cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5517/ccdc.csd.cc28k6dg
title: CCDC 2101905: Experimental Crystal Structure Determination

description: Related Article: Mengchu Zhang, Sifan Yu, Ruyu Hua, Dan Zhang, Huang Qiu, Wenhao Hu|2023|Org.Biomol.Chem.|21|783|doi:10.1039/D2OB02075K
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.cc28mq9y
title: CCDC 2104320: Experimental Crystal Structure Determination

description: Related Article: Mengchu Zhang, Sifan Yu, Ruyu Hua, Dan Zhang, Huang Qiu, Wenhao Hu|2023|Org.Biomol.Chem.|21|783|doi:10.1039/D2OB02075K
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.cc28n8ks
title: CCDC 2104855: Experimental Crystal Structure Determination

description: Related Article: Terence Wu, Matthew R. Tatton, Michael F. Greaney|2022|Angew.Chem.,Int.Ed.|61|e202117524|doi:10.1002/anie.202117524
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: 10.6084/m9.figshare.21937601
title: BHK-21-RABV-M-GST-Pulldown

description: Identification of RABV-M interactome via GST pull-down coupled with LC-MS/MS.
DOI: 10.5281/zenodo.7504830
title: Pupillary dynamics reflect the impact of temporal expectation on detection strategy - data

description: This repository contains data from work that investigated how humans can extract hidden temporal cues from the occurrences of probabilistic targets and utilize them to inform target detection in a complex acoustic stream, using a combination of behavioral measures and pupillometry. It accompanies the article entitled: " <strong>Pupillary dynamics reflect the impact of temporal expectation on detection strategy</strong>" from the same authors. It contains:<br> - preprocessed pupil data for all subjects<br> - similarly matched behavior data for all subjects<br> - custom code for both behavioral and pupil analysis
DOI: 10.5281/zenodo.7504829
title: Pupillary dynamics reflect the impact of temporal expectation on detection strategy - data

description: This repository contains data from work that investigated how humans can extract hidden temporal cues from the occurrences of probabilistic targets and utilize them to inform target detection in a complex acoustic stream, using a combination of behavioral measures and pupillometry. It accompanies the article entitled: " <strong>Pupillary dynamics reflect the impact of temporal expectation on detection strategy</strong>" from the same authors. It contains:<br> - preprocessed pupil data for all subjects<br> - similarly matched behavior data for all subjects<br> - custom code for both behavioral and pupil analysis
DOI: 10.5066/p9zvc4d5
title: Denali Fault Zone Field, Microvein, and Microbeam Data, Kluane Ranges, Yukon, Canada

description: Detailed geologic mapping and sample collection was conducted in rare bedrock exposures of the Denali fault zone during the summer months of 2013, 2014, and 2015 by the U.S. Geological Survey. Data include measurements of structural geologic orientations and documentation of fault zone and host rock characteristics. Representative samples were selected for measurements of fault vein attributes and electron backscatter diffraction studies to characterize deformation mechanisms. All station locations, pertinent sample information, and associated data are included in this data release.
DOI: 10.5281/zenodo.7466606
title: High-resolution oil and gas methane emission inventory for the Permian Basin

description: This dataset consists of a high-resolution (0.01<sup>o</sup> × 0.01<sup>o</sup>) oil and gas methane emission inventory for the Permian Basin, developed at Environmental Defense Fund (www.edf.org). The Permian Basin in western Texas and southern New Mexico is the largest oil producing basin in the U.S., accounting for more than 40% of national oil production in 2021. It is also the nation's largest methane emitting basin, with recent measurement-based estimates of more than three million metric tons per year. Here, we develop an improved inventory of oil and gas methane emissions for the Permian Basin, based on recent facility-scale measurements and updated oil and gas activity data for the year 2021. Full details for the oil and gas methane emission inventory development and key results can be found in the following journal paper, which is under review at Earth System Science Data journal. Please cite the paper when using the methane inventory dataset: Omara, M., Gautam, R., O'Brien, M.A., Himmelberger, A., Franco, A., Meisenhelder, K., Hauser, G., Lyon, D.R., Chulakadaba, A., Miller, C.C., Franklin, J., Wofsy, S., and Hamburg, S.P. Developing a spatially explicit global oil and gas infrastructure database for characterizing methane emission sources at high resolution. <em>In review</em>, Earth System Science Data journal (2023). Points of Contact at Environmental Defense Fund: Mark Omara (momara@edf.org) and Ritesh Gautam (rgautam@edf.org).
DOI: 10.5281/zenodo.7569671
title: DACOS - Dataset

