cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.10069094
title: Supplementary data for Spatial modeling of archaeological site locations based on summed probability distributions and hot-spot analyses: A case study from the Three Kingdoms Period, Korea (Journal of Archaeological Science)

description: These are radiocarbon ages and statistical models from Baekje settlements located in Gyeonggi-do published in Spatial modeling of archaeological site locations based on summed probability distributions and hot-spot analyses: A case study from the Three Kingdoms Period, Korea. Journal of Archaeological Science (https://doi.org/10.1016/j.jas.2019.105036). SM1 contains the raw radiocarbon ages and site locations. SM2 contains the summed probability distributions (SPDs) from the sites used as attribute weights in the paper.
DOI: 10.6084/m9.figshare.10069055
title: Supplementary Material for: Imaging of Carotid Plaque Neovascularization by Contrast-Enhanced Ultrasound and Dynamic Contrast-Enhanced Magnetic Resonance Imaging

description: <b><i>Background:</i></b> Carotid plaque neovascularization (<i>vasa vasorum</i> [VV]) may be useful for detecting high-risk atherosclerotic plaques. Contrast-enhanced ultrasound (CEUS) and dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) are 2 commonly used techniques for imaging VV of the carotid plaque, yet the relationship between their measurements remains unknown. <b><i>Objectives:</i></b> We aimed to blindly evaluate the correlation between CEUS and DCE-MRI in measuring carotid plaque VV. <b><i>Methods:</i></b> We recruited subjects with asymptomatic carotid stenosis (≥50%). VV was graded by CEUS, based on richness of contrast signal, according to 3 different methods named CEUS_A, CEUS_B and CEUS_C on different point scales (the higher the values, the higher the estimated VV). A 3.0 T MRI scanner was used for VV quantification by DCE-MRI using gadolinium contrast kinetic modelling for computing the fractional plasma volume (<i>vp</i>) and transfer constant (<i>K</i><sup><i>trans</i></sup>). <b><i>Results:</i></b> The analysis included 30 patients. A significant correlation between CEUS and DCE-MRI findings was observed when CEUS_C was used for neovessel grading and DCE-MRI was used to determine adventitial (<i>r</i> = 0.460, <i>p</i> = 0.010) and plaque (<i>r</i> = 0.374, <i>p</i> = 0.042) <i>Ktrans</i> values. CEUS_B (<i>r</i> = 0.416, <i>p</i> = 0.022) and CEUS_C (<i>r</i> = 0.443, <i>p</i> = 0.014) grading showed a significant correlation with regard to the maximal <i>K</i><sup><i>trans</i></sup>. <b><i>Conclusions:</i></b> We found a positive but weak correlation and a moderate diagnostic agreement between neovessels as visually graded by CEUS and adventitial neovessels assessed by DCE-MRI <i>K</i><sup><i>trans</i></sup> in carotid atherosclerosis. These findings may help in understanding how VV density, flow, and permeability influence in vivo measurements by CEUS and DCE-MRI as well as in selecting the most appropriate variables and imaging method in future research and potentially in clinical settings. Further confirmative studies are necessary to confirm our results.
DOI: 10.6084/m9.figshare.10069094.v1
title: Supplementary data for Spatial modeling of archaeological site locations based on summed probability distributions and hot-spot analyses: A case study from the Three Kingdoms Period, Korea (Journal of Archaeological Science)

description: These are radiocarbon ages and statistical models from Baekje settlements located in Gyeonggi-do published in Spatial modeling of archaeological site locations based on summed probability distributions and hot-spot analyses: A case study from the Three Kingdoms Period, Korea. Journal of Archaeological Science (https://doi.org/10.1016/j.jas.2019.105036). SM1 contains the raw radiocarbon ages and site locations. SM2 contains the summed probability distributions (SPDs) from the sites used as attribute weights in the paper.
DOI: 10.6084/m9.figshare.10069247.v2
title: EBP1 Regulates the Capacity of Protein Translation

