cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15156/bio/sh3438210.08fu
title: SH3438210.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh3438211.08fu
title: SH3438211.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh3438212.08fu
title: SH3438212.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh3438213.08fu
title: SH3438213.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh3438214.08fu
title: SH3438214.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh3438215.08fu
title: SH3438215.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh3438216.08fu
title: SH3438216.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.17632/7s2cv9kjfs.1
title: py-fmas: A python package for ultrashort optical pulse propagation in terms of forward models for the analytic signal

description: We present a flexible, open-source Python package for the accurate simulation of the z-propagation dynamics of ultrashort optical pulses in nonlinear waveguides, especially valid for few-cycle pulses and their interaction. The simulation approach is based on unidirectional propagation equations for the analytic signal. The provided software allows to account for dispersion, attenuation, four-wave mixing processes including, e.g., third-harmonic generation, and features various models for the Raman response. The propagation equations are solved on a periodic temporal domain. For z-propagation, a selection of pseudospectral methods is available. Propagation scenarios for a custom propagation constant and initial field pulses can either be specified in terms of a HDF5 based input file format or by direct implementation using a python script. We demonstrate the functionality for a test-case for which an exact solution is available, by reproducing exemplary results documented in the scientific literature, and a complex propagation scenario involving multiple pulses.
DOI: 10.17632/dfdcfyg888.1
title: LINF_200021900

description: RESC18
Leishmania infantum (strain JPCM5)
DOI: 10.17632/fm7x2h24m3.1
title: LINF_200022000

description: amidohydrolase
Leishmania infantum (strain JPCM5)
DOI: 10.17632/3yz39935rx.1
title: LINF_200022100

description: amidohydrolase
Leishmania infantum (strain JPCM5)
DOI: 10.17632/khfvjhx4vb.1
title: Automated tip functionalization via machine learning in scanning probe microscopy

description: Auto-CO-AFM is an open-source software package for scanning probe microscopes that enables the automatic functionalization of scanning probe tips with carbon monoxide molecules. This enables machine operators to specify the quality of the tip needed utilizing a pre-trained library with off-the-shelf software. From a single image, the software package can determine which molecules on a surface are carbon monoxide, perform the necessary tip functionalization procedures, interface with microscope software to control the tip position, and determines the centeredness of the tip after a successful functionalization. This is of particular interest for atomic force microscopy imaging of molecules on surfaces, where the tip functionalization is a necessary and time consuming step needed for sub-molecular resolution imaging. This package is freely available under the MIT License.
DOI: 10.17632/86vmptkts6.1
title: LINF_200022200

description: amidohydrolase
Leishmania infantum (strain JPCM5)
DOI: 10.17632/hbk45696nf.1
title: TLBfind: a Thermal Lattice Boltzmann code for concentrated emulsions with FINite-size Droplets

description: In this paper, we present TLBfind, a GPU code for simulating the hydrodynamics of droplets along with a dynamic temperature field. TLBfind hinges on a two-dimensional multi-component lattice Boltzmann (LB) model simulating a concentrated emulsion with finite-size droplets evolving in a thermal convective state, just above the transition from conduction to convection. The droplet concentration of the emulsion system is tunable and at the core of the code lies the possibility to measure a large number of physical observables characterising the flow and droplets. Furthermore, TLBfind includes a parallel implementation on GPU of the Delaunay triangulation useful for the detection of droplets' plastic rearrangements, and several types of boundary conditions, supporting simulations of channels with structured rough walls.
DOI: 10.17632/rw3w87svwd.1
title: Al2O3C: Pulsed OSL and photo transfer TL data

description: This dataset contains the characterization of 33 Al2O3:C crystals for their pulsed optically stimulate luminescence (POSL), thermoluminescence (TL) and photo transferred TL (PTTL) behavior to beta radiation. The accompanying python script produces the figures that are part of the publication "New correlation between PTTL and POSL components in Al2O3:C" submitted to Optical Materials.
DOI: 10.17632/ydf8k8g4vb.1
title: Mathematical discussion in a hybrid environment

description: These data were collected in december 2020 in Italian schools, they are connected to the FEM project M@t.abel 2020.
DOI: 10.25646/9516
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: 10.25646/9519
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: 10.25646/9520
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: 10.17632/9c7f9vbymh.1
title: Graph-based algorithm for common topologies of dynamic lipid clusters 

description: Dataset includes:

1. Tcl scripts to compute H-bonds between lipids, H-bonds between lipid and water molecules (1-water bridges), interactions between lipids and ions from simulations.
2. Matlab scripts to compute lipid H-bond clusters and detect types of cluster topologies using depth-first search (DFS) algorithm.
3. Tcl script to visualize in VMD lipid H-bonds or ion interactions. Lipids are color-coded based on the topology type. 

Workflow is generated and tested in MATLAB R2017b and VMD 1.9.3.
Guidelines for running the scripts are in README text file in the topology_analysis folder.

"When using these scripts, please cite:

"

###########################################################################################################
DFS algorithm:

To cluster lipid H-bond clusters and detect types of topologies, we perform  Connected Component searches based on the Depth-First Search (DFS) algorithm.  The DFS algorithm starts from an initial (source) node and performs exhaustive searches of all the nodes along the current path. When all nodes are visited,  it moves backwards on the same path to find unvisited nodes. When all nodes of the current path are visited, the algorithm selects the next unexplored path. The computation is completed when the entire graph is explored. 

The Degree Centrality (DC) of a node ni gives the number of edges of the node.

Algorithm computes three main types of topologies linear, star and circular and combinations thereof.  All paths are catalogued according to their path length.  For each lipid cluster found in the membrane and for each simulation time,  the length of each path is defined as the longest number of edges between a start and an end node excluding short branches from star paths, and keep for the circular paths only the edge that connects the longest path to the end node.

References:

Cormen, T.H., Leiserson, C.E., Rivest, R.L. and Stein, C., 2009. Introduction to Algorithms (3-rd edition). MIT Press and McGraw-Hill.
Freeman LC: Centrality in social networks. Conceptual clarification. Social Networks 1979, 1:215-239.
V.K. Balakrishnan, Schaum's outline of theory and problems of graph theory, McGraw-Hill, 1997.
J.L. Gross, J. Yellen, Graph theory and its applications, CRC Press, 1998.
DOI: 10.21227/14h3-er18
title: Data Recovery for False Data Injection Attacks of Power Systems Based on Lightweight Variational Convolution Auto-Encoder

description: Power system state estimation (PSSE) plays a vital role in stable operation of modern smart grids, while it is vulnerable to cyber attacks. False data injection attacks (FDIA), one of the most common cyber attacks, can tamper with measurement data and bypass the bad data detection (BDD) mechanism, leading to incorrect PSSE results. This paper proposes a data recovery framework for FDIA based on variational convolution auto-encoder (VCAE) to ensure continuous monitoring of PSSE. VCAE combines deep learning ideas with Bayesian inference. Besides, VCAE uses convolution and deconvolution operations with excellent feature capture capabilities in the encoder and decoder network, respectively, to effectively restore the abnormal values after FDIA to the values close to normal operation. Moreover, knowledge distillation (KD) is used to compress the VCAE model, making it possible to deploy a lightweight model on equipment with limited resources. Case studies are undertaken on IEEE 14-bus system under different attack intensities and degrees to evaluate the recovery performance of VCAE. Simulation results show that the mean absolute error (MAE) and mean absolute percentage error (MAPE) of VCAE are lower than the comparative generative models. Moreover, the satisfactory recovery performance of IEEE 30-bus and 118-bus systems verifies the scalability of the proposed model. In addition, KD allows the lightweight VCAE scale to reach about one-tenth of the original VCAE scale with almost no increase in MAE and MAPE.
DOI: 10.17632/rsk3jvy22f.1
title: Bi-objective design-for-control for improving the resilience of water distribution networks

