cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5354092.v1
title: Natural antisense transcripts drive a regulatory cascade controlling c-MYC transcription

description: <i>Cis</i>-natural antisense transcripts (<i>cis-</i>NATs) are long noncoding RNAs transcribed from the opposite strand and overlapping coding and noncoding genes on the sense strand. <i>cis-</i>NATs are widely present in the human genome and can be involved in multiple mechanisms of gene regulation. Here, we describe the presence of <i>cis-</i>NATs in the 3′ distal region of the c-MYC locus and investigate their impact on transcriptional regulation of this key oncogene in human cancers. We found that <i>cis-</i>NATs are produced as consequence of the activation of cryptic transcription initiation sites in the 3′ distal region downstream of the c-MYC 3′UTR. The process is tightly regulated and leads to the formation of two main transcripts, NAT6531 and NAT6558, which differ in their ability to fold into stem-loop secondary structures. NAT6531 acts as a substrate for DICER and as a source of small RNAs capable of modulating c-MYC transcription. This complex system, based on the interplay between <i>cis</i>-NATs and NAT-derived small RNAs, may represent an important layer of epigenetic regulation of the expression of c-MYC and other genes in human cells.
DOI: 10.6084/m9.figshare.5354053
title: Effects of chronic crude oil exposure on early developmental stages of the Northern krill (<i>Meganyctiphanes norvegica</i>)

description: Rising oil and gas activities in northern high latitudes have led to an increased risk of petroleum pollution in these ecosystems. Further, seasonal high UV radiation at high latitudes may elevate photo-enhanced toxicity of petroleum pollution to marine organisms. Zooplanktons are a key ecological component of northern ecosystems; therefore, it is important to assess their sensitivity to potential pollutants of oil and gas activity. As ontogenetic development may be particularly sensitive, the aim of this study was to examine the impact of chronic exposure to oil water dispersion (OWD) on development and feeding of early life stages of the Northern krill, <i>Meganyctiphanes norvegica</i>. In a range of experiments, embryonic, nonfeeding, and feeding larval stages were exposed to concentrations of between 0.01 and 0.1 mg/L of oil or photo-modified oil for 19 and 21 d. No significant effects on egg respiration, hatching success, development, length and larval survival were observed from these treatments. Similarly, evolution of fatty acid composition patterns during ontogenetic development was unaffected. The results indicates a high degree of resilience of these early developmental stages to such types and concentrations of pollutants. However, feeding and motility in later calyptopis-stage larvae were significantly impaired at exposure of 0.1 mg/L oil. Data indicate that feeding larval stage of krill was more sensitive to OWD than early nonfeeding life stages. This might be attributed to the narcotic effects of oil pollutants, their direct ingestion, or accumulated adverse effects over early development.
DOI: 10.6084/m9.figshare.5354122.v1
title: So similar and yet so different: taxonomic status of Pallid Swift <i>Apus pallidus</i> and Common Swift <i>Apus apus</i>

description: <b>Capsule:</b> Common Swift <i>Apus apus</i> and Pallid Swift <i>Apus Pallidus</i> are morphologically very similar but are genetically distinct and diverged 1.9–2.1 million years ago (mya). <b>Aims:</b> To examine genetic differentiation and to estimate separation time between Common and Pallid Swifts. <b>Methods:</b> Estimation of differences in three different mitochondrial DNA markers (<i>COI</i>, <i>ND2</i> and control region), and a fourth marker, the <i>cytb</i>, that did not differ between taxa. Fossils were used to calibrate the estimate of separation date between the two taxa. <b>Results:</b> The genetic between-species distances were 0.010, 0.006 and 0.033 for the three markers, respectively. These values were from three to ten times higher than within-species distances. Results show that the separation dates back to 1.9–2.1 mya, at the Plio-Pleistocene transition, when global climate underwent a period of significant cooling and Northern latitudes were probably more favourable to the Common than to the Pallid Swift. <b>Conclusion:</b> Differences in breeding biology, migration, moult and vocalizations between the two species are mirrored by a clear genetic separation.
DOI: 10.6084/m9.figshare.5354053.v1
title: Effects of chronic crude oil exposure on early developmental stages of the Northern krill (<i>Meganyctiphanes norvegica</i>)

