cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7910/dvn/v1rjpf/ftdgbz
title: ykc20160812_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/nym7qo
title: ykc20170413_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/3t5ivh
title: ykc20170121_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/he4tow
title: ykc20170105_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/9e0gyl
title: ykc20160101_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/8gkjvu
title: ykc20160908_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4004418
title: Jobs Posts up to October 10th 2016

description: List of Jobs Posts across several job application sites.
DOI: 10.7910/dvn/v1rjpf/7d0cni
title: ykc20160409_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4004415
title: Messy Data Lesson

description: Messy data activity for open science session
DOI: 10.7910/dvn/v1rjpf/qb0vnb
title: ykc20161015_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4004418.v1
title: Jobs Posts up to October 10th 2016

description: List of Jobs Posts across several job application sites.
DOI: 10.7910/dvn/v1rjpf/wafg6o
title: ykc20170620_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4004415.v1
title: Messy Data Lesson

description: Messy data activity for open science session
DOI: 10.6084/m9.figshare.4004418.v2
title: Jobs Posts up to October 10th 2016

description: List of Jobs Posts across several job application sites.
DOI: 10.7910/dvn/v1rjpf/fhefuv
title: ykc20160501_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4004418.v4
title: Jobs Posts up to October 10th 2016

description: List of Jobs Posts across several job application sites.
DOI: 10.6084/m9.figshare.4004418.v3
title: Jobs Posts up to October 10th 2016

description: List of Jobs Posts across several job application sites.
DOI: 10.7910/dvn/v1rjpf/w9exgh
title: ykc20161019_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/0bnnm5
title: ykc20161227_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4004382
title: CONTENIDO DE METALES PESADOS EN ORGANISMOS ACUÍCOLAS EXPENDIDOS EN LOS MERCADOS DE LA CIUDAD DE MACHALA, PROVINCIA DE EL ORO

description: No cabe duda que en los últimos años, el medio ambientemarino se ha ido contaminando visiblemente, como resultado de las actividades del hombre. Grandes cantidades de sustancias, algunas nocivas, llegan al ecosistema acuático y parte de ellas proceden de residuos industriales, agrícolas o domésticos. Dentro de la variable lista de contaminantes, los metales pesados en cantidades de trazas, ocupan una posición única, ya que ellos no pueden ser descompuestos posteriormente y, una vez depositados, permanecerán en el medio acuático, prácticamente sin ningún cambio cualitativo. Históricamente, los niveles de metales pesados existentes en alimentos resultan conocidos y con pocas excepciones,aceptados como constituyentes naturales de los mismos; pero en los últimos 60 años se llegó a la conclusión de que los metales pesados presentes en ciertos alimentos, especialmente en pescados, mariscos y sus derivados, están directamenterelacionados con la contaminación de ríos, lagos y océanos, constituyendo un interesante campo de investigación en la biología del medio ambiente marino. Una de las principales características de este medio ambiente la constituyen sus condiciones físico-químicas relativamente constantes; sin embargo, ciertos organismos marinos adaptados a estas condiciones, podrían aceptar ligeros cambios en su medio, causados por los contaminantes. Por eso la presencia en niveles altos de sustancias o compuestos extraños y metales pesados como contaminantes en el agua de mar, puede ocasionar unproblema para el desarrollo y supervivencia de los organismos marinos que adquieren acusada importancia cuando se destinan a la alimentación humana.
DOI: 10.7910/dvn/v1rjpf/w98aef
title: ykc20171231_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4004379
title: Informe Final. Estudio Zona Costera de Jose

