cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.3243160
title: Training material for the course "Exome analysis with GALAXY"

description: Galaxy is an open source, web-based platform for data intensive biomedical research. It makes accessible bioinformatics applications to users lacking programming skills, enabling them to easily build analysis workflows for NGS data.<br>
 <br>
The course "<strong>Exome analysis using Galaxy</strong>" is aimed at PhD student, biologists, clinicians and researchers who are analysing, or need to analyse in the near future, high throughput exome sequencing data. The aim of the course is to make participants familiarise with the Galaxy platform and prepare them to work independently, using state-of-the art tools for the analysis of exome sequencing data.

The course will be delivered using a mixture of lectures and computer based hands-on practical sessions. Lectures will provide an up-to-date overview of the strategies for the analysis of exome next-generation experiments, starting from the raw sequence data. Analyses include sequence quality control, alignment to a reference genome, refinement of aligned sequences, variant calling, annotation and interpretation, and tools for visual inspection of results. Participants will apply the knowledge gained during the course to the analysis of Illumina’s real exome datasets, and implement workflows to reproduce the complete analysis. After the course, participants will be able to create pipeline for their individual analyses.

Those are the needed datasets for this course.
DOI: 10.21227/ee09-gj83
title: Frequency Spectrum Waterfall Image

description: Frequency spectrum waterfall image dataset
DOI: 10.14457/cu.the.2013.1427
title: ENVIRONMENTAL CONCENTRATION OF CARBONYL COMPOUNDS AND BTEX IN RESIDENTIAL AREAS OF INNER CITY OF BANGKOK AND THEIR POSSIBLE HEALTH RISK

description: This study aimed to determine the concentrations of carbonyl compounds and BTEX in indoor and outdoor environments and estimate the potential health risk of the residents via inhalation exposure. All samples were taken from 5 communities during dry season (21st April to 24th May, 2013) and wet season (22nd September to 25th October, 2013) by using 2, 4 dinitrophenylhydrazine (DNPH) cartridge and charcoal glass tube connected with personal air pump with air flow rate equaled 100 mL/min for carbonyl compounds and BTEX collections, respectively. The equipments were installed at indoor and outdoor environments at 1.5-2.0 meter height above the ground during 24 hours. Carbonyl compounds extracted by using acetonitrile and BTEX extracted by using carbon disulfide were analyzed by using HPLC/UV and GC/FID, respectively. The results shew the indoor concentrations of four main carbonyl compounds which were formaldehyde, acetaldehyde, propionaldehye, and hexanaldehyde were ranked in 0.14-38.73, 0.10-11.02, 0.03-2.08, and 0.03-6.28 µg/m3, respectively. And benzene, toluene, m-,p-xylene, and o-xlyene were ranked in  According to lifetime cancer risk from indoor concentrations based on general scenario, the results revealed that 95% CI of formaldehyde, acetaldehyde, benzene, and ethylbenzene were in the ranges of 5.99x10-5-4.72x10-5, 1.09x10-5-9.93x10-6, 1.03x10-4-8.83x10-5, and 1.45x10-5-1.10x10-5µg/m3, respectively. In case of age interval scenario, the 95% CI of lifetime cancer risk of these chemicals were in the ranges of 1.94x10-4-1.79x10-4, 3.20x10-5-3.00x10-5, 2.72x10-3-2.40x10-3, and 5.78x10-5-5.38x10-5. Most cancer risk from both scenarios were above the acceptable criteria which one people from one million people had possibility of developing cancer (or 10-6). There were some overestimated risk due to exposure during equaled to 24 hours and the exposure frequency equaled to 350 days/year, while the most non-cancer risks were in the acceptable range.
DOI: 10.14457/cu.the.2013.1428
title: THE PREPARATION OF LAO EDUCATION FOR ASEAN ECONOMIC COMMUNITY IN 2015: THE CASE STUDY OF PRIVATE VOCATIONAL SCHOOLS AND COLLEGES

