cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/k7nk86cfbs.1
title: A fast method to compute dispersion diagrams of three-dimensional photonic crystals with rectangular geometry

description: We propose a method and codes for fast computation of complex dispersion relations in three-dimensional photonic crystals (PCs) with rectangular geometry. The main idea of the method is to convert the eigenproblem to a nonlinear equation equivalent to the zero-determinant condition. This equation is then solved iteratively either by fixed-point iteration or by rational approximation method. Additional mathematical elements include fast-converging continued-fraction expansion to compute the interaction tensor (appearing in the above nonlinear equation) and efficient accounting for the rectangular geometry in matrix-vector multiplications, which are involved in computing the continued fraction coefficients. The method allows one to perform realistic three-dimensional computations on a typical laptop computer, including finding the Bloch wave vector in the band gaps and in evanescent mode bands. This paper is focused on the method and includes its detailed explanation and illustration with examples. The associated computational package contains a detailed user guide and a set of further demonstrations, which can be run with the help of provided scripts.
DOI: 10.17632/psm26xxbvd.1
title: TeNeS: Tensor network solver for quantum lattice systems

description: TeNeS (Tensor Network Solver) [1], [2] is a free/libre open-source software program package for calculating two-dimensional many-body quantum states based on the tensor network method and the corner transfer matrix renormalization group (CTMRG) method. This package calculates ground-state wavefunctions for user-defined Hamiltonians and evaluates user-defined physical quantities such as magnetization and correlation functions. For certain predefined models and lattices, there is a tool that makes it easy to generate input files. TeNeS uses an OpenMP/MPI hybrid parallelized tensor operation library and thus can perform large-scale calculations using massively parallel machines.
DOI: 10.17632/srkpysb727.1
title: FELINE: Finite element solver for hydrodynamic lubrication problems using the inexact Newton method

description: In this work we present FELINE, a C++ solver of the Reynolds equation for treating hydrodynamic lubrication problems. To correctly describe cavitation regions, FELINE implements the inexact Newton iteration (INE) algorithm within a finite element method (FEM) framework. The solver was tested and validated against known cases in literature and industrially relevant cases of dimpled textures. Furthermore, we provide a benchmark for a complex dimpled texture case to evaluate the performance and robustness of the implementation. FELINE performs very fast when compared with existing implementations and shows a great degree of stability, while providing physically correct solutions thanks to the INE algorithm.
DOI: 10.17632/xvfvk2zvhw.1
title: Dataset of "Consistency of pacing profile according to performance level in three different editions of the Chicago, London, and Tokyo marathons"

description: Dataset with the data of the manuscript "Consistency of pacing profile according to performance level in three different editions of the Chicago, London, and Tokyo marathons" published in Scientific Reports (DOI: 10.1038/s41598-022-14868-6). The dataset is after pre-processing data (removing outliers, calculate the variables of analysis, etc.).
DOI: 10.17632/b66g5nknk4.3
title: Vulnerability-related Source Code Comments in GitHub

description: This artefact is a repository consisting of the collected dataset including (i) 1,491 vulnerability-related source code comments extracted from GitHub, and (ii) 1,491 code comments of our manual analysis. This artefact aims to enable researchers to replicate our dataset and reuse this dataset for further research.
DOI: 10.17632/cx455t6j6x.1
title: Melanopsin retinal ganglion cells mediate light-promoted brain development through retinal-hypothalamic circuits

description: Raw data of this paper
DOI: 10.17632/drkj8vhdms.1
title: A study of Dynamics of synthetic yeast chromosome evolution shaped by hierarchical chromatin organization. Sijie Zhou et al.

description: 1.We comprehensively sequenced this SCRaMbLEd pool and detected over 260,000 rearrangement events via a loxPsym junction analysis method.By analyzing each rearrangement event, we uncovered a stable rearrangement landscape for synthetic chromosomes.
2.To investigate the mechanisms underlying the rearrangement patterns,we compared the rearrangement map with local chromatin structures and the three-dimensional genome architecture via assay for transposase-accessible chromatin using sequencing (ATAC-seq) and genome-wide chromosome conformation capture (Hi-C), respectively
DOI: 10.17632/p27tzscvb3.1
title: data_acp-2022-125

description: Electromagnetic, particle and meteorological data related to the study "Continental thunderstorm ground enhancement
observed at an exceptionally low altitude" (Atmospheric Chemistry and Physics).
DOI: 10.17632/tcfbd773wv.1
title: A study of Dynamics of synthetic yeast chromosome evolution shaped by hierarchical chromatin organization. Sijie Zhou et al.

