cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.21997178.v1
title: Supplementary Material for: Modulatory Effects of Ketamine and Lamotrigine on Cognition: Emotion Interaction in the Brain

description: <b><i>Introduction:</i></b> Cognition and emotion are fundamentally integrated in the brain and mutually contribute to behavior. The relation between working memory (WM) and emotion is particularly suited to investigate cognition-emotion interaction since WM is an essential component of many higher cognitive functions. Ketamine affects not only WM but also has a profound impact on emotional processing. Effects of acute ketamine challenge are sensitive to modulation by pretreatment with lamotrigine, which inhibits glutamate release. Accordingly, a combination of these approaches should be particularly suited to investigate cognition-emotion interaction. <b><i>Methods:</i></b> Seventy five healthy subjects were investigated in a double-blind, placebo-controlled, randomized, single-dose, parallel-group study with three treatment conditions. All subjects underwent two scanning sessions (acute/post 24 h). <b><i>Results:</i></b> Compared to placebo, acute ketamine administration induced significant dissociative, psychotomimetic, and cognitive effects, as well as an increase in neural activity during WM for positive stimuli. Inhibition of glutamate release by pretreatment with lamotrigine did not influence ketamine’s subjective effects, but significantly attenuated its impact on emotional WM and associated neural activity. There was no effect on these measures 24 h after ketamine administration. <b><i>Conclusion:</i></b> Our results demonstrate differential acute effects of modulated glutamate release and a swift restoration of disturbed neurobehavioral homeostasis in healthy subjects.
DOI: 10.6084/m9.figshare.21968105.v1
title: Supplementary Material for: Temporary Myopic Shift in a Patient with Multiple Parallel-Line Endotheliitis

description: Here, we report the case of a patient with multiple parallel-line endotheliitis with myopic shift, which has not been previously reported. A 36-year-old man visited our clinic with blurred vision in his left eye. A slit lamp examination revealed an interesting pattern of multiple parallel lines of keratic precipitates, along with subtle corneal edema. The spherical equivalents measured in the right and left eyes were -9.25 and -11.875 diopter, respectively, with the left eye showing more myopic progression. On specular microscopy, endothelial cell loss was found in the left eye. After administration of a weak topical steroid, keratic precipitates and corneal edema resolved completely within 2 days. The myopic shift in his left eye recovered to -10.0 diopters. Multiple parallel-line endotheliitis can be easily treated with a weak topical steroid in a short period. A temporary myopic shift may occur, which in this case resolved upon disease recovery. However, corneal endothelial cell loss is inevitable; therefore, careful monitoring is needed.
DOI: 10.6084/m9.figshare.21997175
title: Supplemental Data to "Sample size calculation for a NanoString GeoMx spatial transcriptomics experiment to study predictors of fibrosis progression in non-alcoholic fatty liver disease"

description: Supplemental Data to "Sample size calculation for a NanoString GeoMx spatial transcriptomics experiment to study predictors of fibrosis progression in non-alcoholic fatty liver disease"
DOI: 10.5281/zenodo.7599910
title: Genbank and BOLD accession numbers of sequences from "New insights into the diversity of cryptobenthic Cirripectes blennies in the Mascarene Archipelago sampled using Autonomous Reef Monitoring Structures (ARMS)"

description: <strong>Abstract:</strong> Autonomous Reef Monitoring Structures (ARMS) are artificial mini-reefs designed for standardised sampling of sessile and small motile cryptobenthic organisms. ARMS are also effective for collecting small cryptobenthic fishes, such as the combtooth blennies of the genus <em>Cirripectes</em>. Recent studies discovered several <em>Cirripectes</em> species endemic to islands or archipelagos, in spite of the generally broad distributions of tropical and subtropical blennies. Thus, in order to evaluate the diversity and distribution of <em>Cirripectes</em> species in the Mascarene Archipelago, a little studied region but an important biodiversity hotspot, complete mitochondrial genomes and nuclear rhodopsin genes were sequenced for 39 specimens collected with ARMS deployed on outer reef slopes at Reunion and Rodrigues islands. Mitochondrial COI sequences were analysed to integrate these specimens within the largest dataset of publicly available sequences. Three species were found in the Mascarene Archipelago, <em>Cirripectes castaneus, C. randalli, </em>and <em>C. stigmaticus</em>. <em>C. castaneus</em> and <em>C. stigmaticus</em> both have an Indo-Pacific distribution with several haplotypes shared among distant localities. In agreement with the literature, <em>C. randalli </em>shows a small-range endemism restricted to the Mascarenes. We confirmed the presence of <em>C. castaneus, C. randalli </em>and <em>C. stigmaticus </em>in Rodrigues, and the presence of <em>C. stigmaticus</em> in Reunion. This study contributes to fill the gaps in taxonomic and molecular knowledge of the reef cryptobiome in the South-West Indian Ocean, and provides the first complete mitogenomes for the genus, a crucial step for future molecular-based inventories (e.g. eDNA). <strong>Content of this repository:</strong> Genbank and BOLD accession numbers of sequences from "New insights into the diversity of cryptobenthic <em>Cirripectes</em> blennies in the Mascarene Archipelago sampled using Autonomous Reef Monitoring Structures (ARMS)" published in<em> Ecology and Evolution</em> (2023)
DOI: 10.5281/zenodo.7599909
title: Genbank and BOLD accession numbers of sequences from "New insights into the diversity of cryptobenthic Cirripectes blennies in the Mascarene Archipelago sampled using Autonomous Reef Monitoring Structures (ARMS)"