description: The purpose of this research is to study the preparation of Lao PDR’s education for the ASEAN Economic Community (AEC), which will formally come into existence in 2015. The research focuses on the preparation of Lao PDR’s private vocational schools and colleges in Vientiane Capital and the city of Savannakhet because this aspect of education is crucial for the development of workforce for the expected economic expansion of Laos when the country becomes part of the AEC in 2015. The sampling for this study consists of 80 teachers in private vocational schools and colleges, together with a limited number of investors in private education and directors of private vocational schools and colleges. The study tools include questionnaires for the teachers and in-depth interviews for investors and directors. The research found that Lao PDR’s preparation for the AEC through its private vocational education ranges from the medium to high levels. The highest level of preparation was found in the curriculum, because the private vocational schools and colleges have introduced new technologies to vocational teaching and learning and their focus on real practice to develop skills. The next level of preparation is found in administration and management because the private sector in education places emphasis on the quality of vocational education, as well as the creation of social value and confidence in this type of education. At the same time it is emphasized by the private sector that private education must go hand in hand with that provided by the state. Private vocational education suffers most from its shortages in matters relating to premises for teaching and learning since it lacks budget and sufficient support from the state sector. Moreover, in addition to lack of privileges in any form, the private education sector does not have an opportunity to participate in the formulation of educational policy, and this has in part accounted for those shortages it has been suffering from.
DOI: 10.21227/qqwh-qt77
title: Frequency Spectrum Waterfall Image

description: Frequency spectrum waterfall image dataset
DOI: 10.14457/cu.the.2013.1440
title: Effect of lewis acid on the activity of ziegler-natta catalyst and the properties of polyethylene

description: This dissertation investigated the effects of Lewis acid compounds on ethylene polymerization with MgCl2-supported Ziegler-Natta catalysts. The study could be divided into three parts. Firstly, the modification of Mg(OEt)2-based Ziegler-Natta catalysts with various metal chlorides were examined on ethylene homopolymerization and ethylene copolymerization with 1-hexene. One of selected metal chlorides (FeCl2, MnCl2, and ZnCl2), was added together with SiCl4 in the chlorination stage of Mg(OEt)2. The result showed that among various metal chlorides, the addition of FeCl2 could enhance both BET specific surface area and the surface atomic ratio of Ti/Mg, leading to the highest activity in both ethylene homo- and copolymerization. The exposure of Ti species on outer surfaces could be thought as a sign of easier mass transfer phenomena leading to the improvement of catalyst performances. Secondly, two methods of catalyst preparations modified with FeCl2 including TiCl4/MgCl2 complexes in tetrahydrofuran (THF) soluble and recrystallization method by ethanol (EtOH), were examined. It was found that FeCl2 modification with both two methods could improve the activity. However, Fe-THF catalyst exhibited higher activity than Fe-EtOH catalyst because of a suitable of interaction between TiCl4 and MgCl2 and the proper location of Ti atoms on the surface as proven by thermogravimetric analysis (TGA) and energy dispersive X-spectroscopy (EDX), respectively. Finally, the effect of the ZnCl2-SiCl4 doped TiCl4/MgCl2/THF catalyst for ethylene homopolymerization and ethylene/1-hexene or ethylene/1-octene copolymerization was also studied. It indicated that the ZnCl2-SiCl4 modified catalyst exhibited very high activities in ethylene homo-and copolymerization and high the viscosity average molecular weight (Mv) of polymer obtained.
DOI: 10.14457/cu.the.2013.1442
title: Antiviral responses and biological targets of a kazal-type serine proteinase inhibitor spipm2 from the black tiger shrimp Penaeus monodon

description: White spot syndrome (WSS) is a severe viral disease in Penaeus monodon which causes high mortality. The understanding of shrimp immunity will lead to the knowledge for prevention and solving the disease. In black tiger shrimp, several proteins are expressed in response to viral infection. Among others, a Kazal-type serine proteinase SPIPm2 is abundantly expressed in the hemocytes and shown to be involved in innate immune response against white spot syndrome virus (WSSV). In the healthy hemocyte, the immunofluorescent and immunogold labeling techniques showed that the SPIPm2 was expressed and stored in the granule of semi-granular and granular hemocytes. Immunocytochemical study showed that, after WSSV infection, the percentage of SPIPm2-producing hemocytes was reduced by about half. Expectably, the SPIPm2 was secreted readily from these hemocytes after WSSV challenge. The recombinant SPIPm2 (rSPIPm2) was used to investigate the effect of SPIPm2 on viral infection in shrimp. Injection of rSPIPm2 prior to WSSV injection prolonged the mortality rate of WSSV-infected shrimp. By using shrimp primary hemocyte cell culture, the antiviral activity was neutralization and protection. The rSPIPm2 temporarily and dose-dependently neutralizes the WSSV and protects the hemocytes from viral infection judging from the substantially less expression of WSSV late gene VP28. The antiviral activity was very likely due to the binding of SPIPm2 to the components of viral particle and hemocyte cell membrane. The yeast two-hybrid screening had identified a viral target protein of SPIPm2 in the WSSV cDNA library, namely WSV477. The WSV477 was reported to have ATP/GTPase activity. In vitro pull down assay confirmed the protein-protein interaction between rSPIPm2 and rWSV477. In WSSV-infected culture, silencing of WSV477 by dsRNA-WSV477 reduced the expression of viral late gene VP28 and, hence, the reduction of viral infectivity.
DOI: 10.5281/zenodo.3243165
title: Data + Code for "Evaluating health facility access using Bayesian spatial models and location analysis methods"

description: These files contain r data objects  and R files that represent the key details of the paper, "Evaluating health facility access using Bayesian spatial models and location analysis methods".

