cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.4318783
title: MFS-M-00313 Air temperature at 2m, raised bog-hollow, DS18B20 (temperature logger)

description: Air temperature at 2m measured in a raised bog ecosystem by DS18B20 (temperature logger in APIK complex), 2018, 30 min frequency, N60.89494 E68.66999, as part of meteorological monitoring in Mukhrino Field Station (https://mukhrinostation.com/).
DOI: 10.17632/42cxfnjfp3.1
title: Paleoceanographic evolution of the Japan Sea during the Pleistocene – A benthic foraminiferal perspective
DOI: 10.5281/zenodo.4312236
title: Output Files from Reactive Transport Models (supplement to Solid Earth Manuscript 'se-2020-99')

description: This repository includes the output files (in Tecplot format) of the numerical models in the paper entitled "<em><strong>Understanding controls on hydrothermal dolomitisation: insights from 3D Reactive Transport Modelling of geothermal convection</strong></em>". A key to the output data provided here is summarised in Data_Benjakul_et_al_2020.xlsx. We used <strong>TOUGHREACT</strong>, a numerical simulation program developed by the Lawrence Berkeley National Laboratory (LBNL) which is available at: https://tough.lbl.gov/licensing-download/toughreact-licensing-download/ to numerically model the convection of seawater in a single fault within carbonate-hosted system. The parameters used in the numerical models are given in the paper. https://doi.org/10.5194/se-11-2439-2020 The output files from TOUGHREACT (in Tecplot format) are visualised using <strong>trexplot</strong>, a python script developed by Hamish Robertson which can be found at: https://github.com/hammytheham/trexplot (last access: 5 December 2020). Please contact me via the following e-mail addresses in case you have any questions: rb17526@bristol.ac.uk or rbenjaku@gmail.com
DOI: 10.5281/zenodo.4311925
title: Output Files from Reactive Transport Models (supplement to Solid Earth Manuscript 'se-2020-99')

description: This repository includes the output files (in Tecplot format) of the numerical models in the paper entitled "<em><strong>Understanding controls on hydrothermal dolomitisation: insights from 3D Reactive Transport Modelling of geothermal convection</strong></em>". A key to the output data provided here is summarised in Data_Benjakul_et_al_2020.xlsx. We used <strong>TOUGHREACT</strong>, a numerical simulation program developed by the Lawrence Berkeley National Laboratory (LBNL) which is available at: https://tough.lbl.gov/licensing-download/toughreact-licensing-download/ to numerically model the convection of seawater in a single fault within carbonate-hosted system. The parameters used in the numerical models are given in the paper. https://doi.org/10.5194/se-11-2439-2020 The output files from TOUGHREACT (in Tecplot format) are visualised using <strong>trexplot</strong>, a python script developed by Hamish Robertson which can be found at: https://github.com/hammytheham/trexplot (last access: 5 December 2020). Please contact me via the following e-mail addresses in case you have any questions: rb17526@bristol.ac.uk or rbenjaku@gmail.com
DOI: 10.17632/49hbdyz6zk.2
title: Research data for retention of extracellular polymeric substances (EPS) in EPS-ferrihydrite associations

description: The research dataset includes changes in elements, functional groups, and components of EPS under two formation pathways (adsorption vs coprecipitation) of ferrihydrite-EPS associations. This study provides new insights onto EPS behaviour at the mineral-water interface and is valuable for evaluating how microbial-derived compounds are stabilized by iron (hydr)oxides.
DOI: 10.17632/t7prmcwrsz.2
title: Supplementary Material for Robust Integrated Data-Driven Modeling Strategy for Industrial Gas-Phase Ethylene Polymerization Processes with Noises and Outliers

description: This material contains the additional predicted results of the industrial gas-phase ethylene polymerization process by using ELM, RELM, WRELM and proposed robust integrated SDAE-ENELM strategy in the presence of noises and outliers for article "Robust Integrated Data-Driven Modeling Strategy for Industrial Gas-Phase Ethylene Polymerization Processes with Noises and Outliers ".
DOI: 10.17632/mxwpkdx9jf.1
title: "Multi-organ Proteomic Landscape of COVID-19 Autopsies" A study of Nie et al