description: <strong>Abstract:</strong> Autonomous Reef Monitoring Structures (ARMS) are artificial mini-reefs designed for standardised sampling of sessile and small motile cryptobenthic organisms. ARMS are also effective for collecting small cryptobenthic fishes, such as the combtooth blennies of the genus <em>Cirripectes</em>. Recent studies discovered several <em>Cirripectes</em> species endemic to islands or archipelagos, in spite of the generally broad distributions of tropical and subtropical blennies. Thus, in order to evaluate the diversity and distribution of <em>Cirripectes</em> species in the Mascarene Archipelago, a little studied region but an important biodiversity hotspot, complete mitochondrial genomes and nuclear rhodopsin genes were sequenced for 39 specimens collected with ARMS deployed on outer reef slopes at Reunion and Rodrigues islands. Mitochondrial COI sequences were analysed to integrate these specimens within the largest dataset of publicly available sequences. Three species were found in the Mascarene Archipelago, <em>Cirripectes castaneus, C. randalli, </em>and <em>C. stigmaticus</em>. <em>C. castaneus</em> and <em>C. stigmaticus</em> both have an Indo-Pacific distribution with several haplotypes shared among distant localities. In agreement with the literature, <em>C. randalli </em>shows a small-range endemism restricted to the Mascarenes. We confirmed the presence of <em>C. castaneus, C. randalli </em>and <em>C. stigmaticus </em>in Rodrigues, and the presence of <em>C. stigmaticus</em> in Reunion. This study contributes to fill the gaps in taxonomic and molecular knowledge of the reef cryptobiome in the South-West Indian Ocean, and provides the first complete mitogenomes for the genus, a crucial step for future molecular-based inventories (e.g. eDNA). <strong>Content of this repository:</strong> Genbank and BOLD accession numbers of sequences from "New insights into the diversity of cryptobenthic <em>Cirripectes</em> blennies in the Mascarene Archipelago sampled using Autonomous Reef Monitoring Structures (ARMS)" published in<em> Ecology and Evolution</em> (2023)
DOI: 10.6084/m9.figshare.7503722
title: Inhibition of polarity-regulating kinase PAR1b contributes to <i>Helicobacter pylori</i> inflicted DNA Double Strand Breaks in gastric cells

description: The serine/threonine kinase Par1 is a core component of the machinery that sets up polarity in the embryo and regulates cell fate decisions but its role in the homeostasis of adult tissues is poorly understood. Inhibition of Par1 by the bacterium <i>Helicobacter pylori</i> (<i>H. pylori</i>) represents the only established pathology that affects Par1 function in an adult epithelium. Thus, during chronic <i>H. pylori</i> infection of the gastric mucosa Par1 is one of the targets of the non-obligate <i>H.pylori</i> cytotoxic protein and oncogene CagA, which stimulates inflammation and triggers morphological changes, both believed to contribute to the gastric cancer risk imposed by <i>H. pylori</i> infection. Based on Par1’s role in cell polarity, it has been speculated that Par1 inhibition affects epithelial polarity. Here we report the unexpected finding that CagA-mediated Par1-inhibition promotes the generation of DNA Double Strand Breaks in primary gastric epithelial cells, which likely contributes to the reported accumulation of mutations in chronically infected mucosal cells. <b>Abbreviations:</b> AGS: human gastric adenocarcinoma cell line; CM: CagA Multimerization (and Par1 binding) domain; <i>H. pylori: Helicobacter pylori</i>; DSB: Double Strand Break; HGECs: human (primary) gastric epithelial cells; IB: immunoblot; IF: immunofluorescence; MOI: Multiplicity of Infection; ROS: reactive oxygen species; Par1: Partitioning Defective 1 kinase; WT: wild type
DOI: 10.6084/m9.figshare.7503722.v2
title: Inhibition of polarity-regulating kinase PAR1b contributes to <i>Helicobacter pylori</i> inflicted DNA Double Strand Breaks in gastric cells

