cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1433799.v1
title: Taiwanin A incorporated polyurethane fiber sheets for prevention of postoperative cancer recurrence

description: In this study, we propose a single solution for prevention of postoperative complications and recurrence of highly metastatic gastrointestinal tract cancers. Here, we demonstrate preparation and characterization of Taiwanin A incorporated polyurethane fiber sheets with excellent mechanical properties and sustained drug release. Sheets with elastic modulus of 8 MPa and ultimate tensile strength of 30 MPa will provide support on surgical staple line preventing leakage at anastomosis. Slight burst release of the drug within 7 days (15%) and further sustained release will inhibit proliferation and migration of remaining cancer cells and maintain locoregional high drug concentration to prevent recurrence of the disease. High elasticity of the material will promote healing process without impeding natural peristalsis movement of gastrointestinal organs.
DOI: 10.6084/m9.figshare.1433993.v3
title: Numerical integration of the rate equations of the MerB reaction mechanism

description: Source code, Windows executable, and outputs. Syntax is: HgMerB_kinetics [initial concentration of organomercurial (optional)] [number of steps with timestep tightening] [initial_timestep][pH] [type of molecule] [how many seconds of kinetic information you want] [HgMerB (or free MerB) concentration] [concentration of the Hg-removing molecules tested] [barriers in kcal.mol-1 for the 38 reaction steps] [name of output file] Type of molecule is : 1 for MerA, 2 for dithiothreitol, 3 for GSH or other monothiols Notes on the algorithm: A) concentrations are output whenever : A1) concentration of HgMerB decreases by 1%, or A2) concentration of product increases by 1% of initial MerB concentration, or A3) 10^7 integration timesteps have elapsed since the last output (or 3*10^5, if less than 10^7 integration timestpes have elapsed since the beginning of the simulation) B) Integration timestep is scaled to ensure that the concentration of every intermediate does not increase more than 10% of its previous concentration. After product concentration increases above 0.1% of initial enzyme concentration, this test is disabled. C) Further scaling is always performed to prevent concentrations of any intermediate from becoming negative. C) Numerical noise (or even outright integration error) may occur if the reaction quotient of any reaction increases too abruptly due to numerical increase in the reactant concentrations above the real equilibrium concentrations or (less commonly) extensive depletion of products. This may be needed if consecutive rection steps have extremely small activation energies.The option of setting a number of "Timestep tightening cycles" is present to help overcome these issues. In each of these cycles, the timestep is decreased to ensure that, in the next cycle, the intermediates which currently have positive derivatives (of concentration w.r.t. time) still remain having positive derivatives. The requested number of integration timesteps with timestep-tightening cycles is performed every time that concentrations are output to disk.
DOI: 10.6084/m9.figshare.1433683
title: Disentangling the effects of environmental factors on the distribution of vascular plants in Japan: the importance of land use for common species on a macroscale

description: <b><i>Background</i></b>: All human land use (LU) affects the distribution of plant species; however, the impacts vary with the type/intensity of LU. For managing ecosystems, it is therefore essential to understand the effects of LU types on the distribution of plant species on a macroscale.<b><i>Aims</i>:</b> The objectives of our study were to quantify the effects of various LU types on the distribution of vascular plant species in Japan and to determine in particular the extent to which LU was an important factor for the distribution of common species.<b><i>Methods</i>:</b> Based on a logistic regression model and variation partitioning being applied to each plant species, we evaluated the partial deviance by six LU types, four climatic types and three topographic and geological factors for 647 plant species at 14,412 sites in Japan.<b><i>Results</i>:</b> The effect of LU was significant for species present at multiple sites. Of the six LU types, secondary vegetation and plantation were the most important factors determining species distribution for many species.<b><i>Conclusions</i>:</b> Our results suggest that distribution of the common species is largely affected by LU on macroscale. The design of LU relating to secondary vegetation and plantations will thus be important in determining changes in the vegetation composition within Japan.
DOI: 10.6084/m9.figshare.1433683.v2
title: Disentangling the effects of environmental factors on the distribution of vascular plants in Japan: the importance of land use for common species on a macroscale

