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opencc-by-4.0Dec 2023View details →

Project Database and Environmental and Circularity Database containing information on Basajaun Façade System Modules

1. INTRODUCTION The Basajaun project aims to build a sustainable joint between rural and urban areas through circular and innovative wood construction value chains. Building façade was one of the innovations developed in Basajaun, which were implemented in digital and real scale demo buildings. The main innovation for the façade includes the implementation of  hybrid bio-based polymers and wood over three technological systems that incorporate increased use of wood-based components and a novel bio-composite material: the frame profiles, the insulation equipment, and the seal system. This implies the need to verify the reduction of environmental impact, including the calculation of its Embodied Carbon.   2. REPOSITORY The Project Database and Environmental and Circularity Database presented here serve as repositories of the specific information related to the Basajaun Façade System's life cycles (A1-A5) employed to assess its cradle-to-practical-completion Embodied Carbon. It can also be used to validate the digital Semantic Framework conceived for the facilitation of Façade Environmental Assessment beneath the project. The Project Database contains datasets with technical information on each façade module analysed. This should be regarded as a complete database for the Basajaun commission job, including (1, 2, and 3) the list of materials, components, and processes related to three different modules (Glazed Vision, Opaque, and Window modules); (4) the façade modules assembly off-site; (5) Information on transporting modules to the construction site; and (6) the construction activities related to Opaque and Window modules. The Environmental and Circularity Database is designed to be unique to the production plant and contains the four datasets. The first dataset (1) provides information on the environmental impact of each possible single material, component, or process related to the façade module's life cycle (e.g., carbon factors). Assembly off-site (2) and logistics (3) consumption and emissions data are stored separately in two different datasets. Finally, the dataset related to construction site options (4) contains data on all working activities related to the façade modules.  3. INSTALLATION All datasets are in .csv format with data separated by a ";".  Private data belonging to third parties or under copyright, which cannot be published, have been replaced with "omitted".

opengpl-3.0-or-laterFeb 2024View details →

Toy example for Decoil-viz - vizualization module for ecDNA reconstructions

This zenodo entry is a toy example for the Decoil-viz, the visualization module for ecDNA reconstructions generated by Decoil method. <ul> <li>Find Decoil-viz repository under <a href="https://github.com/madagiurgiu25/decoil-viz">https://github.com/madagiurgiu25/decoil-viz</a>.</li> <li>Learn how to reconstruct ecDNA structures using Decoil (<a href="https://github.com/madagiurgiu25/decoil-pre">https://github.com/madagiurgiu25/decoil-pre)</a></li> </ul> Please cite the paper: Giurgiu et al. 2024. Genome Research. "Reconstructing extrachromosomal DNA structural heterogeneity from long-read sequencing data using Decoil". <a href="https://genome.cshlp.org/content/early/2024/08/21/gr.279123.124">Doi: 10.1101/gr.279123.124</a>

Spring tropical cyclones modulate near-surface isotopic compositions of atmospheric water vapour at Kathmandu, Nepal

All these data have been published in a ACP paper. If you use these data in any conditions, please cite the following publicaiton: Adhikari, N., Gao, J., Zhao, A., Xu, T., Chen, M., Niu, X., and Yao, T.: Spring tropical cyclones modulate near-surface isotopic compositions of atmospheric water vapour at Kathmandu, Nepal, EGUsphere, https://doi.org/10.5194/egusphere-2023-2186, 2023.

Triarylamine modulation for hybrid perovskite photovoltaics

Structural, optoelectronic, photovoltaic, and supplementary characterization data for “Triarylamine modulation for hybrid perovskite photovoltaics”, DOI:10.1002/admi.202301053 Figure_2_XRD.opju: Data described in Figure 2 (XRD patterns) as Origin (.opju) software file. Figure_2_XPS.opju: Data described in Figure 2 (XPS spectra) as Origin (.opju) software file. Figure_2_UV-vis.opju: Data described in Figure 2 (UV-vis spectra) as Origin (.opju) software file. Figure_2_Tauc_plot.opju: Data described in Figure 2 (Tauc plot) as Origin (.opju) software file. Figure_3_PV.opju: Data described in Figure 3 (Photovoltaics metrics) as Origin (.opju) software file. Figure_4_TRPL.opju: Data described in Figure 4 (TRPL) as Origin (.opju) software files. Figure_4_PL_no_spiro.opju: Data described in Figure 4 (steady state PL) as Origin (.opju) software files Figure_4_PL_with_spiro.opju: Data described in Figure 4 (steady state PL with spiro-OMeTAD) as Origin (.opju) software files Figure_5_stability.opju: Data described in Figure 5 (operational stability) as Origin (.opju) software files. Figures_SI.zip: Data described in the Supporting Information Figures S2 (FTIR spectra data as Origin (.opju) software file); Figures S5a (JV curve for champion devices as Origin (.opju) software file); Figures S5b (IPCE as Origin (.opju) software file); Figures S6 (Supplementary photovoltaic metrics as Origin (.opju) software file).

