cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/b369b9hm9d.5
title: NEFM-Data: Input data for the Nigerian Energy-Food Model (NEFM)

description: This Data Article houses secondary data, consisting of the available historic and current farm production data in Nigeria such as crop type, yields, prices, crop production inputs’ (e.g. labour, fertilizer, pesticide, seed, cash capital) as well as the Nigerian food consumption, ethanol demand, and international commodity (crop/food) trade (import and export) data. The data were collected from reputable online databases such as FAOSTAT, World Bank, IMF, USDA, NBS, IITA, etc., and through personal research visits to Nigerian government agencies such as Federal and State Ministries of Agricultural and Rural Development, State Agricultural Development Agency (ADP) in Nigeria, National (Nigerian) Bureau of Statistics (NBS) and others; and were assembled, screened, processed (tabulated them according to GAMS table requirements), and applied via General Algebraic Modelling System (GAMS) to analyse the Nigerian Biofuels (bioethanol production) Potential, assessing its policy impacts on domestic (Nigerian) food and energy securities, job creation, rural development, and the economy. Ndukwe Agbai Dick collected all the data, processed and applied them through GAMS to analyse the Nigerian Biofuels Potential during his PhD research studies at Newcastle University, England, between October 2010 and September, 2014. The research visit took place between March 1st and June, 2012. Research findings from the analysis of these data using GAMS have been partly documented in paper titled "Analysis of the Inherent Energy-Food Dilemma of the Nigerian Biofuels Policy using Partial Equilibrium Model: The Nigerian Energy-Food Model (NEFM)", which has been peer-reviewed and recommended for publication with major revisions in a reputable international high impact journal - Renewable and Sustainable Energy Reviews (RSER). Of course, a revised version of the paper has been resubmitted for final evaluation, acceptance and publication; which we hope to happen soon.
DOI: 10.17632/s4jfjftd49.1
title: A comparison between manual count, flow cytometry and qPCR as a means of determining Babesia rossi parasitaemia in naturally infected dogs

description: Light microscopic manual count is the current gold standard for parasite quantification. The ability to determine parasite density in whole blood is crucial to understanding disease pathogenesis and finding a suitable automated method of B. rossi parasite quantification would facilitate higher throughput and provide results that are more objective. This study investigated both peripheral capillary and central venous whole blood to estimate the correlations between light microscopy, flow cytometry and quantitative real-time PCR (qPCR). Furthermore, the use of SYBR Green I as a nuclear marker for the detection and quantification of B. rossi by flow cytometric analysis was explored. Peripheral capillary and central venous blood were sampled from forty naturally B. rossi-infected dogs and ten healthy control dogs. Samples were analysed by reverse line blot hybridization assay to confirm a mono-B. rossi infection. Capillary blood parasite density was quantified using light microscopic manual counting and venous blood parasitaemia quantified by manual counts, flow cytometry and qPCR. Flow cytometry, using SYBR Green I staining, showed promise in quantifying B. rossi nucleic acid in venous blood. A significant correlation was found between the venous manual counts and adjusted flow cytometric results, as well as qPCR. A significant correlation was also observed between the capillary manual counts compared to venous manual counts, adjusted flow cytometric results, and qPCR. The study results suggest that qPCR is of value as an alternative to the gold standard manual count for quantifying B. rossi parasitaemia in canine whole blood and that flow cytometry may be useful with further refinement of issues such as background fluorescence and the influence of reticulocytes. The data presented in Tables A-C represent the raw field data used during data analysis.
DOI: 10.21961/mdm:31429
title: Acute Myeloid Leukemia

description: Acute Myeloid Leukemia Common Data Elements Holz
DOI: 10.17632/5ffwcbdttm.1
title: Tumblagooda Sandstone

description: Data used during my PhD on the Tumblagooda Sandstone to compare modern paralic systems to one deposited in the absence of plants.
DOI: 10.17632/f6vty3wkwj.1
title: Massively parallel implementation and approaches to simulate quantum dynamics using Krylov subspace techniques

