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Fig. 5 in Formation Factors Of Cytogenetic Violation Of Rutilus Rutilus (Cypriniformes, Cyprinidae) In Transformed River Ecosystems

Fig. 5. Distribution of revealed nucleus structural breaking down in R. rutilus individuals of different age: (1+) — one-year-old; (2+) — two-year-old; (3+) –three-year-old; (4+) — four-year-old.

Fig. 1 in Formation Factors Of Cytogenetic Violation Of Rutilus Rutilus (Cypriniformes, Cyprinidae) In Transformed River Ecosystems

Fig. 1. Possible versions of micronuclei and nuclear material in erythrocytes of peripheral fish blood: a — micronuclei of "standart" type; b — "attached"; c — "linked to the nucleus with chromatine thread"; d-I — nonformed nuclear material shaped as small sticks; d-II — non-formed nuclear material in the form of clews; e — rounded formations of nuclear material of big enough sizes.

Fig. 4 in Formation Factors Of Cytogenetic Violation Of Rutilus Rutilus (Cypriniformes, Cyprinidae) In Transformed River Ecosystems

Fig. 4. Distribution of revealed structural breaking down of nucleus in R. rutilus selections from representative alignments of transformed river hydrosystems in the north-western region of Ukraine.

Fig. 2 in Formation Factors Of Cytogenetic Violation Of Rutilus Rutilus (Cypriniformes, Cyprinidae) In Transformed River Ecosystems

Fig. 2. Frequency of nuclear violations of R. rutilus peripheral blood erythrocytes in representative alignments of river hydrosystems in the north-western region of Ukraine.

opencc-by-4.0Nov 2019View details →

Fig. 5 in Histological Changes In Common Toad, Bufo Bufo (Anura, Bufonidae), Liver Tissue Under Conditions Of Anthropogenically Transformed Ecosystems

Fig. 5. Manifestation of protein dystrophy and hyper- Fig. 6. Abnormally big melano-macrophagal aggrepigmentation in common toad liver tissue. Hematox- gation surrounded by lymphoid infiltrate (inflammayline-eosine staining, ×200. tion) and hyperpigmentation in common toad's liver

Fig. 3 in Morphofunctional Adaption Of The Renal Tissue Of Acipenser Ruthenus (Actinopterygii, Acipenseriformes) Under Transformed Habitation Conditions

Fig. 3. Degenerative changes in the renal corpuscles of the sterlet's mesonephros. Ehrlich's hematoxylin, Hart's fuchselin. ×100.

Fig. 4 in Morphofunctional Adaption Of The Renal Tissue Of Acipenser Ruthenus (Actinopterygii, Acipenseriformes) Under Transformed Habitation Conditions

Fig. 4. Necrosis of the renal corpuscle of the sterlet's mesonephros. Ehrlich's hematoxylin, Hart's fuchselin. ×70.

Fig. 5 in Morphofunctional Adaption Of The Renal Tissue Of Acipenser Ruthenus (Actinopterygii, Acipenseriformes) Under Transformed Habitation Conditions

Fig. 5. The total sterlet's mesonephrolysis. Ehrlich's hematoxylin, Hart's fuchselin. ×100. Рис. 5. Тотальное разрушение мезонефроса стерляди. Гематоксилин Эрлиха, фукселин Харта. ×100.

Fig. 2 in Morphofunctional Adaption Of The Renal Tissue Of Acipenser Ruthenus (Actinopterygii, Acipenseriformes) Under Transformed Habitation Conditions

Fig. 2. Changes in the histological structure of the proximal nephron of the sterlet's mesonephros. Ehrlich's hematoxylin, Hart's fuchselin. ×200.

Fig. 1 in Morphofunctional Adaption Of The Renal Tissue Of Acipenser Ruthenus (Actinopterygii, Acipenseriformes) Under Transformed Habitation Conditions

Fig. 1. The normal structure of the sterlet's mesonephros. Ehrlich's hematoxylin, Hart's fuchselin. ×200.

