cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1152682
title: Molecular Dynamics Simulation of an Allosteric Receptor by Simultaneous Casting and Molding in a Dynamic Combinatorial Library

description: Raw results of the molecular dynamics simulations performed for the paper:
<em>An Allosteric Receptor by Simultaneous Casting and Molding in a Dynamic Combinatorial Library</em>, J. Li, P. Nowak and S. Otto.
This fileset contains results of MD simulations on the macrocyclic isomer III (isoIII), gamma-cyclodextrin (CD), quaternary ammonium template (2) and complexes formed by them (CD-isoIII, isoIII-2, CD-isoIII-2). 
Files with the "structure_" prefix are snaphots from MD simulations at the time indicated in the filename.
Files with the ".traj" extension are Amber trajectory files (without water box) which can be loaded into a trajectory visualisation program (e.g. VMD, http://www.ks.uiuc.edu/Research/vmd/). The corresponding topology/parameter files have the ".prmtop" extension. The structures were saved every 10000 steps and the timestep was 2 fs. Therefore, in order to convert the frame number into simulation time, the former has to be multiplied by 1/50 ns. 
Files with the "distGAX-Y_" prefix contain the distances between the mass centers of glucopyranose residues X and Y of either free or complexed gamma-cyclodextrin as a function of simulation time.
Files with the "rmsfit" extension contain RMSD errors as a function of simulation time.
File "1BB.mol2" is the naphtalene fragment (from building block <strong>1</strong>) used to construct the isomer III macrocycle with the leap program. It was generated using restrained electrostatic fit (RESP) with RED.III.5 program. File "2TM" corresponds to the template <strong>2</strong> and was obtained the same way.
DOI: 10.6084/m9.figshare.1152682.v1
title: Molecular Dynamics Simulation of an Allosteric Receptor by Simultaneous Casting and Molding in a Dynamic Combinatorial Library

description: Raw results of the molecular dynamics simulations performed for the paper:
<em>An Allosteric Receptor by Simultaneous Casting and Molding in a Dynamic Combinatorial Library</em>, J. Li, P. Nowak and S. Otto.
This fileset contains results of MD simulations on the macrocyclic isomer III (isoIII), gamma-cyclodextrin (CD), quaternary ammonium template (2) and complexes formed by them (CD-isoIII, isoIII-2, CD-isoIII-2). 
Files with the "structure_" prefix are snaphots from MD simulations at the time indicated in the filename.
Files with the ".traj" extension are Amber trajectory files (without water box) which can be loaded into a trajectory visualisation program (e.g. VMD, http://www.ks.uiuc.edu/Research/vmd/). The corresponding topology/parameter files have the ".prmtop" extension. The structures were saved every 10000 steps and the timestep was 2 fs. Therefore, in order to convert the frame number into simulation time, the former has to be multiplied by 1/50 ns. 
Files with the "distGAX-Y_" prefix contain the distances between the mass centers of glucopyranose residues X and Y of either free or complexed gamma-cyclodextrin as a function of simulation time.
Files with the "rmsfit" extension contain RMSD errors as a function of simulation time.
File "1BB.mol2" is the naphtalene fragment (from building block <strong>1</strong>) used to construct the isomer III macrocycle with the leap program. It was generated using restrained electrostatic fit (RESP) with RED.III.5 program. File "2TM" corresponds to the template <strong>2</strong> and was obtained the same way.
DOI: 10.6084/m9.figshare.1152695
title: pH Shaping the Composition of <i>sqhC</i>-Containing Bacterial Communities

description: Sediment and tailings samples were collected from sites with a contrasting physicochemical gradient to investigate microbial squalene-hopene cyclase (<i>sqhC</i>) composition and distribution in terrestrial environments. Acidobacteria (66%), Alphaproteobacteria (96%) and Gammaproteobacteria (55%) were found to dominate <i>sqhC</i> communities, respectively, at the acidic Dajiuhu Peatland, the alkaline Heshang Cave and strongly acidic tailings of Tongling copper mine in China. Statistical analysis confirmed that pH was the important factor impacting the geographical distribution of <i>sqhC</i> at phylum level. <i>sqhC</i> gene abundance is comparable at the three sites. However, the total amount of hopanoids in per gram total organic matter content (TOC) is 1.75 times higher in the acidic peatland than that in the alkaline Cave and it is below the detecting limit in tailings of Tongling copper mine, inferring the potential impact of pH in regulating the hopanoid production.
DOI: 10.6084/m9.figshare.1152695.v1
title: pH Shaping the Composition of <i>sqhC</i>-Containing Bacterial Communities