The following datasources are available for simulation of some of the ideas in the paper.

- dat_grid_sim: simulated data of the grid and grid cells<br>
- dat_ohca_cv_sim: simulated data containing the cross validated test/training sets of OHCA data<br>
- dat_ohca_sim: simulated OHCA event data<br>
- dat_aed_sim: simulated AED location data<br>
- dat_bldg_sim: simulated building location data<br>
- dat_municipality_sim: simulated municipality information<br>
- table_1: Table 1 information containing key demographic data

These data were produced using the code in 01-create-sim-data.R, and one of the statistical models is demonstrated in 02-demo-inla-model.

 

In terms of the paper itself, the functions and code used in the manuscript are located in:

* 01_tidy.Rmd - analysis code used to tidy up the data

* 02_fit_fixed_all_cv.Rmd - analysis code used to place AEDs

* 02_model.Rmd - analysis code used to fit the model in INLA

* 03_manuscript.Rmd - Full code and text used to create the paper

* 04_supp_materials.Rmd - full code and text used to create the supplementary materials

 

The following files are a part of an R package "swatial" that was developed along with the paper. These files are:

* DESCRIPTION

* NAMESPACE

* LICENSE

* LICENSE.md

* decay.R 

* spherical-distance.R 

* test-figure-data-matches.R 

* test-table-data-matches.R 

* testthat.R 

* tidy-inla.R 

* tidy-posterior-coefs.R 

* tidy-predictions.R 

* utils-pipe.R 

* All files that end in .Rd are documentation files for the functions.

 

In the future, these functions from the paper may be generalised and put into their own package. If that happens, this repository will be updated with a link to updated functions.
DOI: 10.7910/dvn/2v2lgk/19w4b8
title: beliefs_conj1.R

description: :unav
DOI: 10.7910/dvn/2v2lgk/1lyyhn
title: beliefs_descriptives.R

description: :unav
DOI: 10.7910/dvn/2v2lgk/4lmfdd
title: beliefs_regression1.R

description: :unav
DOI: 10.7910/dvn/2v2lgk/ptcolm
title: beliefs_master.R

description: :unav
DOI: 10.7910/dvn/2v2lgk/32nu9a
title: README.txt

description: :unav
DOI: 10.7910/dvn/2v2lgk/imeoir
title: df_conj_out1.csv

description: :unav
DOI: 10.7910/dvn/2v2lgk/ufkgmd
title: ri.csv

description: :unav
DOI: 10.7910/dvn/2v2lgk/xwc4hp
title: appendix.pdf

description: :unav
DOI: 10.6073/pasta/d64894dfea2c9eb99f01308e9ef43a59
title: Groundwater stage height measurements of ten minute intervals from 9 sites located in Macon County, North Carolina, within the Upper Little Tennessee River Basin

description: The hillslope study was established to directly link land use impacts to streamwater quality in the southern Appalachian Mountains.  Nine sites were selected in the Little Tennessee River watershed in Macon County, NC, representing four land use types: forest, mountain development, traditional valley, and large river valley. At each of these sites, three subsurface flowpaths were identified, and four plots were established along the flowpath following the elevation gradient. At seven of the nine sites, the three lower elevation plots at one of the subsurface flowpaths had ground water wells installed in order to measure groundwater stage along an elevational gradient. Measurements were taken every 60 seconds and output as ten minute averages.  Data were used as part of the Regional HydroEcological Simulation System (RHESSys) ecohydrologic model. Please see the accompanying well construction data for additional groundwater well information.
DOI: 10.7910/dvn/6o3kb8
title: Bikini Body Workouts

description: Bikini Body Workouts is an online system designed to get you in shape in as little as 60 days. I know, you’ve heard it before. I thought the exact same thing but as I began to look at the details of the program, I was pleasantly surprised and even thought to myself that this system could very well be one that provides exactly what it is they’re offering – a beach body in only a couple of weeks. And am I ever glad that I decided to bite the bullet and give it a shot, but don’t take my word for it. Just keep reading and you’ll quickly find out whether or not Bikini Body Workouts is for you.
DOI: 10.7910/dvn/rmihwz
title: Isometrics Mass

