraction experiments and γ-activity measurements, the extraction constant corresponding to the equilibrium Eu<sup>3+</sup>(aq) + 3A<sup>−</sup>(aq) + <b>1</b>(nb) ⇆ <b>1</b><b>·</b>Eu<sup>3+</sup>(nb) + 3A<sup>‑</sup>(nb) occurring in the two-phase water–nitrobenzene system (A<sup>−</sup> = CF<sub>3</sub>SO<sup>−</sup><sub>3</sub>; <b>1</b> = lithium ionophore VIII; aq = aqueous phase, nb = nitrobenzene phase) was determined as log <i>K</i><sub>ex</sub> (<b>1</b><b>·</b>Eu<sup>3+</sup>, 3A<sup>‑</sup>) = 2.5 ± 0.1. Furthermore, the extremely high stability constant of the <b>1</b><b>·</b>Eu<sup>3+</sup> complex in nitrobenzene saturated with water was calculated: log β<sub>nb</sub> (<b>1</b><b>·</b>Eu<sup>3+</sup>) = 15.6 ± 0.1. Finally, by using DFT calculations, the most probable structure of the cationic complex species <b>1</b><b>·</b>Eu<sup>3+</sup> was derived. In the resulting complex, the ‘central’ cation Eu<sup>3+</sup> is bound by six very strong bond interactions to the corresponding six oxygen atoms of the parent ligand <b>1</b>. It is evident that this exceptionally effective receptor <b>1</b> for the Eu<sup>3+</sup> cation could be considered as a potential extraction agent for nuclear waste treatment.
DOI: 10.6084/m9.figshare.1140391.v2
title: Quantum imagination leading to the "theory of everything"

description: Attempt to connect the dots and maybe prove that the theory of everything has been solved.
DOI: 10.6084/m9.figshare.1140330.v2
title: Lithium ionophore VIII as an extraordinarily strong receptor for the trivalent europium cation

description: On the basis of extraction experiments and γ-activity measurements, the extraction constant corresponding to the equilibrium Eu<sup>3+</sup>(aq) + 3A<sup>−</sup>(aq) + <b>1</b>(nb) ⇆ <b>1</b><b>·</b>Eu<sup>3+</sup>(nb) + 3A<sup>‑</sup>(nb) occurring in the two-phase water–nitrobenzene system (A<sup>−</sup> = CF<sub>3</sub>SO<sup>−</sup><sub>3</sub>; <b>1</b> = lithium ionophore VIII; aq = aqueous phase, nb = nitrobenzene phase) was determined as log <i>K</i><sub>ex</sub> (<b>1</b><b>·</b>Eu<sup>3+</sup>, 3A<sup>‑</sup>) = 2.5 ± 0.1. Furthermore, the extremely high stability constant of the <b>1</b><b>·</b>Eu<sup>3+</sup> complex in nitrobenzene saturated with water was calculated: log β<sub>nb</sub> (<b>1</b><b>·</b>Eu<sup>3+</sup>) = 15.6 ± 0.1. Finally, by using DFT calculations, the most probable structure of the cationic complex species <b>1</b><b>·</b>Eu<sup>3+</sup> was derived. In the resulting complex, the ‘central’ cation Eu<sup>3+</sup> is bound by six very strong bond interactions to the corresponding six oxygen atoms of the parent ligand <b>1</b>. It is evident that this exceptionally effective receptor <b>1</b> for the Eu<sup>3+</sup> cation could be considered as a potential extraction agent for nuclear waste treatment.
DOI: 10.6084/m9.figshare.1140391.v3
title: Quantum imagination leading to the "theory of everything"

description: Attempt to connect the dots and maybe prove that the theory of everything has been solved.
DOI: 10.6084/m9.figshare.1140391.v4
title: Quantum imagination leading to the "theory of everything"

description: Attempt to connect the dots and maybe prove that the theory of everything has been solved.
DOI: 10.6084/m9.figshare.1140391.v5
title: Quantum imagination leading to the "theory of everything"

description: Attempt to connect the dots and maybe prove that the theory of everything has been solved.
DOI: 10.6084/m9.figshare.1138736
title: LAS files 2012 Santorini LiDAR dataset EU-12-12-137

description: LAS format LiDAR point cloud data from the NERC Airborne Research and Survey Facility campaign to Santorini, Greece, in May 2012 - EU-12-12-137. 13 flightlines in total. Data are analysed in an open access paper in GeoResJ by Nomikou et al., 2014 - http://dx.doi.org/10.1016/j.grj.2014.02.002
DOI: 10.6084/m9.figshare.1140391.v6
title: Quantum imagination leading to the "theory of everything"