opencc-by-4.0Oct 2022View details →

Data for "Stratospheric Downward Wave Reflection Events Modulate North American Weather Regimes and Cold Spells"

Wave reflection index and regimes time series for DJFM 1979/80 - 2020/21 as used in <a href="https://doi.org/10.5194/wcd-3-1215-2022" target="_blank" rel="noopener">Messori et al. (2022)</a> "Stratospheric Downward Wave Reflection Events Modulate North American Weather Regimes and Cold Spells", Weather and Climate Dynamics. This dataset has been updated following the publication of a corrigendum: <a href="https://doi.org/10.5194/wcd-3-1215-2022-corrigendum" target="_blank" rel="noopener">https://doi.org/10.5194/wcd-3-1215-2022-corrigendum</a>. The correction only applies to the reflection index (the regimes time series are unchanged).

opencc-zeroMar 2024View details →

Demography and environment modulate the effects of genetic diversity on extinction risk in a butterfly metapopulation

Linking genetic diversity to extinction is a common goal in genomic studies. Recently, a debate has arisen regarding the importance of genetic variation in conservation as some studies have failed to find associations between genome-wide genetic diversity and extinction risk. However, only rarely are genetic diversity and fitness measured together in the wild, and typically variation in demographic history or environment are ignored. It is therefore difficult to infer whether a lack of an association is real or obscured by confounding factors. To address these shortcomings, we analysed genetic data from 7,501 individuals with extinction data from 279 meadows and mortality of 1,742 larval nests in a butterfly metapopulation. We found strong negative associations between genetic diversity and extinction when heterozygosity was included alone in models. However, this association was no longer present when ecological covariates were included. Interactions between heterozygosity and demographic variables revealed that associations are context-dependent or only detectable when confounding factors are controlled. For example, extinction declined with increasing heterozygosity in large but not currently small populations, although negative associations between heterozygosity, extinction, and mortality were detected in populations with a recent history of decline. We conclude that low genetic diversity is an important predictor of extinction, predicting >25% increase in extinction beyond ecological factors in certain contexts. This highlights that inferences about the importance of genetic diversity should not rely on genomic data alone but requires investments in obtaining demographic and environmental data from natural populations to jointly assess their impact on population extinction risk.

opencc-zeroMar 2024View details →

Data from: Redox state of NAD modulates the activation of Na-bicarbonate cotransporter NBCe1-B by IRBIT and L-IRBIT

NAD is known as a coenzyme for many enzymes catalyzing redox reactions or as a substrate for enzymes for second messenger cADP-ribose generation or protein deacetylation. IRBIT and L-IRBIT are structurally conserved with dehydrogenases but lacking catalytic activity. By protein interaction, the IRBITs instead modulate many proteins of fundamental biological importance. Among these is the Na+-HCO3− cotransporter NBCe1-B, which plays a central role in intracellular pH (pHi) regulation and epithelial electrolyte transport. Here, we demonstrate that NAD modulates NBCe1-B activation by serving as a cofactor of the IRBITs. Blocking NAD salvage pathway decreases NBCe1-B activation by the IRBITs. NAD+ administration enhances, whereas NADH decreases NBCe1-B activity. Our study reveals a new role of NAD and greatly expands our appreciation of NAD biology. Because NAD redox state fluctuates greatly with metabolic status, our work provides insight into how, via IRBITs, energy metabolism could affect pHi regulation and many other IRBIT-dependent processes.

opencc-zeroMar 2024View details →

Dataset for research paper entitled Adaptive Phase or Variant Formation at the Austenite/Twinned Martensite Interface in Modulated Ni–Mn–Ga Martensite