description: :Sediment and tailings samples were collected from sites with a contrasting physicochemical gradient to investigate microbial squalene-hopene cyclase (<i>sqhC</i>) composition and distribution in terrestrial environments. Acidobacteria (66%), Alphaproteobacteria (96%) and Gammaproteobacteria (55%) were found to dominate <i>sqhC</i> communities, respectively, at the acidic Dajiuhu Peatland, the alkaline Heshang Cave and strongly acidic tailings of Tongling copper mine in China. Statistical analysis confirmed that pH was the important factor impacting the geographical distribution of <i>sqhC</i> at phylum level. <i>sqhC</i> gene abundance is comparable at the three sites. However, the total amount of hopanoids in per gram total organic matter content (TOC) is 1.75 times higher in the acidic peatland than that in the alkaline Cave and it is below the detecting limit in tailings of Tongling copper mine, inferring the potential impact of pH in regulating the hopanoid production.
DOI: 10.6084/m9.figshare.1157860
title: Dataset for Outcomes in Cochrane systematic reviews addressing four common eye conditions: An evaluation of completeness and comparability

description: This is the dataset for the PLoS One paper titled "Outcomes in Cochrane systematic reviews addressing four common eye conditions: An evaluation of completeness and comparability"
DOI: 10.6084/m9.figshare.1157860.v1
title: Dataset for Outcomes in Cochrane systematic reviews addressing four common eye conditions: An evaluation of completeness and comparability

description: This is the dataset for the PLoS One paper titled "Outcomes in Cochrane systematic reviews addressing four common eye conditions: An evaluation of completeness and comparability"
DOI: 10.6084/m9.figshare.1157860.v3
title: Dataset for Outcomes in Cochrane systematic reviews addressing four common eye conditions: An evaluation of completeness and comparability

description: This is the dataset for the PLoS One paper titled "Outcomes in Cochrane systematic reviews addressing four common eye conditions: An evaluation of completeness and comparability"
DOI: 10.6084/m9.figshare.1157860.v2
title: Dataset for Outcomes in Cochrane systematic reviews addressing four common eye conditions: An evaluation of completeness and comparability

description: This is the dataset for the PLoS One paper titled "Outcomes in Cochrane systematic reviews addressing four common eye conditions: An evaluation of completeness and comparability"
DOI: 10.6084/m9.figshare.1162520
title: Molecular interactions of agonist and inverse agonist ligands at serotonin 5-HT<sub>2C</sub> G protein-coupled receptors: computational ligand docking and molecular dynamics studies validated by experimental mutagenesis results

description: To understand molecular determinants for ligand activation of the serotonin 5-HT<sub>2C</sub> G protein-coupled receptor (GPCR), a drug target for obesity and neuropsychiatric disorders, a 5-HT<sub>2C</sub> homology model was built according to an adrenergic β<sub>2</sub> GPCR (β<sub>2</sub>AR) structure and validated using a 5-HT<sub>2B</sub> GPCR crystal structure. The models were equilibrated in a simulated phosphatidyl choline membrane for ligand docking and molecular dynamics studies. Ligands included (2<i>S</i>, 4<i>R</i>)-(–)-<i>trans</i>-4-(3’-bromo- and trifluoro-phenyl)-<i>N</i>,<i>N</i>-dimethyl-1,2,3,4-tetrahydronaphthalene-2-amine (3’-Br-PAT and 3’-CF<sub>3</sub>-PAT), a 5-HT<sub>2C</sub> agonist and inverse agonist, respectively. Distinct interactions of 3’-Br-PAT and 3’-CF<sub>3</sub>-PAT at the wild-type (WT) 5-HT<sub>2C</sub> receptor model were observed and experimental 5-HT<sub>2C</sub> receptor mutagenesis studies were undertaken to validate the modelling results. For example, the inverse agonist 3’-CF<sub>3</sub>-PAT docked deeper in the WT 5-HT<sub>2C</sub> binding pocket and altered the orientation of transmembrane helices (TM) 6 in comparison to the agonist 3’-Br-PAT, suggesting that changes in TM orientation that result from ligand binding impact function. For both PATs, mutation of 5-HT<sub>2C</sub> residues S3.36, T3.37, and F5.47 to alanine resulted in significantly decreased affinity, as predicted from modelling results. It was concluded that upon PAT binding, 5-HT<sub>2C</sub> residues T3.37 and F5.47 in TMs 3 and 5, respectively, engage in inter-helical interactions with TMs 4 and 6, respectively. The movement of TMs 5 and 6 upon agonist and inverse agonist ligand binding observed in the 5-HT<sub>2C</sub> receptor modelling studies was similar to movements reported for the activation and deactivation of the β<sub>2</sub>AR, suggesting common mechanisms among aminergic neurotransmitter GPCRs.
DOI: 10.6084/m9.figshare.1162520.v2
title: Molecular interactions of agonist and inverse agonist ligands at serotonin 5-HT<sub>2C</sub> G protein-coupled receptors: computational ligand docking and molecular dynamics studies validated by experimental mutagenesis results

