cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/t9rcjv5362.4
title: Continuous culture of HEK293 producing the ECD-Her1. Existence steady states´ multiplicity at the same external conditions.Cell culture and metabolic datasets

description: The data correspond to the fermentation process in continuous mode of HEK293 cells producing the heterologous glycoprotein Her1, in a 2L bioreactor. 
Samples were taken daily from the culture for subsequent analysis of cell density, protein concentration and metabolites measurement.
The data were acquired from different sources listed below:
Viable cell density and viability, via microscope by trypan blue dye exclusion method.
Extracellular domain Her1 concentration, via microplate photometer by ELISA sandwich method (GEN5 Reader Control Software). Briefly, 96-microwell plates were previously coated with 5 mg/mL of an anti-Her1 and incubated overnight at 4 °C. Later on, the samples and standard were added to the plates and incubated at 37 °C 1 h. An anti-EGFr antibody conjugated with biotin was added to the plate and incubated at 37 °C 1h. Then, Streptavidin-Peroxidase reagent was added to the plate and incubated at 37 °C 1 h. Finally, TMB substrate was added to the plate. After 20 minutes the reaction was stopped and the plates were read by a spectrophotometer at 450 nm.
Metabolites concentration, via Liquid Chromatography-Mass spectrometry by derivatization method (TraceFinder software). Briefly, metabolites present in supernatant samples were extracted with extraction solvent (ACN:MeOH:H2O, 3:5:2) and transferred to LC-MS vials for separation and detection by employing the LC-MS equipment. Metabolites were firstly separated by the LC column with depend of their retention times. There was used as aqueous mobile phase solvent, 20 mM ammonium carbonate, adjusted to pH 9.4 with 0.1 % ammonium hydroxide solution (25 %), and 100 % Acetonitrile was used as organic mobile phase. A lineal gradient scheme was applied for the separation process at 200 mL/min taking the application around 15 minutes, and followed by an equilibration step. Column was kept in the oven at 45 °C, and samples were maintained at 4 °C prior to injection to the mass spectrometer. Finally, the metabolites were isolated by their mass/charge (m/z) with a mass accuracy below to 5 ppm for all metabolites with the Q-Exactive mass spectrometer.
The metabolic data were autoscaling-standardized (ratio of centered mean and the standard deviation) prior the analysis.
DOI: 10.17632/wr28vs63sf.1
title: Effects of localized fat accumulation on psoriasis and its subtypes: a Mendelian-Randomization study

description: Supplementary Table
DOI: 10.21227/m75z-gp43
title: Examining the Evolution of Air Traffic Research from 2000-2023: A Bibliometric Perspective

description: We have synthesized the latest developments over the past two decades using a bibliometric approach, drawing data from the Web of Science Core Collection database from January 2000 to May 2023. Both VOSviewer and CiteSpace were employed to examine journals, authors, institutions, and countries' contributions. We also identified collaboration networks, research hotspots, and theme evolutions. A total of 4,432 articles were included in this study, revealing a marked increase in global research publications. The United States, China, and the United Kingdom lead in terms of research output. The Journal of Air Transport Management had the highest publication count. Key contributing institutions include MIT, NASA, Nanjing University of Aeronautics and Astronautics, and Delft University of Technology. Moreover, 14 clusters were formed, highlighting four major research themes: Aircraft Sequencing, Urban Air Mobility, Aircraft Trajectory Prediction, and Air Traffic Control System. These insights offer a comprehensive understanding of research directions and provide invaluable guidance for future air traffic research.
DOI: 10.17045/sthlmuni.23735529.v1
title: <strong>Data supplement items I - IV for</strong> <strong>Ring et al. </strong> <strong>Geochronology of high-pressure rocks from the Saih Hatat window, Oman: Age gaps and tectonic implications for the subduction history at the southern margin of Neo-Tethys</strong> <strong>to be submitted to Earth Science-Reviews</strong>

description: Data supplement I provides a detailed cross section with stratigraphic columns of the Arabian rifted margin in Oman. <br> Data supplement II provides an additional, geometrical feasible interpretation of the development of the major shear zones of the Ruwi - Al Hamriyah area. <br> Data supplement item III is a review of literature data for finding a potential protolith for the calcphyllite of the Ruwi Nappe. <br> Data supplement item IV provides a detailed outline of the Rb-Sr method used for dating metamorphic rocks of the Saih Hatat window. It also describes the 22 samples dated by the Rb-Sr method. <br>
DOI: 10.17632/5gcf29tky2.1
title: "Evaluation of water erosion in the soils of the Arroyo Corozo micro-watershed, under different land uses and coverages using the USLE-Arcgis model."