description: We have developed an application and implemented parallel algorithms in order to provide a computational framework suitable for massively parallel supercomputers to study the unitary dynamics of quantum systems. We use renowned parallel libraries such as PETSc/SLEPc combined with high-performance computing approaches in order to overcome the large memory requirements to be able to study systems whose Hilbert space dimension comprises over 9 billion independent quantum states. Moreover, we provide descriptions of the parallel approach used for the three most important stages of the simulation: handling the Hilbert subspace basis, constructing a matrix representation for a generic Hamiltonian operator and the time evolution of the system by means of the Krylov subspace methods. We employ our setup to study the evolution of quasidisordered and clean many-body systems, focussing on the return probability and related dynamical exponents: the large system sizes accessible provide novel insights into their thermalization properties.
DOI: 10.17632/j3thz43k93.1
title: Multi-architecture Monte-Carlo (MC) simulation of soft coarse-grained polymeric materials: SOft coarse grained Monte-Carlo Acceleration (SOMA)

description: Multi-component polymer systems are important for the development of new materials because of their ability to phase-separate or self-assemble into nano-structures. The Single-Chain-in-Mean-Field (SCMF) algorithm in conjunction with a soft, coarse-grained polymer model is an established technique to investigate these soft-matter systems. Here we present an implementation of this method: SOft coarse grained Monte-carlo Acceleration (SOMA). It is suitable to simulate large system sizes with up to billions of particles, yet versatile enough to study properties of different kinds of molecular architectures and interactions. We achieve efficiency of the simulations commissioning accelerators like GPUs on both workstations as well as supercomputers. The implementation remains flexible and maintainable because of the implementation of the scientific programming language enhanced by OpenACC pragmas for the accelerators. We present implementation details and features of the program package, investigate the scalability of our implementation SOMA, and discuss two applications, which cover system sizes that are difficult to reach with other, common particle-based simulation methods.
DOI: 10.17632/v7dhjnd8xg.1
title: Causal inferences in the contemporary economics
DOI: 10.17632/v7dhjnd8xg.2
title: Causal inferences in the contemporary economics

description: The dataset covers tabularic summaries of all the studies putting forth an explicitly causal conclusion included in the systematic literature review of three top economic journals (AER, JPE, QJE; 2005-2015). The table specifies each of the analyzed articles, classifies its research methods and delivers a short description of causal inference that hopefully will prove useful for further research. To cite this dataset, please also refer to my article "Evidence behind causal inference in the contemporary economics". I would like to thankfully acknowledge the support from the National Science Centre, Poland (under grant no. 2015/19/N/HS1/01066). The author received a Ph.D. scholarship from the National Science Centre, Poland under grant no. 2018/28/T/HS1/00007.
DOI: 10.21227/9wmx-kb90
title: Testings of spectrozonal analog lab-on-a-chip with angle-sensitive pixels (ASP) using diode laser sources in combined nanosecond reflectometric and stroboscopic oscilloscopic measurements.

description: Testings of spectrozonal analog lab-on-a-chip with angle-sensitive pixels (ASP) using diode laser sources in combined nanosecond reflectometric and stroboscopic oscilloscopic measurements. FILE 1: Combined nanosecond reflectometric and stroboscopic oscilloscopic analysis for RF lab-on-a-chip.mp400:15 - Wavelength: 405 nm (DPSS);00:57 - Wavelength: 405 nm (laser diode source); FILE 2: Analog angle-sensitive pixel lab-on-a-chip testing using nanosecond stroboscopic oscilloscope.mp400:20 - Zero Point Calibration (ZPC);00:34 - R-channel calibration;01:01 - R-channel in pulse regime;01:37 - R-channel; laser measurements in darkfield conditions;02:17 - reversive transitions reflectometry in nanosecond time range (and more);02:30 - B-channel; 405 nm laser diode source;02:54 - strobiong regime exit  Acknowledgements:“Development of the novel physical methods for complex biomedical diagnostics based on position-sensitive mapping with the angular resolution at the tissue and cellular levels using analytical labs-on-a-chip” (RFBR grant # 16-32-00914) [6 838,27 $ per year];“Lab-on-a-chip development for personalized diagnostics” (FASIE grant 0019125) [3 039,00 $ per year].
DOI: 10.25489/58jmqj
title: DOI Test
DOI: 10.25489/76knd1
title: DOI Test
DOI: 10.5061/dryad.gv144d5/1
title: KNIME workflow to evaluate morphological features using the FishInspector software