description: Isometrics Mass teaches you safe, effective isometric techniques that explode your muscle and strength gains. It’s an online system that focuses specifically on isometric movements that allow you to maximize your results without having to put an insane amount of stress on your joints. But what type of gains can you expect? Let me put it this way: one of the techniques you learn was also used by a secret Russian spy used to bend his prison bars and rip open his heavy shackles to escape prison. Needless to say, Isometrics Mass is going to bulk and build you up. So, put down the magic muscle pills and voodoo spells that never work anyway. Building massive muscle and strength gains takes work, and this program teaches you the exact type of exercises to complete to maximize your results.
DOI: 10.7910/dvn/8uws1r/0nmkzx
title: Mello 2019 EJIS.R

description: :unav
DOI: 10.7910/dvn/8uws1r/mo28b8
title: Mello 2019 EJIS.tab

description: :unav
DOI: 10.7910/dvn/8uws1r/xmhzta
title: Mello 2019 EJIS Supplement.pdf

description: :unav
DOI: 10.21227/kv93-ak67
title: Italian Parkinson's Voice and Speech

description: This dataset is associated with the paper, Giovanni Dimauro et al. 2017, which is open source, and can be found here: https://ieeexplore.ieee.org/document/8070308The DataPort Repository contains the data used primarily for generating Figure 2,3,4,5
DOI: 10.5281/zenodo.3243359
title: The influence of lattice termination on the edge states of the quantum spin Hall insulator monolayer 1T'-WTe_2

description: We study the influence of sample termination on the electronic properties of the novel quantum spin Hall insulator monolayer 1T'-WTe<sub>2</sub>. For this purpose, we construct an accurate, minimal 4-orbital tight-binding model with spin-orbit coupling by employing a combination of density-functional theory calculations, symmetry considerations, and fitting to experimental data. Based on this model, we compute energy bands and 2-terminal conductance spectra for various ribbon geometries with different terminations, with and without magnetic field.

The provided repository contains all code and data to reproduce the results of this study.
DOI: 10.5281/zenodo.3240534
title: Results for chloroplast assembler benchmarking

description: Output fasta files produced by the different tools for real data (retry is a subset of real to test for consistency) and simulated data.
DOI: 10.5258/soton/d0746
title: Dataset for: The Effect of Organoclay Loading and Matrix Morphology on Charge Transport and Dielectric Breakdown in an Ethylene-based Polymer Blend

description: Dataset supports the publication: Shaw, A. V., Vaughan, A., & Andritsch, T. The effect of organoclay loading and matrix morphology on charge transport and dielectric breakdown in an ethylene-based polymer blend. Journal of Materials Science. Readme is contained within the spreadsheet.Article abstract: The effect of an organoclay on the electrical properties of a polymeric host is described. The matrix was composed of a blend of high and low density polyethylene, such that a wide range of different morphologies could be generated, to which an ethylene/(vinyl acetate) copolymer was added, to increase compatibility between the organoclay and the matrix and, thereby, improve the organoclay dispersion. The ratio between the compatibiliser and organoclay was found to be important in forming a well-dispersed system, as evinced by thermogravimetric analysis, X-ray diffraction and scanning electron microscopy, indicating the effectiveness of the chosen compatibilisation strategy. DC conductivity was found to be determined by the precise distribution of the organoclay throughout the system; changes in morphology and phase structure of the matrix polymer resulting from changes in imposed thermal history had little effect per se, but varying degrees of self-assembly of the organoclay facilitated by different residence times within the quiescent melt could result in changes in overall DC conductivity of several orders of magnitude. Consequent increases in DC conductivity led to reductions in DC breakdown strength, implying failure through some avalanche or thermal process. However, a monotonic increase in observed AC breakdown strength implies that the associated underlying failure process is then very different.
DOI: 10.21227/1bm6-wa12
title: The Good, The Bad and The Fair: KPIs from Network Elements

description: Measurements collected from R1 for root cause analyses of the network service states defined from quality and service design perspectives
DOI: 10.21227/mn65-wj07
title: The Good, The Bad and The Fair: KPIs from Network Elements

description: Measurements collected from R1 for root cause analyses of the network service states defined from quality and service design perspectives
DOI: 10.5281/zenodo.3243329
title: POPC with 40 and 50 mol-% of cholesterol at 310 K. Slipids force field.

description: Simulations of a POPC bilayer with varying amounts of cholesterol. This data is employed for the NMRlipids project, see <em>http://nmrlipids.blogspot.fi</em> for more information.