description: La erosión hídrica es uno de los mayores problemas ambientales, sus efectos están relacionados con la degradación de la tierra y las pérdidas de la capacidad productiva de los suelos. En la Republica Dominicana un 70% de las tierras son montañosas y en las mismas están sometidas a un uso agrícola y por ende a cambios de cobertura constante. Esta investigación tiene el objetivo de evaluar la relación entre los cambios en el uso y cobertura de la tierra y los riesgos de erosión hídrica utilizando el modelo USLE-Arcgis. La variabilidad de uso de la tierra se determino a partir de imágenes satelitales, , la longitud y grado de inclinación se calculó del DEM datos oficializados por DIARENA, la isoerosividad de las lluvias es estimo partir del Mapa Nacional de Intensidades máxima de las lluvias para la Republica Dominicana, valores de erodabilidad de os suelos se obtuvo del mapa de suelos de la cuenca de Sabana Yegua. Todos estos valores desde el software ArcGIS fueron sometidos a un proceso de algebra de mapas, tabulación de las salidas. En los resultados se determino que hay cambios significativos de la cobertura entre 1996 y 2010, no siguen patrón ordenado, hay una disminución del área bajo agricultura de subsisgggtencia en un 4% y un incremento del bosque de conífero en 6%. Esta misma tendencia se observó en los valores de riesgo un 48% del área estaba afectada por una erosión de alta a severa, mientras que en 2010 se disminuyó a 40% el área con ese grado de erosión.
DOI: 10.17632/mt94786pgg.1
title: Effects of localized fat accumulation on psoriasis and its subtypes: a Mendelian-Randomization study

description: Supplementary Table
DOI: 10.17632/pxp2w28zkm.1
title: OSCE data on the research study "A PROSPECTIVE RANDOMIZED CONTROLLED TRIAL ON HIGH-FIDELITY PATIENT SIMULATION VERSUS VIDEO-ASSISTED LECTURE FOR UNDERGRADUATE MEDICAL STUDENTS" (main study)

description: The data was collected from a Randomized Controlled Trial study on the effectiveness of High-Fidelity Simulation (HFS) among undergraduate medical students. The study was conducted in the Clinical Simulation Lab of Manipal University College Malaysia, Melaka from March 2019 to February 2020. This data was the collection of the students' OSCE scores (in small groups) -  video-assisted learning (control group)  and HFS-based teaching (intervention group) at 1st, 4th & 7/8th weeks. The data was analysed with SPSS software (v25).
The analysis revealed increased OSCE scores for both control and intervention groups.
DOI: 10.17632/x844x4ky8x.2
title: Aerobic glycolysis is the predominant means of glucose metabolism in neuronal somata, which protects against oxidative damage

description: Different distribution of PKM2 drives neurons to use aerobic glycolysis in somata to prevent oxidative damage and OXPHOS in terminals to meet high energy demands.
DOI: 10.17632/kdhfkdt2sg.1
title: ACFNR

description: Codes and experiment results of ACFNR.
DOI: 10.17632/4z3r79m2cn.1
title: Extrapolation procedure algorithm

description: This is the algorithm designed in Matlab for the execution of the extrapolation procedure explained in the article "Fractional viscoelastic models for the estimation of the frequency response of rubber bushings based on relaxation tests".
DOI: 10.17632/fsn6dkcvrv.1
title: Atom-centered machine-learning force field package

description: In recent years, machine learning algorithms have been widely used for constructing force fields with an accuracy of ab initio methods and the efficiency of classical force fields. Here, we developed a python-based atom-centered machine-learning force field (PyAMFF) package to provide a simple and efficient platform for fitting and using machine learning force fields by implementing an atom-centered neural-network algorithm with Behler-Parrinello symmetry functions as structural fingerprints. The following three features are included in PyAMFF: (1) integrated Fortran modules for fast fingerprint calculations and Python modules for user-friendly integration through scripts and facile extension of future algorithms; (2) a pure Fortran backend to interface with the software, including the long-timescale dynamic simulation package EON, enabling both molecular dynamic simulations and adaptive kinetic Monte Carlo simulations with machine-learning force fields; and (3) integration with the Atomic Simulation Environment package for active learning and ML-based algorithm development. Here, we demonstrate an efficient parallelization of PyAMFF in terms of CPU and memory usage and show that the Fortran-based PyAMFF calculator exhibits a linear scaling relationship with the number of symmetry functions and the system size.
DOI: 10.17632/jjjmvzy3tw.1
title: Fungal communities' ITSF1 gene profiles in soil.