description: Las actividades del hombre están afectando prácticamente todas las riberas marinas y la zonas costeras a nivel mundial. La construcción de puertos e instalaciones industriales, el desarrollo de servicios turísticos, el crecimiento de los asentamiento y ciudades producen la pérdida irremediable de los hábitats. Si bien difícil de cuantificar, es notorio la destrucción de playas, de los arrecifes coralinos y las zonas pantanosas, incluyendo los manglares, y la creciente erosión del litoral.. De no controlarse esta situación, se deteriorara la calidad y productividad del medio marino. La creciente explotación de las costas refleja la explosión demográfica, el aumento de la urbanización y la mayor afluencia y rapidez del transporte, tendencias que indudablemente continuarán. Controlar las actividades costeras y proteger los hábitats demandará cambios en la planificación tanto en las zonas terrestres como costeras, con opciones políticas y sociales frecuentemente difíciles. La diversidad de actividades terrestres contribuye a la contaminación marina, ya sea en forma directa o indirecta por el transporte en los cursos fluviales y la atmósfera de los contaminantes. Sólo una pequeña porción de estos contaminantes se propaga más allá de los límites de la plataforma continental. La mayor parte permanece en las aguas costeras, habiendo alcanzado niveles importantes en ciertas zonas especialmente con poca circulación de las aguas.
DOI: 10.7910/dvn/v1rjpf/zk8ze9
title: ykc20160522_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4004379.v1
title: Informe Final. Estudio Zona Costera de Jose

description: Las actividades del hombre están afectando prácticamente todas las riberas marinas y la zonas costeras a nivel mundial. La construcción de puertos e instalaciones industriales, el desarrollo de servicios turísticos, el crecimiento de los asentamiento y ciudades producen la pérdida irremediable de los hábitats. Si bien difícil de cuantificar, es notorio la destrucción de playas, de los arrecifes coralinos y las zonas pantanosas, incluyendo los manglares, y la creciente erosión del litoral.. De no controlarse esta situación, se deteriorara la calidad y productividad del medio marino. La creciente explotación de las costas refleja la explosión demográfica, el aumento de la urbanización y la mayor afluencia y rapidez del transporte, tendencias que indudablemente continuarán. Controlar las actividades costeras y proteger los hábitats demandará cambios en la planificación tanto en las zonas terrestres como costeras, con opciones políticas y sociales frecuentemente difíciles. La diversidad de actividades terrestres contribuye a la contaminación marina, ya sea en forma directa o indirecta por el transporte en los cursos fluviales y la atmósfera de los contaminantes. Sólo una pequeña porción de estos contaminantes se propaga más allá de los límites de la plataforma continental. La mayor parte permanece en las aguas costeras, habiendo alcanzado niveles importantes en ciertas zonas especialmente con poca circulación de las aguas.
DOI: 10.7910/dvn/v1rjpf/k1xorn
title: ykc20170728_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4004370
title: Enhanced autophagy in pulmonary endothelial cells on exposure to HIV-Tat and morphine: Role in HIV-related pulmonary arterial hypertension

description: Intravenous drug use is one of the major risk factors for HIV-infection in HIV-related pulmonary arterial hypertension patients. We previously demonstrated exaggerated pulmonary vascular remodeling with enhanced apoptosis followed by increased proliferation of pulmonary endothelial cells on simultaneous exposure to both opioids and HIV protein(s). Here we hypothesize that the exacerbation of autophagy may be involved in the switching of endothelial cells from an early apoptotic state to later hyper-proliferative state. Treatment of human pulmonary microvascular endothelial cells (HPMECs) with both the HIV-protein Tat and morphine resulted in an oxidative stress-dependent increase in the expression of various markers of autophagy and formation of autophagosomes when compared to either Tat or morphine monotreatments as demonstrated by western blot, transmission electron microscopy and immunofluorescence. Autophagy flux experiments suggested increased formation rather than decreased clearance of autolysosomes. Inhibition of autophagy resulted in a significant increase in apoptosis and reduction in proliferation of HPMECs with combined morphine and Tat (M+T) treatment compared to monotreatments whereas stimulation of autophagy resulted in opposite effects. Significant increases in the expression of autophagy markers as well as the number of autophagosomes and autolysosomes was observed in the lungs of SIV-infected macaques and HIV-infected humans exposed to opioids. Overall our findings indicate that morphine in combination with viral protein(s) results in the induction of autophagy in pulmonary endothelial cells that may lead to an increase in severity of angio-proliferative remodeling of the pulmonary vasculature on simian and human immunodeficiency virus infection in the presence of opioids.
DOI: 10.7910/dvn/v1rjpf/nzvtdk
title: ykc20170818_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4004370.v1
title: Enhanced autophagy in pulmonary endothelial cells on exposure to HIV-Tat and morphine: Role in HIV-related pulmonary arterial hypertension