description: Rising oil and gas activities in northern high latitudes have led to an increased risk of petroleum pollution in these ecosystems. Further, seasonal high UV radiation at high latitudes may elevate photo-enhanced toxicity of petroleum pollution to marine organisms. Zooplanktons are a key ecological component of northern ecosystems; therefore, it is important to assess their sensitivity to potential pollutants of oil and gas activity. As ontogenetic development may be particularly sensitive, the aim of this study was to examine the impact of chronic exposure to oil water dispersion (OWD) on development and feeding of early life stages of the Northern krill, <i>Meganyctiphanes norvegica</i>. In a range of experiments, embryonic, nonfeeding, and feeding larval stages were exposed to concentrations of between 0.01 and 0.1 mg/L of oil or photo-modified oil for 19 and 21 d. No significant effects on egg respiration, hatching success, development, length and larval survival were observed from these treatments. Similarly, evolution of fatty acid composition patterns during ontogenetic development was unaffected. The results indicates a high degree of resilience of these early developmental stages to such types and concentrations of pollutants. However, feeding and motility in later calyptopis-stage larvae were significantly impaired at exposure of 0.1 mg/L oil. Data indicate that feeding larval stage of krill was more sensitive to OWD than early nonfeeding life stages. This might be attributed to the narcotic effects of oil pollutants, their direct ingestion, or accumulated adverse effects over early development.
DOI: 10.6084/m9.figshare.5353846
title: Supplementary Material for: An Ecological Study of the Association between Air Pollution and Hepatocellular Carcinoma Incidence in Texas

description: <strong><em>Introduction:</em></strong> Primary liver cancer is a significant cause of cancer-related death in both the United States and the world at large. Hepatocellular carcinoma comprises 90% of these primary liver cancers and has numerous known etiologies. Evaluation of these identified etiologies and other traditional risk factors cannot explain the high incidence rates of hepatocellular carcinoma in Texas. Texas is home to the second largest petrochemical industry and agricultural industry in the nation; industrial activity and exposure to pathogenic chemicals have never been assessed as potential links to the state's increased incidence rate of hepatocellular carcinoma. <b><i>Methods:</i></b> The association between the county-level concentrations of 4 air pollutants known to be linked to liver cancer, vinyl chloride, arsenic, benzene, and 1,3-butadiene, and hepatocellular carcinoma rates was evaluated using nonparametric generalized additive logistic regression and gamma regression models. Hepatocellular carcinoma incidence rates for 2000-2013 were evaluated in comparison to 1996 and 1999 pollution concentrations and hepatocellular carcinoma rates for the subset of 2006-2013 were evaluated in comparison to 2002 and 2005 pollution concentrations, respectively. <b><i>Results:</i></b> The analysis indicates that the relationship between the incidence of liver cancer and air pollution and risk factors is nonlinear. There is a consistent significant positive association between the incidence of liver cancer and hepatitis C prevalence rates (gamma all years, <i>p</i> &lt; 0.05) and vinyl chloride concentrations (logistic 2002 and 2005, <i>p</i> &lt; 0.0001; gamma 2002 and 2005, <i>p</i> &lt; 0.05). <b><i>Conclusions:</i></b> This study suggests that vinyl chloride is a significant contributor to the incidence of liver cancer in Texas. The relationship is notably nonlinear. Further, the study supports the association between incidence of liver cancer and prevalence of hepatitis B.
DOI: 10.6084/m9.figshare.5353843
title: Supplementary Material for: Two Novel Pathogenic MID1 Variants and Genotype-Phenotype Correlation Reanalysis in X-Linked Opitz G/BBB Syndrome

description: X-linked Opitz G/BBB syndrome (XLOS) is a multisystemic congenital condition, caused by mutations in the midline-1 gene (<i>MID1</i>), characterized by a large inter- and intrafamilial phenotypic variability and often associated with intellectual disability (ID). We report clinical, genetic, and molecular findings in 4 patients with typical XLOS dysmorphic features belonging to 2 unrelated families. Two novel pathogenic loss-of-function <i>MID1</i> variants, a maternally inherited c.1656del and a de novo c.1215_1228dup, were identified. Subsequently, we performed a genotype-phenotype analysis using data from 91 male XLOS patients. To test the mutation impact on the phenotype; the type of mutation, the MID1-impaired domain and function were compared with the presence of each of the major clinical features (hypertelorism, clefts of the lip and/or palate, laryngo-tracheo-esophageal abnormalities, hypospadias and ID ) and minor clinical features (brain, heart, and anal defects). No statistically significant correlation was found with these features. Further investigations, as well as exhaustive and unequivocal phenotyping, may be required to improve our knowledge of the biological mechanisms underlying this syndrome and to provide more adequate disease management.
DOI: 10.6084/m9.figshare.5353999.v1
title: Raw and Denoised Sequences with their Reference Datasets

description: Raw and Denoised sequences of the two environmental samples (MPE4, MPE5) and the reference datasets used in taxonomic assignment methods.
DOI: 10.6084/m9.figshare.5353789
title: Supplementary Material for: Comparison of Different Sources of Mesenchymal Stem Cells: Palatal versus Lipoaspirated Adipose Tissue