description: This workflow allows to measure morphological features of zebrafish larvae (48hpf or 96 hpf) using the output file (json format) from the FishInspector software. The file should be imported to the KNIME open source analytical platform.
DOI: 10.5061/dryad.gv144d5/3
title: Heart rate analysis zebrafish

description: This workflow allows to measure the heart frequence of zebrafih larvae from videos obtained with the VAST BioImager system. The workflow should be imported to the KNIME open analytical platform.
DOI: 10.5061/dryad.gv144d5/4
title: Knime workflow to rotate and crop zebrafish images

description: This workflow automatically rotates, crop the images and draws a virtual capillary based on a ImageJ macro.The workflow can easily be adapted to accommodate different image properties depending on the source of the image (e.g. intensity, contrast).
DOI: 10.17632/8vpwwh8th5.2
title: gpuSPHASE—A shared memory caching implementation for 2D SPH using CUDA (new version announcement)

description: Smoothed particle hydrodynamics (SPH) is a meshless Lagrangian method that has been successfully applied to computational fluid dynamics (CFD), solid mechanics and many other multi-physics problems. gpuSPHASE is a graphics processing unit (GPU) accelerated solver for 2D SPH simulations that is optimised for relatively small numbers of particles but long physical simulation times as required to solve transport phenomena in process engineering applications. The software aims at a low latency execution pipeline with thousands of iterations per second on contemporary GPU accelerator cards, while using symplectic time integration for long term stability of the simulations. For this, a novel caching algorithm for CUDA shared memory is proposed and implemented. gpuSPHASE is validated against SPHERIC test cases and the performance is evaluated and compared to state of the art implementations of the SPH method.
DOI: 10.17632/xhgyp6ncvt.1
title: mVMC—Open-source software for many-variable variational Monte Carlo method

description: mVMC (many-variable Variational Monte Carlo) is an open-source software based on the variational Monte Carlo method applicable for a wide range of Hamiltonians for interacting fermion systems. In mVMC, we introduce more than ten thousands variational parameters and simultaneously optimize them by using the stochastic reconfiguration (SR) method. In this paper, we explain basics and user interfaces of mVMC. By using mVMC, users can perform the calculation by preparing only one input file of about ten lines for widely studied quantum lattice models, and can also perform it for general Hamiltonians by preparing several additional input files. We show the benchmark results of mVMC for the Hubbard model, the Heisenberg model, and the Kondo-lattice model. These benchmark results demonstrate that mVMC provides ground-state and low-energy-excited-state wave functions for interacting fermion systems i th high accuracy.
DOI: 10.17632/3kkc9yp8k7.1
title: Mouse fetal liver/bone marrow transduced with NOTCH1-dE

description: Acute leukemias are aggressive malignancies of developmentally arrested hematopoietic progenitors. We sought here to explore the possibility that changes in hematopoietic stem/progenitor cells during development might alter the biology of leukemias arising from this tissue compartment. Using a mouse model of acute T-cell leukemia, we found that leukemias generated from fetal liver (FL) and adult bone marrow (BM) differed dramatically in their leukemia stem cell activity with FL leukemias showing markedly reduced serial transplantability as compared to BM leukemias. We present evidence that this difference is due to NOTCH1-driven autocrine IGF1 signaling which is active in FL cells, but restrained in BM cells by EZH2-dependent H3K27 trimethylation.
DOI: 10.17632/6x37kcvvrp.1
title: QSWalk.jl: Julia package for quantum stochastic walks analysis

description: The paper describes QSWalk.jl package for Julia programming language, developed for the purpose of simulating the evolution of open quantum systems. The package enables the study of quantum procedures developed using stochastic quantum walks on arbitrary directed graphs. We provide a detailed description of the implemented functions, along with a number of usage examples. The package is compared with the existing software offering a similar functionality.
DOI: 10.17632/8vjpf69zch.1
title: ris4: A program for relativistic isotope shift calculations