description: Attempt to connect the dots and maybe prove that the theory of everything has been solved.
DOI: 10.6084/m9.figshare.1138734
title: LAS point cloud LiDAR data flightline 13

description: Santorini LiDAR data from 2012 NERC ARSF flight EU-12-12-137
DOI: 10.6084/m9.figshare.1138743
title: TXT files - raw LiDAR data from the 2012 LiDAR campaign to Santorini, Greece

description: Text files of the raw LiDAR data from the 2012 NERC ARSF survey of the Kameni islands, Santorini, Greece EU-12-12-137 Data are from 13 flightlines
DOI: 10.6084/m9.figshare.1138730
title: LAS point cloud LiDAR data flightline 10

description: Santorini LiDAR data from 2012 NERC ARSF flight EU-12-12-137
DOI: 10.6084/m9.figshare.1140391.v7
title: Quantum imagination leading to the "theory of everything"

description: Attempt to connect the dots and maybe prove that the theory of everything has been solved.
DOI: 10.6084/m9.figshare.1138730.v1
title: LAS point cloud LiDAR data flightline 10

description: Santorini LiDAR data from 2012 NERC ARSF flight EU-12-12-137
DOI: 10.6084/m9.figshare.1138718
title: 2012 Santorini LiDAR data

description: Datasets from a LiDAR survey of the Greek volcanic islands of Nea Kameni and Palea Kameni, Santorini, Greece. Data were collected during a NERC ARSF flight campaign EU-12-12-137. See the open access paper in GeoResJ by Evi Nomikou et al., (2014) for details; http://dx.doi.org/10.1016/j.grj.2014.02.002
DOI: 10.6084/m9.figshare.1138729
title: LAS point cloud LiDAR data flightline 12

description: LAS point cloud LiDAR data flightline 12 NERC ARSF LiDAR survey of the Kameni islands, Santorini, 2012 EU-12-12-137
DOI: 10.6084/m9.figshare.1140391.v8
title: Quantum imagination leading to the "theory of everything"

description: Attempt to connect the dots and maybe prove that the theory of everything has been solved.
DOI: 10.6084/m9.figshare.1140391.v9
title: Quantum imagination leading to the "theory of everything"

description: Attempt to connect the dots and maybe prove that the theory of everything has been solved.
DOI: 10.6084/m9.figshare.1138671
title: Raw data: Body weight

description: Paper available at PlosOne
DOI: 10.6084/m9.figshare.1138672
title: Raw data: Food consumption

description: Paper available at PlosOne
DOI: 10.6084/m9.figshare.1138673
title: Raw data: Plasma corticosterone

description: Paper available at PlosOne
DOI: 10.6084/m9.figshare.1138672.v1
title: Raw data: Food consumption

description: Paper available at PlosOne
DOI: 10.6084/m9.figshare.1138673.v1
title: Raw data: Plasma corticosterone

description: Paper available at PlosOne
DOI: 10.6084/m9.figshare.1140391.v10
title: Quantum imagination leading to the "theory of everything"

description: Attempt to connect the dots and maybe prove that the theory of everything has been solved.
DOI: 10.6084/m9.figshare.1140391.v11
title: Quantum imagination leading to the "theory of everything"

description: Attempt to connect the dots and maybe prove that the theory of everything has been solved.
DOI: 10.6084/m9.figshare.1138621
title: Tamsulosin: quality of clinical trials (research methods and reporting); conflict of interests; research impact (citations)

description: For more información please read: Ramirez, Jorge H (2014): Expression of concern about tamsulosin: over three quarters of human studies are unpublished. figshare.<br>http://dx.doi.org/10.6084/m9.figshare.1094338 Note related to Paywalls: it was no possible for me to analyze the whole scenario. I'm disclosing this data so anyone could continue the analysis. This data is publicly available (I do not own this data) feel welcome to analyze it without asking anyone. However, I'll advice you to do it according to the terms of service from which this data was collected (ClinicalTrials.gov, WHO ICTRP, PubMed, Embase, Propublica, among other databases). Please contact me if you have any question, I'll be very happy to cooperate with you.
DOI: 10.6084/m9.figshare.1138532
title: Robustness of tests for directional mean

description: In this paper we study the robustness of the likelihood ratio, circular mean and circular trimmed mean test functionals in the context of tests of hypotheses regarding the mean direction of circular normal and wrapped normal distributions. We compute the level and power breakdown properties of the three test functionals and compare them. We find that the circular trimmed mean test functional has the best robustness properties for both the above-mentioned distributions. The level and power properties of the test statistics corresponding to these functionals are also studied. Two examples with real data are given for illustration. We also consider the problem of testing the mean direction of the von-Mises–Fisher distribution on the unit sphere and explore the robustness properties of the spherical mean direction and likelihood ratio test functionals.
DOI: 10.6084/m9.figshare.1138531
title: Google Trends - Evidence Based Medicine