description: <strong>DACOS - DAtaset of COde Smells</strong> The dataset offers annotated code snippets for three code smells— multifaceted abstraction, complex method, and long parameter list. In addition to a manually annotated dataset on potentially subjective snippets, we offer a larger set of snippets containing the snippets that are either definitely benign or smelly. The upload contains three files : DACOSMain.sql - This is the SQL file containing the main DACOS dataset. DACOSExtended.sql - This is the SQL file containing the Extended DACOS dataset. Files.zip - The zip file containing all the source code files. <strong>Required Software</strong> The dataset is created in MySQL. Hence a local or remote installation of MySQL is needed with privileges to create and modify schemas. <strong>Importing the Dataset</strong> The dataset is a self-contained SQL file. To import the dataset, run the following command: <pre><code>mysql -u username -p database_name &lt; DACOSMain.sql mysql -u username -p database_name &lt; DACOSExtended.sql</code></pre> <strong>Understanding the Datasets</strong> Both the datasets differ in architecture. The main dataset contains a table named annotations that contains every annotation collected from users. The sample table contains the samples presented to the user for annotation. The class_metrics and method_metrics contain the tables for class and method metrics respectively. These were used to filter samples that are likely to contain smells and hence can be shown to users. The extended dataset is created by selecting samples that are below or above the selected metric range for each smell. Hence, these samples are definitely smelly or benign. The extended version of the dataset does not contain a table for annotation since they were not presented to user. It instead has an 'entry' table where each sample is classified according to the smell it contains. The codes for identifying smells are as below: Condition smell Id Multifaceted Abstraction Present 1 Multifaceted Abstraction not detected 4 Long Parameter List Present 2 Long Parameter List Absent 5 Complex Method Present 3 Complex Method Absent 6
DOI: 10.5281/zenodo.7569672
title: DACOS - Dataset

description: <strong>DACOS - DAtaset of COde Smells</strong> The dataset offers annotated code snippets for three code smells— multifaceted abstraction, complex method, and long parameter list. In addition to a manually annotated dataset on potentially subjective snippets, we offer a larger set of snippets containing the snippets that are either definitely benign or smelly. The upload contains three files : DACOSMain.sql - This is the SQL file containing the main DACOS dataset. DACOSExtended.sql - This is the SQL file containing the Extended DACOS dataset. Files.zip - The zip file containing all the source code files. <strong>Required Software</strong> The dataset is created in MySQL. Hence a local or remote installation of MySQL is needed with privileges to create and modify schemas. <strong>Importing the Dataset</strong> The dataset is a self-contained SQL file. To import the dataset, run the following command: <pre><code>mysql -u username -p database_name &lt; DACOSMain.sql mysql -u username -p database_name &lt; DACOSExtended.sql</code></pre> <strong>Understanding the Datasets</strong> Both the datasets differ in architecture. The main dataset contains a table named annotations that contains every annotation collected from users. The sample table contains the samples presented to the user for annotation. The class_metrics and method_metrics contain the tables for class and method metrics respectively. These were used to filter samples that are likely to contain smells and hence can be shown to users. The extended dataset is created by selecting samples that are below or above the selected metric range for each smell. Hence, these samples are definitely smelly or benign. The extended version of the dataset does not contain a table for annotation since they were not presented to user. It instead has an 'entry' table where each sample is classified according to the smell it contains. The codes for identifying smells are as below: Condition smell Id Multifaceted Abstraction Present 1 Multifaceted Abstraction not detected 4 Long Parameter List Present 2 Long Parameter List Absent 5 Complex Method Present 3 Complex Method Absent 6
DOI: 10.5281/zenodo.7570428
title: DACOS - Dataset