description: <strong><em>Objectives:</em></strong> The purpose of this study was to compare the proliferation and differentiation potential of mesenchymal stem cells (MSCs) derived from palatal adipose tissue (PAT) and lipoaspirated adipose tissue (LAT). <b><i>Materials and Methods:</i></b> PATs were obtained from 2 healthy female patients undergoing surgery for gingival recession, and LATs were obtained from 2 healthy female patients undergoing plastic surgery. LAT- and PAT-derived MSCs were confirmed by flow cytometry using MSC-specific surface markers. The multilineage differentiation capacity of the MSCs was analyzed. The expression of immunophenotyping, embryonic, and differentiation markers was compared between both MSC lines. The proliferation of PAT- and LAT-MSCs was evaluated using a real-time cell analyzer, and telomerase activity was determined using an ELISA-based TRAP assay. Stem cells isolated from PAT and LAT were analyzed by real-time PCR and whole genome array analysis. <b><i>Results:</i></b> The cells isolated from PAT had MSC characteristics. In addition, PAT-MSCs had significantly higher alkaline phosphatase activity and osteogenic potential than LAT-MSCs. Although the proliferation and telomerase activities of LAT-MSCs were higher than those of PAT-MSCs, the difference was not statistically significant. The level of embryonic stem cell markers (Oct4 and Nanog) was higher in LAT-MSCs than in PAT-MSCs. The whole genome array analysis demonstrated that 255 gene sequences were differentially expressed, with more than a twofold change in expression. <b><i>Conclusions:</i></b> This is the first comparative analysis of the isolation and characterization of MSCs from PAT and LAT. PAT is an accessible source of MSCs, which could be used in periodontal and craniofacial tissue engineering.
DOI: 10.6084/m9.figshare.5353843.v1
title: Supplementary Material for: Two Novel Pathogenic MID1 Variants and Genotype-Phenotype Correlation Reanalysis in X-Linked Opitz G/BBB Syndrome

description: X-linked Opitz G/BBB syndrome (XLOS) is a multisystemic congenital condition, caused by mutations in the midline-1 gene (<i>MID1</i>), characterized by a large inter- and intrafamilial phenotypic variability and often associated with intellectual disability (ID). We report clinical, genetic, and molecular findings in 4 patients with typical XLOS dysmorphic features belonging to 2 unrelated families. Two novel pathogenic loss-of-function <i>MID1</i> variants, a maternally inherited c.1656del and a de novo c.1215_1228dup, were identified. Subsequently, we performed a genotype-phenotype analysis using data from 91 male XLOS patients. To test the mutation impact on the phenotype; the type of mutation, the MID1-impaired domain and function were compared with the presence of each of the major clinical features (hypertelorism, clefts of the lip and/or palate, laryngo-tracheo-esophageal abnormalities, hypospadias and ID ) and minor clinical features (brain, heart, and anal defects). No statistically significant correlation was found with these features. Further investigations, as well as exhaustive and unequivocal phenotyping, may be required to improve our knowledge of the biological mechanisms underlying this syndrome and to provide more adequate disease management.
DOI: 10.6084/m9.figshare.5353774
title: Supplementary Material for: Venous Stasis and Cerebrovascular Complications in Cerebral Venous Sinus Thrombosis

description: <strong><em>Background/Aims:</em></strong> The factors related to cerebrovascular complications in cerebral venous sinus thrombosis (CVST) are controversial. We focused on venous stasis and investigated its relationship with cerebrovascular complications in CVST. <b><i>Methods:</i></b> CVST patients between June 2013 and October 2016 were enrolled. Relationships between cerebrovascular complications, defined as cerebral venous infarction, intracerebral hemorrhage, or subarachnoid hemorrhage, and cerebrum venous stasis and other clinical information were retrospectively analyzed. Venous stasis was evaluated by the prominence of the veins on susceptibility-weighted imaging (SWI). The cerebrum was divided into 10 regions according to the venous drainage territories, and venous stasis was quantified by adding one point for venous prominence on SWI for each region (CVST SWI score). <b><i>Results:</i></b> All 5 cases in the noncomplicated group had a CVST SWI score of 0. The 3 patients with CVST SWI scores higher than 0 had cerebrovascular complications. The CVST SWI scores were higher in the complicated group than in the noncomplicated group (3.0 vs. 0, <i>p</i> = 0.010). Seizures were seen in all patients with complications and in none of the patients without complications (3 vs. 0, <i>p</i> = 0.018). <b><i>Conclusion:</i></b> Venous stasis evaluated by SWI can help predict cerebrovascular complications in CVST. A seizure is an important initial symptom that suggests cerebrovascular complications in CVST.
DOI: 10.6084/m9.figshare.5353774.v1
title: Supplementary Material for: Venous Stasis and Cerebrovascular Complications in Cerebral Venous Sinus Thrombosis