description: To understand molecular determinants for ligand activation of the serotonin 5-HT<sub>2C</sub> G protein-coupled receptor (GPCR), a drug target for obesity and neuropsychiatric disorders, a 5-HT<sub>2C</sub> homology model was built according to an adrenergic β<sub>2</sub> GPCR (β<sub>2</sub>AR) structure and validated using a 5-HT<sub>2B</sub> GPCR crystal structure. The models were equilibrated in a simulated phosphatidyl choline membrane for ligand docking and molecular dynamics studies. Ligands included (2<i>S</i>, 4<i>R</i>)-(–)-<i>trans</i>-4-(3’-bromo- and trifluoro-phenyl)-<i>N</i>,<i>N</i>-dimethyl-1,2,3,4-tetrahydronaphthalene-2-amine (3’-Br-PAT and 3’-CF<sub>3</sub>-PAT), a 5-HT<sub>2C</sub> agonist and inverse agonist, respectively. Distinct interactions of 3’-Br-PAT and 3’-CF<sub>3</sub>-PAT at the wild-type (WT) 5-HT<sub>2C</sub> receptor model were observed and experimental 5-HT<sub>2C</sub> receptor mutagenesis studies were undertaken to validate the modelling results. For example, the inverse agonist 3’-CF<sub>3</sub>-PAT docked deeper in the WT 5-HT<sub>2C</sub> binding pocket and altered the orientation of transmembrane helices (TM) 6 in comparison to the agonist 3’-Br-PAT, suggesting that changes in TM orientation that result from ligand binding impact function. For both PATs, mutation of 5-HT<sub>2C</sub> residues S3.36, T3.37, and F5.47 to alanine resulted in significantly decreased affinity, as predicted from modelling results. It was concluded that upon PAT binding, 5-HT<sub>2C</sub> residues T3.37 and F5.47 in TMs 3 and 5, respectively, engage in inter-helical interactions with TMs 4 and 6, respectively. The movement of TMs 5 and 6 upon agonist and inverse agonist ligand binding observed in the 5-HT<sub>2C</sub> receptor modelling studies was similar to movements reported for the activation and deactivation of the β<sub>2</sub>AR, suggesting common mechanisms among aminergic neurotransmitter GPCRs.
DOI: 10.6084/m9.figshare.1162520.v1
title: Molecular interactions of agonist and inverse agonist ligands at serotonin 5-HT<sub>2C</sub> G protein-coupled receptors: computational ligand docking and molecular dynamics studies validated by experimental mutagenesis results

description: To understand molecular determinants for ligand activation of the serotonin 5-HT<sub>2C</sub> G protein-coupled receptor (GPCR), a drug target for obesity and neuropsychiatric disorders, a 5-HT<sub>2C</sub> homology model was built according to an adrenergic β<sub>2</sub> GPCR (β<sub>2</sub>AR) structure and validated using a 5-HT<sub>2B</sub> GPCR crystal structure. The models were equilibrated in a simulated phosphatidyl choline membrane for ligand docking and molecular dynamics studies. Ligands included (2<i>S</i>, 4<i>R</i>)-(–)-<i>trans</i>-4-(3’-bromo- and trifluoro-phenyl)-<i>N</i>,<i>N</i>-dimethyl-1,2,3,4-tetrahydronaphthalene-2-amine (3’-Br-PAT and 3’-CF<sub>3</sub>-PAT), a 5-HT<sub>2C</sub> agonist and inverse agonist, respectively. Distinct interactions of 3’-Br-PAT and 3’-CF<sub>3</sub>-PAT at the wild-type (WT) 5-HT<sub>2C</sub> receptor model were observed and experimental 5-HT<sub>2C</sub> receptor mutagenesis studies were undertaken to validate the modelling results. For example, the inverse agonist 3’-CF<sub>3</sub>-PAT docked deeper in the WT 5-HT<sub>2C</sub> binding pocket and altered the orientation of transmembrane helices (TM) 6 in comparison to the agonist 3’-Br-PAT, suggesting that changes in TM orientation that result from ligand binding impact function. For both PATs, mutation of 5-HT<sub>2C</sub> residues S3.36, T3.37, and F5.47 to alanine resulted in significantly decreased affinity, as predicted from modelling results. It was concluded that upon PAT binding, 5-HT<sub>2C</sub> residues T3.37 and F5.47 in TMs 3 and 5, respectively, engage in inter-helical interactions with TMs 4 and 6, respectively. The movement of TMs 5 and 6 upon agonist and inverse agonist ligand binding observed in the 5-HT<sub>2C</sub> receptor modelling studies was similar to movements reported for the activation and deactivation of the β<sub>2</sub>AR, suggesting common mechanisms among aminergic neurotransmitter GPCRs.
DOI: 10.6084/m9.figshare.1165483
title: The Early Triassic eosauropterygian <i>Majiashanosaurus discocoracoidis</i>, gen. et sp. nov. (Reptilia, Sauropterygia), from Chaohu, Anhui Province, People’s Republic of China