description: Intravenous drug use is one of the major risk factors for HIV-infection in HIV-related pulmonary arterial hypertension patients. We previously demonstrated exaggerated pulmonary vascular remodeling with enhanced apoptosis followed by increased proliferation of pulmonary endothelial cells on simultaneous exposure to both opioids and HIV protein(s). Here we hypothesize that the exacerbation of autophagy may be involved in the switching of endothelial cells from an early apoptotic state to later hyper-proliferative state. Treatment of human pulmonary microvascular endothelial cells (HPMECs) with both the HIV-protein Tat and morphine resulted in an oxidative stress-dependent increase in the expression of various markers of autophagy and formation of autophagosomes when compared to either Tat or morphine monotreatments as demonstrated by western blot, transmission electron microscopy and immunofluorescence. Autophagy flux experiments suggested increased formation rather than decreased clearance of autolysosomes. Inhibition of autophagy resulted in a significant increase in apoptosis and reduction in proliferation of HPMECs with combined morphine and Tat (M+T) treatment compared to monotreatments whereas stimulation of autophagy resulted in opposite effects. Significant increases in the expression of autophagy markers as well as the number of autophagosomes and autolysosomes was observed in the lungs of SIV-infected macaques and HIV-infected humans exposed to opioids. Overall our findings indicate that morphine in combination with viral protein(s) results in the induction of autophagy in pulmonary endothelial cells that may lead to an increase in severity of angio-proliferative remodeling of the pulmonary vasculature on simian and human immunodeficiency virus infection in the presence of opioids.
DOI: 10.7910/dvn/v1rjpf/ur5sml
title: ykc20160720_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/tpe8dt
title: ykc20161224_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/qqcsep
title: ykc20170929_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4004322
title: Interaction between flavin mononucleotide-containing azoreductase and azo dyes

description: Azoreductase, a flavin mononucleotide-containing oxidoreductase from <i>Escherichia coli</i>, can catalyze the reduction of azo dyes to form aromatic amine compounds. Few spectroscopic studies have explored the binding mode of azo dyes or the role of the arginine at site 59 in Azoreductase. In this article, protein engineering strategy has been used to construct one mutant in which the arginine residue at site 59 was mutated to glycine. Fluorescence spectroscopic data showed that the addition of Methyl Red and Methyl Orange resulted in the fluorescence quenching of the cofactor flavin mononucleotide bound to Azoreductase. The association constant was fitted using the standard binding equation instead of the Stern-Volmer equation. The results showed that the mutation from the arginine to glycine at site 59 weakened the association constant from 2.21 × 10<sup>5</sup> L.mol<sup>−1</sup> to 4.55 × 10<sup>4</sup> L.mol<sup>−1</sup> at 25°C. A similar phenomenon was also observed when Methyl Orange was used as a substrate. In each case, the association constant tended to decrease as the temperature increased from 25°C to 37°C. Thermodynamic parameter analysis revealed that the interaction type changed from a van der Waals interaction (between Azoreductase and the dyes) to a hydrogen bonding interaction (between the mutant and the dyes). Moleculcar docking was also performed in this work to provide some support for the binding mode and binding stability between Azoreductase/mutant and azo dyes.
DOI: 10.7910/dvn/v1rjpf/ylsrph
title: ykc20160718_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4004322.v1
title: Interaction between flavin mononucleotide-containing azoreductase and azo dyes

description: Azoreductase, a flavin mononucleotide-containing oxidoreductase from <i>Escherichia coli</i>, can catalyze the reduction of azo dyes to form aromatic amine compounds. Few spectroscopic studies have explored the binding mode of azo dyes or the role of the arginine at site 59 in Azoreductase. In this article, protein engineering strategy has been used to construct one mutant in which the arginine residue at site 59 was mutated to glycine. Fluorescence spectroscopic data showed that the addition of Methyl Red and Methyl Orange resulted in the fluorescence quenching of the cofactor flavin mononucleotide bound to Azoreductase. The association constant was fitted using the standard binding equation instead of the Stern-Volmer equation. The results showed that the mutation from the arginine to glycine at site 59 weakened the association constant from 2.21 × 10<sup>5</sup> L.mol<sup>−1</sup> to 4.55 × 10<sup>4</sup> L.mol<sup>−1</sup> at 25°C. A similar phenomenon was also observed when Methyl Orange was used as a substrate. In each case, the association constant tended to decrease as the temperature increased from 25°C to 37°C. Thermodynamic parameter analysis revealed that the interaction type changed from a van der Waals interaction (between Azoreductase and the dyes) to a hydrogen bonding interaction (between the mutant and the dyes). Moleculcar docking was also performed in this work to provide some support for the binding mode and binding stability between Azoreductase/mutant and azo dyes.
DOI: 10.7910/dvn/v1rjpf/ss9qfg
title: ykc20160614_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/abloxv
title: ykc20170410_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/ozgahk
title: ykc20170716_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/v1jp4s
title: ykc20171010_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4004274
title: Robust Improper Maximum Likelihood: Tuning, Computation, and a Comparison With Other Methods for Robust Gaussian Clustering

