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Experimental raw data sets associated with certified reference material BAM-P116 (titanium dioxide) for comparison of nitrogen and argon sorption, available in the universal adsorption information format (AIF)

These data sets serve as models for calculating the specific surface area (BET method) using gas sorption in accordance with ISO 9277. The present measurements were carried out with nitrogen at 77 Kelvin and argon at 87 Kelvin. It is recommended to use the following requirements for the molecular cross-sectional area: Nitrogen: 0.1620 nm² Argon: 0.1420 nm² Expected specific surface area for nitrogen (BET): 305 to 345 m²/g Expected specific surface area for argon (BET): 300 to 310 m²/g Titanium dioxides certified with nitrogen sorption and additionally measured with argon for research purposes were used as sample material. The resulting data sets are intended to serve as comparative data for own measurements and show the differences in sorption behaviour and evaluations between nitrogen and argon. These data are stored in the universal AIF format (adsorption information format), which allows flexible use of the data.

Gene prioritization scores and drug target information

This data folder accompanies the article Sadler MC, Auwerx C, Deelen P, Kutalik Z. Multi-layered genetic approaches to identify approved drug targets. Cell Genomics 3, no. 7 (July 2023): 100341(https://doi.org/10.1016/j.xgen.2023.100341).It contains disease-drug-target links as well as gene prioritisation scores of all the assessed methods.

Data and Scripts for Publication: Information Bottleneck in Peptide Conformation Determination by X-ray Absorption Spectroscopy

Data and scripts for the publication titled Information Bottleneck in Peptide Conformation Determination by X-ray Absorption Spectroscopy. Article available at <a href="https://doi.org/10.1088/2399-6528/ad1f73">10.1088/2399-6528/ad1f73</a>

openmit-licenseDec 2023View details →

Pathformer: a biological pathway informed Transformer for disease diagnosis and prognosis using multi-omics data

Integrating multi-omics data offers a more comprehensive view of gene regulation, which would be helpful in achieving accurate diagnosis of diseases like cancer. To improve the accuracy of disease diagnosis and prognosis, we developed Pathformer, a multi-omics integration method for both tissue and liquid biopsy data. We implemented Pathformer's network architecture using the “PyTorch” package in Python v3.6.9, and our codes can be found in the GitHub repository (https://github.com/lulab/Pathformer). This repository contains preprocessed TCGA dataset data, preprocessedliquid biopsy dataset data, result of Pathformer and comparison_methods, mentioned in GitHub project and article.

opencc-zeroJan 2024View details →

Detection of ghost introgression requires exploiting topological and branch length information

In recent years, the study of hybridization and introgression has made significant progress, with ghost introgression—the transfer of genetic material from extinct or unsampled lineages to extant species—emerging as a key area for research. Accurately identifying ghost introgression, however, presents a challenge. To address this issue, we focused on simple cases involving three species with a known phylogenetic tree. Using mathematical analyses and simulations, we evaluated the performance of popular phylogenetic methods, including HyDe and PhyloNet/MPL, and the full-likelihood method, Bayesian Phylogenetics and Phylogeography (BPP), in detecting ghost introgression. Our findings suggest that heuristic approaches relying on site-pattern counts or gene-tree topologies struggle to differentiate ghost introgression from introgression between sampled non-sister species, frequently leading to incorrect identification of donor and recipient species. The full-likelihood method BPP using multilocus sequence alignments directly—hence taking into account both gene-tree topologies and branch lengths, by contrast, is capable of detecting ghost introgression in phylogenomic datasets. We analyzed a real-world phylogenomic dataset of 14 species of Jaltomata (Solanaceae) to showcase the potential of full-likelihood methods for accurate inference of introgression.

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".

opencc-by-4.0Nov 2023View details →

Exploring the Automatic Classification of Usage Information in Feedback

Datasets and list of relevant papers for the publication "Exploring the Automatic Classification of Usage Information in Feedback".Please read the included readMe for more information on formatting of Json-Files

opencc-by-4.0Jan 2024View details →

Data and Figures for "Glacier Terminus Morphology Informs Calving Style"

Data and figures for the submitted study "Glacier Terminus Morphology Informs Calving Style" (Pending review at GRL).   Folders correspond to directories in notebooks provided on https://github.com/sgoliber/TerminusMorpho.   The folder "figures" provides the figures in the manuscript. The folder "data" provides both primary and derived data for the study. Original<a href="https://www.pgc.umn.edu/guides/stereo-derived-elevation-models/pgc-dem-products-arcticdem-rema-and-earthdem/"> PGC DEMs</a> are not provided here due to size restriction, but can be downloaded directly from PGC. Please contact the author if you need the original files.