description: <b><i>Background</i></b>: All human land use (LU) affects the distribution of plant species; however, the impacts vary with the type/intensity of LU. For managing ecosystems, it is therefore essential to understand the effects of LU types on the distribution of plant species on a macroscale.<b><i>Aims</i>:</b> The objectives of our study were to quantify the effects of various LU types on the distribution of vascular plant species in Japan and to determine in particular the extent to which LU was an important factor for the distribution of common species.<b><i>Methods</i>:</b> Based on a logistic regression model and variation partitioning being applied to each plant species, we evaluated the partial deviance by six LU types, four climatic types and three topographic and geological factors for 647 plant species at 14,412 sites in Japan.<b><i>Results</i>:</b> The effect of LU was significant for species present at multiple sites. Of the six LU types, secondary vegetation and plantation were the most important factors determining species distribution for many species.<b><i>Conclusions</i>:</b> Our results suggest that distribution of the common species is largely affected by LU on macroscale. The design of LU relating to secondary vegetation and plantations will thus be important in determining changes in the vegetation composition within Japan.
DOI: 10.6084/m9.figshare.1433683.v1
title: Disentangling the effects of environmental factors on the distribution of vascular plants in Japan: the importance of land use for common species on a macroscale

description: <b><i>Background</i></b>: All human land use (LU) affects the distribution of plant species; however, the impacts vary with the type/intensity of LU. For managing ecosystems, it is therefore essential to understand the effects of LU types on the distribution of plant species on a macroscale.<b><i>Aims</i>:</b> The objectives of our study were to quantify the effects of various LU types on the distribution of vascular plant species in Japan and to determine in particular the extent to which LU was an important factor for the distribution of common species.<b><i>Methods</i>:</b> Based on a logistic regression model and variation partitioning being applied to each plant species, we evaluated the partial deviance by six LU types, four climatic types and three topographic and geological factors for 647 plant species at 14,412 sites in Japan.<b><i>Results</i>:</b> The effect of LU was significant for species present at multiple sites. Of the six LU types, secondary vegetation and plantation were the most important factors determining species distribution for many species.<b><i>Conclusions</i>:</b> Our results suggest that distribution of the common species is largely affected by LU on macroscale. The design of LU relating to secondary vegetation and plantations will thus be important in determining changes in the vegetation composition within Japan.
DOI: 10.6084/m9.figshare.1433993.v4
title: Numerical integration of the rate equations of the MerB reaction mechanism

description: Source code, Windows executable, and outputs. Syntax is: HgMerB_kinetics [initial concentration of organomercurial (optional)] [number of steps with timestep tightening] [initial_timestep][pH] [type of molecule] [how many seconds of kinetic information you want] [HgMerB (or free MerB) concentration] [concentration of the Hg-removing molecules tested] [barriers in kcal.mol-1 for the 38 reaction steps] [name of output file] Type of molecule is : 1 for MerA, 2 for dithiothreitol, 3 for GSH or other monothiols Notes on the algorithm: A) concentrations are output whenever : A1) concentration of HgMerB decreases by 1%, or A2) concentration of product increases by 1% of initial MerB concentration, or A3) 10^7 integration timesteps have elapsed since the last output (or 3*10^5, if less than 10^7 integration timestpes have elapsed since the beginning of the simulation) B) Integration timestep is scaled to ensure that the concentration of every intermediate does not increase more than 10% of its previous concentration. After product concentration increases above 0.1% of initial enzyme concentration, this test is disabled. C) Further scaling is always performed to prevent concentrations of any intermediate from becoming negative. C) Numerical noise (or even outright integration error) may occur if the reaction quotient of any reaction changes too abruptly due to numerical increase in the reactant concentrations above the real equilibrium concentrations or (less commonly) extensive depletion of products. This is most likey to occur when consecutive rection steps have extremely small activation energies.The option of setting a number of "Timestep tightening cycles" is present to help overcome these issues. In each of these cycles, the timestep is decreased to ensure that, in the next cycle, the intermediates which currently have positive derivatives (of concentration w.r.t. time) still have positive derivatives. The requested number of integration timesteps with timestep-tightening cycles is performed every time that concentrations are output to disk.
DOI: 10.6084/m9.figshare.1433993.v5
title: Numerical integration of the rate equations of the MerB reaction mechanism