description: ABSTRACT—Records of Early Triassic marine reptiles, when they first emerged after the end Permian mass extinction, are rare. During an excavation at Majiashan, Chaohu, Anhui Province, a new sauropterygian specimen was found co-occurring with the ichthyopterygian <i>Chaohusaurus</i> from the Upper Member of the Nanlinghu Formation, of Olenekian (Spathian, Early Triassic) age, for which a new taxon, <i>Majiashanosaurus discocoracoidis</i>, gen. et sp. nov., is erected. This skeleton is exposed in ventral view, with the last three cervical vertebrae together with 19 dorsal, three sacral, and more than 18 caudal vertebrae preserved. The cervical centra are keeled ventrally, and cervical ribs are double-headed, carrying a free anterior process. The transverse processes of the dorsal vertebrae are not distinctively elongated. The dorsal ribs are single-headed, and the clavicles articulate on the anteromedial aspect of the scapula. The humerus is curved. These features allow assignment to a new sauropterygian taxon. The interclavicle has no posterior process, and the scapula is of typical eosauropterygian shape, with a broad and ventrally expanded glenoidal portion that is separated from a narrow posterodorsal blade by a distinct constriction. The coracoid is round and plate-like without a waist. This feature is different from that of all other known eosauropterygians, but resembles that of placodonts.SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP
DOI: 10.6084/m9.figshare.1165483.v1
title: The Early Triassic eosauropterygian <i>Majiashanosaurus discocoracoidis</i>, gen. et sp. nov. (Reptilia, Sauropterygia), from Chaohu, Anhui Province, People’s Republic of China

description: ABSTRACT—Records of Early Triassic marine reptiles, when they first emerged after the end Permian mass extinction, are rare. During an excavation at Majiashan, Chaohu, Anhui Province, a new sauropterygian specimen was found co-occurring with the ichthyopterygian <i>Chaohusaurus</i> from the Upper Member of the Nanlinghu Formation, of Olenekian (Spathian, Early Triassic) age, for which a new taxon, <i>Majiashanosaurus discocoracoidis</i>, gen. et sp. nov., is erected. This skeleton is exposed in ventral view, with the last three cervical vertebrae together with 19 dorsal, three sacral, and more than 18 caudal vertebrae preserved. The cervical centra are keeled ventrally, and cervical ribs are double-headed, carrying a free anterior process. The transverse processes of the dorsal vertebrae are not distinctively elongated. The dorsal ribs are single-headed, and the clavicles articulate on the anteromedial aspect of the scapula. The humerus is curved. These features allow assignment to a new sauropterygian taxon. The interclavicle has no posterior process, and the scapula is of typical eosauropterygian shape, with a broad and ventrally expanded glenoidal portion that is separated from a narrow posterodorsal blade by a distinct constriction. The coracoid is round and plate-like without a waist. This feature is different from that of all other known eosauropterygians, but resembles that of placodonts.SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP
DOI: 10.6084/m9.figshare.1165483.v3
title: The Early Triassic eosauropterygian <i>Majiashanosaurus discocoracoidis</i>, gen. et sp. nov. (Reptilia, Sauropterygia), from Chaohu, Anhui Province, People’s Republic of China