opencc-zeroJan 2024View details →

Supporting information for: Discrimination ability of central visual field testing using stimulus size I, II, and III and relationship with macular ganglion cell thickness in chiasmal compression

Purpose: To compare the relationship between macular ganglion cell layer (mGCL) thickness and 10-2 visual field (VF) sensitivity using different stimulus sizes in patients with temporal hemianopia from chiasmal compression. Methods: A cross-sectional study was conducted involving 30 eyes from 25 patients with temporal VF loss on 24-2 SITA standard automated perimetry due to previous chiasmal compression and 30 healthy eyes (23 controls). Optical coherence tomography (OCT) of the macular area and 10-2 VF testing using Goldmann stimulus size I (GI), II (GII), and III (GIII) were performed in the Octopus 900 perimeter. For the sake of analysis, mGCL thickness and VF data were segregated into four quadrants (two temporal and two nasal) and two halves (temporal and nasal) centered on the fovea, and the groups were compared using generalized estimated equations. The discrimination ability of GI, GII, and GIII was evaluated, as was the correlation between mGCL and 10-2 VF sensitivity using GI, GII, and GIII. Results: All mGCL parameters were significantly reduced in patients compared to controls. 10-2 VF test sensitivity using GI, GII, and GIII was significantly lower in patients than in controls (p≤0.008) for all parameters, except the three nasal divisions when using GI (p=0.41, 0.07 and 0.18) Significant correlations were found between temporal VF sectors (all stimulus sizes) and the corresponding nasal mGCL measurements, with similar discrimination ability. Significant correlations were also observed between all three nasal VF divisions and the corresponding temporal mGCL thickness when using stimulus sizes I and II, but not stimulus size III. Conclusions: On 10-2 VF testing, GII outperformed GI and GIII with regard to discrimination ability and structure-function correlation with mGCL thickness in chiasmal compression. Our findings suggest that the use of GII can enhance the diagnostic power of 10-2 VF testing, although further studies are necessary to support this conclusion.

opencc-by-4.0Nov 2023View details →

Supplementary information: Specific versus Nonspecific Solvent Interactions of a Biomolecule in Water [Dataset]

Data availability to the manuscript "Specific versus Nonspecific Solvent Interactions of a Biomolecule in Water" by Lanhai He, Luká&scaron; Tomaník, Sebastian Malerz, Florian Trinter, Sebastian Trippel, Michal Belina, Petr Slavíček, Bernd Winter, and Jochen Küpper, pubulished at JPCL  The dataset contains the complete x-ray photoelectron-emission spectra of indoleaq in a liquid microjet. The uploaded files include: <ul> <li>Valence band PES data (<a href="../api/files/eec96d6e-1972-463a-bc54-ee320bb2280e/May02_0053VB.ibw">May02_0053VB.ibw</a>, <a href="../api/files/eec96d6e-1972-463a-bc54-ee320bb2280e/May02_0058VB_background.ibw">May02_0058VB_background.ibw</a>),</li> <li>core level PES data (<a href="../api/files/eec96d6e-1972-463a-bc54-ee320bb2280e/May02_0045C1s.ibw">May02_0045C1s.ibw</a>, <a href="../api/files/eec96d6e-1972-463a-bc54-ee320bb2280e/May02_0049N1s.ibw">May02_0049N1s.ibw</a>),</li> <li>Auger PES  pectra (<a href="../api/files/eec96d6e-1972-463a-bc54-ee320bb2280e/May02_0052CAuger.ibw">May02_0052CAuger.ibw</a>, <a href="../api/files/eec96d6e-1972-463a-bc54-ee320bb2280e/May02_0057CAuger.ibw">May02_0057CAuger.ibw</a>, <a href="../api/files/eec96d6e-1972-463a-bc54-ee320bb2280e/May02_0056NAuger.ibw">May02_0056NAuger.ibw</a>)</li> <li>rough-scanned full spectra (<a href="../api/files/eec96d6e-1972-463a-bc54-ee320bb2280e/May02_0046Full.ibw">May02_0046Full.ibw</a>, <a href="../api/files/eec96d6e-1972-463a-bc54-ee320bb2280e/May02_0047Full.ibw">May02_0047Full.ibw</a>).</li> </ul> In addition, a python script (Read_ibw_file.py) has been uploaded, which can be used to read raw PES data files in .ibw format and export the intergraded PES data as a .txt file.

