cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/wxvtnnczcs.1
title: Single-lysine precursor ion labelling in KARMA assays for a subset of proteins (10 NUP baits)

description: Supplementary analyzed data from Manuscript: TITLE: Maturation kinetics of a multiprotein complex revealed by metabolic labeling. JOURNAL: CELL. Article Type: Research Article Authors: Evgeny Onischenko*, Elad Noor*, Jonas S. Fischer*, Ludovic Gillet, Matthias Wojtynek, Pascal Vallotton, Karsten Weis *Equally Contributing Authors Corresponding Authors: Evgeny Onischenko and Karsten Weis Related to Figure S2; Table S4 Single-lysine precursor ion labelling in KARMA assays for a subset of proteins (10 NUP baits). The target protein complex is isolated from cell lysates by affinity pulldowns at several time points following the onset of metabolic labeling, tryptically digested and analyzed with LC-MS on an Orbitrap mass-spectrometer. The MS2 fragmentation spectra are acquired in a DIA mode for all samples. Zero time point samples (containing only light lysine) are additionally analyzed in a DDA mode to produce assay spectral libraries. Peptide intensities are extracted from the DIA datasets with Spectronaut software (Biognosis) using complementary assay spectral libraries. Individual plots: Protein labeling H/(H+L) in each post-labeling sample (red track) is determined based on the summed intensities of light (L) and heavy (H) constituent high quality precursor ions (green tracks). Low-quality precursor ions are excluded from quantification (gry tracks). y-axis: fractional labeling H/(H+L); x-axis: individual samples (10 handles, 3 replicates, 3 timepoints).
DOI: 10.17632/bhnx77wx94.1
title: LTSRP

description: This dataset is used for the working paper “Routing automated lane-guided transport vehicles in a warehouse handling returns” (LTSRP) authored by Emde, Tahirov, Gendreau and Glock. We generate three different instance sets namely, S, M, and L that correspond proportionally to the real industry case. Instance set S contains small instances with 9 stations. Set M contains medium size instances with 60 stations. These instances correspond most closely to the real-world case. Finally, with 150 stations set L is the largest instances set. The number of depots is 3 in all cases and each set contains 20 instances. There are 60 instances in total. We use two-dimensional coordinates (x_i,y_i) for each station. For set S and L the value of the coordinates are randomly drawn numbers from the interval (1,15) and (1,100), respectively. Depot i=1,…m, is placed in location (2.5+(i-1)∙ 5, 0) (S) and (16.67+(i-1)∙ 33.33, 0) (L), respectively. For the real-world M instances, we reuse the data from our industry partner, randomly fudging the numbers such that they are proportionally correct. Note that, the first 3 nodes (coordinates) of each instance of M set represent depots. Distances between stations (and depots) are then measured via the Euclidean metric. Each text file is structured as follows: NAME: DIMENSION: EDGE_WEIGHT_TYPE: NODE_COORD_SECTION: EOF:
DOI: 10.17632/w3f4kksy69.1
title: Relative signal intensities of NUP peptides in pre-labeling KARMA assay samples

description: Supplementary analyzed data from Manuscript: TITLE: Maturation kinetics of a multiprotein complex revealed by metabolic labeling. JOURNAL: CELL. Article Type: Research Article Authors: Evgeny Onischenko*, Elad Noor*, Jonas S. Fischer*, Ludovic Gillet, Matthias Wojtynek, Pascal Vallotton, Karsten Weis *Equally Contributing Authors Corresponding Authors: Evgeny Onischenko and Karsten Weis Related to Figure S2; Table S4 Relative signal intensities of NUP peptides in pre-labeling KARMA assay samples. The target protein complex is isolated from cell lysates by affinity pulldowns, tryptically digested and analyzed with LC-MS on an Orbitrap mass-spectrometer. The MS2 fragmentation spectra are acquired in a DIA mode for all samples. Peptide intensities are extracted from the DIA datasets with Spectronaut software (Biognosis) using complementary assay spectral libraries. Individual plots: The fraction of protein's signal intensity in each sample (red track) is given by the median of the signal fraction across all high quality precursor ions (green tracks). Low quality precursor ions (grey tracks) are excluded from quantification. x-axis: individual samples, y-axis: fraction of precursor ion signal in a sample (precursor signal intensity in a sample normalised for the total across all 34 samples). Individual precursor ion values across samples are connected, forming a track.
DOI: 10.17632/89cct7t7tk.1
title: HQ peptide labeling of KARMA baits relative to their position in the protein sequence

