cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.6519525
title: Supplementary information: Specific versus non-specific interactions of indole in water revealed by x-ray photoemission spectroscopy [Dataset]

description: Data availability to the manuscript "Specific versus non-specific interactions of indole in water revealed by x-ray photoemission spectroscopy" by Lanhai He, Lukáš Tomaník, Sebastian Malerz, Florian Trinter, Sebastian Trippel, Michal Belina, Petr Slavíček, Bernd Winter, and Jochen Küpper, to be submitted to JPCL 

The dataset contains the complete x-ray photoelectron-emission spectra of indoleaq in a liquid microjet. The uploaded files include:



Valence band PES data (May02_0053VB.ibw, May02_0058VB_background.ibw),

core level PES data (May02_0045C1s.ibw, May02_0049N1s.ibw),

Auger PES  pectra (May02_0052CAuger.ibw, May02_0057CAuger.ibw, May02_0056NAuger.ibw)

rough-scanned full spectra (May02_0046Full.ibw, May02_0047Full.ibw).


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.
description: We acknowledge support by Deutsches Elektronen-Synchrotron DESY, a member of the Helmholtz Association (HGF), and the use of the Maxwell computational resources operated at Deutsches Elektronen-Synchrotron DESY. Parts of this research were carried out at PETRA III at DESY; beamtime was allocated for proposal II-20180012. This work was supported by the Cluster of Excellence "Advanced Imaging of Matter" (AIM, EXC 2056, ID 390715994) of the Deutsche Forschungsgemeinschaft (DFG) and by the European Research Council under the European Union's Seventh Framework Program (FP7/2007-2013) through the Consolidator Grant COMOTION (614507). L.H. acknowledges the support by the National Natural Science Foundation of China (11704147) and a fellowship within the framework of the Helmholtz-OCPC postdoctoral exchange program. P.S., L.T., and M.B. thank Czech Science Foundation (EXPRO project no. 21-26601X). B.W. acknowledges funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and investigation programme (grant agreement 883759). F.T. and B.W. acknowledge support by the MaxWater initiative of the Max-Planck-Gesellschaft.
DOI: 10.6084/m9.figshare.25132280
title: July-23 training OR.xlsx

description: Presentation skills, education
DOI: 10.21227/5j31-8a73
title: Dataset for Smart Precision Agriculture System in Bangladesh

description: The dataset comprises many variables like area, production, season, minimum humidity, maximum humidity, minimum temperature, maximum temperature, district, crop name which impact the agricultural output of different crops in the region of Bangladesh. Surveys were conducted in various areas of Bangladesh to gather data on different types of crops. The primary aim of this collection is to facilitate research in the domain of precision agriculture. The gathered data will assist in developing algorithms and solutions that are more accurate and efficient for making data-driven judgments. This dataset was used to train different machine learning models. The trained models can provide suggestion on most efficient crop yield.
DOI: 10.25919/ewtx-nr19
title: Parkes pulsar observations with undefined project IDs for 2023OCTS_06

description: Parkes pulsar observations with undefined project IDs for 2023OCTS. This collection contains observations from project IDs PX112 and PX119.
DOI: 10.5281/zenodo.10608282
title: Tactile-Vision-Language (TVL) Dataset
DOI: 10.5281/zenodo.10608283
title: Tactile-Vision-Language (TVL) Dataset
DOI: 10.6084/m9.figshare.25132295
title: Seguchi_&_Izawa_Rawdata

description: Raw datasets of social behaviour results from triadic cohabitation (Experiment 1) and V1aR antagonism (Experiment 2) .
DOI: 10.6084/m9.figshare.25132295.v1
title: Seguchi_&_Izawa_Rawdata

description: Raw datasets of social behaviour results from triadic cohabitation (Experiment 1) and V1aR antagonism (Experiment 2) .
DOI: 10.17615/7x9x-0q90
title: Metabolomics Dataset

description: We applied unbiased metabolomics using liquid chromatography coupled to high-resolution mass spectrometry (LC-HRMS) to identify metabolites in heart and serum saline or isoproterenol- treated WT and genetically modified mice with cardiac-restricted depletion of the RhoA GAP, GRAF1. The dataset provided are raw data generated from this analysis.
DOI: 10.34740/kaggle/dsv/7536319
title: AnonymousReviewDataset
DOI: 10.6084/m9.figshare.25028366
title: Heat per gdp - Extension of Japan prefectural emission accounting and enrich socioeconomic data 1990 to 2020