description: The molecular pathology of multi-organ injuries in COVID-19 patients remains unclear, preventing effective therapeutics development. Here, we report an in-depth multi-organ proteomic landscape of COVID-19 autopsy samples. By integrative analysis of seven-organ proteomes, namely lung, spleen, liver, heart, kidney, thyroid and testis, we quantified 11,394 proteins, in which 5336 were perturbed in theCOVID-19 patients compared to controls. Our data showed that CTSL, rather than ACE2, was significantly upregulated in the lung from the COVID-19 patients. Dysregulation of protein translation, glucose metabolism, fatty acid metabolism was detected in multiple organs. Our data suggested upon SARS-CoV-2 infection, hyperinflammation might be triggered, leading to hypoxia, angiogenesis, blood coagulation and fibrosis in the multiple organs. Evidence for testicular injuries includes reduced Leydig cells, suppressed cholesterol biosynthesis and sperm mobility. In summary, this study depicts the multi-organ proteomic landscape of COVID-19 autopsies, and uncovered dysregulated proteins and biological processes, offering potential therapeutic clues.
DOI: 10.17632/m6xzygyvjt.1
title: A unified alternative telomere lengthening pathway in yeast survivor cells

description: Alternative lengthening of telomeres (ALT) is a recombination process that maintains telomeres in the absence of telomerase, and is an important survival mechanism for cancer cells. Yeast has been used as a robust model of ALT; however, the inability to determine the frequency and chromosomal structure of ALT hindered the understanding of its mechanism. Here, using populational and molecular genetics approaches we overcome these problems and demonstrate that, contrary to the current view, both RAD51 -dependent and -independent mechanisms are required for a single ALT survivor pathway. This conclusion is based on the calculation of ALT frequencies as well as on ultra-long sequencing of ALT products that revealed “hybrid” sequences containing features attributed to both recombination pathways. Sequencing of ALT intermediates demonstrate that recombination begins with RAD51 -mediated strand invasion to form DNA substrates that are matured by a Rad51-independent ssDNA annealing pathway. We propose that similar to yeast, a single major pathway may be driving ALT in other organisms including humans.
DOI: 10.17632/4w9rt699d9.1
title: Damage detection, localization and extent of damage in beams from noisy static measurements using data smoothing and regularization

description: These four Mathematica files present the method of damage localization by statistical methods along with the determination of the extent of damage by the Tikhonov regularization. The results are used in the lone excel file. The results could be reproduced by the Mathematica files.
DOI: 10.17632/8w4vrpttpc.1
title: The Monte Carlo Program KKMC, for the Lepton or Quark Pair Production at LEP/SLC Energies—Updates of electroweak calculations

description: Since the KKMC program was published for the first time over 20 years ago, it has gained popularity and was exploited in a broad spectrum of applications. The core part of the program itself did not change much. In contrast, some of the libraries have evolved substantially. The aim of this publication is to archive four versions, alternative to the one published 20 years ago versions of the electroweak libraries (or just parameter initialization versions), which were instrumental for the precision Standard Model calculation from the end of LEP era till now and for the sake of the future applications/comparisons for the future electron–positron colliders, in particular for the FCC-ee related studies. These electroweak libraries are useful for the hadron collider applications as well, for instance for KKMC-hh or TauSpinner projects. The previous version of this program (ADMD_v1_0) may be found at https://doi.org/10.1016/S0010-4655(00)00048-5.
DOI: 10.17632/jcpj3j83rt.1
title: PARCE: Protocol for Amino acid Refinement through Computational Evolution

description: The in silico design of peptides and proteins as binders is useful for diagnosis and therapeutics due to their low adverse effects and major specificity. To select the most promising candidates, a key matter is to understand their interactions with protein targets. In this work, we present PARCE, an open source Protocol for Amino acid Refinement through Computational Evolution that implements an advanced and promising method for the design of peptides and proteins. The protocol performs a random mutation in the binder sequence, then samples the bound conformations using molecular dynamics simulations, and evaluates the protein–protein interactions using multiple scoring functions. Finally, it accepts or rejects the mutation by applying a consensus criterion based on the binding scores. The procedure is iterated with the aim to explore efficiently novel sequences with potential better affinities towards their targets. We also provide a tutorial for running and reproducing the methodology.
DOI: 10.17632/grp8njy6gz.1
title: UNDI: An open-source library to simulate muon-nuclear interactions in solids