description: Research Hypothesis:
The research hypothesis centers around the investigation of fungal communities in surface soils contaminated by heavy metals in the Zambian Copperbelt region. The hypothesis posits that fungal communities in polluted areas (specifically TD25 and TD26) will exhibit distinct taxonomic compositions compared to uncontaminated surface soils from Mwekera Forest (MW). Additionally, the study anticipates the identification of fungal species that demonstrate resilience to copper (Cu) and cobalt (Co), the primary contaminants in the Copperbelt. The data collected through metagenomic analysis of ITSF1 gene amplicons seeks to test these hypotheses.
Data Description:
The data comprises fungal community profiles obtained from various soil samples. These samples include MW (Mwekera Natural Forest) soil from a planted area (P1), TD25 (Kitwe Tailing Dam) soil from both bare surface soil (B2) and planted surface soil (P2), and TD26 (Uchi Tailing Dam) soil from bare surface areas (B2, B1). The fungal community structure at both the phylum and genus levels was characterized through metagenomic analysis.

Interpretation of Data:
The data reveals significant insights into the fungal communities in the studied soils. At the phylum level, Basidiomycota dominates the fungal profiles in the tailings (TD25 and TD26), followed by Ascomycota, Glomeromycota, and Rozellomycota. This dominance suggests that these fungal phyla are well-adapted to metal-contaminated environments.

Notably, several fungal genera, including Vanrija, Paraconiothyrium, Toxicladosporium, Neocosmospora, Septoglomus, and Fusarium, were more abundant in contaminated tailings soils. These genera are known for their potential in leaching, absorbing, and transforming heavy metals, indicating their crucial role in bioremediation efforts.

Furthermore, specific fungal species, such as Aspergillus, Penicillium, Fusarium, and Oidiodendron, demonstrate resilience to copper (Cu) and cobalt (Co). This suggests that these fungi have adapted to thrive in the presence of these contaminants and could potentially be harnessed for bioremediation initiatives in similar environments.

Notable Findings:
1. Basidiomycota predominates in metal-contaminated soils, with Ascomycota prevailing in reference soil.
2. Glomeromycota, known for forming beneficial associations with plant roots, were found in contaminated soils.
3. Rozellomycota, with potential ecological roles, were identified, including their presence in crude oil-contaminated soils, indicating bioremediation potential.
4. Several fungal genera, especially in contaminated soils, may play crucial roles in metal transformation and bioremediation.

Implications:
These findings provide valuable insights for environmental management and bioremediation strategies in areas affected by mining activities. The identified fungal species, particularly those exhibiting metal tolerance, hold promise for enhancing the recovery of contaminated sites.
DOI: 10.17632/whcnvm2mc9.2
title: TUMME 2023: Tsinghua University Minnesota Master Equation program. New version announcement

description: This is an updated version of TUMME (Tsinghua University Minnesota Master Equation program), which is a computer program for setting up and solving master equations for chemical kinetics of unimolecular and bimolecular reactions. The master equation is discretized in terms of energy bins, and rate constants are calculated from chemically significant eigenmodes. TUMME has interfaces to Gaussian 16, Polyrate 2023, and MSTor 2023 output files that allow the master equation code to obtain the microcanonical flux coefficients needed for the kernel of the master equation as calculated by conventional transition state theory (TST), variational transition state theory (VTST) with various tunneling methods, or multi-structural or multi-path VTST (MS-VTST or MP-VTST) with various tunneling methods. The tunneling methods supported include zero-curvature tunneling (ZCT), small-curvature tunneling (SCT), large-curvature tunneling (LCT), and microcanonically optimized multidimensional tunneling (μOMT). For mechanisms involving only unimolecular isomerization (no bimolecular pairs), TUMME can set up and solve a conservative master equation for both rate constants and time-dependent energy-bin populations. For mechanisms involving bimolecular pairs, TUMME 2023 can set up and solve two kinds of master equation: (i) a nonconservative master equation for calculating rate constants of bimolecular reactions and (ii) a conservative master equation that includes bimolecular association in the transition matrix and that can be used for calculating the time evolution of the concentration of a pseudo-first-order bimolecular reactant. TUMME is written in double precision with Python 3; quadruple and octuple precision are also available for some subtasks in C++. The Python code can run in serial or parallel (MP or MPI), and C++ code can run on a single processor or on multiple processors with OpenMP. The program includes a manual and a tutorial.
DOI: 10.17632/5xm9pm24cz.1
title: QuDPy: A Python-based tool for computing ultrafast non-linear optical responses