description: Supplementary analyzed data from Manuscript: TITLE: Maturation kinetics of a multiprotein complex revealed by metabolic labeling. JOURNAL: CELL. Article Type: Research Article Authors: Evgeny Onischenko*, Elad Noor*, Jonas S. Fischer*, Ludovic Gillet, Matthias Wojtynek, Pascal Vallotton, Karsten Weis *Equally Contributing Authors Corresponding Authors: Evgeny Onischenko and Karsten Weis Related to Figure S4; Table S4 HQ peptide labeling of KARMA baits relative to their position in the protein sequence. Individual Plots: Dependence of high-quality precursor labelling upon their position in the polypeptide chain was analysed for all ten KARMA bait proteins across all labelling time points. Note that the linear regression analysis does not show significant dependence between a peptide's labelling and its position in the polypeptide chain.
DOI: 10.17632/5ngccfr479.1
title: KSM fits for 320 bait-prey pairs of NUPs in KARMA assays

description: Supplementary analyzed data from Manuscript: TITLE: Maturation kinetics of a multiprotein complex revealed by metabolic labeling. JOURNAL: CELL. Article Type: Research Article Authors: Evgeny Onischenko*, Elad Noor*, Jonas S. Fischer*, Ludovic Gillet, Matthias Wojtynek, Pascal Vallotton, Karsten Weis *Equally Contributing Authors Corresponding Authors: Evgeny Onischenko and Karsten Weis Related to Figures S4, Figure S5, and Table S3; KSM fitting curves for 320 bait-prey pairs characterised in the KARMA assays. Individual plots: The red line represents the expected labeling of the reference proteins as a function of time, and is used to find the effective sampling time for each sample (i.e. the x-value of each point). Then, we try to fit the 3-step KSM (purple line). Preys with metabolic labeling exceeding the reference protein were fitted with a 4-step model. 𝜙1: effective maturation pool, 𝜙2: accessible fraction of the mature state.
DOI: 10.17632/wp6d6nbnr3.1
title: Top 0.1 percent best scoring trees for the NPC maturation order

description: Supplementary analyzed data from Manuscript: TITLE: Maturation kinetics of a multiprotein complex revealed by metabolic labeling. JOURNAL: CELL. Article Type: Research Article Authors: Evgeny Onischenko*, Elad Noor*, Jonas S. Fischer*, Ludovic Gillet, Matthias Wojtynek, Pascal Vallotton, Karsten Weis *Equally Contributing Authors Corresponding Authors: Evgeny Onischenko and Karsten Weis Related to Figures 5 and S5. Possible maturation orders in NPC biogenesis, are represented by a binary tree whose leaves are the 9 identified NUP assembly groups. The leafs are allowed to gradually merge representing the co-assembly events among NUPs until they form a complete NPC (tree root). Each leaf and each vertex (i.e. a mature complex of several such leaves) in the tree is assigned a single variable which represents its relative pool size. For every possible tree configuration this set of variables is optimised to match the effective maturation pool data from the KSM fitting. RMSE (Root Mean Squared Error) between the computed maturation pools from the binary tree and the ones estimated by KSM is used as the tree score. The graphs represent 0.1% best scoring trees (i.e. with the lowest RMSE values) arranged in an ascending order.
DOI: 10.17632/n8gsxc2s6j.3
title: Commitment to Rice Cooperatives in Zambia

description: The data is about commitment to cooperatives by smallholder rice farmers in the Western Zambia. The aim of this study, therefore, is to analyze the economic impact of commitment to rice cooperatives by smallholder farmers. The cooperatives in question is from a rice value chain in the Western province of Zambia.
DOI: 10.17632/pkgf78r9yb.1
title: REV - 3D models of the pores structure

description: The pores’ geometric representation of some of the configurations proposed in the work "Expanding manufacturing strategies to advance in porous media planning with material extrusion additive manufacturing". The REV gives an idea of how complex a lattice-type porous structure can become when the advanced parameters are applied. The interpretation of these paths is not always trivial and, therefore, the 3D models of the REV are available in STL and STEP formats as additional material. They might be useful for pore-scale simulations.
DOI: 10.17632/8jt8cshzsx.2
title: Characterization of Regional Drought over Water and Energy Limited Zones of India using Potential and Actual Evapotranspiration

description: Suitability of use of Actual Evapotranspiration in the drought asessment over water and energy-limited regions of India
DOI: 10.17632/4jfgz3z5pd.2
title: Jurujuba Sound pore water and sediment Data - RJ - Brazil