description: We present UNDI, an open-source program to analyze the time dependent spin polarization of an isolated muon interacting with the surrounding nuclear magnetic dipoles in the context of standard muon spin rotation and relaxation spectroscopy experiments. The code can perform both exact and approximated estimates of the muon polarization function in presence of external fields and electric field gradients on the nuclei surrounding the muon. We show that this tool, combined to ab initio estimations of the electric field gradient at the nuclei interacting with the muon, can become a valuable complement to supercell based identifications of muon sites in crystals when large nuclear magnetic moments are present in the sample. In addition, it allows to properly investigate physical properties influenced by the presence of a non-negligible electric field gradient such as avoided level crossing resonance, nature of the ground state, disentanglement of electronic and nuclear magnetic moments or charge ordered states. The efficiency and effectiveness of this method is shown along the lines of three realistic examples.
DOI: 10.17632/rgv4hkrxjw.1
title: FEMS – A Mechanics-oriented Finite Element Modeling Software

description: This paper is a presentation of a Finite Element Modeling Software named FEMS that integrates mesh generation and adaption features in order to alleviate significantly the difficulty of designing a Finite Element (FE) mesh for a particular problem. FEMS is targeted at engineers and scientists addressing localization problems in mechanics, although it should be suited to many other applications. FEMS is particularly relevant for problems with internal interfaces, both in solid and fluid mechanics, as it has both explicit and implicit interface representation. The former can be generated from signed distance functions using body-fitted meshing capabilities implemented in FEMS, while the latter relies on the level-set method. The choice between the one or the other can be made by the user depending on the severity of deformations in the neighborhood of an interface. During the simulation, FEMS adapts the FE mesh automatically to achieve the best accuracy for a prescribed number of nodes. This is possible for both linear and quadratic interpolation. Additionally, in an updated Lagrangian setting, FEMS triggers mesh adaption automatically to avoid element flipping during node motion. The capabilities of FEMS are demonstrated in this paper for fluid and solid mechanics problems featuring turbulence, multiphase flow, large deformations and plasticity. This wide range of problems that can be handled by FEMS should prove its great interest for the computational mechanics community.
DOI: 10.17632/r8jsx4xxgv.1
title: QSW_MPI: A framework for parallel simulation of quantum stochastic walks

description: QSW_MPI is a Python package developed for time-series simulation of continuous-time quantum stochastic walks. This model allows for the study of Markovian open quantum systems in the Lindblad formalism, including a generalisation of the continuous-time random walk and continuous-time quantum walk. Consisting of a Python interface accessing parallelised Fortran libraries utilising sparse data structures, QSW_MPI is scalable to massively parallel computers, which makes possible the simulation of a wide range of walk dynamics on directed and undirected graphs of arbitrary complexity.
DOI: 10.17632/cybfcj53d5.1
title: Data on dynamics of landscape structure and fragmentation in Ambo district, central highlands of Ethiopia

description: The data is concerned with landscape changes and fragmentation
DOI: 10.5281/zenodo.4318802
title: MFS-M-00368 Air temperature at 2m, raised eriophorum-sphagnum bog, DS18B20 (APIK)

description: Air temperature at 2m measured in a raised bog ecosystem (eriophorum-Sphagnum bog) by DS18B20 (temperature logger), 2018-2020, 30 min frequency, N60.89439 E68.68113, OTC-dry experimental site,<br> as part of meteorological monitoring in Mukhrino Field Station (https://mukhrinostation.com/).
DOI: 10.5281/zenodo.4318801
title: MFS-M-00368 Air temperature at 2m, raised eriophorum-sphagnum bog, DS18B20 (APIK)

description: Air temperature at 2m measured in a raised bog ecosystem (eriophorum-Sphagnum bog) by DS18B20 (temperature logger), 2018-2020, 30 min frequency, N60.89439 E68.68113, OTC-dry experimental site,<br> as part of meteorological monitoring in Mukhrino Field Station (https://mukhrinostation.com/).
DOI: 10.6084/m9.figshare.13369898
title: Determinants of Neural Tube Defects among Mothers Who Gave Birth in North Shoa Zone Hospitals, Amhara Region, Ethiopia 2020: Case control study