description: The two main topics of this article are the introduction of the “optimally tuned robust improper maximum likelihood estimator” (OTRIMLE) for robust clustering based on the multivariate Gaussian model for clusters, and a comprehensive simulation study comparing the OTRIMLE to maximum likelihood in Gaussian mixtures with and without noise component, mixtures of <i>t</i>-distributions, and the TCLUST approach for trimmed clustering. The OTRIMLE uses an improper constant density for modeling outliers and noise. This can be chosen optimally so that the nonnoise part of the data looks as close to a Gaussian mixture as possible. Some deviation from Gaussianity can be traded in for lowering the estimated noise proportion. Covariance matrix constraints and computation of the OTRIMLE are also treated. In the simulation study, all methods are confronted with setups in which their model assumptions are not exactly fulfilled, and to evaluate the experiments in a standardized way by misclassification rates, a new model-based definition of “true clusters” is introduced that deviates from the usual identification of mixture components with clusters. In the study, every method turns out to be superior for one or more setups, but the OTRIMLE achieves the most satisfactory overall performance. The methods are also applied to two real datasets, one without and one with known “true” clusters. Supplementary materials for this article are available online.
DOI: 10.7910/dvn/v1rjpf/qepdnj
title: ykc20161202_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4004265
title: Ketamine up-regulates a cluster of intronic miRNAs within the serotonin receptor 2C gene by inhibiting glycogen synthase kinase-3

description: <b>Objectives:</b> We examined mechanisms that contribute to the rapid antidepressant effect of ketamine in mice that is dependent on glycogen synthase kinase-3 (GSK3) inhibition. <b>Methods:</b> We measured serotonergic (5HT)-2C-receptor (5HTR2C) cluster microRNA (miRNA) levels in mouse hippocampus after administering an antidepressant dose of ketamine (10 mg/kg) in wild-type and GSK3 knockin mice, after GSK3 inhibition with L803-mts, and in learned helpless mice. <b>Results:</b> Ketamine up-regulated cluster miRNAs 448-3p, 764-5p, 1264-3p, 1298-5p and 1912-3p (2- to 11-fold). This up-regulation was abolished in GSK3 knockin mice that express mutant constitutively active GSK3. The GSK3 specific inhibitor L803-mts was antidepressant in the learned helplessness and novelty suppressed feeding depression-like behaviours and up-regulated the 5HTR2C miRNA cluster in mouse hippocampus. After administration of the learned helplessness paradigm mice were divided into cohorts that were resilient (non-depressed) or were susceptible (depressed) to learned helplessness. The resilient, but not depressed, mice displayed increased hippocampal levels of miRNAs 448-3p and 1264-3p. Administration of an antagonist to miRNA 448-3p diminished the antidepressant effect of ketamine in the learned helplessness paradigm, indicating that up-regulation of miRNA 448-3p provides an antidepressant action. <b>Conclusions:</b> These findings identify a new outcome of GSK3 inhibition by ketamine that may contribute to antidepressant effects.
DOI: 10.6084/m9.figshare.4004274.v1
title: Robust Improper Maximum Likelihood: Tuning, Computation, and a Comparison With Other Methods for Robust Gaussian Clustering