The impact of Indonesian Throughflow constrictions on eastern Pacific upwelling and water-mass transformation

Netcdf data and Matlab processing scripts for the article:  Eabry, Holmes and Sen Gupta (2022): The impact of Indonesian Throughflow constrictions on eastern Pacific upwelling and water-mass transformation. Journal of Geophysical Research: Oceans. <a href="https://doi.org/10.1029/2022JC018509">https://doi.org/10.1029/2022JC018509</a> Included are netcdf files with output from the ACCESS-OM2 1-degree ocean model averaged over years 500-600 of the spin-up simulation. CONTROL indicates the control simulation (realistic ITF topography), OPENITF indicates the Open ITF experiment and DIFF indicates difference files between the two. Please refer to the meta-data within the netcdf files for more information. Scripts to help with plotting standard variables are part of the COSIMA cookbook repository at <a href="https://github.com/COSIMA/cosima-recipes">https://github.com/COSIMA/cosima-recipes</a>. An example script Control_WMT_budget.m is provided to plot the control WMT budget and can be easily modified to plot the Open ITF or anomalous WMT budget. This script uses the Pacific masks found in mask.mat. The small tendency term is provided separately as dV_dt_nrho.mat.

opencc-by-4.0Apr 2022View details →

Data for Scan-Centric, Frequency-Based Method for Characterizing Peaks from Direct Injection Fourier transform Mass Spectrometry Experiments

Input and output files from the manuscript analysis titled "Scan-Centric, Frequency-Based Method for Characterizing Peaks from Direct Injection Fourier transform Mass Spectrometry Experiments"

DProQ: A Gated-Graph Transformer for Protein Complex Structure Assessment

The file contains two benchmark sets: Heterodimer-AF2 and Docking benchmark 5.5-AF2 test. Each set includes (1) doecy folder, (2) native folder, and (3) label_info.csv.

DProQ: A Gated-Graph Transformer for Protein Complex Structure Assessment: MAF2 set

Multimer AF2  set. For more information, please read our paper on biorxiv: <a href="https://www.biorxiv.org/content/10.1101/2022.05.19.492741v2">https://www.biorxiv.org/content/10.1101/2022.05.19.492741v2</a>

Forschungsdaten zur Masterarbeit "Open Science und wissenschaftliche Bibliotheken. Disruptive Potentiale digitaler Transformation am Beispiel der Sächsischen Landesbibliothek — Staats- und Universitätsbibliothek Dresden"