description: The sequencing of SCRaMbLEd populations.
SCRaMbLE of the strain yZSJ025 to generate a SCRaMbLEd pool(yZSJ400). yZSJ400 has a different sequencing depth from yZSJ490
DOI: 10.17632/wkhsvt4fpg.2
title: Investigation of the effect of Coriander (Coriandrum savitum) on hematological and immune system of Rainbow Trout (Oncorhynchus mykiss)

description: This study includes the investigation of the effect of coriander (Coriandrum savitum) on haematological parameters and immune system of rainbow trout (Oncorhynchus mykiss). For this purpose, fish with an average weight of 40±25 g were used. Coriander was added to the feed as 0, 0.5, 1.0, 2.0 mg/g, and experimental groups were formed. Prepared feed was fed in the morning and evening and weighed as 2% of fish weight daily. Blood samples were taken from the fish on the 21st and 42nd days from the first feeding. After the feeding experiment (21st and 42nd days), hematological and immunological parameters were examined. As a result, adding up to 2% of coriander to the feed of Rainbow trout did not cause any problems in terms of fish growth. In the study, it was observed that there was no difference between the control group and the experimental group in terms of erythrocyte, leukocyte, hemoglobin, hematocrit, average erythrocyte volume, mean erythrocyte hemoglobin, mean erythrocyte hemoglobin concentration, total immunoglubin, lysozyme activity, nitroblue tetrazolium activity, protein values, whereas in terms of myeloperoxidase activity (P >0.05), a difference was observed between the control group and the experimental group (P <0.05).
DOI: 10.17632/63wx3vd7hx.2
title: iScience

description: Mycobacterium tuberculosis (Mtb) evades host clearance by inhibiting autophagy. MicroRNA-25 (miR-25) expression was significantly up-regulated in the lung tissues of mice infected with Bacillus Calmette-Guerin (BCG) and macrophages infected with Mtb or BCG, especially in the early stages of infection. MiR-25 can significantly increase the survival of Mtb and BCG in macrophages. We validated that miR-25 targets the NPC1 protein located on the lysosomal membrane, resulting in damage to lysosomal function, thereby inhibiting autophagolysosome formation and promoting the survival of Mtb and BCG. Consistently, mice lacking miR-25 exhibited more resistant to BCG infection. In addition, we found that Rv1759c induces the expression of miR-25 through NFKB inhibitor zeta (NFKBIZ). This study demonstrates that the role of miR-25 during Mtb infection contributes to a better understanding of the pathogenesis of tuberculosis (TB).
DOI: 10.17632/f48mxkzz3c.1
title: LINF_290008500

description: protein of unknown function - conserved
Leishmania infantum (strain JPCM5)
DOI: 10.5517/ccdc.csd.cc29kzql
title: CCDC 2132450: Experimental Crystal Structure Determination

description: Related Article: Pankaj Kumar, Navpreet Kaur, Rakesh Kumar, Prabal Banerjee|2022|J.Org.Chem.|87|7167|doi:10.1021/acs.joc.2c00379
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2b0h2y
title: CCDC 2145419: Experimental Crystal Structure Determination

description: Related Article: Peyman Hamidizadeh, Reza Babadi Aghakhanpour, Samira Chamyani, Sareh Paziresh, Hamid R. Shahsavari, S. Masoud Nabavizadeh|2022|Organometallics|41|1325|doi:10.1021/acs.organomet.2c00064
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2b0h3z
title: CCDC 2145420: Experimental Crystal Structure Determination

description: Related Article: Peyman Hamidizadeh, Reza Babadi Aghakhanpour, Samira Chamyani, Sareh Paziresh, Hamid R. Shahsavari, S. Masoud Nabavizadeh|2022|Organometallics|41|1325|doi:10.1021/acs.organomet.2c00064
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.17632/r5scn89cgv.1
title: LINF_290008400

description: UBX domain-containing protein
Leishmania infantum (strain JPCM5)
DOI: 10.6084/m9.figshare.20010191
title: Bee communities net collected from New Jersey watermelon crop flowers