description: <strong>DACOS - DAtaset of COde Smells</strong> The dataset offers annotated code snippets for three code smells— multifaceted abstraction, complex method, and long parameter list. In addition to a manually annotated dataset on potentially subjective snippets, we offer a larger set of snippets containing the snippets that are either definitely benign or smelly. The upload contains three files : DACOSMain.sql - This is the SQL file containing the main DACOS dataset. DACOSExtended.sql - This is the SQL file containing the Extended DACOS dataset. Files.zip - The zip file containing all the source code files. <strong>Required Software</strong> The dataset is created in MySQL. Hence a local or remote installation of MySQL is needed with privileges to create and modify schemas. <strong>Importing the Dataset</strong> The dataset is a self-contained SQL file. To import the dataset, run the following command: <pre><code>mysql -u username -p database_name &lt; DACOSMain.sql mysql -u username -p database_name &lt; DACOSExtended.sql</code></pre> <strong>Understanding the Datasets</strong> Both the datasets differ in architecture. The main dataset contains a table named annotations that contains every annotation collected from users. The sample table contains the samples presented to the user for annotation. The class_metrics and method_metrics contain the tables for class and method metrics respectively. These were used to filter samples that are likely to contain smells and hence can be shown to users. The extended dataset is created by selecting samples that are below or above the selected metric range for each smell. Hence, these samples are definitely smelly or benign. The extended version of the dataset does not contain a table for annotation since they were not presented to user. It instead has an 'entry' table where each sample is classified according to the smell it contains. The codes for identifying smells are as below: Condition smell Id Multifaceted Abstraction Present 1 Multifaceted Abstraction not detected 4 Long Parameter List Present 2 Long Parameter List Absent 5 Complex Method Present 3 Complex Method Absent 6
DOI: 10.21227/cm13-p079
title: SUPPLEMENTARY MATERIAL - Analysis of Coil Coupling in the Near-field Far-field Hybrid Region

description: This supplementary material includes the derivation of static coupling and radiative coupling between coils working at near-field/far-field hybrid regions.
DOI: 10.6084/m9.figshare.19729990
title: Multimodal Rayleigh and Love wave joint inversion for S-wave velocity structures in Kanto Basin, Japan

description: <pre><code>You can download the FJ spectrograms, observed dispersion curves, local 1D S-wave velocity model, and interpolated 3D model.</code></pre> <pre><code>Each file includes following information.</code></pre> <pre><code><br></code></pre> <pre><code>*LatLon.txt</code></pre> <pre><code>Coordinates of gravity of all stations in each array. Fist and second columns indicate Latitude and Longitude. Each row includes result of each array.</code></pre> <pre><code><br></code></pre> <pre><code>*Thickness.txt</code></pre> <pre><code>The estimated thickness of each 1D S-wave velocity structure. Fist, second and third columns indicate the thickness of fist, second and third layer, respectively. Each row includes result of each array. The coordinates were explained in LatLon.txt.</code></pre> <pre><code><br></code></pre> <pre><code>*Vs1D.txt</code></pre> <pre><code>The estimated S-wave velocity of each 1D S-wave velocity structure. Fist, second, third and fourth columns indicate the S-wave velocity of fist, second, third and fouth layer, respectively. Each row includes result of each array. The coordinates were explained in LatLon.txt.</code></pre> <pre><code><br></code></pre> <pre><code>*frequency.txt</code></pre> <pre><code>The frequency of observed dispersion curves.</code></pre> <pre><code><br></code></pre> <pre><code>*Dispersion_curves.txt</code></pre> <pre><code>This file includes multimodal Rayleigh and Love wave dispersion curves obsrved in each array (The coordinates were explained in LatLon.txt). The number of array is same as the row of LatLon.txt.</code></pre> <pre><code><br></code></pre> <pre><code>*Vs3D.txt</code></pre> <pre><code>The interpolated 3D S-wave velocity model. This file is described as follows.</code></pre> <code> 1 2 3 4</code> <br> <code>1 Latitude Longitude depth Vs</code> <br> <code>2 Latitude Longitude depth Vs</code> <br> <code>: : : : :</code> <br> <code>: : : : :</code> <pre><code><br></code></pre> <pre><code>*FJ.m and FJ.mat</code></pre> <pre><code>The FJ spectrogram is described in MATLAB (FJ.mat). You can check the FJ spectrogram which we calculated by using FJ.m.</code></pre>
DOI: 10.5281/zenodo.6472266
title: Substrate stiffness reduces particle uptake by epithelial cells and macrophages in a size-dependent manner through mechanoregulation