description: The two main topics of this paper are the introduction of the “optimally tuned improper maximum likelihood estimator” (OTRIMLE) for robust clustering based on the multivariate Gaussian model for clusters, and a comprehensive simulation study comparing the OTRIMLE to Maximum Likelihood in Gaussian mixtures with and without noise component, mixtures of t-distributions, and the TCLUST approach for trimmed clustering. The OTRIMLE uses an improper constant density for modelling outliers and noise. This can be chosen optimally so that the non-noise part of the data looks as close to a Gaussian mixture as possible. Some deviation from Gaussianity can be traded in for lowering the estimated noise proportion. Covariance matrix constraints and computation of the OTRIMLE are also treated. In the simulation study, all methods are confronted with setups in which their model assumptions are not exactly fulfilled, and in order to evaluate the experiments in a standardized way by misclassification rates, a new model-based definition of “true clusters” is introduced that deviates from the usual identification of mixture components with clusters. In the study, every method turns out to be superior for one or more setups, but the OTRIMLE achieves the most satisfactory overall performance. The methods are also applied to two real datasets, one without and one with known “true” clusters.
DOI: 10.7910/dvn/v1rjpf/ynpy6b
title: ykc20170304_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/aqvfqv
title: ykc20161216_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4004274.v2
title: Robust Improper Maximum Likelihood: Tuning, Computation, and a Comparison With Other Methods for Robust Gaussian Clustering

description: The two main topics of this paper are the introduction of the “optimally tuned improper maximum likelihood estimator” (OTRIMLE) for robust clustering based on the multivariate Gaussian model for clusters, and a comprehensive simulation study comparing the OTRIMLE to Maximum Likelihood in Gaussian mixtures with and without noise component, mixtures of t-distributions, and the TCLUST approach for trimmed clustering. The OTRIMLE uses an improper constant density for modelling outliers and noise. This can be chosen optimally so that the non-noise part of the data looks as close to a Gaussian mixture as possible. Some deviation from Gaussianity can be traded in for lowering the estimated noise proportion. Covariance matrix constraints and computation of the OTRIMLE are also treated. In the simulation study, all methods are confronted with setups in which their model assumptions are not exactly fulfilled, and in order to evaluate the experiments in a standardized way by misclassification rates, a new model-based definition of “true clusters” is introduced that deviates from the usual identification of mixture components with clusters. In the study, every method turns out to be superior for one or more setups, but the OTRIMLE achieves the most satisfactory overall performance. The methods are also applied to two real datasets, one without and one with known “true” clusters.
DOI: 10.7910/dvn/v1rjpf/5cemmo
title: ykc20161030_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4004208
title: Regionall Nettworrk in Marriine Science and Technollogy forr tthe Carribbean:: Know –Why Nettwork

description: The Marine Sciences and Technologies Regional Project for the Wider Caribbean Region, known as ”Know Why Network”, came into being as part of the financial support provided by the Swedish Development Agency (SIDA) and is administered and directed by the AMEP subprogramme(Evaluation and Management of Marine Pollution) of the Caribbean Environmental Programme (CEP). The general aim of this project is the exchange of capacities between countries with the objectives of implementing the Pollution from Land-based Sources Protocol (LBS) and improving knowledge about the environmental quality of the marine ecosystems and their resources in the Wider Caribbean Region (WRC).
DOI: 10.6084/m9.figshare.4004208.v1
title: Regionall Nettworrk in Marriine Science and Technollogy forr tthe Carribbean:: Know –Why Nettwork

description: The Marine Sciences and Technologies Regional Project for the Wider Caribbean Region, known as ”Know Why Network”, came into being as part of the financial support provided by the Swedish Development Agency (SIDA) and is administered and directed by the AMEP subprogramme(Evaluation and Management of Marine Pollution) of the Caribbean Environmental Programme (CEP). The general aim of this project is the exchange of capacities between countries with the objectives of implementing the Pollution from Land-based Sources Protocol (LBS) and improving knowledge about the environmental quality of the marine ecosystems and their resources in the Wider Caribbean Region (WRC).
DOI: 10.7910/dvn/v1rjpf/n7yutz
title: ykc20160227_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/jqulca
title: ykc20171102_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4004187
title: Human G4 Sequences (BED and txt format)

description: Contains G4 sequences identified by quadparser for hg16, hg19, and hg38 human genome assemblies.
DOI: 10.7910/dvn/v1rjpf/sg6foe
title: ykc20160604_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/oqetrz
title: ykc20160910_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/l1iiud
title: ykc20160624_03.txt.gz

description: :unav