description: <strong><em>Background/Aims:</em></strong> The factors related to cerebrovascular complications in cerebral venous sinus thrombosis (CVST) are controversial. We focused on venous stasis and investigated its relationship with cerebrovascular complications in CVST. <b><i>Methods:</i></b> CVST patients between June 2013 and October 2016 were enrolled. Relationships between cerebrovascular complications, defined as cerebral venous infarction, intracerebral hemorrhage, or subarachnoid hemorrhage, and cerebrum venous stasis and other clinical information were retrospectively analyzed. Venous stasis was evaluated by the prominence of the veins on susceptibility-weighted imaging (SWI). The cerebrum was divided into 10 regions according to the venous drainage territories, and venous stasis was quantified by adding one point for venous prominence on SWI for each region (CVST SWI score). <b><i>Results:</i></b> All 5 cases in the noncomplicated group had a CVST SWI score of 0. The 3 patients with CVST SWI scores higher than 0 had cerebrovascular complications. The CVST SWI scores were higher in the complicated group than in the noncomplicated group (3.0 vs. 0, <i>p</i> = 0.010). Seizures were seen in all patients with complications and in none of the patients without complications (3 vs. 0, <i>p</i> = 0.018). <b><i>Conclusion:</i></b> Venous stasis evaluated by SWI can help predict cerebrovascular complications in CVST. A seizure is an important initial symptom that suggests cerebrovascular complications in CVST.
DOI: 10.6084/m9.figshare.5353765.v2
title: Overlap of highly FDG-avid and FMISO hypoxic tumor subvolumes in patients with head and neck cancer

description: <b>Background:</b> PET imaging may be used to personalize radiotherapy (RT) by identifying radioresistant tumor subvolumes for RT dose escalation. Using the tracers [<sup>18</sup>F]-fluorodeoxyglucose (FDG) and [<sup>18</sup>F]-fluoromisonidazole (FMISO), different aspects of tumor biology can be visualized. FDG depicts various biological aspects, e.g., proliferation, glycolysis and hypoxia, while FMISO is more hypoxia specific. In this study, we analyzed size and overlap of volumes based on the two markers for head-and-neck cancer patients (HNSCC). <b>Material and methods:</b> Twenty five HNSCC patients underwent a CT scan, as well as FDG and dynamic FMISO PET/CT prior to definitive radio-chemotherapy in a prospective FMISO dose escalation study. Three PET-based subvolumes of the primary tumor (GTV<sub>prim</sub>) were segmented: a highly FDG-avid volume <i>V</i><sub>FDG</sub>, a hypoxic volume on the static FMISO image acquired four hours post tracer injection (<i>V</i><sub>H</sub>) and a retention/perfusion volume (<i>V</i><sub>M</sub>) using pharmacokinetic modeling of dynamic FMISO data. Absolute volumes, overlaps and distances to agreement (DTA) were evaluated. <b>Results:</b> Sizes of PET-based volumes and the GTV<sub>prim</sub> are significantly different (GTV<sub>prim</sub>&gt;<i>V</i><sub>FDG</sub>&gt;<i>V</i><sub>H</sub> &gt;<i>V</i><sub>M</sub>; <i>p</i> V<sub>H</sub> is covered by <i>V</i><sub>FDG</sub> or DTAs are small (mean coverage 74.4%, mean DTA 1.4 mm). Coverage of <i>V</i><sub>M</sub> is less pronounced. With respect to <i>V</i><sub>FDG</sub> and <i>V</i><sub>H</sub>, the mean coverage is 48.7% and 43.1% and the mean DTA is 5.3 mm and 6.3 mm, respectively. For two patients, DTAs were larger than 2 cm. <b>Conclusions:</b> Hypoxic subvolumes from static PET imaging are typically covered by or in close proximity to highly FDG-avid subvolumes. Therefore, dose escalation to FDG positive subvolumes should cover the static hypoxic subvolumes in most patients, with the disadvantage of larger volumes, resulting in a higher risk of dose-limiting toxicity. Coverage of subvolumes from dynamic FMISO PET is less pronounced. Further studies are needed to explore the relevance of mismatches in functional imaging.
DOI: 10.6084/m9.figshare.5353762.v2
title: A new method to assess pulmonary changes using <sup>18</sup>F-fluoro-2-deoxyglucose positron emission tomography for lung cancer patients following radiotherapy