description: <b>Introduction:</b> Neural tube defects affect the brain and the spinal column of the developing embryo. The defects occur due to incomplete or failure of closure of the neural tube. The condition eventually causes death and lifelong disability. Worldwide, more than 300,000 babies are born with neural tube defects each year. The highest burden is in low and middle income countries. Therefore, this study aims to identify the determinant factors of neural tube defects among mothers who gave birth in North Shoa Zone Hospitals. <b>Methods</b>: A hospital based unmatched case-control study was conducted among 243(81 cases and 162 controls) study participants in North Shoa Zone Hospitals. The hospitals were selected using simple random sampling and all cases and randomly selected controls in the selected hospitals were included in the study. The data were collected by using pre-tested structured questionnaire. <b>Results</b>: Different factors were identified to have association with neural tube defect. Family annual cash income less than 24000ETB (AOR: 3.73, 95%CI: 1.35, 10.26), history of still birth (AOR: 3.63, 95%CI: 1.03, 12.2), history of abortion (AOR: 6.15, 95%CI: 2.63, 18.56), preconception tea use (AOR: 2.36, 95%CI: 1.15, 4.86) and pesticides/chemical exposer (AOR: 5.34, 95%CI: 1.77, 16.05) were positively associated factors. In the contrart, preconception care (AOR: 0.14, 95%CI: 0.05, 0.39) and taking iron/folic acid/multivitamin during the current pregnancy (AOR: 0.16, 95%CI: 0.07, 0.33) showed a protective effect. <b>Conclusion</b>: Family annual income less than 24000ETB, history of still birth, history of abortion, preconception tea use and pesticides/chemical exposer were predictors of neural tube defects. Preconception counseling and screening should be recommended for women who plan for pregnancy. <b>Key words</b>: Neural tube defect, Determinant factors, Hospitals, Ethiopia
DOI: 10.6084/m9.figshare.13369898.v1
title: Determinants of Neural Tube Defects among Mothers Who Gave Birth in North Shoa Zone Hospitals, Amhara Region, Ethiopia 2020: Case control study

description: <b>Introduction:</b> Neural tube defects affect the brain and the spinal column of the developing embryo. The defects occur due to incomplete or failure of closure of the neural tube. The condition eventually causes death and lifelong disability. Worldwide, more than 300,000 babies are born with neural tube defects each year. The highest burden is in low and middle income countries. Therefore, this study aims to identify the determinant factors of neural tube defects among mothers who gave birth in North Shoa Zone Hospitals. <b>Methods</b>: A hospital based unmatched case-control study was conducted among 243(81 cases and 162 controls) study participants in North Shoa Zone Hospitals. The hospitals were selected using simple random sampling and all cases and randomly selected controls in the selected hospitals were included in the study. The data were collected by using pre-tested structured questionnaire. <b>Results</b>: Different factors were identified to have association with neural tube defect. Family annual cash income less than 24000ETB (AOR: 3.73, 95%CI: 1.35, 10.26), history of still birth (AOR: 3.63, 95%CI: 1.03, 12.2), history of abortion (AOR: 6.15, 95%CI: 2.63, 18.56), preconception tea use (AOR: 2.36, 95%CI: 1.15, 4.86) and pesticides/chemical exposer (AOR: 5.34, 95%CI: 1.77, 16.05) were positively associated factors. In the contrart, preconception care (AOR: 0.14, 95%CI: 0.05, 0.39) and taking iron/folic acid/multivitamin during the current pregnancy (AOR: 0.16, 95%CI: 0.07, 0.33) showed a protective effect. <b>Conclusion</b>: Family annual income less than 24000ETB, history of still birth, history of abortion, preconception tea use and pesticides/chemical exposer were predictors of neural tube defects. Preconception counseling and screening should be recommended for women who plan for pregnancy. <b>Key words</b>: Neural tube defect, Determinant factors, Hospitals, Ethiopia
DOI: 10.6084/m9.figshare.13366814
title: all-β

description: STINGRDB descriptors for all-beta structures<br>
DOI: 10.6084/m9.figshare.13366814.v1
title: all-β

description: STINGRDB descriptors for all-beta structures<br>
DOI: 10.6084/m9.figshare.13369541
title: β-sheet in (α + β) + (α / β)

description: STINGRDB descriptors for β-sheet in (α+β) + (α/β) structures<br>
DOI: 10.6084/m9.figshare.13369541.v1
title: β-sheet in (α + β) + (α / β)

description: STINGRDB descriptors for β-sheet in (α+β) + (α/β) structures<br>
DOI: 10.25646/7737
title: Tagesdaten-CSV aus dem DIVI-Intensivregister