description: Wild bee communities were sampled at watermelon (<em>Citrullus lanatus</em>) farms in the eastern USA. We netted all bees visiting crop flowers within a predefined 50- to 200-m<sup>2</sup> transect. Netting was repeated in three 20-minute periods each sampling day. Specimens were identified to species using published taxonomic keys and assistance by expert taxonomists. <br> Data collection methods are further described in Lemanski et al, 2022, Greater bee diversity is needed to maintain crop pollination over time, Nature Ecology and Evolution. <br> Both files contain the same data, but the file "watermelon_visit_table.csv" is formatted for the main analysis in the manuscript, while the file "njwat_obs.csv" is formatted for use in a null model analysis. <br>
DOI: 10.6084/m9.figshare.20010179
title: Bee communities net collected from New Jersey blueberry crop flowers

description: Wild bee communities were sampled at highbush blueberry (<em>Vaccinium corymbosum</em> L., cultivars Duke and Bluecrop) farms in the eastern USA. We netted all bees visiting crop flowers within a predefined 50- to 200-m2 transect. Netting was repeated in three 20-minute periods each sampling day. Specimens were identified to species using published taxonomic keys and assistance by expert taxonomists. <br> Data collection methods are further described in Lemanski et al, 2022, Greater bee diversity is needed to maintain crop pollination over time, Nature Ecology and Evolution. <br> Both files contain the same data, but the file "blueberry_visit_table.csv" is formatted for the main analysis in the manuscript, while the file "blue_obs.csv" is formatted for use in a null model analysis.
DOI: 10.6084/m9.figshare.20083916
title: Bee communities net collected from California watermelon crop flowers

description: Wild bee communities were sampled at watermelon (<em>Citrullus lanatus, </em>cultivars Crimson Sweet and Yellow Baby) farms in the western USA. We netted all bees visiting crop flowers within a predefined 50- to 200-m2 transect. Netting was repeated in four ten-minute periods each sampling day. Specimens were identified to species using published taxonomic keys and assistance by expert taxonomists. <br> Data collection methods are further described in Lemanski et al, 2022, Greater bee diversity is needed to maintain crop pollination over time, Nature Ecology and Evolution. <br> Both files contain the same data, but the file "ca_wat_visits_corr.csv" is formatted for the main analysis in the manuscript, while the file "3years_wbees_oncrop.csv" is formatted for use in a null model analysis.
DOI: 10.5281/zenodo.6631536
title: NPM Packages (~1.9M packages)

description: - input.json.gz contains the raw NPM data dump from the replicate.npmjs.org database (downloaded on June 4th, 2022) in the following format: <pre><code class="language-json">{ "total_rows": 1997865, "offset": 0, "rows": [ { "id": "-", "key": "-", "value": { "rev": "5-92e28c1ea7f24d165faa202aabd92669" }, "doc": { "_id": "-", "_rev": "5-92e28c1ea7f24d165faa202aabd92669", "name": "-", "dist-tags": { "latest": "0.0.1" }, "versions": { "0.0.1": { "name": "-", "version": "0.0.1", "license": "UNLICENSED", "keywords": [], "main": "dist/index.js", "types": "dist/index.d.ts", "scripts": { "test": "echo \"Error: no test specified\" && exit 1", "start": "node --require ts-node/register src", "build": "tsc" }, "devDependencies": { "@types/node": "13.9.0", "ts-node": "8.6.2", "typescript": "3.8.3" }, "description": "...", "_id": "-@0.0.1", "_nodeVersion": "13.3.0", "_npmVersion": "6.14.4", "dist": {...}, "maintainers": [ { "name": "parzhitsky", "email": "parzhitsky@gmail.com" } ], "_npmUser": { "name": "parzhitsky", "email": "parzhitsky@gmail.com" }, "directories": {}, "_npmOperationalInternal": { "host": "s3://npm-registry-packages", "tmp": "tmp/-_0.0.1_1585828132159_0.6185838126718755" }, "_hasShrinkwrap": false } }, "time": { "created": "2020-04-02T11:48:52.159Z", "0.0.1": "2020-04-02T11:48:52.339Z", "modified": "2022-04-04T10:06:01.120Z" }, "maintainers": [ { "email": "support@npmjs.com", "name": "npm-support" } ], "description": "...", "keywords": [], "license": "UNLICENSED", "readme": "...", "readmeFilename": "README.md" } }, ... ] }</code></pre> - streamedout.json.gz contains a processed file that has the following format <pre><code class="language-json">{"pkgs": [ { "name": "react", "versions": { "1.00": { "timestamp": "06-05-2022T10:00:01", "dependencies": { "name": "^1.0.2" } } } }, ... ]}</code></pre>
DOI: 10.5281/zenodo.6631535
title: NPM Packages (~1.9M packages)