Data for: Information accessibility, accounting manipulation, and sustainable development of digital enterprises: Based on double moderating effect model and panel PSM-DID method

A theoretical mechanism was analyzed from the micro perspective of the enterprise to explore how information accessibility moderates the effect of accounting manipulation on the sustainable development of digital enterprises. Using data from 1200 listing digital enterprises in China and the DEA-Malmquist index method, the efficiency value of digital enterprises in 2007–2021 was estimated to represent the index of sustainable development of digital enterprises. The accounting manipulation was detected using the panel PSM-DID method based on the Administrative Measures for the Recognition of High-tech Enterprise's policy. The information accessibility value was estimated based on the MDA method. Empirical studies were conducted using text analysis, the panel PSM-DID method, and the double moderating effect model. The results showed that: (1) Accounting manipulation had a negative impact on the sustainable development of "true" digital enterprises and the "fake" digital enterprises; (2) Information accessibility directly and positively enhanced the technological progress and scale efficiency of digital enterprises, and its moderating effect was heterogeneous, with a significant moderating effect on the "true" digital enterprises and a negative effect on the "fake" ones.

Data from: Lineage diversity within a widespread endemic Australian skink to better inform conservation in response to regional-scale disturbance

This dataset was used to examine the phylogeographic genetic structure of Eastern three lined skink Bassiana duperreyi. It comprises SNP data used for population genetics and phylogenetic reconstruction. The data were used to provide foundational work for the detailed taxonomic re-evaluation of this species complex and to reinforce the need for biodiversity assessment to include an examination of cryptic species and/or cryptic diversity below the level of species. Such information on lineage diversity within species and its distribution in the context of disturbance at a regional scale can be factored into conservation planning regardless of whether a decision is made to formally diagnose new species taxonomically and nomenclaturally.

opencc-by-4.0Mar 2022View details →

Supporting information for "Automated ChIPmentation procedure on limited biological material of the human blood fluke Schistosoma mansoni"

<ul> <li>Files “CG_Ro_1_High Sensitivity DNA Assay_DE13805677_2019-06-20_09-10-48.pdf” and “CG_Ro_2_High Sensitivity DNA Assay_DE13805677_2019-06-20_10-12-12.pdf” uncropped files used in figure 2</li> <li>File “gel qpcr test input sds_01.tif” : uncropped file used in figure 8.</li> <li>File "20200612-1_Report.pdf" : qPCR report for inputs 1µL and available chromatine ("Row7"), figure 6 </li> <li>File "20200919-1_Report.pdf" : qPCR report for for testing SDS after Tn5, figure 7B and figure 8</li> <li>File "20200921-1_Report.pdf" : qPCR report for for comparing inputs with enzyme of Diagenode kit and our protocol with other enzyme Tn5 </li> <li>File "wilcoxon_curves.tgz" contains compressed versions of R-script "wilcoxon_curves.Rmd" that was used to compared metagene profiles and generate "wilcoxon_curves.html" and underlying ressources that are also in this compressed archive</li> </ul> Produced at IHPE (http://ihpe.univ-perp.fr)

Supplementary information for: The artefactual branch effect and phylogenetic conflict: Species delimitation with gene flow in mangrove pit vipers (Trimeresurus purpureomaculatus-erythrurus complex)

Mangrove pit vipers of the Trimeresurus purpureomaculatus-erythrurus complex are the only species of viper known to naturally inhabit mangroves. Despite serving integral ecological functions in mangrove ecosystems, the evolutionary history, distribution, and species boundaries of mangrove pit vipers remain poorly understood, partly due to overlapping distributions, confusing phenotypic variations, and the lack of focused studies. Here, we present the first genomic study on mangrove pit vipers and introduce a robust hypothesis-driven species delimitation framework that considers gene flow and phylogenetic uncertainty in conjunction with a novel application of a new class of speciation-based delimitation model implemented through the program Delineate. Our results showed that gene flow produced phylogenetic conflict in our focal species and substantiated the artefactual branch effect where highly admixed populations appear as divergent nonmonophyletic lineages arranged in a stepwise manner at the basal position of clades. Despite the confounding effects of gene flow, we were able to obtain unequivocal support for the recognition of a new species based on the intersection and congruence of multiple lines of evidence. This study demonstrates that an integrative hypothesis-driven approach predicated on the consideration of multiple plausible evolutionary histories, population structure/ differentiation, gene flow, and the implementation of a speciation-based delimitation model can effectively delimit species in the presence of gene flow and phylogenetic conflict.

Integration of genomic and ecologic methods inform management of an undescribed, yet highly exploited, sardine species

Assessing genetic diversity within species is key for conservation strategies in the context of human-induced biotic changes. This is important in marine systems where many species remain undescribed while being overfished, and conflicts between resource-users and conservation agencies are common. Combining niche modelling with population genomics can contribute to resolving those conflicts by identifying management units and understanding how past climatic cycles resulted in current patterns of genetic diversity. We addressed these issues on an undescribed but already overexploited species of sardine of the genus Harengula. We find that the species distribution is determined by salinity and depth, with a continuous distribution along the Brazilian mainland and two disconnected oceanic archipelagos. Genomic data indicates that such biogeographic barriers are associated with two divergent intraspecific lineages. Changes in habitat availability during the last glacial cycle led to different demographic histories among stocks. One coastal population experienced a 3.6-fold expansion, whereas an island-associated population contracted 3-fold, relative to the size of the ancestral population. Our results indicate that the island population should be managed separately from the coastal population, and that a Marine Protected Area covering part of the island population distribution can support the viability of this lineage.

