cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3439589.v1
title: Helminths of 13 species of microhylid frogs (Anura: Microhylidae) from Papua New Guinea

description: In an attempt to better document the invertebrate biodiversity of the threatened fauna of Papua New Guinea (PNG), 208 microhylid frogs representing 13 species collected in 2009 and 2010 in PNG were examined for endoparasitic helminths. This study found mature individuals of one species of Digenea (<i>Opisthioglyphe cophixali</i>), adults of two species of Cestoda (<i>Nematotaenia hylae, Cylindrotaenia</i> sp.) and cysticerci of an unidentified cestode species; adults of nine species of Nematoda (<i>Aplectana krausi</i>, <i>Bakeria bakeri</i>, <i>Cosmocerca novaeguineae</i>, <i>Cosmocercella phrynomantisi</i>, <i>Falcaustra papuensis</i>, <i>Icosiella papuensis</i>, <i>Ochtoterenella papuensis</i>, <i>Parathelandros allisoni</i>, <i>Parathelandros andersoni</i>), and one species of Acanthocephala (cystacanths in the family Centrorhynchidae). There was a high degree of endemism among the helminth species infecting the microhylids, with 83% of the species known only from PNG. Yet the helminth fauna infecting Papuan microhylids are generalists with direct life cycles (no intermediate host) that also infect other anuran species. We thus conclude infection is more dependent upon habitat conditions than diet. Twenty-nine new host records are reported.
DOI: 10.6084/m9.figshare.3439568
title: Improved control of blood pressure and albuminuria among patients with type-2 diabetes in Finnish open care

description: Risk of cardiovascular events within the diabetic population has decreased and survival increased with patients living longer and thus facing the development of end-stage renal disease (ESRD). This calls for good care of patient with diabetes with a focus on hypertension. Patient data were collected from 42 Finnish primary care centres. Each was asked to enrol 10–12 consecutive patients with type-2 diabetes between March 2011 and August 2012. Along with the office blood pressure measurements and laboratory tests, the presence of albuminuria was measured and glomerular filtration rate estimated (eGFR). The 2013 ESH criteria for diabetic hypertensive patients (&lt;140/85 mmHg) was reached by 39% of all 625 study patients and 38% of the pharmacologically treated 520 patients. The absence of detectable albumin in urine was significantly associated with the control of systolic blood pressure and achievement of treatment goals. Beta blockers were the most common antihypertensive agents and patients treated with them had lower eGFR compared to those not treated with these agents. The blood pressure of patients was not in full concordance with the present guideline recommendations. However, satisfactory improvement in blood pressure control, reduction of albuminuria and hence ESRD prevention was achieved.
DOI: 10.6084/m9.figshare.3439568.v2
title: Improved control of blood pressure and albuminuria among patients with type-2 diabetes in Finnish open care

description: Risk of cardiovascular events within the diabetic population has decreased and survival increased with patients living longer and thus facing the development of end-stage renal disease (ESRD). This calls for good care of patient with diabetes with a focus on hypertension. Patient data were collected from 42 Finnish primary care centres. Each was asked to enrol 10–12 consecutive patients with type-2 diabetes between March 2011 and August 2012. Along with the office blood pressure measurements and laboratory tests, the presence of albuminuria was measured and glomerular filtration rate estimated (eGFR). The 2013 ESH criteria for diabetic hypertensive patients (&lt;140/85 mmHg) was reached by 39% of all 625 study patients and 38% of the pharmacologically treated 520 patients. The absence of detectable albumin in urine was significantly associated with the control of systolic blood pressure and achievement of treatment goals. Beta blockers were the most common antihypertensive agents and patients treated with them had lower eGFR compared to those not treated with these agents. The blood pressure of patients was not in full concordance with the present guideline recommendations. However, satisfactory improvement in blood pressure control, reduction of albuminuria and hence ESRD prevention was achieved.
DOI: 10.6084/m9.figshare.3439511
title: Differences in the equine fecal microbiome using different sampling times and sites

description: To investigate the effect of different sampling techniques (rectum vs. stall floor ), locations (center vs. surface of the fecal ball) and time of sample collection post-defecation on the equine fecal microbiome.<br>
DOI: 10.6084/m9.figshare.3439511.v1
title: Differences in the equine fecal microbiome using different sampling times and sites