description: Die Tagesdaten-CSV entspricht einem Auszug der Daten des DIVI-Intensivregisters. Die Datei enthält eine Aggregation der aktuellsten Meldungen pro Landkreis. Es werden die aktuell gemeldeten Anzahlen der COVID-19 Intensivfälle sowie die gemeldeten intensivmedizinischen Behandlungskapazitäten angezeigt. Die Tagesdaten-CSV liefert dabei ausschließlich einen Blick auf die Daten gemäß dem Stand des betrachteten Tages. Die Daten sind im situationsbedingten Kontext aufbereitet, damit sind verschiedene Tagesdaten-CSVs u.U. nicht direkt miteinander vergleichbar. Die aktuellsten Meldungen werden im gewählten Betrachtungszeitfenster über alle Meldebereiche und Standorte aufsummiert. Weitere Informationen sind zu finden unter https://www.intensivregister.de/#/faq
DOI: 10.17632/ms9y3wdjjc.1
title: A rate threshold mechanism regulates MAPK stress signaling and survival
DOI: 10.17632/wd66b4gb4d.1
title: Supplementary Data
DOI: 10.17632/bm59f4nddy.4
title: Distribution of eight forest habitats of European Interest in mainland Spain, and R code for Korcak fragmentation analysis

description: 1. Vector coverages (shapefiles, 1:50,000, EPSG 25830) of the distribution of eight zonal forest types in mainland Spain. The dominant species and Habitat Type code (European Habitats Directive 92/43 EEC) are: • Fagus sylvatica (9120, 9130 and 9150) • Quercus robur and Q. pyrenaica (9230) • Q. suber (9330) • Pinus uncinata (9430) • P. nigra ssp. salzmannii (9530) • P. pinea (subset of 9540) 2. R scripts to determine patchiness using the Korcak exponent B. This is computed both for the entire range of patch sizes and for size intervals using a segmented regression approach. Such intervals are automatically detected.
DOI: 10.17632/jn6mf3s868.1
title: Phenotypic and Genotypic Characterization of Antibiotic Resistance in Military Hospital-Associated Bacteria from War-Injuries in the Eastern Ukraine Conflict between 2014 to 2020

description: Objectives: To describe the phenotypic and genotypic mechanisms of antibiotic resistance in pathogens associated with war-injuries in the Ukraine conflict. Retrospective multicenter microbiological survey in four Ukrainian Military hospitals between 2014 – 2020. A total of 1,061 microbiology results with 813 organisms from 162 different patients were eligible for this study. Only 250 de-duplicated bacterial isolates were selected for further analysis. The proportion and percentage of microorganisms recovered from clinical samples from different military hospitals are described in detail in Supplementary File1. Multi-drug resistant (MDR) strains harbored an abundance of antibiotic resistant genes. K. pneumoniae co-produce class A and D β-lactamases, in one case with blaNDM-1 and rmtC 16S rRNA methyltransferase (RmtASE). A. baumannii also carried class A and D β-lactamases but not metallo-β-lactamases; in four isolates the carbapenemases were present with the RmtASE gene, armA gen. P. aeruginosa harbored wide range of class A and D β-lactamases, along with metallo-β-lactamases, singly with RmtB4 RmtASE . Gram-positive cocci were generally sensitive to tested antibiotics. The whole-genome sequences of investigated microorganisms were deposited to Genbank, the GenBank Accession Numbers can be found in Supplementary File #2. All genes which were retrieved from the genome of investigated microorganisms are listed in Supplementary File3.
DOI: 10.17632/wttpypkctg.1
title: Resting State EEG Biomarkers of Cognitive Decline (PLOS ONE - INSPECDS)
DOI: 10.17632/htgr7k5b79.1
title: Data for spatio-temporal modelling and optimisation of multi-product rice value chains

description: The data is supplement to the Data in Brief article "Data on resources and technologies for the multi-objective spatio-temporal optimisation of Philippine rice value chains". They serve as input to the rice value chains modelling and optimisation studies for the Philippines that is published in the Journal of Cleaner Production article "Integrated production of food, energy, fuels and chemicals from rice crops: Multi-objective optimisation for efficient and sustainable value chains". The data were acquired by literature search in academic journals, technical papers and government agencies. They are presented in tables or worksheets (MS Excel format) and fully referenced. There are eight worksheets. The first worksheet shows the contents of each worksheet. The following worksheets, A to F, tabulate the various data acquired for the resources, processing technologies and transporting technologies in order to model and optimise multi-product rice value chains. The last worksheet lists the references for all data collected.