description: Arabidopsis pgEBP1-YFP line expressing EBP1-YFP under the EBP1 promoter were grown in 3 repeats alongside with the same number of repeats of the control 35CaMVS:GFP (ref) for 7 days at 16/8 light and 150-200 seedlings were frozen in liquid N2 and total proteins were extracted in 1 mL of lysis buffer(150 mM NaCl, 1% Igepal CA-630, 50 mM Tris HCl (pH 8.0), 1 mM DTT, 3 mM PMSF, protease inhibitor cocktail, 3mM pNPP 10 uM MG132). The total protein extracts (4mg/IP) were cleared by centrifugation at 13,000g and 4°C for 20 min to remove remaining membrane and DNA, and the supernatant was incubated with 50 µl magnetic beads coupled to monoclonal mouse anti-GFP antibody (Miltenyi Biotec) for 15 min on ice. Magnetic columns were equilibrated using 250 µl lysis buffer. Cell lysates were added to the column after incubation and washed two times with 1 ml ice-cold lysis buffer, five times with 2 ml of 1xPBS (Dulbecco’s Phosphate Buffered Saline), and 2 times 1 ml 25 mM ABC (Ammonium bicarbonate), pH 7.5. Purified proteins were predigested by adding 20 µl 25 mM ABC , pH 7.5, 1 mM DTT, and 150 ng trypsin (Promega) for label-free experiments. After in-column digestion for 30 min at room temperature, proteins were eluted by adding two times 50 µl 25 mM ABC, pH 7.5, and 2.2 mM Iodoacetamide. Proteins were digested overnight at room temperature. The digestion was stopped by adding 5 µl 10 % formic acid, and peptides of each experiment were split and purified on two C18 Stage Tips and stored at 4°C.<br><br>The peptide mixture was analyzed by LC-MS/MS using a nanoflow RP-HPLC (LC program: linear gradient of 3-40 % B in 100 min, solvent A: 0.1% formic acid in water, solvent B: 0.1% formic acid in acetonitrile) on-line coupled to a linear ion trap-Orbitrap (Orbitrap-Fusion-Lumos, Thermo Fisher Scientific) mass spectrometer operating in positive ion mode.<br><br>o determine bait specific interactors, MaxQuant proteomics software version 1.6.6.0 (Cox and 131Mann 2008)based label-free quantification analysis was carried out on the corresponding MS data 132files (.raw) representing 6 repeats of each pull down against the Arabidopsis thaliana protein and 133common laboratory contaminant databases, concatenated with the reverse sequences. Standard 134parameters were kept unchanged with false discovery rates (FDRs) of 0.01 for peptide and protein 135identification, and the minimum ratio set at 1. Unique and razor peptides were used for quantification 136with “match between runs” option enabled to permit for peptide identification transfer between the 137corresponding LC-MS raw files.
DOI: 10.6084/m9.figshare.10069247
title: EBP1 Regulates the Capacity of Protein Translation

description: Arabidopsis pgEBP1-YFP line expressing EBP1-YFP under the EBP1 promoter were grown in 3 repeats alongside with the same number of repeats of the control 35CaMVS:GFP (ref) for 7 days at 16/8 light and 150-200 seedlings were frozen in liquid N2 and total proteins were extracted in 1 mL of lysis buffer(150 mM NaCl, 1% Igepal CA-630, 50 mM Tris HCl (pH 8.0), 1 mM DTT, 3 mM PMSF, protease inhibitor cocktail, 3mM pNPP 10 uM MG132). The total protein extracts (4mg/IP) were cleared by centrifugation at 13,000g and 4°C for 20 min to remove remaining membrane and DNA, and the supernatant was incubated with 50 µl magnetic beads coupled to monoclonal mouse anti-GFP antibody (Miltenyi Biotec) for 15 min on ice. Magnetic columns were equilibrated using 250 µl lysis buffer. Cell lysates were added to the column after incubation and washed two times with 1 ml ice-cold lysis buffer, five times with 2 ml of 1xPBS (Dulbecco’s Phosphate Buffered Saline), and 2 times 1 ml 25 mM ABC (Ammonium bicarbonate), pH 7.5. Purified proteins were predigested by adding 20 µl 25 mM ABC , pH 7.5, 1 mM DTT, and 150 ng trypsin (Promega) for label-free experiments. After in-column digestion for 30 min at room temperature, proteins were eluted by adding two times 50 µl 25 mM ABC, pH 7.5, and 2.2 mM Iodoacetamide. Proteins were digested overnight at room temperature. The digestion was stopped by adding 5 µl 10 % formic acid, and peptides of each experiment were split and purified on two C18 Stage Tips and stored at 4°C.<br><br>The peptide mixture was analyzed by LC-MS/MS using a nanoflow RP-HPLC (LC program: linear gradient of 3-40 % B in 100 min, solvent A: 0.1% formic acid in water, solvent B: 0.1% formic acid in acetonitrile) on-line coupled to a linear ion trap-Orbitrap (Orbitrap-Fusion-Lumos, Thermo Fisher Scientific) mass spectrometer operating in positive ion mode.<br><br>o determine bait specific interactors, MaxQuant proteomics software version 1.6.6.0 (Cox and 131Mann 2008)based label-free quantification analysis was carried out on the corresponding MS data 132files (.raw) representing 6 repeats of each pull down against the Arabidopsis thaliana protein and 133common laboratory contaminant databases, concatenated with the reverse sequences. Standard 134parameters were kept unchanged with false discovery rates (FDRs) of 0.01 for peptide and protein 135identification, and the minimum ratio set at 1. Unique and razor peptides were used for quantification 136with “match between runs” option enabled to permit for peptide identification transfer between the 137corresponding LC-MS raw files.
DOI: 10.6084/m9.figshare.10067297
title: Raw Data (L-ASNase activity for Taguchi analysis).xlsx