description: Spectral lines from different isotopes display a small separation in energy, commonly referred to as the line isotope shift. The program RIS 4 (Relativistic Isotope Shift) calculates normal and specific mass shift parameters as well as field shift electronic factors from relativistic multiconfiguration Dirac-Hartree–Fock wave functions. These quantities, together with available nuclear data, determine isotope-dependent energy shifts. Using a reformulation of the field shift, it is possible to study, in a model-independent way, the atomic energy shifts arising from changes in nuclear charge distributions, e.g. deformations. The previous version of this program (ADEK_v2_0) may be found at http://dx.doi.org/10.1016/j.cpc.2013.02.015.
DOI: 10.17632/y4rfjtjw3g.1
title: Exonuclease domain-containing 1 enhances PIWI slicing-triggered piRNA biogenesis via its interaction with TDRD12

description: Figures
DOI: 10.5281/zenodo.1438114
title: Properties Of Negative Initial Leaders And Lightning Flash Size In A Cluster Of Supercells

description: It is the figure data of the paper titled as "Properties of negative initial leaders and lightning flash size in a cluster of supercells". The abstract of this paper is as follows:

Properties of negative initial leaders (NILs) and flash size in a cluster of supercells with generally inverted charge structure in Oklahoma on 10 − 11 May 2010 are examined, primarily using Lightning Mapping Array data. A method to identify NILs from LMA source is proposed, and helps to reveal the multiple NILs properties and their distributions. The NILs in the supercell cluster have smaller speed (median 3D displacement speed: 0.65 × 10<sup>5</sup> m s<sup>−1</sup>), relative to the previous reports in “normal” thunderstorms. Furthermore, median NIL speeds initially decrease with increasing height, but begin increasing above 12 km. The NILs tend to decelerate during the early stage. The parameters characterizing flash duration and spatial size are also investigated. It is found they all follow lognormal distributions and the spatial flash size is relatively small on average (median horizontal distance: 5.54 km). Most flashes (83.18%) extend primarily in the horizontal direction. Flash area shows an inverse relationship with flash density at their fast changes during storm evolution. Although large flash initiation density (FID) generally occurs in regions with small flash size, the smallest flash size is nearly not collocated with large FID value. In the regions with large FID, average flash duration roughly increases with increasing FID, while average flash area changes little. We proposed that the pattern of charge pockets and variation of charge density dominated by the strong kinematics are responsible for some new findings about the properties of NIL and flash size in the supercell cluster.
DOI: 10.5281/zenodo.1438115
title: Properties Of Negative Initial Leaders And Lightning Flash Size In A Cluster Of Supercells

description: It is the figure data of the paper titled as "Properties of negative initial leaders and lightning flash size in a cluster of supercells". The abstract of this paper is as follows:

Properties of negative initial leaders (NILs) and flash size in a cluster of supercells with generally inverted charge structure in Oklahoma on 10 − 11 May 2010 are examined, primarily using Lightning Mapping Array data. A method to identify NILs from LMA source is proposed, and helps to reveal the multiple NILs properties and their distributions. The NILs in the supercell cluster have smaller speed (median 3D displacement speed: 0.65 × 10<sup>5</sup> m s<sup>−1</sup>), relative to the previous reports in “normal” thunderstorms. Furthermore, median NIL speeds initially decrease with increasing height, but begin increasing above 12 km. The NILs tend to decelerate during the early stage. The parameters characterizing flash duration and spatial size are also investigated. It is found they all follow lognormal distributions and the spatial flash size is relatively small on average (median horizontal distance: 5.54 km). Most flashes (83.18%) extend primarily in the horizontal direction. Flash area shows an inverse relationship with flash density at their fast changes during storm evolution. Although large flash initiation density (FID) generally occurs in regions with small flash size, the smallest flash size is nearly not collocated with large FID value. In the regions with large FID, average flash duration roughly increases with increasing FID, while average flash area changes little. We proposed that the pattern of charge pockets and variation of charge density dominated by the strong kinematics are responsible for some new findings about the properties of NIL and flash size in the supercell cluster.
DOI: 10.17632/5thy2mcwn7.3
title: Data for Alcohol use and burden for 195 countries and territories, 1990–2016: a systematic analysis for the Global Burden of Disease Study 2016