description: Source code, Windows executable, and outputs. Syntax is: HgMerB_kinetics [initial concentration of organomercurial (optional)] [number of steps with timestep tightening] [initial_timestep][pH] [type of molecule] [how many seconds of kinetic information you want] [HgMerB (or free MerB) concentration] [concentration of the Hg-removing molecules tested] [barriers in kcal.mol-1 for the 38 reaction steps] [name of output file] Type of molecule is : 1 for MerA, 2 for dithiothreitol, 3 for GSH or other monothiols Notes on the algorithm: A) concentrations are output whenever : A1) concentration of HgMerB decreases by 1%, or A2) concentration of product increases by 1% of initial MerB concentration, or A3) 10^7 integration timesteps have elapsed since the last output (or 3*10^5, if less than 10^7 integration timestpes have elapsed since the beginning of the simulation) B) Integration timestep is scaled to ensure that the concentration of every intermediate does not increase more than 10% of its previous concentration. After product concentration increases above 0.1% of initial enzyme concentration, this test is disabled. C) Further scaling is always performed to prevent concentrations of any intermediate from becoming negative. C) Numerical noise (or even outright integration error) may occur if the reaction quotient of any reaction changes too abruptly due to numerical increase in the reactant concentrations above the real equilibrium concentrations or (less commonly) extensive depletion of products. This is most likey to occur when consecutive rection steps have extremely small activation energies.The option of setting a number of "Timestep tightening cycles" is present to help overcome these issues. In each of these cycles, the timestep is decreased to ensure that, in the next cycle, the intermediates which currently have positive derivatives (of concentration w.r.t. time) still have positive derivatives. The requested number of integration timesteps with timestep-tightening cycles is performed every time that concentrations are output to disk.
DOI: 10.6084/m9.figshare.1431931
title: A Virtuosa Anna Mesquita - Peça

description: Pequena peça em 12 atos, onde retratam partes importantes da vida de Anna Mesquita Laurini, nascimento e morte que é patronesse da Escola Estadual de São Paulo do Bairro Novo Bonfim em Cabreúva, SP - Brasil
DOI: 10.6084/m9.figshare.1433993.v6
title: Numerical integration of the rate equations of the MerB reaction mechanism

description: Source code, Windows executable, and outputs. Syntax is: HgMerB_kinetics [initial concentration of organomercurial (optional)] [number of steps with timestep tightening] [initial_timestep][pH] [type of molecule] [how many seconds of kinetic information you want] [HgMerB (or free MerB) concentration] [concentration of the Hg-removing molecules tested] [barriers in kcal.mol-1 for the 38 reaction steps] [name of output file] Type of molecule is : 1 for MerA, 2 for dithiothreitol, 3 for GSH or other monothiols Notes on the algorithm: A) concentrations are output whenever : A1) concentration of HgMerB decreases by 1%, or A2) concentration of product increases by 1% of initial MerB concentration, or A3) 10^7 integration timesteps have elapsed since the last output (or 3*10^5, if less than 10^7 integration timestpes have elapsed since the beginning of the simulation) B) Integration timestep is scaled to ensure that the concentration of every intermediate does not increase more than 10% of its previous concentration. After product concentration increases above 0.1% of initial enzyme concentration, this test is disabled. C) Further scaling is always performed to prevent concentrations of any intermediate from becoming negative. C) Numerical noise (or even outright integration error) may occur if the reaction quotient of any reaction changes too abruptly due to numerical increase in the reactant concentrations above the real equilibrium concentrations or (less commonly) extensive depletion of products. This is most likey to occur when consecutive rection steps have extremely small activation energies.The option of setting a number of "Timestep tightening cycles" is present to help overcome these issues. In each of these cycles, the timestep is decreased to ensure that, in the next cycle, the intermediates which currently have positive derivatives (of concentration w.r.t. time) still have positive derivatives. The requested number of integration timesteps with timestep-tightening cycles is performed every time that concentrations are output to disk.
DOI: 10.6084/m9.figshare.1433993.v7
title: Numerical integration of the rate equations of the MerB reaction mechanism