description: The serine/threonine kinase Par1 is a core component of the machinery that sets up polarity in the embryo and regulates cell fate decisions but its role in the homeostasis of adult tissues is poorly understood. Inhibition of Par1 by the bacterium <i>Helicobacter pylori</i> (<i>H. pylori</i>) represents the only established pathology that affects Par1 function in an adult epithelium. Thus, during chronic <i>H. pylori</i> infection of the gastric mucosa Par1 is one of the targets of the non-obligate <i>H.pylori</i> cytotoxic protein and oncogene CagA, which stimulates inflammation and triggers morphological changes, both believed to contribute to the gastric cancer risk imposed by <i>H. pylori</i> infection. Based on Par1’s role in cell polarity, it has been speculated that Par1 inhibition affects epithelial polarity. Here we report the unexpected finding that CagA-mediated Par1-inhibition promotes the generation of DNA Double Strand Breaks in primary gastric epithelial cells, which likely contributes to the reported accumulation of mutations in chronically infected mucosal cells. <b>Abbreviations:</b> AGS: human gastric adenocarcinoma cell line; CM: CagA Multimerization (and Par1 binding) domain; <i>H. pylori: Helicobacter pylori</i>; DSB: Double Strand Break; HGECs: human (primary) gastric epithelial cells; IB: immunoblot; IF: immunofluorescence; MOI: Multiplicity of Infection; ROS: reactive oxygen species; Par1: Partitioning Defective 1 kinase; WT: wild type
DOI: 10.6084/m9.figshare.7503722.v1
title: Inhibition of Polarity-Regulating Kinase PAR1b contributes to <i>Helicobacter pylori</i> inflicted DNA Double Strand Breaks in Gastric Cells

description: The serine/threonine kinase Par1 is a core component of the machinery that sets up polarity in the embryo and regulates cell fate decisions but its role in the homeostasis of adult tissues is poorly understood. Inhibition of Par1 by the bacterium <i>Helicobacter pylori</i> (<i>H. pylori</i>) represents the only established pathology that affects Par1 function in an adult epithelium. Thus, during chronic <i>H. pylori</i> infection of the gastric mucosa Par1 is one of the targets of the non-obligate <i>H.pylori</i> cytotoxic protein and oncogene CagA, which stimulates inflammation and triggers morphological changes, both believed to contribute to the gastric cancer risk imposed by <i>H. pylori</i> infection. Based on Par1’s role in cell polarity, it has been speculated that Par1 inhibition affects epithelial polarity. Here we report the unexpected finding that CagA-mediated Par1-inhibition promotes the generation of DNA Double Strand Breaks in primary gastric epithelial cells, which likely contributes to the reported accumulation of mutations in chronically infected mucosal cells.
DOI: 10.6073/pasta/a70abb486440fbb8fbf5553a7431f74d
title: Role of Moose and Deer Browsing in Harvested Forests of Southern New England since 2008

description: In the past 20 years, moose have spread south from Vermont and New Hampshire and recolonized their pre-historical range limit in southern New England from which they had been extirpated almost 200 years earlier. Intensive moose browsing in the boreal forest has caused declines in forest density and shifts in species composition in some areas, generating considerable interest and concern among foresters, wildlife managers, and ecologists as to how moose along with white-tailed deer will impact forest development in this region. Harvard Forest in collaboration with researchers at the USGS Massachusetts Cooperative Research Unit has initiated a long-term study of the role of moose and deer in SNE forests using experimental exclosures. The design is a randomized block with 3 factors -- full exclosure, partial exclosure, and control plot. Full exclosures exclude both moose and deer but allow access to small mammals such as mice, squirrels, and rabbits. Partial exclosures have a 60cm opening around the bottom perimeter of the fence, which excludes moose but allows access to deer and other small and medium-sized animals. The design enables us to quantify forest composition and structure in areas (1) exposed to moose and deer browsing,(2) protected from moose and deer browsing, and (3) exposed to deer browsing but protected from moose browsing.
DOI: 10.34740/kaggle/dsv/4937117
title: Internet of Vehicles Dataset
DOI: 10.3886/e183869
title: São Lourenço, Minas Gerais, Estância Hidromineral