description: This dataset includes the hydraulic model of the case study network BWPnet studied in the publication "Bi-objective design-for-control for improving the resilience of water distribution networks", by Aly-Joy Ulusoy, Herman Mahmoud, Filippo Pecci, Ivan Stoivanov and Edward Keedwell. The information provided in this dataset, which consists of an .inp file, to access using EPANET or a text editor, with characteristics of network pipes (diameter, length, roughness coefficients) and nodes (elevation, demand), aims to facilitate future comparison of our work against alternative solution methods. We refer the reader to the main manuscript for a detailed presentation of the problem formulation and results obtained for BWPnet.
DOI: 10.17632/vy4ccz4hxz.1
title: PyPhotonics: A python package for the evaluation of luminescence properties of defects

description: The prediction of the photoluminescence line-shape of defect systems from first principles is becoming an important tool for the discovery of quantum emission defects in semiconductors. Using a sequence of density functional theory calculations based on the VASP code, PyPhotonics calculates the Huang-Rhys factor and plots the photoluminescence line-shape of the defect by processing the VASP output.
DOI: 10.17632/8prgdffv92.1
title: Polymorphism promotes edge utilization by marsh crabs

description: These data and R code files derive from the research article "Polymorphism promotes edge utilization by marsh crabs" to be published in Oecologia. Hypotheses, results and data interpretation can be found in the research article.
DOI: 10.17632/9kdb2p76hv.1
title: N ways to simulate short-range particle systems: Automated algorithm selection with the node-level library AutoPas

description: AutoPas is an open-source C++ library delivering optimal node-level performance by providing the ideal algorithmic configuration for an arbitrary scenario in a given short-range particle simulation. It acts as a black-box container, internally implementing an extensive set of algorithms, parallelization strategies, and optimizations that are combined dynamically according to the state of the simulation via auto-tuning. This paper gives an overview of the high-level user perspective, as well as the internal view, covering the implemented techniques and features. The library is showcased by incorporating it into the codes LAMMPS and ls1 mardyn, and by investigating various applications. We further outline node-level shared-memory performance and scalability of our auto-tuning software which is comparable to LAMMPS.
DOI: 10.17632/p8vj83xg4p.2
title: Data for: Immobilization of Streptomyces griseoloalbus alpha galactosidase and soymilk hydrolysis

description: This data is regarding the characterization of immobilized alpha galactosidase from Streptomyces griseolalbus in gelatin-alginate blended beads and hydrolysis of raffinose oligosaccharides in soymilk.
DOI: 10.17632/wzy67jd56d.1
title: A brute-force code searching for cell of non-identical displacement for CSL grain boundaries and interfaces

description: Atomic simulation of coincidence-site lattice (CSL) grain boundaries (GBs) and interfaces is of importance for understanding GBs in polycrystalline materials and for making functional films. A common process of high-throughput simulation for CSL GBs and interfaces is to explore rigid body translation (RBT) of one crystal respect to the other. Cell of non-identical displacement (CNID) is the minimum cell including all non-identical RBTs in the GB or interface plane and is important for effective sampling. This work proposes an algorithm to compute the CNID of any two-dimensional CSL GB or interface based on a reciprocity relation between the displacement shift complete (DSC) and CSL.
DOI: 10.17632/2hxhw9zjg9.1
title: EDIpack: A parallel exact diagonalization package for quantum impurity problems

description: We present EDIpack, an exact diagonalization package to solve generic quantum impurity problems. The algorithm includes a generalization of the look-up method introduced in Ref. [1] and enables a massively parallel execution of the matrix-vector linear operations required by Lanczos and Arnoldi algorithms. We show that a suitable Fock basis organization is crucial to optimize the inter-processors communication in a distributed memory setup and to reach sub-linear scaling in sufficiently large systems. We discuss the algorithm in details indicating how to deal with multiple orbitals and electron-phonon coupling. Finally, we outline the download, installation and functioning of the package.