--- english version below --- Im Rahmen des Fernstudiengangs Bibliotheks- und Informationswissenschaften habe ich die Masterarbeit mit dem Titel "Open Science und wissenschaftliche Bibliotheken. Disruptive Potentiale digitaler Transformation am Beispiel der Sächsischen Landesbibliothek — Staats- und Universitätsbibliothek Dresden" im Zeitraum vom 17.02.2022 bis 17.06.2022 angefertigt.  Für die Arbeit wurden Mitarbeitende in Interviews zum Thema "Open Science" befragt. Die Interviews wurden nach der Repertory-Grid-Technik durchgeführt und analysiert nach der Interpretive-Clustering-Methode, die erstmals <a href="http://doi.org/10.1080/14780887.2020.1794088">2020 von Burr, King und Heckmann</a> beschrieben wurde. Unterstützend konnte ein von Mark Heckmann entwickeltes Tool zur IC-Analyse verwendet werden: <a href="http://ic.openrepgrid.org/">http://ic.openrepgrid.org/</a>. Im Vorfeld der Interviews mussten Elemente als Basis gefunden werden. Die Elemente wurden mithilfe einer Korpusanalyse eines SLUB-Textkorpus mit dem Tool <a href="https://www.sketchengine.eu/">Sketch Engine</a> und nachfolgender Kuratierung gefunden. Es handelt sich um Nomina, die - nach logDice gewichtet- die höchste Kollokation zu den Begriffen "offen, Offenheit, offenbar" haben. Gewählt wurden: <ul> <li>Werkstatt</li> <li>Kulturdaten</li> <li>Schnittstelle</li> <li>Zugang</li> <li>Meinungsfreiheit</li> <li>Lizenz</li> <li>Standard</li> <li>Wissenschaft</li> <li>Wissen</li> <li>Austausch</li> <li>Makerspace</li> </ul> Als Forschungsdaten zur Arbeit liegen vor: <ul> <li>Ergebnisse der Kollokationsanalyse zu "offen", "Offenheit" und "offenbar"</li> <li>Interviewleitfaden für die Interviews nach Repertory-Grid-Technik</li> <li>Vorlage für den ersten Teil der Interviews (Konstruktbildung)</li> <li>Vorlage für den zweiten Teil der Interviews (Skaleneinordnung der Elemente)</li> <li>Ergebnisse des ersten Teils der Interviews (Konstruktbildung)</li> <li>Ergebnisse des zweiten Teils der Interviews (Skaleneinordnung der Elemente)</li> <li>Ergebnisse der Analyse der Interviews nach der Interpretive-Clustering-Methode</li> <li>Beispiel für die (ungenügende) automatische Transkription eines Interviewanfangs mithilfe der Google Speech to Text API</li> </ul> ----- english version As part of the distance learning course in Library and Information Science, I wrote the Master's thesis entitled "Open Science and academic libraries. Disruptive potentials of digital transformation using the example of the Saxon State Library - State and University Library Dresden" in the period from 17.02.2022 to 17.06.2022.  For the work, employees were questioned in interviews on the topic of "Open Science". The interviews were conducted using the repertory grid technique and analysed using the interpretive clustering method, which was first described by <a href="http://doi.org/10.1080/14780887.2020.1794088">Burr, King and Heckmann in 2020</a>. A tool developed by Mark Heckmann for IC analysis could be used as a support: <a href="http://ic.openrepgrid.org/">http://ic.openrepgrid.org/</a>. In the run-up to the interviews, elements had to be found as a basis. The elements were found with the help of a corpus analysis of an SLUB text corpus with the tool <a href="http://www.sketchengine.eu/">Sketch Engine</a> and subsequent curation. These are nouns which - weighted according to logDice - have the highest collocation to the terms "open, openness, apparent". The following were chosen: <ul> <li>Werkstatt</li> <li>Kulturdaten</li> <li>Schnittstelle</li> <li>Zugang</li> <li>Meinungsfreiheit</li> <li>Lizenz</li> <li>Standard</li> <li>Wissenschaft</li> <li>Wissen</li> <li>Austausch</li> <li>Makerspace</li> </ul> The research data available for the work are: <ul> <li>Results of the collocation analysis on "open", "openness" and "apparently".</li> <li>Interview guide for the interviews according to the repertory grid technique</li> <li>Template for the first part of the interviews (construct formation)</li> <li>Template for the second part of the interviews (scale classification of the elements)</li> <li>Results of the first part of the interviews (construct formation)</li> <li>Results of the second part of the interviews (scale classification of the elements)</li> <li>Results of the analysis of the interviews according to the interpretive clustering method</li> <li>Example of (insufficient) automatic transcription of an interview beginning using the Google Speech to Text API</li> </ul>

opencc-by-4.0Dec 2021View details →

Rapid assessment of lipidomics sample quality and quantity using attenuated total reflectance Fourier-transform infrared spectroscopy