description: The data is the raw data for production improvement of L-Asparaginase from Lysinibacillus fusiformis.
DOI: 10.6084/m9.figshare.10067036
title: Genetic repertoire of Pseudomonas putida KT2440

description: Known for its versatile metabolism and capabilities in degrading organic pollutants, <i>Pseudomonas putida</i> KT2440 is emerging as a suitable microbial chassis for both metabolic engineering and environmental remediation applications. To understand the physiological and metabolic capabilities of a microorganism, the contemporary approach posits a look into its annotated genome. In particular, the types of genes present as well as their sequence constitute the basic information upon which metabolic pathways are discerned as well as genome scale metabolic network are constructed. To this end, the annotated genome sequence of <i>P. putida</i> KT2440 (Genbank accession number: NCBI Reference Sequence: NC_002947.4) was read by an in-house MATLAB software to enable the construction of a gene database comprising all annotated genes in the genome of the organism. Together with gene identifier, descriptor of the gene as well as its gene sequence were also curated in the gene database. The resource should be useful for researchers interested in the basic biology of <i>P. putida</i> KT2440 as well as metabolic engineers seeking to construct better biotechnology strains using the base strain as engineering chassis.<br><br>
DOI: 10.6084/m9.figshare.10067297.v1
title: Raw Data (L-ASNase activity for Taguchi analysis).xlsx

description: The data is the raw data for production improvement of L-Asparaginase from Lysinibacillus fusiformis.
DOI: 10.6084/m9.figshare.10066643
title: Rasters indoor residual spraying (IRS) coverage Sub-Saharan Africa from 1997 until 2017

description: Raster for indoor residual spray coverage from 1997-2017. Rasters at a 2.5 arc-minute (approximately 5 km) resolution are provided for each insecticide class and for total IRS, for each year. Each raster provides values for coverage from 0 to 100% and unknown values are represented as no-data.<br>Structure of the title is "insecticide class"_IRS_"year of coverage"<br>car_ Carbamatesoch_ organochlorinesoph_ organophosphatespyr_ pyrethroidsNo class_ Total IRS coverage<br>
DOI: 10.6084/m9.figshare.10066910
title: Indoor residual spraying (IRS) coverage data from 1997-2017

description: The datafile includes the year, country, most disaggregated administrative level, shapefile source with the unique identifier for each admin unit, IRS activity, insecticide brand name, insecticide formulation, insecticide class, proportion of structures sprayed, raw data type, source for coverage data, source for insecticide class data and a note of whether the raw data are publicly available. If the data for insecticide brand name, insecticide formulation, insecticide class or proportion of structures sprayed were unknown, they are marked as such.<br>Data discription is included.
DOI: 10.6084/m9.figshare.10066910.v1
title: Indoor residual spraying (IRS) coverage data from 1997-2017

description: The datafile includes the year, country, most disaggregated administrative level, shapefile source with the unique identifier for each admin unit, IRS activity, insecticide brand name, insecticide formulation, insecticide class, proportion of structures sprayed, raw data type, source for coverage data, source for insecticide class data and a note of whether the raw data are publicly available. If the data for insecticide brand name, insecticide formulation, insecticide class or proportion of structures sprayed were unknown, they are marked as such.<br>Data discription is included.
DOI: 10.6084/m9.figshare.10066643.v1
title: Rasters indoor residual spraying (IRS) coverage Sub-Saharan Africa from 1997 until 2017

description: Raster for indoor residual spray coverage from 1997-2017. Rasters at a 2.5 arc-minute (approximately 5 km) resolution are provided for each insecticide class and for total IRS, for each year. Each raster provides values for coverage from 0 to 100% and unknown values are represented as no-data.<br>Structure of the title is "insecticide class"_IRS_"year of coverage"<br>car_ Carbamatesoch_ organochlorinesoph_ organophosphatespyr_ pyrethroidsNo class_ Total IRS coverage<br>
DOI: 10.6084/m9.figshare.12866060
title: original data.xlsx