The dataset contains the experimental result concerning in-situ synchrotron and SEM/EBSD measurements as a function of temperature. The list of files is listed below: The dataset is composed of both the raw and processed data: X-ray phase analysis - performed with a synchrotron radiation energy 87.1 KeV. <ul> <li>Origin file 1 - Diffraction experiments made on NiMnGa single crystals below and above Ms temperature</li> <li>2D Diffraction pattern for 10M 10M’ Mt, and A structures.</li> </ul> TEM experiments - Microstructural observations were carried out by ThermoFisher Scientific TitanThemis Cs corrected 200 kV scanning /transmission electron microscope (S/TEM) equipped with SuperX <a title="Learn more about EDX from ScienceDirect's AI-generated Topic Pages" href="https://www.sciencedirect.com/topics/materials-science/energy-dispersive-x-ray-spectroscopy">EDX</a> detector system. Thin foil for analysis was prepared by TEM observations were prepared with a TenuPol-5 double jet electropolisher using an electrolyte of nitric acid (70%) and methanol (30%) at -25 °C. ·      File 1 set of HRTEM images showing modulation boundaries ·      File 2 set of HRTEM images showing a/b boundaries SEM/EBSD - FEI Quanta 3D FEG SEM equipped with a TSL system and a Murano heating stage. To analyze the lattice parameter changes, a crystallographic analysis of lattice metric (CALM) was used. This method does not need a standard for indexing or lattice constant determination. The lattice metric (lattice parameters) was derived through the reconstruction of the experimental EBSD pattern. In the first step, centers of Kikuchi band traces were detected from the EBSD diffraction pattern. Then, using information about the diffraction projection center, 20 to 100 independent reflectors were reconstructed in the reciprocal space. The final step involves a search for primitive lattice vectors which are fulfilling translational symmetry conditions for all reflectors. Reconstructed vectors are recomputed to the higher symmetry lattices with a relative error lower than 0.1%Thermogravimetric curves obtained for the decomposition of powder after synthesis at 500 rpm. <ul> <li>Origin file 2 Relation between a/c lattice parameters</li> <li>Origin file 3 Relation between a/c lattice parameters</li> <li>SEM/BSE pictures showing austenite twinned/martensite interface</li> <li>Video 1 shows in-situ SEM/BSE with martensitic transformation and one planar austenite/twinned martensite interface during cooling</li> <li>Video 2 shows set of Kikuchi pattern across Austenite martensite phase indicating elastic nature of the martensitic transformation</li> </ul>

Researcher interview Jennifer Veitch on Temporal Light Modulation, MetTLM 20NRM01

In this researcher interview on the effect called temporal light modulation or TLM with Jennifer Veitch, we delve into how it affects humans, how it arose in lighting, disappeared and then reappeared, the difficulties of researching a subject that involves experts from many fields and many other aspects. The video was produced by the EMPIR project MetTLM 20NRM01, for more information on the project see the webpage http://mettlm.eu/ MetTLM 20NRM01 has received funding from the EMPIR programme co-financed by the Participating States and from the European Union's Horizon 2020 research and innovation programme. Disclaimer: Any opinions, findings, and conclusion or recommendations expressed in this material are those of the participants and do not necessarily reflect the views of the MetTLM consortium.

opencc-zeroApr 2024View details →

Data for: A novel and ubiquitous miRNA-involved regulatory module ensures precise phosphorylation of RNA polymerase II and proper transcription

Proper transcription orchestrated by RNA polymerase II (RNPII) is crucial for cellular development, which relies on the phosphorylation state of RNPII's carboxyl-terminal domain (CTD). Sporangia, developed from mycelia, are essential for the destructive oomycetes Phytophthora, remarkable transcriptional changes are observed during the morphological transition. However, how these changes are rapidly triggered and their relationship with the versatile RNPII-CTD phosphorylation remain enigmatic. Herein, we found that Phytophthora capsici had undergone an elevation of Ser5-phosphorylation in its uncanonical heptapeptide repeats of RNPII-CTD during sporangia development, which subsequently changed the chromosomal occupation of RNPII and primarily activated transcription of certain genes. A cyclin-dependent kinase, PcCDK7, was highly induced and phosphorylated RNPII-CTD during this morphological transition. Mechanistically, a novel DCL1-dependent microRNA, pcamiR1, was found to be a feedback modulator for the precise phosphorylation of RNPII-CTD by complexing with PcAGO1 and regulating the accumulation of PcCDK7. Moreover, this study revealed that the pcamiR1-CDK7-RNPII regulatory module is evolutionarily conserved and the impairment of the balance between pcamiR1 and PcCDK7 could efficiently reduce the growth and virulence of P. capsici. Collectively, this study uncovers a novel and evolutionarily conserved mechanism of transcription regulation that could facilitate correct development and identifies pcamiR1 as a promising target for disease control.