description: Cells continuously exert forces on their environment and respond to changes in mechanical forces by altering their behavior. Many pathologies such as cancer and fibrosis are hallmarked by dysregulation in the extracellular matrix, driving aberrant behavior through mechanotransduction pathways. We demonstrate that substrate stiffness can be used to regulate cellular endocytosis of particles in a size-dependent fashion. Culture of A549 epithelial cells and J774A.1 macrophages on polystyrene/glass (stiff) and polydimethylsiloxane (soft) substrates indicated that particle uptake is increased up to six times for A549 and two times for macrophages when cells are grown in softer environments. Furthermore, we altered surface characteristics through the attachment of submicron-sized particles as a method to locally engineer substrate stiffness and topography. To investigate the biomechanical changes which occurred within adherent epithelial cells, i.e. characterization of A549 cell spreading and focal adhesion maturation. Consequently, decreasing substrate rigidity and particle-based topography lead to a reduction of focal adhesion size. Moreover, expression levels of Yes-associated protein were found to correlate with the degree of particle endocytosis. A thorough appreciation of the mechanical cues may lead to improved solutions to optimize nanomedicine approaches for treatment of cancer and other diseases with abnormal mechanosignaling.
DOI: 10.5281/zenodo.7464241
title: Substrate stiffness reduces particle uptake by epithelial cells and macrophages in a size-dependent manner through mechanoregulation

description: Cells continuously exert forces on their environment and respond to changes in mechanical forces by altering their behavior. Many pathologies such as cancer and fibrosis are hallmarked by dysregulation in the extracellular matrix, driving aberrant behavior through mechanotransduction pathways. We demonstrate that substrate stiffness can be used to regulate cellular endocytosis of particles in a size-dependent fashion. Culture of A549 epithelial cells and J774A.1 macrophages on polystyrene/glass (stiff) and polydimethylsiloxane (soft) substrates indicated that particle uptake is increased up to six times for A549 and two times for macrophages when cells are grown in softer environments. Furthermore, we altered surface characteristics through the attachment of submicron-sized particles as a method to locally engineer substrate stiffness and topography. To investigate the biomechanical changes which occurred within adherent epithelial cells, i.e. characterization of A549 cell spreading and focal adhesion maturation. Consequently, decreasing substrate rigidity and particle-based topography lead to a reduction of focal adhesion size. Moreover, expression levels of Yes-associated protein were found to correlate with the degree of particle endocytosis. A thorough appreciation of the mechanical cues may lead to improved solutions to optimize nanomedicine approaches for treatment of cancer and other diseases with abnormal mechanosignaling.
DOI: 10.5281/zenodo.4922652
title: Particle Stiffness and Surface Topography Determine Macrophage-Mediated Removal of Surface Adsorbed Particles

description: Cellular surface recognition and behavior are driven by a host of physical and chemical features which have been exploited to influence particle–cell interactions. Mechanical and topographical cues define the physical milieu which plays an important role in defining a range of cellular activities such as material recognition, adhesion, and migration through cytoskeletal organization and signaling. In order to elucidate the effect of local mechanical and topographical features generated by the adsorption of particles to an underlying surface on primary human monocyte-derived macrophages (MDM), a series of poly(<em>N</em>-isopropylacrylamide) (pNIPAM) particles with differing rigidity are self-assembled to form a defined particle-decorated surface. Assembly of particle-decorated surfaces is facilitated by modification of the underlying glass to possess a positive charge through functionalization using 3-aminopropyltriethoxysilane (APTES) or coating with poly(L-lysine) (PLL). MDMs are noted to preferentially remove particles with higher degrees of crosslinking (stiffer) than those with lower degrees of crosslinking (softer). Alterations to the surface density of particles enabled a greater area of the particle-decorated surface to be cleared. Uniquely, the impact of particle adsorption is evinced to have a direct impact on topographical recognition of the surface, suggesting a novel approach for controllably affecting cell-surface recognition and response.
DOI: 10.5281/zenodo.4922653
title: Particle Stiffness and Surface Topography Determine Macrophage-Mediated Removal of Surface Adsorbed Particles