description: Nonlinear Optical Spectroscopy is a well-developed field with theoretical and experimental advances that have benefited multiple disciplines, including chemistry, biology, and physics. However, for the accurate interpretation of the corresponding multi-dimensional spectra, there is a need for precise quantum dynamical simulations based on model Hamiltonians. In this article, we present the initial release of our code, QuDPy (Quantum Dynamics in Python), which provides a robust numerical platform for performing quantum dynamics simulations based on model systems, including open quantum systems. A distinguishing feature of our approach is the ability to specify various high-order optical response pathways in the form of double-sided Feynman diagrams through a straightforward input syntax. This syntax outlines the time-ordering of ket-sided or bra-sided optical interactions acting on the time-evolving density matrix of the system. We utilize the quantum dynamics capabilities of QuTip to simulate the spectral response of complex systems, allowing us to compute virtually any n-th order optical response of the model system. To illustrate the utility of our approach, we provide a series of example calculations.
DOI: 10.5517/ccdc.csd.cc2fcw3t
title: CCDC 2245736: Experimental Crystal Structure Determination

description: Related Article: Ryoji Tanaka|2023|CSD Communication|||
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.cc2ffvc3
title: CCDC 2247635: Experimental Crystal Structure Determination

description: Related Article: Ryoji Tanaka|2023|CSD Communication|||
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.cc2fvs58
title: CCDC 2260060: Experimental Crystal Structure Determination

description: Related Article: Jessica Bruhn|2023|CSD Communication|||
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.cc2fx2t8
title: CCDC 2261320: Experimental Crystal Structure Determination

description: Related Article: Xuan Zhang|2023|CSD Communication|||
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/k9v4hjb5xj.1
title: NEMOH: Open-source boundary element solver for computation of first- and second-order hydrodynamic loads in the frequency domain

description: NEMOH is developed to solve potential flow problems using the boundary element method for computing wave loads on offshore structures. The solver solves the first-order problem in the frequency domain. An extended module enables computation of the second-order loads on a structure in bi-chromatic bi-directional waves. NEMOH is released as open-source, developed, and distributed under the terms of GNU General Public License (GPLv3). Along with the source code, a user manual is available which facilitates the compilation and execution of the source files. In this new release, NEMOH v3.0 has new features; irregular frequencies removal method, new linear system solvers for enhancing computational efficiency, and a new module for computing the full quadratic transfer function (QTF) of drift forces. Verification cases are shown for a truncated cylinder, a truncated cylinder with a thin heave plate, a spar buoy platform (SOFTWIND), and a semi-submersible platform (OC4). The results are compared with reference data from commercial software, WAMIT, DIODORE, and HYDROSTAR, and the comparison showed that NEMOH v3.0 is accurate and efficient.
DOI: 10.5517/ccdc.csd.cc2fx43m
title: CCDC 2261360: Experimental Crystal Structure Determination

description: Related Article: Józef Utko, Patrycja Wytrych, Tadeusz Lis|2023|CSD Communication|||
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.cc2fx45p
title: CCDC 2261362: Experimental Crystal Structure Determination

description: Related Article: Józef Utko, Patrycja Wytrych, Tadeusz Lis|2023|CSD Communication|||
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.cc2fx46q
title: CCDC 2261363: Experimental Crystal Structure Determination

description: Related Article: Józef Utko, Patrycja Wytrych, Tadeusz Lis|2023|CSD Communication|||
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.cc2fx5dy
title: CCDC 2261400: Experimental Crystal Structure Determination

description: Related Article: Rima Kiche, Riadh Bourzami, Louiza Ouksel, Hakima Ait Youcef|2023|CSD Communication|||
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.cc2fx5h1
title: CCDC 2261403: Experimental Crystal Structure Determination

description: Related Article: Hkima Ait Youcef, Riadh Bourzami, Louiza Ouksel, Kiche Rima|2023|CSD Communication|||
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/w5y32cs5zx.1
title: https://data.mendeley.com/drafts/zmx9x8828z

description: 
https://data.mendeley.com/drafts/zmx9x8828z
DOI: 10.5517/ccdc.csd.cc2fx5q8
title: CCDC 2261410: Experimental Crystal Structure Determination

description: Related Article: Xing Duan|2023|CSD Communication|||
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.cc2fx9h5
title: CCDC 2261527: Experimental Crystal Structure Determination

description: Related Article: Ryoji Tanaka|2023|CSD Communication|||
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.