description: Source code, Windows executable, and outputs. Syntax is: HgMerB_kinetics [initial concentration of organomercurial (optional)] [number of steps with timestep tightening] [initial_timestep][pH] [type of molecule] [how many seconds of kinetic information you want] [HgMerB (or free MerB) concentration] [concentration of the Hg-removing molecules tested] [barriers in kcal.mol-1 for the 38 reaction steps] [name of output file] Type of molecule is : 1 for MerA, 2 for dithiothreitol, 3 for GSH or other monothiols Notes on the algorithm: A) concentrations are output whenever : A1) concentration of HgMerB decreases by 1%, or A2) concentration of product increases by 1% of initial MerB concentration, or A3) 10^7 integration timesteps have elapsed since the last output (or 3*10^5, if less than 10^7 integration timestpes have elapsed since the beginning of the simulation) B) Integration timestep is scaled to ensure that the concentration of every intermediate does not increase more than 10% of its previous concentration. After product concentration increases above 0.1% of initial enzyme concentration, this test is disabled. C) Further scaling is always performed to prevent concentrations of any intermediate from becoming negative. C) Numerical noise (or even outright integration error) may occur if the reaction quotient of any reaction changes too abruptly due to numerical increase in the reactant concentrations above the real equilibrium concentrations or (less commonly) extensive depletion of products. This is most likey to occur when consecutive rection steps have extremely small activation energies.The option of setting a number of "Timestep tightening cycles" is present to help overcome these issues. In each of these cycles, the timestep is decreased to ensure that, in the next cycle, the intermediates which currently have positive derivatives (of concentration w.r.t. time) still have positive derivatives. The requested number of integration timesteps with timestep-tightening cycles is performed every time that concentrations are output to disk.
DOI: 10.6084/m9.figshare.1433993.v8
title: Numerical integration of the rate equations of the MerB reaction mechanism

description: Source code, Windows executable, and outputs. Syntax is: HgMerB_kinetics [initial concentration of organomercurial (optional)] [number of steps with timestep tightening] [initial_timestep][pH] [type of molecule] [how many seconds of kinetic information you want] [HgMerB (or free MerB) concentration] [concentration of the Hg-removing molecules tested] [barriers in kcal.mol-1 for the 38 reaction steps] [name of output file] Type of molecule is : 1 for MerA, 2 for dithiothreitol, 3 for GSH or other monothiols Notes on the algorithm: A) concentrations are output whenever : A1) concentration of HgMerB decreases by 1%, or A2) concentration of product increases by 1% of initial MerB concentration, or A3) 10^7 integration timesteps have elapsed since the last output (or 3*10^5, if less than 10^7 integration timestpes have elapsed since the beginning of the simulation) B) Integration timestep is scaled to ensure that the concentration of every intermediate does not increase more than 10% of its previous concentration. After product concentration increases above 0.1% of initial enzyme concentration, this test is disabled. C) Further scaling is always performed to prevent concentrations of any intermediate from becoming negative. C) Numerical noise (or even outright integration error) may occur if the reaction quotient of any reaction changes too abruptly due to numerical increase in the reactant concentrations above the real equilibrium concentrations or (less commonly) extensive depletion of products. This is most likey to occur when consecutive rection steps have extremely small activation energies.The option of setting a number of "Timestep tightening cycles" is present to help overcome these issues. In each of these cycles, the timestep is decreased to ensure that, in the next cycle, the intermediates which currently have positive derivatives (of concentration w.r.t. time) still have positive derivatives. The requested number of integration timesteps with timestep-tightening cycles is performed every time that concentrations are output to disk. Program HgMerB_kinetics_fast follows the same syntax and uses the same algorithms, with a sinlge difference: in each integration step, reaction fluxes which are smaller than 10^(-12) of the larger flux are set to zero. This makes the program faster by ca. two orders of magnitude.
DOI: 10.6084/m9.figshare.1431922
title: Xml BEAUTii file used for BEAST analysis

description: Xml file
DOI: 10.6084/m9.figshare.1433993.v9
title: Numerical integration of the rate equations of the MerB reaction mechanism