description: A sub-set for the dataset concerning 'Extension of Japan prefectural emission accounting and enrich socioeconomic data 1990 to 2020'.This database offers an in-depth view of Japan's carbon emission trends and distribution across its 47 prefectures over three decades, from 1990 to 2020. Developed in response to Japan's shift from nuclear to fossil fuel-based energy post-Fukushima, it highlights the challenges in meeting emission reduction targets. The database meticulously compiles emissions data based on the consumption of three primary fossil fuels across 29 sectors, including a separate accounting for emissions from local power generation. It uniquely blends energy consumption data from prefectural natural resources and energy departments with emissions data from power plants, providing a granular view of the energy landscape. Moreover, the database enriches this emission data with corresponding socioeconomic factors such as population, GDP, land prices, green space, and road infrastructure, sourced from official Japanese statistical resources. This fusion of environmental and economic data offers a multi-faceted perspective, crucial for formulating targeted carbon reduction strategies and sustainable development policies.
DOI: 10.6084/m9.figshare.25028366.v1
title: Heat per gdp - Extension of Japan prefectural emission accounting and enrich socioeconomic data 1990 to 2020

description: A sub-set for the dataset concerning 'Extension of Japan prefectural emission accounting and enrich socioeconomic data 1990 to 2020'.This database offers an in-depth view of Japan's carbon emission trends and distribution across its 47 prefectures over three decades, from 1990 to 2020. Developed in response to Japan's shift from nuclear to fossil fuel-based energy post-Fukushima, it highlights the challenges in meeting emission reduction targets. The database meticulously compiles emissions data based on the consumption of three primary fossil fuels across 29 sectors, including a separate accounting for emissions from local power generation. It uniquely blends energy consumption data from prefectural natural resources and energy departments with emissions data from power plants, providing a granular view of the energy landscape. Moreover, the database enriches this emission data with corresponding socioeconomic factors such as population, GDP, land prices, green space, and road infrastructure, sourced from official Japanese statistical resources. This fusion of environmental and economic data offers a multi-faceted perspective, crucial for formulating targeted carbon reduction strategies and sustainable development policies.
DOI: 10.6084/m9.figshare.25028366.v2
title: Heat per gdp - Extension of Japan prefectural emission accounting and enrich socioeconomic data 1990 to 2020

description: A sub-set for the dataset concerning 'Extension of Japan prefectural emission accounting and enrich socioeconomic data 1990 to 2020'.This database offers an in-depth view of Japan's carbon emission trends and distribution across its 47 prefectures over three decades, from 1990 to 2020. Developed in response to Japan's shift from nuclear to fossil fuel-based energy post-Fukushima, it highlights the challenges in meeting emission reduction targets. The database meticulously compiles emissions data based on the consumption of three primary fossil fuels across 29 sectors, including a separate accounting for emissions from local power generation. It uniquely blends energy consumption data from prefectural natural resources and energy departments with emissions data from power plants, providing a granular view of the energy landscape. Moreover, the database enriches this emission data with corresponding socioeconomic factors such as population, GDP, land prices, green space, and road infrastructure, sourced from official Japanese statistical resources. This fusion of environmental and economic data offers a multi-faceted perspective, crucial for formulating targeted carbon reduction strategies and sustainable development policies.
DOI: 10.25345/c53x83x1m
title: MassIVE MSV000093978 - De novo nine-species benchmark peptide identifications for Casanovo and other methods
title: Predicted peptides for the 9-species de novo sequencing benchmark MSV000090982 as described in Yilmaz et al. [Yilmaz2023]. FTP directory contains outputs of 5 de novo peptide sequencing methods on the 9-species benchmark: Casanovo, Casanovo_bm (benchmark), PointNovo, DeepNovo and Novor. [Yilmaz2023] M. Yilmaz*, W. Fondrie*, W. Bittremieux*, R. Nelson, V. Ananth, S. Oh, and W. Noble,"Sequence-to-sequence translation from mass spectra to peptides with a transformer model", bioRxiv, 2023
DOI: 10.5281/zenodo.10596973
title: AKScore2