In this work, we aimed to develop a simple lipid quality and quantification method for biological lipid extracts, as a step in lipidomics workflows, with minimal sample requirement. We chose FTIR spectroscopy with an Attenuate Total Reflectance (ATR) sampling method as it requires just 1 microliter of MS-ready sample without additional sample preparation. We validated the proposed lipidomics sample quality control workflow using a set of plasma samples (n=107, with 3-4 technical replicates) with comparison to LC-MS-based lipidomics. The following file contains the resulting spectra acquired by ATR-FTIR spectrometry for these plasma samples, standard curves and contaminated samples used for method development. Spectrometer was ambient blanked and detector cleaned between each measurement. Lipid samples were extracted by butanol-methanol (3:1) precipitation, and dried directly onto the ATR-FTIR detector. Absorbance was measured between 4,000 and 650 cm-1 wavenumbers, at a resolution of 8cm-1. Each spectra has been baseline corrected (whole spectra).

opencc-by-4.0Jun 2022View details →

Detection of early seeding of Richter transformation in chronic lymphocytic leukemia: scRNA-seq data

Richter transformation (RT) is a paradigmatic evolution of chronic lymphocytic leukemia (CLL) into a very aggressive large B cell lymphoma conferring a dismal prognosis. The mechanisms driving RT remain largely unknown. We characterized the whole genome, epigenome and transcriptome, combined with single-cell DNA/RNA-sequencing analyses and functional experiments, of 19 cases of CLL developing RT. Studying 54 longitudinal samples covering up to 19 years of disease course, we uncovered minute subclones carrying genomic, immunogenetic and transcriptomic features of RT cells already at CLL diagnosis, which were dormant for up to 19 years before transformation. We also identified new driver alterations, discovered a new mutational signature (SBS-RT), recognized an oxidative phosphorylation (OXPHOS)high–B cell receptor (BCR)low-signaling transcriptional axis in RT and showed that OXPHOS inhibition reduces the proliferation of RT cells. These findings demonstrate the early seed- ing of subclones driving advanced stages of cancer evolution and uncover potential therapeutic targets for RT. This repository contains the processed scRNA-seq data (expression matrices, Seurat objects, metadata) related with this publication.

opencc-by-4.0Jun 2022View details →

Data repository - Land use change and carbon emissions of a transformation to timber cities

Data and model source code for the publication: Land use change and carbon emissions of a transformation to timber cities (Nature Communications, 2022) DOI: 10.1038/s41467-022-32244-w Abhijeet Mishra1,2,*, Florian Humpenöder1, Galina Churkina1, Christopher P.O. Reyer1, Felicitas Beier1,2, Benjamin Leon Bodirsky1, Hans Joachim Schellnhuber1, Hermann Lotze-Campen1,2, and Alexander Popp1 1 Potsdam Institute for Climate Impact Research (PIK), Member of Leibniz Association, P.O.Box 60 12 03, 14412,6 Potsdam, Germany 2 Humboldt University of Berlin, Department of Agricultural Economics, Unter den Linden 6, 10099 Berlin,8 Germany Abhijeet Mishra *mishra@pik-potsdam.de May 2022 See README.txt for further details.

opencc-by-4.0Jun 2022View details →

Acoustic models of Brazilian Portuguese Speech based on Neural Transformers - Refinement dataset SPIRA

This dataset was collected over the internet and in hospital wards with the goal of detecting respiratory insufficiency (typically caused by COVID-19). This data collection is part of the SPIRA Project, whose goal is developing a system for recognizing respiratory insufficiency through speech analysis. The datasets presented here were used in the paper: Acoustic models of Brazilian Portuguese Speech based on Neural Transformers by Marcelo Gauy and Marcelo Finger. The spira_trimmed_data file contains the original ~1 hour dataset collected over the internet (control) and in hospital wards (patients) by the SPIRA Project. This is as described in the paper: Deep learning against COVID-19: Respiratory insufficiency detection in Brazilian Portuguese Speech. We include it here for completeness. The spira_control_full_mp3 file contains the complete ~18 hours control data collected over the internet by the SPIRA project. While not useful for respiratory insufficiency detection, the dataset may be used for identifying age and gender as we mention in our paper: Acoustic models of Brazilian Portuguese Speech based on Neural Transformers.