description: Source code, Windows executable, and outputs. Syntax is: HgMerB_kinetics [initial concentration of organomercurial (optional)] [number of steps with timestep tightening] [initial_timestep][pH] [type of molecule] [how many seconds of kinetic information you want] [HgMerB (or free MerB) concentration] [concentration of the Hg-removing molecules tested] [barriers in kcal.mol-1 for the 38 reaction steps] [name of output file] Type of molecule is : 1 for MerA, 2 for dithiothreitol, 3 for GSH or other monothiols Notes on the algorithm: A) concentrations are output whenever : A1) concentration of HgMerB decreases by 1%, or A2) concentration of product increases by 1% of initial MerB concentration, or A3) 10^7 integration timesteps have elapsed since the last output (or 3*10^5, if less than 10^7 integration timestpes have elapsed since the beginning of the simulation) B) Integration timestep is scaled to ensure that the concentration of every intermediate does not increase more than 10% of its previous concentration. After product concentration increases above 0.1% of initial enzyme concentration, this test is disabled. C) Further scaling is always performed to prevent concentrations of any intermediate from becoming negative. C) Numerical noise (or even outright integration error) may occur if the reaction quotient of any reaction changes too abruptly due to numerical increase in the reactant concentrations above the real equilibrium concentrations or (less commonly) extensive depletion of products. This is most likey to occur when consecutive rection steps have extremely small activation energies.The option of setting a number of "Timestep tightening cycles" is present to help overcome these issues. In each of these cycles, the timestep is decreased to ensure that, in the next cycle, the intermediates which currently have positive derivatives (of concentration w.r.t. time) still have positive derivatives. The requested number of integration timesteps with timestep-tightening cycles is performed every time that concentrations are output to disk.
DOI: 10.6084/m9.figshare.1431922.v2
title: Xml BEAUTii file used for BEAST analysis

description: Xml file
DOI: 10.6084/m9.figshare.1431922.v1
title: Xml BEAUTii file used for BEAST analysis

description: Xml file
DOI: 10.6084/m9.figshare.1431873
title: The Functional Connectome of Speech Control

description: Connectivity matrices used to construct the functional connenctome and community structure of the resting state, sequential finger tapping, auditory pure tone discrimination, syllable production, and speech production.
DOI: 10.6084/m9.figshare.1431881
title: AL_RDM_DILL

description: The dataset contains the answers provided to a questionnaire which was aimed to study academic libraries' readiness for research data management.
DOI: 10.6084/m9.figshare.1431903.v1
title: Nuclear localized Akt enhances breast cancer stem-like cells through counter-regulation of p21<sup>Waf1/Cip1</sup> and p27<sup>kip1</sup>

description: Cancer stem-like cells (CSCs) are a rare subpopulation of cancer cells capable of propagating the disease and causing cancer recurrence. In this study, we found that the cellular localization of PKB/Akt kinase affects the maintenance of CSCs. When Akt tagged with nuclear localization signal (Akt-NLS) was overexpressed in SKBR3 and MDAMB468 cells, these cells showed a 10–15% increase in the number of cells with CSCs enhanced ALDH activity and showing CD44<sup>+High</sup>/CD24<sup>−Low</sup> phenotype. This effect was completely reversed in the presence of Akt-specific inhibitor, Triciribine. Furthermore, cells overexpressing Akt or Akt-NLS were less likely to be in G0/G1 phase of the cell cycle by inactivating p21<sup>Waf1/Cip1</sup> and exhibited increased clonogenicity and proliferation as assayed by colony-forming assay (mammosphere formation). Thus, our data emphasize the importance the intracellular localization of Akt has on stemness in human breast cancer cells. It also indicates a new robust way for improving the enrichment and culture of CSCs for experimental purposes. Hence, it allows for the development of simpler protocols to study stemness, clonogenic potency, and screening of new chemotherapeutic agents that preferentially target cancer stem cells.
DOI: 10.6084/m9.figshare.1431868
title: Suramin inhibits Chikungunya virus entry and transmission

description: This file contain time course, time course and additional table-PlonOne-Data for PONE-D-15-07382