description: This repository contains the training docked conformation data to train AK-Score2 model. The zip file contains the all near-native and conformational and cross-docked decoy complex structures. Decoy is divided into conformatinoal decoy of the native ligand, cross-docked decoy docked with other ligands in pdbbind v2020, and random-docked decoy generated randomly from the Enamin dataset. All decoy docking poses were created using AutoDock-GPU v1.5.3. In the case of AutoDock-GPU, the grid center was used as the center coordinate of the native ligand. The grid box size of AutoDock-GPU was used as 22.5 Å X 22.5 Å X 22.5 Å.
DOI: 10.5281/zenodo.10596974
title: AKScore2

description: This repository contains the training docked conformation data to train AK-Score2 model. The zip file contains the all near-native and conformational and cross-docked decoy complex structures. Decoy is divided into conformatinoal decoy of the native ligand, cross-docked decoy docked with other ligands in pdbbind v2020, and random-docked decoy generated randomly from the Enamin dataset. All decoy docking poses were created using AutoDock-GPU v1.5.3. In the case of AutoDock-GPU, the grid center was used as the center coordinate of the native ligand. The grid box size of AutoDock-GPU was used as 22.5 Å X 22.5 Å X 22.5 Å.
DOI: 10.5281/zenodo.10608361
title: BoreCapture-JGR-Oceans

description: Dataset supporting research submitted to JGR Oceans titled 'Investigations on Bore Capture Modulation on a Macrotidal Beach'.
DOI: 10.17615/8yjy-w790
title: ZOE 2.0: A community-based, epidemiologic study of early childhood oral health

description: Early childhood caries (ECC) is an aggressive form of dental caries occurring in the first five years of life. Despite its prevalence and consequences, little progress has been made in its prevention and even less is known about individuals' susceptibility or genomic risk factors. The genome-wide association study (GWAS) of ECC ("ZOE 2.0") is a community-based, multi-ethnic, cross-sectional, genetic epidemiologic study seeking to address this knowledge gap. This paper describes the study's design, the cohort's demographic profile, data domains, and key oral health outcomes. Between 2016 and 2019, the study enrolled 8059 3-5-year-old children attending public preschools in North Carolina, United States. Participants resided in 86 of the state's 100 counties and racial/ethnic minorities predominated-for example, 48% (n = 3872) were African American, 22% white, and 20% (n = 1611) were Hispanic/Latino. Seventy-nine percent (n = 6404) of participants underwent clinical dental examinations yielding ECC outcome measures-ECC (defined at the established caries lesion threshold) prevalence was 54% and the mean number of decayed, missing, filled surfaces due to caries was eight. Nearly all (98%) examined children provided sufficient DNA from saliva for genotyping. The cohort's community-based nature and rich data offer excellent opportunities for addressing important clinical, epidemiologic, and biological questions in early childhood.
DOI: 10.15151/esrf-es-1413554496
title: Advanced Photon Source, Sector 21 - The Life Sciences Collaborative Access Team (LS-CAT) - CAT Member Macromolecular Crystallography

description: The Life Sciences Collaborative Access Team (LS-CAT) provides Macromolecular Crystallography support to our CAT members from eight Universities in the USA, including Northwestern University, University of Michigan, Wayne State University, Michigan State University, University Wisconsin, Vanderbilt University, and University of Illinois at Chicago, and also to General Users. With a one-year dark period approaching for the upgrade of the Advanced Photon Source (APS-U), we are seeking beam time for our CAT Member laboratories at ESRF by way of this Block Allocation Group, consisting of a portion of our CAT Member PIs and their laboratory members, in order to keep supporting their research and future funding. LS-CAT is organizing our CAT Members into this BAG Proposal, and other proposals we will submit, in order to streamline the process for our CAT Members, and for the Staff of Lightsources to which we are applying for access to beam time.
DOI: 10.15151/esrf-es-1409457864
title: Structural Biology at EMBL Grenoble, IBS-CIBB and IAB