description: The original data came from the laboratory test and imaging examination results of the patients, which were true and effective. The study was approved by the Ethics Committee of all centers. Written informed consent was waived by the Ethics Commission of each hospital for emerging infections. <br>
DOI: 10.6084/m9.figshare.12866060.v2
title: original data.xlsx

description: The original data came from the laboratory test and imaging examination results of the patients, which were true and effective. The study was approved by the Ethics Committee of all centers. Written informed consent was waived by the Ethics Commission of each hospital for emerging infections. <br>
DOI: 10.5281/zenodo.4001688
title: PortLib Instances for the Port Scheduling Problem.

description: In the following we present the <em>PortLib</em> instances for the <em>Port Scheduling Problem</em> (PSP), which have been presented in the paper <em>An Adaptive Large Neighbourhood Search Heuristic for Routing and Scheduling Feeder Vessels in Multi-terminal Ports,</em> written by Erik Hellsten, David Sacramento and David Pisinger, and published in <em>European Journal of Operational Research</em>. The repository includes the results for <em>PortLib </em>instances for the <em>Adaptive Large Neighbourhood Search (ALNS)</em> heuristic and the commercial solver <em>CPLEX.</em> Additionally, we further include the results for the <em>Constraint Programming</em> and the <em>ALNS Math-heuristic</em> approaches from the paper <em>Constraint Programming and Local Search Heuristic: A Math-heuristic Approach for Routing and Scheduling Feeder Vessels in Multi-Terminal Ports</em>, written by David Sacramento, Christine Solnon and David Pisinger, and pending for publication in <em>SN Operations Research Forum</em>. Furthermore, this version includes the results for the <em>Constraint Programming</em> models from the paper <em>Integrated Planning of Feeder Vessels at Multi-Terminal Ports</em>, written by David Sacramento and David Pisinger, and pending for publication in <em>4OR</em> <em>- A Quarterly Journal of Operations Research</em>. The PSP represents a new scheduling problem for feeder vessels in multi-terminal ports, which has been defined in close collaboration with the industry. The proposed problem is a General Shop-like problem, and it accounts for most of the practical restrictions faced by the carriers in scheduling the operations. Given a fleet of feeder vessels, which each of them has a number of operations to perform at different terminals, and each terminal can only serve one vessels at a time, the task is to define an operational schedule, i.e. a starting time for each operation, which satisfies the time window and precedence constraints as well as minimises the departure times of the vessels and packs the schedule as tight as possible. The instances are named <strong>PSP.</strong><strong>n.m.r</strong>, where <strong>n</strong> is the number of container-terminals, <strong>m</strong> is the number of vessels, and <strong>r</strong> is the generic name of the scenario. The instances are randomly generated to be realistic, but in addition we ensured that each instance has a feasible solution as well as strove towards that each constraint should have a significant impact. In general, the instances are made to be slightly harder to solve than the problems faced by industry, in order to properly challenge the developed methods, as well as spurring further development.
DOI: 10.5281/zenodo.2572739
title: PortLib Instances for the Port Scheduling Problem.

description: In the following we present the <em>PortLib</em> instances for the <em>Port Scheduling Problem</em> (PSP), which have been presented in the paper <em>An Adaptive Large Neighbourhood Search Heuristic for Routing and Scheduling Feeder Vessels in Multi-terminal Ports,</em> written by Erik Hellsten, David Sacramento and David Pisinger, and published in <em>European Journal of Operational Research</em>. The repository includes the results for <em>PortLib </em>instances for the <em>Adaptive Large Neighbourhood Search (ALNS)</em> heuristic and the commercial solver <em>CPLEX.</em> Additionally, we further include the results for the <em>Constraint Programming</em> and the <em>ALNS Math-heuristic</em> approaches from the paper <em>Constraint Programming and Local Search Heuristic: A Math-heuristic Approach for Routing and Scheduling Feeder Vessels in Multi-Terminal Ports</em>, written by David Sacramento, Christine Solnon and David Pisinger, and pending for publication in <em>SN Operations Research Forum</em>. Furthermore, this version includes the results for the <em>Constraint Programming</em> models from the paper <em>Integrated Planning of Feeder Vessels at Multi-Terminal Ports</em>, written by David Sacramento and David Pisinger, and pending for publication in <em>4OR</em> <em>- A Quarterly Journal of Operations Research</em>. The PSP represents a new scheduling problem for feeder vessels in multi-terminal ports, which has been defined in close collaboration with the industry. The proposed problem is a General Shop-like problem, and it accounts for most of the practical restrictions faced by the carriers in scheduling the operations. Given a fleet of feeder vessels, which each of them has a number of operations to perform at different terminals, and each terminal can only serve one vessels at a time, the task is to define an operational schedule, i.e. a starting time for each operation, which satisfies the time window and precedence constraints as well as minimises the departure times of the vessels and packs the schedule as tight as possible. The instances are named <strong>PSP.</strong><strong>n.m.r</strong>, where <strong>n</strong> is the number of container-terminals, <strong>m</strong> is the number of vessels, and <strong>r</strong> is the generic name of the scenario. The instances are randomly generated to be realistic, but in addition we ensured that each instance has a feasible solution as well as strove towards that each constraint should have a significant impact. In general, the instances are made to be slightly harder to solve than the problems faced by industry, in order to properly challenge the developed methods, as well as spurring further development.
DOI: 10.6084/m9.figshare.10065788
title: Supplementary Material for: Learning Curves for Training in Ultrasonography-Based Examination of Umbilical Catheter Placement: A Piglet Study