restrictedcc-by-4.0Apr 2024View details →

Data from: Chemotherapy Modulation by a Cancer-Associated Microbiota Metabolite

Data from the manuscript:  Chemotherapy Modulation by a Cancer-Associated Microbiota Metabolite Summary - Revealed once accepted The data in this repository covers the following datasets: <ul> <li>4-way screening of BW, pyrE and the triple mutant (TM) -> 4_way.csv files</li> <li>RNA-seq raw and normalised counts (from salmon), with their metadata -> files starting with RNAseq</li> <li>Proteomics data from Perseus</li> <li>Biolog metabolites for PM plates PM-PM11 to PM14 with a curated classification of their targets, molecule types and processes -> biolog_metabolites_cancer.xlsx</li> <li>Drug (Biolog and DrugBank) fingerprints -> Drug_FP.xlsx</li> </ul>

opencc-zeroApr 2024View details →

Cholecystokinin facilitates motor skill learning by modulating neuroplasticity in the motor cortex

Cholecystokinin (CCK) is an essential modulator for neuroplasticity in sensory and emotional domains. Here, we investigated the role of CCK in motor learning using a single pellet reaching task in mice. Mice with a knockout of cck gene (CCK-/-) or blockade of CCK-B receptor (CCKBR) showed defective motor learning ability; the success rate of retrieving reward remained at the baseline level compared to the wildtype mice with significantly increased success rate. We observed no long-term potentiation (LTP) upon high-frequency stimulation (HFS) in the motor cortex of CCK-/- mice, indicating a possible association between motor learning deficiency and neuronal plasticity in the motor cortex. In vivo calcium imaging demonstrated that the deficiency of CCK signalling disrupted the refinement of population neuronal activity in the motor cortex during motor skill training. Anatomical tracing revealed direct projections from CCK-expressing neurons in the rhinal cortex to the motor cortex. Inactivating the CCK neurons in the rhinal cortex using chemogenetic methods significantly suppressed motor learning, and intraperitoneal application of CCK4, a tetrapeptide CCK agonist, rescued the motor learning deficits of CCK-/- mice. In summary, our results suggest that CCK, which could be provided from the rhinal cortex, enables neuroplasticity in the motor cortex leading to motor skill learning.

opencc-zeroApr 2024View details →

Data from: Major group-B enterovirus populations deleted in the noncoding 5' region of genomic RNA modulate activation of the type I interferon pathway in cardiomyocytes and induce myocarditis

Major 5'-terminally deleted (5'TD) RNA forms of group-B coxsackievirus (CVB-5'TD) has been associated with myocarditis in both mice and humans. Although it is known that interferon-β (IFN-β) signaling is critical for an efficient innate immune response against CVB-induced myocarditis, the link between CVB-5'TD RNA forms and type I IFN signaling in cardiomyocytes remains to be explored. In a mouse model of CVB3/28-induced myocarditis, major early-emerging forms of CVB-5'TD RNA have been characterized as replicative viral populations that impair IFN-β production in the heart. Synthetic CVB3/28 RNA forms mimicking each of these major 5'TD virus populations were transfected in mice and have been shown to modulate innate immune responses in the heart and to induce myocarditis in mice. Remarkably, transfection of synthetic viral RNA with deletions in the secondary structures of the 5'-terminal CVB3 RNA domain I, modifying stem-loops "b", "c" or "d", were found to impair IFN-β production in human cardiomyocytes. In addition, the activation of innate immune response by Poly(I:C), was found to restore IFN-β production and to reduce the burden of CVB-5'TD RNA-forms in cardiac tissues, thereby reducing the mortality rate of infected mice. Overall, our results indicate that major early-emerging CVB3 populations deleted in the domain I of genomic RNA, in the 5' noncoding region, modulate the activation of the type I IFN pathway in cardiomyocytes and induce myocarditis in mice. These findings shed new light on the role of replicative CVB-5'TD RNA forms as key pathophysiological factors in CVB-induced human myocarditis.

opencc-by-4.0Sep 2024View details →

Rapid modulation of striatal cholinergic interneurons and dopamine release by satellite astrocytes