description: To investigate the effect of different sampling techniques (rectum vs. stall floor ), locations (center vs. surface of the fecal ball) and time of sample collection post-defecation on the equine fecal microbiome.<br>
DOI: 10.6084/m9.figshare.3439448
title: 3-(benzo[<i>d</i>]thiazol-2-YL)phenol and 4-(benzo[<i>d</i>]thiazol-2-YL)phenol: Crystal Structure Determination, DFT Calculations and Visualizing Intermolecular Interactions Using Hirshfeld Surface Analysis

description: This article describes the synthesis and X-ray crystal structure analysis of <b>3-(benzo[<i>d</i>]thiazol-2-yl) phenol (I) and 4-(benzo[<i>d</i>]thiazol-2-yl)phenol (II)</b>, crystallized in centrosymmetric triclinic and orthorhombic space groups respectively. The packing in the unit cell of these two positional isomers are different resulting difference in various types of intermolecular interactions (C-H…S, O-H…O<sub>w</sub> and O-H…N) connect the molecules into 2D frameworks. Due to presence of lattice water in compound (<b>I</b>), H-bonding interactions are strong and melting point of (<b>I</b>) is comparatively higher than (<b>II</b>). The DFT optimized molecular geometries in (<b>I</b>) and (<b>II</b>) agree closely with those obtained from crystallographic studies. The compounds <b>(I)</b> and <b>(II)</b> have been crystallized in centrosymmetric space groups. The DFT optimized molecular geometries in both compounds agree closely with those obtained from the crystallographic studies. An interplay of O-H…O<sub>w</sub> and O-H…N type strong hydrogen bonds and C-H…S type weak interactions connect the molecules of (<b>I</b>) and (<b>II</b>) into 2D framework. Hirshfeld surface analysis of (<b>I</b>) indicates that the H…H and H…π contacts can account for 47.4% and 18.7%, respectively, of the Hirshfeld surface area, whereas the corresponding fraction in (<b>II</b>) is 36.5% and 29.5%, respectively.
DOI: 10.6084/m9.figshare.3439448.v1
title: 3-(benzo[<i>d</i>]thiazol-2-YL)phenol and 4-(benzo[<i>d</i>]thiazol-2-YL)phenol: Crystal Structure Determination, DFT Calculations and Visualizing Intermolecular Interactions Using Hirshfeld Surface Analysis

description: This article describes the synthesis and X-ray crystal structure analysis of <b>3-(benzo[<i>d</i>]thiazol-2-yl) phenol (I) and 4-(benzo[<i>d</i>]thiazol-2-yl)phenol (II)</b>, crystallized in centrosymmetric triclinic and orthorhombic space groups respectively. The packing in the unit cell of these two positional isomers are different resulting difference in various types of intermolecular interactions (C-H…S, O-H…O<sub>w</sub> and O-H…N) connect the molecules into 2D frameworks. Due to presence of lattice water in compound (<b>I</b>), H-bonding interactions are strong and melting point of (<b>I</b>) is comparatively higher than (<b>II</b>). The DFT optimized molecular geometries in (<b>I</b>) and (<b>II</b>) agree closely with those obtained from crystallographic studies. The compounds <b>(I)</b> and <b>(II)</b> have been crystallized in centrosymmetric space groups. The DFT optimized molecular geometries in both compounds agree closely with those obtained from the crystallographic studies. An interplay of O-H…O<sub>w</sub> and O-H…N type strong hydrogen bonds and C-H…S type weak interactions connect the molecules of (<b>I</b>) and (<b>II</b>) into 2D framework. Hirshfeld surface analysis of (<b>I</b>) indicates that the H…H and H…π contacts can account for 47.4% and 18.7%, respectively, of the Hirshfeld surface area, whereas the corresponding fraction in (<b>II</b>) is 36.5% and 29.5%, respectively.
DOI: 10.6084/m9.figshare.3439412.v1
title: Figure 1.tif

description: HIV-1 unintegrated DNAs have significant impact on productive retroviral replication.<br>
DOI: 10.6084/m9.figshare.3439355
title: MARCH2 regulates autophagy by promoting CFTR ubiquitination and degradation and PIK3CA-AKT-MTOR signaling