description: <b><i>Background:</i></b> The training required for accurate assessment of umbilical catheter placement by ultrasonography (US) is unknown. <b><i>Objective:</i></b> To describe the learning curve and provide an estimate of the accuracy of physicians’ US examinations (US skills) and self-confidence when examining umbilical catheter tip placement. <b><i>Methods:</i></b> Twenty-one physicians with minimal experience in US completed a 1.5-hour eLearning module. Ten piglets with catheters inserted in the umbilical vessels were used as training objects. Following eLearning each physician performed up to twelve 10-min US examinations of the piglets. Expert examinations were reference standards. Sensitivity and specificity of physicians’ skills in detecting catheter tip placement by US was used to describe the learning curve. Self-confidence was reported by Likert scale after each examination. <b><i>Results:</i></b> Physicians’ detection of a correctly placed and misplaced umbilical artery catheter tip increased by an odds ratio of 1.6 (95% CI: 1.1, 2.3) and 3.6 (95% CI: 1.7, 7.8) per examination performed. A sensitivity of 0.97 (95% CI: 0.80, 0.99) and specificity of 0.95 (95% CI: 0.84, 0.99) was reached after 6 examinations. For the venous catheter, US skills in detecting a misplaced catheter tip increased with an odds ratio of 2.4 (95% CI: 1.2, 4.8) per US examination. Overall, performance and self-confidence plateaus were reached after 6 examinations. <b><i>Conclusion:</i></b> We found steep learning curves for targeted US examination of umbilical catheter placement. eLearning followed by 6 examinations was found to be adequate training to perform with a sufficiently high accuracy and self-confidence to allow for point-of-care use.
DOI: 10.6084/m9.figshare.10065788.v1
title: Supplementary Material for: Learning Curves for Training in Ultrasonography-Based Examination of Umbilical Catheter Placement: A Piglet Study

description: <b><i>Background:</i></b> The training required for accurate assessment of umbilical catheter placement by ultrasonography (US) is unknown. <b><i>Objective:</i></b> To describe the learning curve and provide an estimate of the accuracy of physicians’ US examinations (US skills) and self-confidence when examining umbilical catheter tip placement. <b><i>Methods:</i></b> Twenty-one physicians with minimal experience in US completed a 1.5-hour eLearning module. Ten piglets with catheters inserted in the umbilical vessels were used as training objects. Following eLearning each physician performed up to twelve 10-min US examinations of the piglets. Expert examinations were reference standards. Sensitivity and specificity of physicians’ skills in detecting catheter tip placement by US was used to describe the learning curve. Self-confidence was reported by Likert scale after each examination. <b><i>Results:</i></b> Physicians’ detection of a correctly placed and misplaced umbilical artery catheter tip increased by an odds ratio of 1.6 (95% CI: 1.1, 2.3) and 3.6 (95% CI: 1.7, 7.8) per examination performed. A sensitivity of 0.97 (95% CI: 0.80, 0.99) and specificity of 0.95 (95% CI: 0.84, 0.99) was reached after 6 examinations. For the venous catheter, US skills in detecting a misplaced catheter tip increased with an odds ratio of 2.4 (95% CI: 1.2, 4.8) per US examination. Overall, performance and self-confidence plateaus were reached after 6 examinations. <b><i>Conclusion:</i></b> We found steep learning curves for targeted US examination of umbilical catheter placement. eLearning followed by 6 examinations was found to be adequate training to perform with a sufficiently high accuracy and self-confidence to allow for point-of-care use.