description: This proposal clusters crystallography and bioSAXS projects at the EMBL Grenoble, IBS-CIBB and IAB. It combines groups working on different topics with a major focus on cell signaling proteins, drug discovery, long non-coding RNAs, nucleic acid-protein complexes, and host-pathogen interactions. The proposers have long-standing experience in the use, as well as the development of beam lines for macromolecular crystallography and biological small angle X-ray scattering and have participated in successive BAG applications over the years, mostly at the ESRF but also at other synchrotrons (i.e. Soleil, Petra III, and Diamond). As Stephen Cusack (former head of EMBL Grenoble) will be retiring at the end of 2023 we propose to change the BAG responsible to Andrew McCarthy for this application round.
DOI: 10.15151/esrf-es-1422535710
title: Structure of metalloproteins, membrane proteins, filamentous sarcomer proteins, and virus particles

description: Our work focusses on biological nitrogen fixation by Nitrogenase, on metalloenzymes and integral membrane proteins of bacterial and archaeal respiratory systems (Andrade/Einsle/Wohlwend), the working mechanism and regulation of medically relevant membrane proteins and complexes and their defects leading to pathologies (Hunte), bacterial antibiotic resistance factors and viral and bacterial proteins bound to their targets or inhibitors, and their interactions with glycans (Stehle/Zocher), human S100 proteins involved in nutritional immunity, USP18 enforcing the endogenous antiviral interferon response, and the respiratory complex NQR of V. cholerae (Fritz), DNA Polymerases with artificial substrates (Benz), and on multi-domain components of the sarcomeric filamentous protein titin and their binding to the E3 ubiquitin ligase MuRF1 and the central myosin rod-domain (Mayans).
DOI: 10.15151/esrf-es-1432220985
title: A synchrotron-based biomechanical and bone microstructural approach to investigate the origin of tetrapod bipedalism

description: Bipedalism represents one of the most striking forms of locomotor convergence in the history of terrestrial tetrapods. However, it remains unclear whether bipedalism occurred because it conveyed an adaptive advantage over quadrupedal locomotion or that it may have simply resulted as a biomechanical consequence of higher acceleration, or if it was the result of multiple factors. The oldest taxa hypothesized to have employed bipedalism date back to the early Permian, including Eudibamus cursoris and Cabarzia trostheidei. Nonetheless, interpretations regarding the bipedal aptitude of these species have primarily leaned on rather subjective evidence, and this hypothesis has never been tested directly using rigorous biomechanical analyses. The current project thus aims at better understanding the morphofunctional abilities of these species, and to test the degree of their proposed bipedalism using innovative biomechanical analyses combined with paleohistological and ichnological data.
DOI: 10.15151/esrf-es-1432053366
title: FastScan - Fast Correlative Scanning SAXS and Visible Light Fluorescence Imaging of Biological Matter

description: The aim of this project is to combine highly complementary imaging methods – i.e., scanning small angle x-ray scattering, fast bright field microscopy and visible light fluorescence microscopy - for the structure determination of components inside biological cells, in particular the cytoskeleton and the nucleus. Importantly, the planned setup will in the future be applicable to a multitude of different sample types, from biological to soft matter and hard condensed matter. Our focus for the upcoming three years will be on (i) model cell lines with a pronounced keratin network, and (ii) biologically relevant heart muscle cells with and without desmin mutants that cause cardiomyopathy. The setup shall be made available to the user community after set-up and commissioning.
DOI: 10.15151/esrf-es-1432054397
title: In situ powder X-ray diffraction of a flexible perfluorinated metal-organic framework during gas adsorption

description: We propose to perform an in situ PXRD experiment during thermal cycling and gas adsorption on a perfluorinated AlIII-based metal-organic framework (MOF) with MIL-53 topology, dubbed F4_MIL-53(Al), at beamline BM01. The aim of the experiment is to gain detailed insight into the phase transitions occurring when the MOF is either thermally cycled or exposed to adsorptives such as N2, Ar and CO2. This is motivated by the interest in further understanding the flexible behaviour of this MOF, which features a temperature-induced phase transition and whose adsorption isotherms display several steps, suggestive of adsorption-induced phase changes. Of special interest is the fact that both the calorimetric profile and the adsorption isotherms display much smaller hysteresis than the fully hydrogenated version of the same MOF, which is the prototypical “breathing” material.
DOI: 10.15151/esrf-es-1432054936
title: New instrument for nano-XRD and nano-XRF at extreme conditions at ID27