description: - input.json.gz contains the raw NPM data dump from the replicate.npmjs.org database (downloaded on June 4th, 2022) in the following format: <pre><code class="language-json">{ "total_rows": 1997865, "offset": 0, "rows": [ { "id": "-", "key": "-", "value": { "rev": "5-92e28c1ea7f24d165faa202aabd92669" }, "doc": { "_id": "-", "_rev": "5-92e28c1ea7f24d165faa202aabd92669", "name": "-", "dist-tags": { "latest": "0.0.1" }, "versions": { "0.0.1": { "name": "-", "version": "0.0.1", "license": "UNLICENSED", "keywords": [], "main": "dist/index.js", "types": "dist/index.d.ts", "scripts": { "test": "echo \"Error: no test specified\" && exit 1", "start": "node --require ts-node/register src", "build": "tsc" }, "devDependencies": { "@types/node": "13.9.0", "ts-node": "8.6.2", "typescript": "3.8.3" }, "description": "...", "_id": "-@0.0.1", "_nodeVersion": "13.3.0", "_npmVersion": "6.14.4", "dist": {...}, "maintainers": [ { "name": "parzhitsky", "email": "parzhitsky@gmail.com" } ], "_npmUser": { "name": "parzhitsky", "email": "parzhitsky@gmail.com" }, "directories": {}, "_npmOperationalInternal": { "host": "s3://npm-registry-packages", "tmp": "tmp/-_0.0.1_1585828132159_0.6185838126718755" }, "_hasShrinkwrap": false } }, "time": { "created": "2020-04-02T11:48:52.159Z", "0.0.1": "2020-04-02T11:48:52.339Z", "modified": "2022-04-04T10:06:01.120Z" }, "maintainers": [ { "email": "support@npmjs.com", "name": "npm-support" } ], "description": "...", "keywords": [], "license": "UNLICENSED", "readme": "...", "readmeFilename": "README.md" } }, ... ] }</code></pre> - streamedout.json.gz contains a processed file that has the following format <pre><code class="language-json">{"pkgs": [ { "name": "react", "versions": { "1.00": { "timestamp": "06-05-2022T10:00:01", "dependencies": { "name": "^1.0.2" } } } }, ... ]}</code></pre>
DOI: 10.17632/rgwzydrg92.1
title: Dissolved (< 0.45 µm) major and trace elements and landscape parameters of Ket and Taz Rivers, Wetsern Siberia

description: Complete data set of dissolved (< 0.45 µm) concentrations of major and trace elements in the Ket River and the Taz River of Western Siberia, together with land cover parameters of watersheds
DOI: 10.6084/m9.figshare.20083910
title: Private vs. public value of U.S. residential battery storage operated for solar self-consumption

description: Please see "Note" or project description. These folders contain the input files and models (optimization and non-optimization base case) for battery dispatch, accompanying Forrester, Barbose, and Miller (2022) iScience article: "<strong>Private vs. public value of U.S. residential battery storage operated for solar self-consumption</strong>"
DOI: 10.6084/m9.figshare.20083910.v1
title: Private vs. public value of U.S. residential battery storage operated for solar self-consumption

description: Please see "Note" or project description. These folders contain the input files and models (optimization and non-optimization base case) for battery dispatch, accompanying Forrester, Barbose, and Miller (2022) iScience article: "<strong>Private vs. public value of U.S. residential battery storage operated for solar self-consumption</strong>"
DOI: 10.17632/3n5gj3s2cx.1
title: Simultaneous head and neck and lung cancers

description: This retrospective study included all patients with simultaneous HNSCC and lung cancer treated between 2003 and 2020 in two academic hospitals. They were compared to a 1:2 matched group of patients with single HNSCC.
DOI: 10.17632/zpr89hpv6g.2
title:  Acousto-Optic Dispersive Delay Line programmer via Dispersive Fourier Synthesis (AODDL_DFS)