A POPC bilayer consisting of 200 lipids (100 per leaflet) is simulated in the presence of 40% (134 molecules) or 50 % (200 molecules) of cholesterol. The Slipids model [1–3] is employed for lipids, and the tip3p model for water.

The Slipids force field parameters were downloaded from http://mmkluster.fos.su.se/slipids/

––––––––––––––––––––––––––––––––––––––––––––––––––––––

The files are in GROMACS format. Trajectory (.xtc) is 100 ns long with data saved every 100 ps. Additionally, the final structure (.gro), topology (.top), index file (.ndx), binary run input file for GROMACS v. 4.6–&gt; (.tpr) and the energy output file (.edr) are provided together with the run parameter file (.mdp) employed to run all the simulations.

UPDATE: Longer 500 ns trajectories are updated together with the checkpoint files.

––––––––––––––––––––––––––––––––––––––––––––––––––––––

[1] Derivation and Systematic Validation of a Refined <br>
All-Atom Force Field for Phosphatidylcholine Lipids<br>
Joakim P. M. Jämbeck and Alexander P. Lyubartsev<br>
The Journal of Physical Chemistry B 2012 116 (10), 3164-3179<br>
DOI: 10.1021/jp212503e

[2] An Extension and Further Validation of an All-Atomistic <br>
Force Field for Biological Membranes<br>
Joakim P. M. Jämbeck and Alexander P. Lyubartsev<br>
Journal of Chemical Theory and Computation 2012 8 (8), 2938-2948<br>
DOI: 10.1021/ct300342n

[3] Another Piece of the Membrane Puzzle: Extending Slipids Further<br>
Joakim P. M. Jämbeck and Alexander P. Lyubartsev<br>
Journal of Chemical Theory and Computation 2013 9 (1), 774-784<br>
DOI: 10.1021/ct300777p
DOI: 10.25407/jacbts.8255276
title: Figure 7: Simulated Surgery for Complex Total Cavopulmonary Connection Planning Using Flexible, Intact-Heart Model

description: See Supplemental Video 1. LPA = left pulmonary artery; RPA = right pulmonary artery; RSVC = right superior vena cava; other abbreviations as in Figures 5 and 6.
DOI: 10.25407/jacbts.8255276.v1
title: Figure 7: Simulated Surgery for Complex Total Cavopulmonary Connection Planning Using Flexible, Intact-Heart Model

description: See Supplemental Video 1. LPA = left pulmonary artery; RPA = right pulmonary artery; RSVC = right superior vena cava; other abbreviations as in Figures 5 and 6.
DOI: 10.5281/zenodo.3243213
title: Data Set of Playing with Protons

description: Data Set of Playing with Protons
description: This data set is anonymised. It was collected in the Playing with Protons study within the CREATIONS project.
DOI: 10.5281/zenodo.3243214
title: Data Set of Playing with Protons

description: Data Set of Playing with Protons
description: This data set is anonymised. It was collected in the Playing with Protons study within the CREATIONS project.
DOI: 10.5519/qd.wkqtiw9h
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (316 records)
DOI: 10.25387/g3.12252719.v1
title: Supplemental Material for Yanagawa et al., 2020

description: File S1. Video of high grooming DGRP line.File S2. Video of low grooming DGRP line.Table S1. ANOVA of spontaneous grooming behavior.Table S2. GWA analyses of spontaneous grooming behavior.Table S3. GWA analysis candidate gene list.Table S4. RNAi functional assessment results.<br>
DOI: 10.25387/g3.12252719
title: Supplemental Material for Yanagawa et al., 2020

description: File S1. Video of high grooming DGRP line.File S2. Video of low grooming DGRP line.Table S1. ANOVA of spontaneous grooming behavior.Table S2. GWA analyses of spontaneous grooming behavior.Table S3. GWA analysis candidate gene list.Table S4. RNAi functional assessment results.<br>
DOI: 10.25407/jacbts.8255327
title: Figure 15: Simulated Arterial Switch Operation From a Hands-on Surgical Training Course for Cardiothoracic Surgeons

description: Reproduced with permission from Yoo et al. (72). See Supplemental Video 2. LCA = left coronary artery; other abbreviations as in Figures 5 and 6.
DOI: 10.25407/jacbts.8255327.v1
title: Figure 15: Simulated Arterial Switch Operation From a Hands-on Surgical Training Course for Cardiothoracic Surgeons

description: Reproduced with permission from Yoo et al. (72). See Supplemental Video 2. LCA = left coronary artery; other abbreviations as in Figures 5 and 6.