description: MARCH2 (membrane-associated RING-CH protein 2), an E3 ubiquitin ligase, is mainly associated with the vesicle trafficking. In the present study, for the first time, we demonstrated that MARCH2 negatively regulates autophagy. Our data indicated that overexpression of MARCH2 impaired autophagy, as evidenced by attenuated levels of LC3B-II and impaired degradation of endogenous and exogenous autophagic substrates. By contrast, loss of <i>MARCH2</i> expression had the opposite effects. In vivo experiments demonstrate that <i>MARCH2</i> knockout mediated autophagy results in an inhibition of tumorigenicity. Further investigation revealed that the induction of autophagy by <i>MARCH2</i> deficiency was mediated through the PIK3CA-AKT-MTOR signaling pathway. Additionally, we found that MARCH2 interacts with CFTR (cystic fibrosis transmembrane conductance regulator), promotes the ubiquitination and degradation of CFTR, and inhibits CFTR-mediated autophagy in tumor cells. The functional PDZ domain of MARCH2 is required for the association with CFTR. Thus, our study identified a novel negative regulator of autophagy and suggested that the physical and functional connection between the MARCH2 and CFTR in different conditions will be elucidated in the further experiments.
DOI: 10.6084/m9.figshare.3439355.v2
title: MARCH2 regulates autophagy by promoting CFTR ubiquitination and degradation and PIK3CA-AKT-MTOR signaling

description: MARCH2 (membrane-associated RING-CH protein 2), an E3 ubiquitin ligase, is mainly associated with the vesicle trafficking. In the present study, for the first time, we demonstrated that MARCH2 negatively regulates autophagy. Our data indicated that overexpression of MARCH2 impaired autophagy, as evidenced by attenuated levels of LC3B-II and impaired degradation of endogenous and exogenous autophagic substrates. By contrast, loss of <i>MARCH2</i> expression had the opposite effects. In vivo experiments demonstrate that <i>MARCH2</i> knockout mediated autophagy results in an inhibition of tumorigenicity. Further investigation revealed that the induction of autophagy by <i>MARCH2</i> deficiency was mediated through the PIK3CA-AKT-MTOR signaling pathway. Additionally, we found that MARCH2 interacts with CFTR (cystic fibrosis transmembrane conductance regulator), promotes the ubiquitination and degradation of CFTR, and inhibits CFTR-mediated autophagy in tumor cells. The functional PDZ domain of MARCH2 is required for the association with CFTR. Thus, our study identified a novel negative regulator of autophagy and suggested that the physical and functional connection between the MARCH2 and CFTR in different conditions will be elucidated in the further experiments.
DOI: 10.6084/m9.figshare.3439355.v1
title: MARCH2 regulates autophagy by promoting CFTR ubiquitination and degradation, and PIK3CA-AKT-MTOR signaling

description: MARCH2 (membrane-associated RING-CH protein 2), an E3 ubiquitin ligase, is mainly associated with the vesicle trafficking. In the present study, for the first time, we demonstrated that MARCH2 negatively regulates autophagy. Our data indicated that overexpression of MARCH2 impaired autophagy, as evidenced by attenuated levels of LC3B-II and impaired degradation of endogenous and exogenous autophagic substrates. By contrast, loss of <i>MARCH2</i> expression had the opposite effects. In vivo experiments demonstrate that <i>MARCH2</i> knockout mediated autophagy results in an inhibition of tumorigenicity. Further investigation revealed that the induction of autophagy by <i>MARCH2</i> deficiency was mediated through the PIK3CA-AKT-MTOR signaling pathway. Additionally, we found that MARCH2 interacts with CFTR (cystic fibrosis transmembrane conductance regulator), promotes the ubiquitination and degradation of CFTR, and inhibits CFTR-mediated autophagy in tumor cells. The functional PDZ domain of MARCH2 is required for the association with CFTR. Thus, our study identified a novel negative regulator of autophagy and suggested that the physical and functional connection between the MARCH2 and CFTR in different conditions will be elucidated in the further experiments.
DOI: 10.6084/m9.figshare.3439301
title: Identifying Mixtures of Mixtures Using Bayesian Estimation

description: The use of a finite mixture of normal distributions in model-based clustering allows to capture non-Gaussian data clusters. However, identifying the clusters from the normal components is challenging and in general either achieved by imposing constraints on the model or by using post-processing procedures. Within the Bayesian framework we propose a different approach based on sparse finite mixtures to achieve identifiability. We specify a hierarchical prior where the hyperparameters are carefully selected such that they are reflective of the cluster structure aimed at. In addition, this prior allows to estimate the model using standard MCMC sampling methods. In combination with a post-processing approach which resolves the label switching issue and results in an identified model, our approach allows to simultaneously (1) determine the number of clusters, (2) flexibly approximate the cluster distributions in a semi-parametric way using finite mixtures of normals and (3) identify cluster-specific parameters and classify observations. The proposed approach is illustrated in two simulation studies and on benchmark data sets.
DOI: 10.6084/m9.figshare.3439301.v1
title: Identifying Mixtures of Mixtures Using Bayesian Estimation