description: Data underlying figures and relative risk curves within the article. Provides readers the mean value and uncertainty intervals for prevalence of current drinking, drinks per day by location, relative risks by outcome and dose, along with results for the weighted all-cause relative risk curve used to justify TMREL within the study. Based off sources mentioned in Appendix I. From Abstract in linked paper: Background Alcohol use is a leading risk factor for death and disability, but its overall association with health remains complex given the possible protective effects of moderate alcohol consumption on some conditions. With our comprehensive approach to health accounting within the Global Burden of Diseases, Injuries, and Risk Factors Study 2016, we generated improved estimates of alcohol use and alcohol-attributable deaths and disability-adjusted life-years (DALYs) for 195 locations from 1990 to 2016, for both sexes and for 5-year age groups between the ages of 15 years and 95 years and older. Methods Using 694 data sources of individual and population-level alcohol consumption, along with 592 prospective and retrospective studies on the risk of alcohol use, we produced estimates of the prevalence of current drinking, abstention, the distribution of alcohol consumption among current drinkers in standard drinks daily (defined as 10 g of pure ethyl alcohol), and alcohol-attributable deaths and DALYs. We made several methodological improvements compared with previous estimates: first, we adjusted alcohol sales estimates to take into account tourist and unrecorded consumption; second, we did a new meta-analysis of relative risks for 23 health outcomes associated with alcohol use; and third, we developed a new method to quantify the level of alcohol consumption that minimises the overall risk to individual health
DOI: 10.17632/fb54rzyttz.1
title: Data to accompany JoEP manuscript "The longitudinal associations of sound financial management behaviors and marital quality"

description: This was the data set that we used to complete the analyses for the JoEP manuscript, "The longitudinal associations of sound financial management behaviors and marital quality". I have also included the associated MPlus input files The data come from the Flourishing Families data set. I do not have permission from the PI's on the project to share the entire data set, only the data that the models analyzed.
DOI: 10.17632/v6rs7nfyjp.1
title: Data for monitoring the curing of blended polyurethane powder coatings

description: This dataset consists of optical and electron micrographs that were not included in the manuscript. Other files include spreadsheets of raw viscosity data, gloss measurements, and domain areas from optical micrographs, which were used for the histograms.
DOI: 10.17632/bcf3p3hv7j.1
title: Production Data from a Dual-Porosity Gas Reservoir Simulator Implementing Pseudopressure-Based Transfer Function

description: This data is specifically generated by a dual-porosity numerical simulator for naturally fractured gas reservoirs implementing a pseudopressure-based transfer function. The data are used in Figures 1 to 7 in the paper "Analytical Dual-Porosity Gas Model for Reserve Evaluation of Naturally Fractured Gas Reservoirs Using a Density-Based Approach" by Zhang, Z. and Ayala H., L. F.
DOI: 10.17632/xc4pj5py86.2
title: Supplemental Data for "Urea cycle dysregulation generates clinically relevant genomic and biochemical signatures"

description: This is the Supplemental Data associated with the article: J.S.Lee, L.Adler et al "Urea cycle dysregulation generates clinically relevant genomic and biochemical signatures." in Cell.
DOI: 10.17632/n5rvr435gn.1
title: Sialylation of OprD hinders antibiotic entry

description: We have conducted molecular dynamics simulations to obtain information about the structural aspects of sialylated glycans incorporated into the OprD protein. Four N-glycosylation sites on Asn196 (NLS), Asn218 (NYT), Asn251 (NTT) and Asn288 (NGS). Out of the four sites, Asn288 site is present in the extracellular loop region having high solvent accessibility, for its proper glycosylation. Molecular dynamic studies revealed that the core glycan moiety can properly fit into Asn288 with no spatial overlap for its proper glycosylation. Simulation of sialylated-glycan in free and conjugated states depicted that the population distribution of different conformers were in good agreement with the experimental structures. The permeability of the docked antibiotic into the OprD channel revealed its binding in loop2 region and interaction with a ladder of basic amino acids helps in traversing the channel. Furthermore, we demonstrated that sialylated-glycan core structure at Asn288 blocks the channel and hinders the antibiotic binding to loop2.
DOI: 10.17632/prrpd5r62w.1
title: Data for: Correlation Coefficient Based Grouping and Model Complex Control for Scaling Up CMA-ES

description: results of CCG-CMAES-MCC on CEC‘2010