description: O objetivo deste artigo é investigar, através da historiografia existente, quem foi o primeiro proprietário das terras onde está situado no município de São Lourenço, Minas Gerais. A metodologia adotada neste estudo fundamentou-se no cruzamento das fontes históricas encontradas, sobretudo nos arquivos digitais do IBGE e do Arquivo Público Mineiro - APM, entre outras fontes que compõem a rica literatura historiográfica do município. O resultado esperado é que esta pesquisa estabeleça um levantamento histórico capaz de auxiliar na preservação da memória social e cultural da estância hidromineral de São Lourenço e contribuir para o preenchimento com documentos históricos adicionais ou vazios existentes na história do município.
DOI: 10.5281/zenodo.7499365
title: Fluctuation-dissipation relation for a Bose-Einstein condensate of photons

description: This repository contains the data presented in the manuscript titled "Fluctuation-dissipation relation for a Bose-Einstein condensate of photons" by F. E. Öztürk et al., <em>Phys. Rev. Lett. </em><strong>130</strong>, 033602 (2023) The files named 'fig{1,2,3,4}.xlsx' contain the final data sets relevant to reproduce all plots shown in the paper.
DOI: 10.5281/zenodo.7499364
title: Fluctuation-dissipation relation for a Bose-Einstein condensate of photons

description: This repository contains the data presented in the manuscript titled "Fluctuation-dissipation relation for a Bose-Einstein condensate of photons" by F. E. Öztürk et al., <em>Phys. Rev. Lett. </em><strong>130</strong>, 033602 (2023) The files named 'fig{1,2,3,4}.xlsx' contain the final data sets relevant to reproduce all plots shown in the paper.
DOI: 10.6096/6002
title: Dust_model_intercomparison_RegCM-Dust

description: No abstract available
DOI: 10.5281/zenodo.7600042
title: Call to Action: Overcoming Enrollment Disparities in Cancer Clinical Trials with Modernized Eligibility Criteria

description: Dataset used for paper: "Call to Action: Overcoming Enrollment Disparities in Cancer Clinical Trials with Modernized Eligibility Criteria." Data extracted from clinicaltrials.gov.
DOI: 10.5281/zenodo.7600041
title: Call to Action: Overcoming Enrollment Disparities in Cancer Clinical Trials with Modernized Eligibility Criteria

description: Dataset used for paper: "Call to Action: Overcoming Enrollment Disparities in Cancer Clinical Trials with Modernized Eligibility Criteria." Data extracted from clinicaltrials.gov.
DOI: 10.18112/openneuro.ds004460.v1.0.0
title: EEG and motion capture data set for a full-body/joystick rotation task
DOI: 10.5281/zenodo.7600030
title: Dataset Peak Delay

description: Header Pre and SeqTOT are the file containing information about the dataset (location, picking, magnitude) for the pre sequence and the sequence, respectively. peakdelay_Presequence and Sequence are the results of peak delay for the pre sequence and the sequence, respectively. First three columns are the coordinates, the fourth and fifth are the peak delay and the number of rays passing in the cell and sampling the peak delay.
DOI: 10.5281/zenodo.7600029
title: Dataset Peak Delay

description: Header Pre and SeqTOT are the file containing information about the dataset (location, picking, magnitude) for the pre sequence and the sequence, respectively. peakdelay_Presequence and Sequence are the results of peak delay for the pre sequence and the sequence, respectively. First three columns are the coordinates, the fourth and fifth are the peak delay and the number of rays passing in the cell and sampling the peak delay.
DOI: 10.6084/m9.figshare.13656175
title: Upregulated circRNA hsa_circ_0071036 promotes tumourigenesis of pancreatic cancer by sponging miR-489 and predicts unfavorable characteristics and prognosis

description: Circular RNAs (circRNAs), the new stars of endogenous non-coding RNAs, are dysregulated in various tumors including pancreatic cancer. Here, we aimed to investigate the biological functions of hsa_circ_0071036 in the tumourigenesis and progression of pancreatic ductal adenocarcinoma (PDAC) and its clinical implications. The differential expression profile of circRNAs in 4 pairs of PDAC tissues was analyzed by microarray assay. Quantitative real-time PCR and fluorescence in situ hybridization (FISH) were utilized to determine the expression patterns and their clinical significance. Functional experiments <i>in vitro</i> and <i>in vivo</i> were performed to explore whether hsa_circ_0071036 functions as an oncogenic circRNA in PDAC. Mechanistically, RT-qPCR, dual luciferase reporter and RNA pull-down assays were conducted to identify the interaction between hsa_circ_0071036 and miR-489 in PDAC. Hsa_circ_0071036 was remarkably overexpressed in PDAC cell lines and tissue samples, which negatively correlated with miR-489 expression. Aberrant expression of hsa_circ_0071036 correlated with poor clinicopathological characteristics and prognoses of PDAC patients. Knockdown of hsa_circ_0071036 suppressed proliferation and invasion and induced apoptosis <i>in vitro</i>. Moreover, the <i>in vivo</i> xenograft model confirmed that silencing of hsa_circ_0071036 attenuated tumor growth. Mechanistic analyses indicated that hsa_circ_0071036 acted as an efficient miRNA sponge for miR-489 in PDAC. In summary, our study revealed that upregulated hsa_circ_0071036 promotes PDAC pathogenesis and progression by directly sponging miR-489, which implies an important role for this circRNA-miRNA functional network.
DOI: 10.6084/m9.figshare.13699237
title: Nitric oxide attenuates microglia proliferation by sequentially facilitating calcium influx through TRPV2 channels, activating NFATC2, and increasing p21 transcription