description: The use of a finite mixture of normal distributions in model-based clustering allows to capture non-Gaussian data clusters. However, identifying the clusters from the normal components is challenging and in general either achieved by imposing constraints on the model or by using post-processing procedures. Within the Bayesian framework we propose a different approach based on sparse finite mixtures to achieve identifiability. We specify a hierarchical prior where the hyperparameters are carefully selected such that they are reflective of the cluster structure aimed at. In addition, this prior allows to estimate the model using standard MCMC sampling methods. In combination with a post-processing approach which resolves the label switching issue and results in an identified model, our approach allows to simultaneously (1) determine the number of clusters, (2) flexibly approximate the cluster distributions in a semi-parametric way using finite mixtures of normals and (3) identify cluster-specific parameters and classify observations. The proposed approach is illustrated in two simulation studies and on benchmark data sets.
DOI: 10.5258/soton/d1194
title: Data for Synthetic band-structure engineering in polariton crystals with non-Hermitian topological phases

description: Experimental data and numerical simulation results used to create the figures in the paper Pickup, L., Sigurdsson, H., Ruostekoski, J. & Lagoudakis, P. (2020) Synthetic band-structure engineering in polariton crystals with non-Hermitian topological phases. Nature Communications.
DOI: 10.6084/m9.figshare.3439268
title: PacBio full-length transcriptome profiling of insect mitochondrial gene expression

description: In this study, we sequenced the first full-length insect transcriptome using the <i>Erthesina fullo</i> Thunberg based on the PacBio platform. We constructed the first quantitative transcription map of animal mitochondrial genomes and built a straightforward and concise methodology to investigate mitochondrial gene transcription, RNA processing, mRNA maturation and several other related topics. Most of the results were consistent with the previous studies, while to the best of our knowledge some findings were reported for the first time in this study. The new findings included the high levels of mitochondrial gene expression, the 3′ polyadenylation and possible 5′ m<sup>7</sup>G caps of rRNAs, the isoform diversity of 12S rRNA, the polycistronic transcripts and natural antisense transcripts of mitochondrial genes <i>et al</i>. These findings could challenge and enrich fundamental concepts of mitochondrial gene transcription and RNA processing, particularly of the rRNA primary (sequence) structure. The methodology constructed in this study can also be used to study gene expression or RNA processing of nuclear genomes.
DOI: 10.6084/m9.figshare.3439268.v2
title: PacBio full-length transcriptome profiling of insect mitochondrial gene expression

description: In this study, we sequenced the first full-length insect transcriptome using the <i>Erthesina fullo</i> Thunberg based on the PacBio platform. We constructed the first quantitative transcription map of animal mitochondrial genomes and built a straightforward and concise methodology to investigate mitochondrial gene transcription, RNA processing, mRNA maturation and several other related topics. Most of the results were consistent with the previous studies, while to the best of our knowledge some findings were reported for the first time in this study. The new findings included the high levels of mitochondrial gene expression, the 3′ polyadenylation and possible 5′ m<sup>7</sup>G caps of rRNAs, the isoform diversity of 12S rRNA, the polycistronic transcripts and natural antisense transcripts of mitochondrial genes <i>et al</i>. These findings could challenge and enrich fundamental concepts of mitochondrial gene transcription and RNA processing, particularly of the rRNA primary (sequence) structure. The methodology constructed in this study can also be used to study gene expression or RNA processing of nuclear genomes.
DOI: 10.6084/m9.figshare.3439268.v1
title: PacBio Full-length transcriptome profiling of insect mitochondrial gene expression