description: A new, unique nano-focus instrumentation for rapid parallel XRF and XRD as well as X-ray imaging measurements at extreme pT conditions will be constructed on ID27. Funding for this project was partially obtained from German authorities in the framework of a BMBF project by M. Wilke (Potsdam), S. Jahn (Cologne) and D. Andrault (Clermont-Ferrand). The planned work is outlined in a collaboration contract between ESRF, University Potsdam and Cologne University (CL 0309). 
The instrument benefits from the very small beam size and the ultimate brilliance provided by the new diffraction-limited synchrotron radiation source at ESRF. During the LTP the new instrument will be benchmarked and employed to perform cutting-edge experiments for understanding materials relevant to processes of the deep Earth. Additionally, this unique setup offers the possibility for applications ranging from materials sciences in the field of superhard or superdense materials to high-pressure solid-state physics.
DOI: 10.15151/esrf-es-1479846280
title: Structure and dynamics in different colloidal suspensions

description: Several model colloidal systems will be investigated using XPCS and USAXS. In particular, near the dynamic arrest transition induced by strong attraction between particles.
DOI: 10.17615/zyrb-9916
title: Spatiotemporal Variability of Gas Transfer Velocity in a Tropical High-Elevation Stream Using Two Independent Methods

description: *** This work was funded by the National Science Foundation under award 1847331: Streams in high-elevation tropical ecosystems known as páramos may be significant sources of carbon dioxide (CO2) to the atmosphere by transforming terrestrial carbon to gaseous CO2. Studies of these environments are scarce and estimates of CO2 fluxed are poorly constrained. In this study, we use two independent methods for measuring gas transfer velocity (k), a critical variable in the estimation of CO2 evasion and other biogeochemical processes. The first method, ‘Kinematic k600’ (k600-K), is derived from an empirical relationship between temperature-adjusted k (k600) and the physical characteristics of the stream. The second method, ‘Measured k600’ (k600-M), estimates gas transfer velocity in the stream by in situ measurements of dissolved CO2 (pCO2) and CO2 evasion to the atmosphere, adjusting for temperature. Measurements were collected throughout a 5-week period during the wet season of a peatland-stream transition within a páramo ecosystem located above 4,000m in elevation in northeastern Ecuador. We characterized the spatial heterogeneity of the 250-m reach on five occasions, and both methods showed a wide range of variability in k600 at small spatial scales. Values of k600-K ranged from 7.42 to 330 m d-1 (mean =116 ± 95.1 m d-1), whereas values of k600-M ranged from 23.5 to 444 m d-1 (mean = 121 ± 127 m d-1). Temporal variability in k600 was driven by increases in stream discharge caused by rain events, whereas spatial variability was driven by channel morphology, including stream width and slope. The two methods were in good agreement (less than 16% difference) at high and medium stream discharge (above 7.0 L s-1). However, the two methods considerably differed from one another (up to 73% difference) at low stream discharge (below 7.0 L s-1). Our study provides the first estimates of k600 values in a high elevation tropical catchment across steep environmental gradients and highlights the combined effects of hydrology and stream morphology in coregulating gas transfer velocities in páramo streams.
DOI: 10.17615/wjqg-v365
title: Face Covering Survey among North Carolina residents

description: State and local health departments have been tasked with promoting the use of face coverings to decrease the spread of COVID-19 in their respective communities. However, little is known about motivations and barriers to wearing face coverings in the context of COVID-19 prevention, particularly among communities of color who are at an increased risk of serious illness from the disease. The purpose of this study was to identify common motivations and barriers to face covering use, as well as explore perceptions of messages encouraging the use of face coverings among a racially and ethnically diverse sample. A survey was distributed electronically to North Carolina (NC) residents through NC Department of Health and Human Services listservs in July 2020. Participants self-categorized as Latino/a (33.5%), Black (39.1%), or white or another race (27.5%). The most commonly endorsed motivations for wearing face coverings were to avoid spreading COVID-19 (77%), as well as to protect people who are vulnerable (76%) and one’s community (72%). Being uncomfortable (40%) was the most commonly endorsed barrier. Messages that included a clear request (ex. please wear a face covering) and a direct benefit (ex. keep community safe) were more commonly endorsed than those that did not. Commonly endorsed motivations, behaviors, and messages differed by race and ethnicity. Increased attention to message content, message structure, and access to information and resources may aid local officials in increasing consistent use of face coverings.