description: Microglia proliferation is critical for proper development and function of the central nervous system (CNS), while dysregulation of proliferation contributes to pathology. We recently reported that male inducible nitric oxide synthase knockout (iNOS<sup>−/−</sup>) mice displayed significantly more proliferating microglia in their postnatal cortex than age-matched wildtype (WT) male mice. Moreover, nitric oxide (NO) signaling in mouse microglia greatly upregulates calcium entry through transient receptor potential vanilloid type 2 (TRPV2) channels. Considering that TRPV2 activity restricts astrocytic proliferation within glioma tissues, we investigated the roles of iNOS/NO signaling and TRPV2 expression in the regulation of microglial proliferation in vitro using assays of calcium imaging, immunocytochemistry, western blot, and polymerase chain reaction. Results showed that non-dividing microglia exhibited substantially higher expression of TRPV2 on the plasma membrane and significantly larger calcium influx through TRPV2 channels in comparison to dividing microglia. Additionally, non-dividing WT microglia exhibited significantly more NO production than dividing WT microglia. Furthermore, the NO-donor NOC18 increased the nuclear translocation of nuclear factor of activated T-cells cytoplasmic 2 (NFATC2) and the mRNA of the cyclin-dependent kinase inhibitor p21 and decreased the percentage of dividing WT and iNOS<sup>–/–</sup> microglia in culture. Importantly, the presence of the TRPV2 inhibitor tranilast abolished these effects of NOC18. Together, results from this study indicated that iNOS/NO signaling inhibits microglial proliferation through TRPV2-mediated calcium influx, nuclear translocation of the transcription factor NFATC2, and p21 expression. Proposed molecular mechanism by which NO-TRPV2 signaling regulates microglia proliferation <i>in vitro.</i> Proposed molecular mechanism by which NO-TRPV2 signaling regulates microglia proliferation <i>in vitro.</i>
DOI: 10.6084/m9.figshare.13656175.v1
title: Upregulated circRNA hsa_circ_0071036 promotes tumourigenesis of pancreatic cancer by sponging miR-489 and predicts unfavorable characteristics and prognosis

description: Circular RNAs (circRNAs), the new stars of endogenous non-coding RNAs, are dysregulated in various tumors including pancreatic cancer. Here, we aimed to investigate the biological functions of hsa_circ_0071036 in the tumourigenesis and progression of pancreatic ductal adenocarcinoma (PDAC) and its clinical implications. The differential expression profile of circRNAs in 4 pairs of PDAC tissues was analyzed by microarray assay. Quantitative real-time PCR and fluorescence in situ hybridization (FISH) were utilized to determine the expression patterns and their clinical significance. Functional experiments <i>in vitro</i> and <i>in vivo</i> were performed to explore whether hsa_circ_0071036 functions as an oncogenic circRNA in PDAC. Mechanistically, RT-qPCR, dual luciferase reporter and RNA pull-down assays were conducted to identify the interaction between hsa_circ_0071036 and miR-489 in PDAC. Hsa_circ_0071036 was remarkably overexpressed in PDAC cell lines and tissue samples, which negatively correlated with miR-489 expression. Aberrant expression of hsa_circ_0071036 correlated with poor clinicopathological characteristics and prognoses of PDAC patients. Knockdown of hsa_circ_0071036 suppressed proliferation and invasion and induced apoptosis <i>in vitro</i>. Moreover, the <i>in vivo</i> xenograft model confirmed that silencing of hsa_circ_0071036 attenuated tumor growth. Mechanistic analyses indicated that hsa_circ_0071036 acted as an efficient miRNA sponge for miR-489 in PDAC. In summary, our study revealed that upregulated hsa_circ_0071036 promotes PDAC pathogenesis and progression by directly sponging miR-489, which implies an important role for this circRNA-miRNA functional network.