description: In this study, we sequenced the first full-length insect transcriptome using the <i>Erthesina fullo</i> Thunberg based on the PacBio platform. We constructed the first quantitative transcription map of animal mitochondrial genomes and built a straightforward and concise methodology to investigate mitochondrial gene transcription, RNA processing, mRNA maturation and several other related topics. Most of the results were consistent with the previous studies, while to the best of our knowledge some findings were reported for the first time in this study. The new findings included the high levels of mitochondrial gene expression, the 3′ polyadenylation and possible 5′ m<sup>7</sup>G caps of rRNAs, the isoform diversity of 12S rRNA, the polycistronic transcripts and natural antisense transcripts of mitochondrial genes <i>et al.</i> These findings could challenge and enrich fundamental concepts of mitochondrial gene transcription and RNA processing, particularly of the rRNA primary (sequence) structure. The methodology constructed in this study can also be used to study gene expression or RNA processing of nuclear genomes.
DOI: 10.6084/m9.figshare.3439265
title: UV radiation impairs the cognitive ability of White children in the USA

description: This is an SPSS data set with 48 contiguous USA states as units of analysis. The main variables encompassed are: UV Index, temperature, proportion of White population, disease burden, income, total fertility rate, and math and reading scores of 4th and 8th grade White, African American, and Hispanic children in 2003, 2009, 2015 and other years.
DOI: 10.6084/m9.figshare.3439265.v1
title: UV radiation impairs the cognitive ability of White children in the USA

description: This is an SPSS data set with 48 contiguous USA states as units of analysis. The main variables encompassed are: UV Index, temperature, proportion of White population, disease burden, income, total fertility rate, and math and reading scores of 4th and 8th grade White, African American, and Hispanic children in 2003, 2009, 2015 and other years.
DOI: 10.6084/m9.figshare.3439259
title: Molecular dissection of valproic acid effects in acute myeloid leukemia identifies predictive networks

description: Histone deacetylase inhibitors (HDACIs) like valproic acid (VPA) display activity in leukemia models and induce tumor-selective cytotoxicity against acute myeloid leukemia (AML) blasts. As there are limited data on HDACIs effects, we aimed to dissect VPA effects <i>in vitro</i> using myeloid cell lines with the idea to integrate findings with <i>in vivo</i> data from AML patients treated with VPA additionally to intensive chemotherapy (n = 12). By gene expression profiling we identified an <i>in vitro</i> VPA response signature enriched for genes/pathways known to be implicated in cell cycle arrest, apoptosis, and DNA repair. Following VPA treatment <i>in vivo</i>, gene expression changes in AML patients showed concordant results with the <i>in vitro</i> VPA response despite concomitant intensive chemotherapy. Comparative miRNA profiling revealed VPA-associated miRNA expression changes likely contributing to a VPA-induced reversion of deregulated gene expression. In addition, we were able to define markers predicting VPA response <i>in vivo</i> such as <i>CXCR4</i> and <i>LBH</i>. These could be validated in an independent cohort of VPA and intensive chemotherapy treated AML patients (n = 114) in which they were inversely correlated with relapse-free survival. In summary, our data provide new insights into the molecular mechanisms of VPA in myeloid blasts, which might be useful in further advancing HDAC inhibition based treatment approaches in AML.
DOI: 10.6084/m9.figshare.3439259.v1
title: Molecular dissection of valproic acid effects in acute myeloid leukemia identifies predictive networks

description: Histone deacetylase inhibitors (HDACIs) like valproic acid (VPA) display activity in leukemia models and induce tumor-selective cytotoxicity against acute myeloid leukemia (AML) blasts. As there are limited data on HDACIs effects, we aimed to dissect VPA effects <i>in vitro</i> using myeloid cell lines with the idea to integrate findings with <i>in vivo</i> data from AML patients treated with VPA additionally to intensive chemotherapy (n = 12). By gene expression profiling we identified an <i>in vitro</i> VPA response signature enriched for genes/pathways known to be implicated in cell cycle arrest, apoptosis, and DNA repair. Following VPA treatment <i>in vivo</i>, gene expression changes in AML patients showed concordant results with the <i>in vitro</i> VPA response despite concomitant intensive chemotherapy. Comparative miRNA profiling revealed VPA-associated miRNA expression changes likely contributing to a VPA-induced reversion of deregulated gene expression. In addition, we were able to define markers predicting VPA response <i>in vivo</i> such as <i>CXCR4</i> and <i>LBH</i>. These could be validated in an independent cohort of VPA and intensive chemotherapy treated AML patients (n = 114) in which they were inversely correlated with relapse-free survival. In summary, our data provide new insights into the molecular mechanisms of VPA in myeloid blasts, which might be useful in further advancing HDAC inhibition based treatment approaches in AML.