description: Acousto-Optic Dispersive Delay Line programmer via Dispersive Fourier Synthesis (AODDL_DFS) is a MATLAB script generating RF waveforms for ultrafast laser pulse shaping using an Acosuto-Optic Dispersive Delay Line (AODDL). The script creates sampled RF waveforms to be uploaded to the arbitrary waveform generator (AWG). AODDL_DFS features generation of broadband transmission functions of the AODDL with multiple programmable stopbands in the transmission window. Two alternative algorithms for waveform generation are implemented: Dispersive Fourier Synthesis (DFS) for explicit waveform calculation and the Gerchberg-Saxton (GS) algorithm for iterative computing the waveform with linear frequency modulation. Preset transmission functions include single and multiple binary rejection bands, triangular and cosine-shaped modulation, and PRBS spectral modulation.
DOI: 10.17632/6vp4h5yzck.1
title: A novel combination (“CHAP”) regimen for management of livedoid vasculopathy in 12 patients

description: Figure 1. Representative before (A) and after (B) images of patient 11 three months after initiation of the "CHAP" regimen (and discontinuation of prednisone and sulfasalazine), showing resolution of painful ulcerations and jagged purpuric macules without formation of new lesions.
DOI: 10.17632/tf9j4xymj2.1
title: Heat transfer data of supercritical carbon dioxide flowing upwards in tubes

description: The data is uploaded to study heat transfer characteristics of SCO2 vertically flowing in a tube. The experiments were conducted by CNNC Key Laboratory Nuclear Reactor Thermal Hydraulics Technology, Nuclear Power Institute of China. More information can be found in the uploaded file.
DOI: 10.6084/m9.figshare.13693707
title: A Bayesian Latent Variable Selection Model for Nonignorable Missingness

description: Missing data are exceedingly common across a variety of disciplines, such as educational, social, and behavioral science areas. Missing not at random (MNAR) mechanism where missingness is related to unobserved data is widespread in real data and has detrimental consequence. However, the existing MNAR-based methods have potential problems such as leaving the data incomplete and failing to accommodate incomplete covariates with interactions, non-linear terms, and random slopes. We propose a Bayesian latent variable imputation approach to impute missing data due to MNAR (and other missingness mechanisms) and estimate the model of substantive interest simultaneously. In addition, even when the incomplete covariates involves interactions, non-linear terms, and random slopes, the proposed method can handle missingness appropriately. Computer simulation results suggested that the proposed Bayesian latent variable selection model (BLVSM) was quite effective when the outcome and/or covariates were MNAR. Except when the sample size was small, estimates from the proposed BLVSM tracked closely with those from the complete data analysis. With a small sample size, when the outcome was less predictable from the covariates, the missingness proportions of the covariates and the outcome were larger, and the missingness selection processes of the covariates and the outcome were more MNAR and MAR, the performance of BLVSM was less satisfactory. When the sample size was large, BLVSM always performed well. In contrast, the method with an MAR assumption provided biased estimates and undercoverage confidence intervals when the missingness was MNAR. The robustness and the implementation of BLVSM in real data were also illustrated. The proposed method is available in the Blimp software application, and the paper includes a data analysis example illustrating its use.
DOI: 10.6084/m9.figshare.13693707.v2
title: A Bayesian Latent Variable Selection Model for Nonignorable Missingness

description: Missing data are exceedingly common across a variety of disciplines, such as educational, social, and behavioral science areas. Missing not at random (MNAR) mechanism where missingness is related to unobserved data is widespread in real data and has detrimental consequence. However, the existing MNAR-based methods have potential problems such as leaving the data incomplete and failing to accommodate incomplete covariates with interactions, non-linear terms, and random slopes. We propose a Bayesian latent variable imputation approach to impute missing data due to MNAR (and other missingness mechanisms) and estimate the model of substantive interest simultaneously. In addition, even when the incomplete covariates involves interactions, non-linear terms, and random slopes, the proposed method can handle missingness appropriately. Computer simulation results suggested that the proposed Bayesian latent variable selection model (BLVSM) was quite effective when the outcome and/or covariates were MNAR. Except when the sample size was small, estimates from the proposed BLVSM tracked closely with those from the complete data analysis. With a small sample size, when the outcome was less predictable from the covariates, the missingness proportions of the covariates and the outcome were larger, and the missingness selection processes of the covariates and the outcome were more MNAR and MAR, the performance of BLVSM was less satisfactory. When the sample size was large, BLVSM always performed well. In contrast, the method with an MAR assumption provided biased estimates and undercoverage confidence intervals when the missingness was MNAR. The robustness and the implementation of BLVSM in real data were also illustrated. The proposed method is available in the Blimp software application, and the paper includes a data analysis example illustrating its use.
DOI: 10.5519/qd.xdy8aujj
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (11 records)