<h3>ABSTRACT</h3> Astrocytes are increasingly thought to possess underestimated and important roles in modulating neuronal circuits. Astrocytes in striatum can regulate dopamine transmission by governing the extracellular tone of axonal neuromodulators, including GABA and adenosine. However, here we reveal that striatal astrocytes occupy a cell type-specific anatomical and functional relationship with cholinergic interneurons (ChIs), through which they rapidly excite ChIs and govern dopamine release via nicotinic acetylcholine receptors on subsecond timescales. We identify that ChI somata are in unexpectedly close proximity to astrocyte somata, in mouse and human, forming a “soma-to-soma” satellite-like configuration not typically observed for other striatal neurons. Transient depolarization of astrocytes in mouse striatum reversibly regulated ChI excitability by decreasing extracellular calcium. These findings reveal a privileged satellite astrocyte-interneuron interaction for striatal ChIs operating on subsecond timescales via regulation of extracellular calcium dynamics to shape downstream striatal circuit activity and dopamine signaling.   <h3>FILE DESCRIPTIONS</h3> This repository contains the following files: <ul> <li>Key Resources Table (.xlsx) - Table containing details on key resources (antibodies, mouse lines, virus strains, software, equipment, and reagents), and the persistent identifiers for protocols and code used and generated in this study. </li> <li>Source Data Folder (.zip): <ul> <li>_README_Source_Data (.txt) with detailed information about each dataset.</li> <li>Individual tabular datasets corresponding to each panel shown in the Main Figures 1 to 5 (.csv).</li> <li>Excel spreadsheet containing all tabular datasets plotted in Main Figures 1 to 5 (.xlsx)</li> </ul> </li> <li>Supplementary Data Folder (.zip): <ul> <li>_README_Supplementary_Data (.txt) with detailed information about each dataset.</li> <li>Individual tabular datasets corresponding to each panel shown in the Supplementary Figures 1-9, 11-14 (.csv).</li> <li>Excel spreadsheet containing all tabular datasets plotted in Supplementary Figures 1-9, 11-14 (.xlsx)</li> </ul> </li> </ul>

opencc-by-4.0May 2024View details →

Semantic audio-visual congruence modulates visual sensitivity to biological motion across awareness levels

This repository contains all experimental scripts, analysis and data files for the manuscript "Semantic audio-visual congruence modulates visual sensitivity to biological motion across awareness levels".

Test models and test results to evaluate CAD assembly modules capabilities to generate component interfaces

Set of 3D CAD assembly models in STEP AP 203 format. Assembly test models are devoted to evaluations of interfaces between components. The interfaces can be of type surface, rectilinear contacts, circular contacts, or point contacts. Test results obtained from some commercially available CAD assembly modules are given as a set of tables organized in accordancce with contact categories (surface, rectilinear, circular, point). The content and use of the test models are described into the pdf document: Test models and test results to evaluate CAD assembly modules capabilities to generate component interfaces.

opencc-zeroNov 2021View details →

Out from under the wing: reconceptualizing the insect wing gene regulatory network as a versatile, general module for body-wall lobes in arthropods

Body plan evolution often occurs through the differentiation of serially homologous body parts, particularly in the evolution of arthropod body plans. Recently, homeotic transformations resulting from experimental manipulation of gene expression have been interpreted as evidence that portions of dorsal and lateral arthropod body-wall are serially homologous to wings. These results, along with comparative data on the expression and function of genes in the wing regulatory network, provided a new perspective on an old question in insect evolution—how did the insect wing, evolve? A proposed ancestral role for the wing regulatory network in patterning body-wall margins motivated a broader comparison of gene function in wings and body-wall. We investigated the roles of a suite of ten wing- and body-wall related genes in a hemimetabolous insect, Oncopeltus fasciatus. Our results indicate that genes involved in wing development in O. fasciatus play similar roles in the development of adult body-wall flattened cuticular evaginations. We found extensive functional similarity between the development of wings and other bilayered evaginations of the body wall. Overall, our results support the existence of a versatile development module for building bilayered cuticular epithelial structures, which may have played a central role in the evolution of wings.

openother-openAug 2021View details →

Data and Codes used in Alonso-Crespo et al (2021) Assembly history modulates vertical root distribution in a grassland experiment.

This repository contains the raw data, the RootPainter model and the annotated R and Python codes supporting the results reported in the following paper: Alonso-Crespo et al (2021) Assembly history modulates vertical root distribution in a grassland experiment.

opencc-by-nc-sa-2.0Jul 2021View details →

Raw data and scripts for "The Period-Modulated Harmonic Locked Loop (PM-HLL): A low-effort algorithm for rapid time-domain multi-periodicity estimation"

This package contains all required scripts to generate the simulations and figures from the study "The Period-Modulated Harmonic Locked Loop (PM-HLL): A low-effort algorithm for rapid time-domain multi-periodicity estimation" by Volker Hohmann, published in Acta Acustica: The Period-Modulated Harmonic Locked Loop (PM-HLL): A low-effort algorithm for rapid time-domain multi-periodicity estimation Volker  Hohmann Acta Acust. 5 56 (2021) DOI: 10.1051/aacus/2021050 When referring to this work, please cite the journal paper. Note that additive noise is generated at random, i.e., small differences in the estimation accuracy occur when repeating a simulation. For further details see the journal paper. Thank you for downloading the package. Your comments are very welcome! Method patented: DE Patent DE102021207339B3 Author: Volker Hohmann, Carl von Ossietzky Universität Oldenburg, Germany