description: Archive (csv) corresponding to the title description. Download date: Aug 14, 2014. Trends: - Evidence based medicine - Practice guidelines - EBM - Medicina basada en la evidencia - Guía de práctica clínica - Médecine factuelle
DOI: 10.6084/m9.figshare.1138531.v2
title: Google Trends - Evidence Based Medicine

description: Archive (csv) corresponding to the title description. Download date: Aug 14, 2014. Trends: - Evidence based medicine - Practice guidelines - EBM - Medicina basada en la evidencia - Guía de práctica clínica - Médecine factuelle
DOI: 10.6084/m9.figshare.1138532.v1
title: Robustness of tests for directional mean

description: In this paper we study the robustness of the likelihood ratio, circular mean and circular trimmed mean test functionals in the context of tests of hypotheses regarding the mean direction of circular normal and wrapped normal distributions. We compute the level and power breakdown properties of the three test functionals and compare them. We find that the circular trimmed mean test functional has the best robustness properties for both the above-mentioned distributions. The level and power properties of the test statistics corresponding to these functionals are also studied. Two examples with real data are given for illustration. We also consider the problem of testing the mean direction of the von-Mises–Fisher distribution on the unit sphere and explore the robustness properties of the spherical mean direction and likelihood ratio test functionals.
DOI: 10.6084/m9.figshare.1138531.v1
title: Google Trends - Evidence Based Medicine

description: Archive (csv) corresponding to the description in the title. Download date: Aug 14, 2014. Trends: - Evidence based medicine - Practice guidelines - EBM - Medicina basada en la evidencia - Guía de práctica clínica - Médecine factuelle
DOI: 10.6084/m9.figshare.1138532.v3
title: Robustness of tests for directional mean

description: In this paper we study the robustness of the likelihood ratio, circular mean and circular trimmed mean test functionals in the context of tests of hypotheses regarding the mean direction of circular normal and wrapped normal distributions. We compute the level and power breakdown properties of the three test functionals and compare them. We find that the circular trimmed mean test functional has the best robustness properties for both the above-mentioned distributions. The level and power properties of the test statistics corresponding to these functionals are also studied. Two examples with real data are given for illustration. We also consider the problem of testing the mean direction of the von-Mises–Fisher distribution on the unit sphere and explore the robustness properties of the spherical mean direction and likelihood ratio test functionals.
DOI: 10.6084/m9.figshare.1138621.v1
title: Tamsulosin: quality of clinical trials (research methods and reporting); conflict of interests; research impact (citations)

description: For more información please read: Ramirez, Jorge H (2014): Expression of concern about tamsulosin: over three quarters of human studies are unpublished. figshare.<br>http://dx.doi.org/10.6084/m9.figshare.1094338
DOI: 10.6084/m9.figshare.1138532.v2
title: Robustness of tests for directional mean

description: In this paper we study the robustness of the likelihood ratio, circular mean and circular trimmed mean test functionals in the context of tests of hypotheses regarding the mean direction of circular normal and wrapped normal distributions. We compute the level and power breakdown properties of the three test functionals and compare them. We find that the circular trimmed mean test functional has the best robustness properties for both the above-mentioned distributions. The level and power properties of the test statistics corresponding to these functionals are also studied. Two examples with real data are given for illustration. We also consider the problem of testing the mean direction of the von-Mises–Fisher distribution on the unit sphere and explore the robustness properties of the spherical mean direction and likelihood ratio test functionals.
DOI: 10.6084/m9.figshare.1138621.v3
title: Tamsulosin: quality of clinical trials (research methods and reporting); conflict of interests; research impact (citations)

description: For more información please read: Ramirez, Jorge H (2014): Expression of concern about tamsulosin: over three quarters of human studies are unpublished. figshare.<br>http://dx.doi.org/10.6084/m9.figshare.1094338 Note related to Paywalls: it was no possible for me to analyze the whole scenario. I'm disclosing this data so anyone could continue the analysis. This data is publicly available (I do not own this data) feel welcome to analyze it without asking anyone. However, I'll advice you to do it according to the terms of service from which this data was collected (ClinicalTrials.gov, WHO ICTRP, PubMed, Embase, Propublica, among other databases). Please contact me if you have any question, I'll be very happy to cooperate with you.
DOI: 10.6084/m9.figshare.1138621.v2
title: Tamsulosin: quality of clinical trials (research methods and reporting); conflict of interests; research impact (citations)

description: For more información please read: Ramirez, Jorge H (2014): Expression of concern about tamsulosin: over three quarters of human studies are unpublished. figshare.<br>http://dx.doi.org/10.6084/m9.figshare.1094338