description: ABSTRACT—Records of Early Triassic marine reptiles, when they first emerged after the end Permian mass extinction, are rare. During an excavation at Majiashan, Chaohu, Anhui Province, a new sauropterygian specimen was found co-occurring with the ichthyopterygian <i>Chaohusaurus</i> from the Upper Member of the Nanlinghu Formation, of Olenekian (Spathian, Early Triassic) age, for which a new taxon, <i>Majiashanosaurus discocoracoidis</i>, gen. et sp. nov., is erected. This skeleton is exposed in ventral view, with the last three cervical vertebrae together with 19 dorsal, three sacral, and more than 18 caudal vertebrae preserved. The cervical centra are keeled ventrally, and cervical ribs are double-headed, carrying a free anterior process. The transverse processes of the dorsal vertebrae are not distinctively elongated. The dorsal ribs are single-headed, and the clavicles articulate on the anteromedial aspect of the scapula. The humerus is curved. These features allow assignment to a new sauropterygian taxon. The interclavicle has no posterior process, and the scapula is of typical eosauropterygian shape, with a broad and ventrally expanded glenoidal portion that is separated from a narrow posterodorsal blade by a distinct constriction. The coracoid is round and plate-like without a waist. This feature is different from that of all other known eosauropterygians, but resembles that of placodonts.SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP
DOI: 10.6084/m9.figshare.1165483.v2
title: The Early Triassic eosauropterygian <i>Majiashanosaurus discocoracoidis</i>, gen. et sp. nov. (Reptilia, Sauropterygia), from Chaohu, Anhui Province, People’s Republic of China

description: ABSTRACT—Records of Early Triassic marine reptiles, when they first emerged after the end Permian mass extinction, are rare. During an excavation at Majiashan, Chaohu, Anhui Province, a new sauropterygian specimen was found co-occurring with the ichthyopterygian <i>Chaohusaurus</i> from the Upper Member of the Nanlinghu Formation, of Olenekian (Spathian, Early Triassic) age, for which a new taxon, <i>Majiashanosaurus discocoracoidis</i>, gen. et sp. nov., is erected. This skeleton is exposed in ventral view, with the last three cervical vertebrae together with 19 dorsal, three sacral, and more than 18 caudal vertebrae preserved. The cervical centra are keeled ventrally, and cervical ribs are double-headed, carrying a free anterior process. The transverse processes of the dorsal vertebrae are not distinctively elongated. The dorsal ribs are single-headed, and the clavicles articulate on the anteromedial aspect of the scapula. The humerus is curved. These features allow assignment to a new sauropterygian taxon. The interclavicle has no posterior process, and the scapula is of typical eosauropterygian shape, with a broad and ventrally expanded glenoidal portion that is separated from a narrow posterodorsal blade by a distinct constriction. The coracoid is round and plate-like without a waist. This feature is different from that of all other known eosauropterygians, but resembles that of placodonts.SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP
DOI: 10.6084/m9.figshare.1172366
title: Gene regulation network inference with joint sparse Gaussian graphical models

description: Revealing biological networks is one key objective in systems biology. With microarrays, researchers now routinely measure expression profiles at the genome level under various conditions, and, such data may be utilized to statistically infer gene regulation networks. Gaussian graphical models (GGMs) have proven useful for this purpose by modeling the Markovian dependence among genes. However, a single GGM may not be adequate to describe the potentially differing networks across various conditions, and hence it is more natural to infer multiple GGMs from such data. In the present study, we propose a class of nonconvex penalty functions aiming at the estimation of multiple GGMs with a flexible <i>joint sparsity</i> constraint. We illustrate the property of our proposed nonconvex penalty functions by simulation study. We then apply the method to a gene expression data set from the GenCord Project, and show that our method can identify prominent pathways across different conditions.
DOI: 10.6084/m9.figshare.1172366.v1
title: Gene regulation network inference with joint sparse Gaussian graphical models

description: Revealing biological networks is one key objective in systems biology. With microarrays, researchers now routinely measure expression profiles at the genome level under various conditions, and, such data may be utilized to statistically infer gene regulation networks. Gaussian graphical models (GGMs) have proven useful for this purpose by modeling the Markovian dependence among genes. However, a single GGM may not be adequate to describe the potentially differing networks across various conditions, and hence it is more natural to infer multiple GGMs from such data. In the present study, we propose a class of nonconvex penalty functions aiming at the estimation of multiple GGMs with a flexible <i>joint sparsity</i> constraint. We illustrate the property of our proposed nonconvex penalty functions by simulation study. We then apply the method to a gene expression data set from the GenCord Project, and show that our method can identify prominent pathways across different conditions.