description: Cellular surface recognition and behavior are driven by a host of physical and chemical features which have been exploited to influence particle–cell interactions. Mechanical and topographical cues define the physical milieu which plays an important role in defining a range of cellular activities such as material recognition, adhesion, and migration through cytoskeletal organization and signaling. In order to elucidate the effect of local mechanical and topographical features generated by the adsorption of particles to an underlying surface on primary human monocyte-derived macrophages (MDM), a series of poly(<em>N</em>-isopropylacrylamide) (pNIPAM) particles with differing rigidity are self-assembled to form a defined particle-decorated surface. Assembly of particle-decorated surfaces is facilitated by modification of the underlying glass to possess a positive charge through functionalization using 3-aminopropyltriethoxysilane (APTES) or coating with poly(L-lysine) (PLL). MDMs are noted to preferentially remove particles with higher degrees of crosslinking (stiffer) than those with lower degrees of crosslinking (softer). Alterations to the surface density of particles enabled a greater area of the particle-decorated surface to be cleared. Uniquely, the impact of particle adsorption is evinced to have a direct impact on topographical recognition of the surface, suggesting a novel approach for controllably affecting cell-surface recognition and response.
DOI: 10.5281/zenodo.7570398
title: Layer-by-Layer siRNA Particle Assemblies for Localized Delivery of siRNA to Epithelial Cells through Surface-Mediated Particle Uptake

description: Localized delivery of small interfering RNA (siRNA) is a promising approach for spatial control of cell responses at biomaterial interfaces. Layer-by-layer (LbL) assembly of siRNA with cationic polyelectrolytes has been used in film and nanoparticle vectors for transfection. Herein, we combine the ability of particles to efficiently deliver siRNA with the ability of film polyelectrolyte multilayers to act locally. LbL particles were prepared with alternating layers of poly(l-arginine) and siRNA and capped with hyaluronic acid. Negatively charged LbL particles were subsequently assembled on the poly(l-lysine)-functionalized substrate to form a LbL particle-decorated surface. Cells grown in contact with the particle-decorated surface were able to survive, internalize particles, and undergo gene silencing. This work shows that particle-decorated surfaces can be engineered by using electrostatic interactions and used to deliver therapeutic payloads for cell-instructive biointerfaces.
DOI: 10.5281/zenodo.7570399
title: Layer-by-Layer siRNA Particle Assemblies for Localized Delivery of siRNA to Epithelial Cells through Surface-Mediated Particle Uptake

description: Localized delivery of small interfering RNA (siRNA) is a promising approach for spatial control of cell responses at biomaterial interfaces. Layer-by-layer (LbL) assembly of siRNA with cationic polyelectrolytes has been used in film and nanoparticle vectors for transfection. Herein, we combine the ability of particles to efficiently deliver siRNA with the ability of film polyelectrolyte multilayers to act locally. LbL particles were prepared with alternating layers of poly(l-arginine) and siRNA and capped with hyaluronic acid. Negatively charged LbL particles were subsequently assembled on the poly(l-lysine)-functionalized substrate to form a LbL particle-decorated surface. Cells grown in contact with the particle-decorated surface were able to survive, internalize particles, and undergo gene silencing. This work shows that particle-decorated surfaces can be engineered by using electrostatic interactions and used to deliver therapeutic payloads for cell-instructive biointerfaces.
DOI: 10.6084/m9.figshare.20419401
title: DATASET _ NEUTROPHIL/LYMPHOCYTE RATIO AND OVERALL SURVIVAL IN PATIENTS WITH BREAST CANCER: A COHORT STUDY IN A LATIN-AMERICAN HOSPITAL

description: The data collection instrument and the data obtained from the statistical analysis are presented, as well as the study protocol and the STROBE checklist for cohort studies.