description: <b>Background:</b><sup>18</sup>F-fluoro-2-deoxyglucose positron emission tomography (<sup>18</sup>F-FDG-PET) may be used for assessing radiation induced alterations in the lung. However, there is a need to further develop methodologies to improve quantification. Using computed tomography (CT), a local structure method has been shown to be superior to conventional CT-based analysis. Here, we investigate whether the local structure method based on <sup>18</sup>F-FDG-PET improves radiotherapy (RT) dose–response quantification for lung cancer patients. <b>Material and methods:</b> Sixteen patients with lung cancer undergoing fractionated RT were examined by <sup>18</sup>F-FDG-PET/CT at three sessions (pre, mid, post) and the lung was delineated in the planning CT images. The RT dose matrix was co-registered with the PET images. For each PET image series, mean (μ) and standard deviation (<i>σ</i>) maps were calculated based on cubes in the lung (3 × 3 × 3 voxels), where the spread in pre-therapy μ and <i>σ</i> was characterized by a covariance ellipse in a sub-volume of 3 × 3 × 3 cubes. Mahalanobis distance was used to measure the distance of individual cube values to the origin of the ellipse and to further form local structure ‘<i>S</i>’ maps. The structural difference maps (Δ<i>S</i>) and mean difference maps (Δμ) were calculated by subtracting pre-therapy maps from maps at mid- and post-therapy. Corresponding maps based on CT images were also generated. <b>Results:</b> Δ<i>S</i> identified new areas of interest in the lung compared to conventional Δμ maps. Δ<i>S</i> for PET and CT gave a significantly elevated lung signal compared to a control group during and post-RT (<i>p</i> S between pre- and post-therapy for <sup>18</sup>F-FDG-PET was the only parameter significantly associated with local lung dose (<i>p</i> = .04). <b>Conclusions:</b> The new method using local structures on <sup>18</sup>F-FDG-PET provides a clearer uptake dose–response compared to conventional analysis and CT-based approaches and may be valuable in future studies addressing lung toxicity.
DOI: 10.6084/m9.figshare.14183973
title: Additional file 1 of Genetic variation and microRNA targeting of A-to-I RNA editing fine tune human tissue transcriptomes

description: Additional file 1: Table S1. List of analyzed datasets.
DOI: 10.6084/m9.figshare.14183973.v1
title: Additional file 1 of Genetic variation and microRNA targeting of A-to-I RNA editing fine tune human tissue transcriptomes

description: Additional file 1: Table S1. List of analyzed datasets.
DOI: 10.6084/m9.figshare.14183949.v1
title: Additional file 11 of Genetic variation and microRNA targeting of A-to-I RNA editing fine tune human tissue transcriptomes

description: Additional file 11: Table S10. List of miRNA-mediated tissue-specific edQTL:eQTL colocalization events.
DOI: 10.6084/m9.figshare.14183958.v1
title: Additional file 13 of Genetic variation and microRNA targeting of A-to-I RNA editing fine tune human tissue transcriptomes

description: Additional file 13: Table S12. List of edQTL p-value cutoffs for FDR of 10% across the 49 tissues.
DOI: 10.6084/m9.figshare.14183964
title: Additional file 15 of Genetic variation and microRNA targeting of A-to-I RNA editing fine tune human tissue transcriptomes

description: Additional file 15: Table S14. Description of plasmids used for 3′-UTR luciferase reporter assays.
DOI: 10.6084/m9.figshare.14183982.v1
title: Additional file 4 of Genetic variation and microRNA targeting of A-to-I RNA editing fine tune human tissue transcriptomes

description: Additional file 4: Table S3. List of ASED sites across the 49 tissues.
DOI: 10.6084/m9.figshare.14183985
title: Additional file 5 of Genetic variation and microRNA targeting of A-to-I RNA editing fine tune human tissue transcriptomes

description: Additional file 5: Table S4. List of edQTL sites with effect sizes correlated (R2 ≥ 0.5) to median ADARB1 levels across the 49 tissues.
DOI: 10.6084/m9.figshare.14183949
title: Additional file 11 of Genetic variation and microRNA targeting of A-to-I RNA editing fine tune human tissue transcriptomes

description: Additional file 11: Table S10. List of miRNA-mediated tissue-specific edQTL:eQTL colocalization events.
DOI: 10.6084/m9.figshare.14183961
title: Additional file 14 of Genetic variation and microRNA targeting of A-to-I RNA editing fine tune human tissue transcriptomes

description: Additional file 14: Table S13. Primer sequences used for 3′-UTR luciferase reporter assays.