Supplemental information for: Inhibition of CSF1R and KIT with pexidartinib reduces inflammatory signaling and cell viability in endometriosis

Endometriosis is a common and debilitating disease, affecting ~170 million women worldwide. Affected patients have limited therapeutic options such as hormonal suppression or surgical excision of the lesions, though therapies are often not completely curative. Targeting receptor tyrosine-kinases (RTKs) could provide a nonhormonal treatment option for endometriosis. We determined that two RTKs, Macrophage colony stimulating factor receptor (CSF1R) and Mast/stem cell growth factor receptor KIT (KIT), are overexpressed in endometriotic lesions and could be novel nonhormonal therapeutic targets for endometriosis. The kinase activity of CSF1R and KIT is suppressed by pexidartinib, a small molecule inhibitor that was recently approved by the US Food and Drug Administration (FDA). Using immunohistochemistry, we detected CSF1R and KIT in endometriotic tissues obtained from peritoneal lesions, colorectal lesions, and endometriomas. Specifically, we show that KIT is localized to the epithelium of the lesions, while CSF1R is expressed in the stroma and macrophages of the endometriotic lesions. Given the high epithelial expression of CSF1R and KIT, 12Z endometriotic epithelial cells were used to evaluate the efficacy of dual CSF1R and KIT inhibition with pexidartinib. We found that pexidartinib suppressed activation in 12Z cells of JNK, STAT3 and AKT signaling pathways, which control key pro-inflammatory and survival networks within the cell. Using quantitative real time PCR, we determined that pexidartinib suppressed interleukin 8 (IL8) and cyclin D1 (CCND1) expression. Lastly, we demonstrated that pexidartinib decreased cell growth and viability. Overall, these results indicate that pexidartinib-mediated CSF1R and KIT inhibition reduces pro-inflammatory signaling and cell viability in endometriosis.

opencc-by-4.0Feb 2024View details →

Dataset of 'Physics-informed neural networks for high-resolution weather reconstruction from sparse weather stations'

Dataset of the article 'Physics-informed neural networks for high-resolution weather reconstruction from sparse weather stations', recently published in Open Research Europe (DOI 10.12688/openreseurope.17388.1). The code which implements the physics-informed neural network can be found at https://github.com/AlvaroMS90/PINNs-for-high-resolution-weather-reconstruction-from-sparse-weather-stations. Funded by the European Union under action HORIZON TMA MSCA Postdoctoral Fellowships - European Fellowships, call HORIZON-MSCA-2021-PF-01 (project number 101059984 with acronym PERSEVERE). Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union. Neither the European Union nor the granting authority can be held responsible for them. <pre> </pre>

opencc-by-4.0Nov 2023View details →

Formalized information from the study protocols of three decentralized studies on rare diseases within the CORD project

The file contains formalized information from the study protocols of decentralized studies on rare diseases within the CORD project. This includes the diagnoses that are coded with ICD-10-GM. The following diseases or use cases are described:<ul><li>Cystic Fibrosis and Pregnancy or Delivery</li><li>Phenylketonuria, Comorbidities and Pregnancy or Delivery</li><li>Kawasaki and Pediatric Inflammatory Multisystem Syndrome (PIMS)</li></ul>

opencc-zeroMar 2024View details →

Male dingo urinary scents code for age class and wild dingoes respond to this information

Chemical information in canid urine has been implicated in territoriality and influences the spacing of individuals. We identified the key volatile organic compound (VOC) components in dingo (Canis lupus dingo) urine and investigated the potential role of scents in territorial spacing. VOC analysis, using headspace gas chromatography-mass spectrometry (GC-MS), demonstrated that the information in fresh urine from adult male dingoes was sufficient to allow statistical classification into age categories. Discriminant function analyses demonstrated that the relative amounts or combinations of key VOCs from pre-prime (3-4 years), prime (5-9 years), and post-prime (≥10 years) males varied between these age categories, and that scents exposed to the environment for 4 (but not 33) days could still be classified to age categories. Further, a field experiment showed that dingoes spent less time in the vicinity of prime male dingo scents than other scents. Collectively, these results indicate that age-related scent differences may be discriminable by dingoes. Previous authors have suggested the potential to use scent as a management tool for wild canids by creating an artificial territorial boundary/barrier. Our results suggest that identifying the specific signals in prime-age male scents could facilitate the development of scent-based tools for non-lethal management.