description: The Jurujuba Sound is located within Guanabara Bay (Rio de Janeiro - Brazil), this overpopulated region probably may have contributed to the accumulation of chemical compounds in the sediments by diffuse sources (the Cachoeira and Icaraí rivers). Jurujuba Sound also supports a considerable area of mussel farms. In this research two main investigation approaches had been chosen, pore water and sediments nutrients. This work aims to indicate the characteristic distribution of the superficial sediment (pH, Eh, particular size, carbonate, organic matter and phosphorus, and nutrients present in pore-water (C, N, P) along Jurujuba Sound area. . The pH and Eh were measured in-situ using a Hanna Multiparameter probe. In the laboratory, nutrients in pore-ware water were measured by the colorimetric method with a KASUAKI UV / VIS spectrometer at different wavelengths for phosphate (and total phosphorous) (880 nm), nitrate (505 nm), nitrite (540 nm), and ammonium (630 nm). The grain size analysis was determined on a laser analyzer, carbonate was performed by mass difference. Spatial distribution maps were produced for each parameter, to assess nutrients spatial behavior and their relationships with other parameters. The results demonstrate high N and P concentrations in pore water, indicating the possible release of the relevant nutrient amount in the water column. The high rate of domestic effluent input (Confirmed by TOC/TN ratio) led to high nutrient levels in sediments and porewater, potential release from the bottom sea could cause fish mortality events and other toxic effects.
DOI: 10.17632/gbvhzbjnsm.1
title: Appropriateness of antibiotic prescription among Italian dental practitioners: results from a cross-sectional study

description: The dataset was used in a cross-sectional study primarily aimed to to investigate the pattern of antibiotic prescription for prophylaxis purposes among Italian DPs. From April to October 2019, a nationwide cross-sectional study was conducted in a representative sample of the Italian general and specialist DPs. The information is collected through a mixed technique, which uses an online questionnaire that is filled in by respondents, a direct telephone interview with the questionnaire administered by an interviewer, and a self-administered paper questionnaire. A structured questionnaire was used, comprising of four sections: (1) an introductory section presenting study aims and motivation at the end of which DPs could give their written consent in joining the study; (2) a socio-demographic data collection section; (3) the main research section about practices regarding prophylactic antibiotic prescriptions; (4) and sources of information used to update knowledge on antibiotic use in dental practices. Bivariate (t-tests, chi-square and Fisher exact test) and multivariate analyses were conducted to examine the potential association with the DP correct prescription practice. Moreover, a logistic regression model was used to estimate the odds of correct prescription practice depending on the invasive dental procedures and the presence of indication or not. The interaction between the two factors was also investigated. 563 DPs answered the general questionnaire (response rate 52.6%).
DOI: 10.17632/wz59sf6ck8.1
title: Data for: Spectral Verification of the Mechanisms behind FBG-based Ultrasonic Guided Wave Detection

description: This data set consists of the filtered and averaged UGW data, and the extracted Gaussian fit data (UGW_fit.mat) for the Bragg wavelength and FWHM of the Bragg peak.
DOI: 10.17632/j3wr4wn946.1
title: Spin-1 spin–orbit- and Rabi-coupled Bose–Einstein condensate solver

description: We present OpenMP versions of FORTRAN programs for solving the Gross–Pitaevskii equation for a harmonically trapped three-component spin-1 spinor Bose–Einstein condensate (BEC) in one (1D) and two (2D) spatial dimensions with or without spin–orbit (SO) and Rabi couplings. Several different forms of SO coupling are included in the programs. We use the split-step Crank–Nicolson discretization for imaginary- and real-time propagation to calculate stationary states and BEC dynamics, respectively. The imaginary-time propagation programs calculate the lowest-energy stationary state. The real-time propagation programs can be used to study the dynamics. The simulation input parameters are provided at the beginning of each program. The programs propagate the condensate wave function and calculate several relevant physical quantities. Outputs of the programs include the wave function, energy, root-mean-square sizes, different density profiles (linear density for the 1D program, linear and surface densities for the 2D program). The imaginary- or real-time propagation can start with an analytic wave function or a pre-calculated numerical wave function. The imaginary-time propagation usually starts with an analytic wave function, while the real-time propagation is often initiated with the previously calculated converged imaginary-time wave function.
DOI: 10.17632/x2m4c3zkjz.1
title: Data for: Early Cretaceous lower crustal thickening and delamination: Constraints from cumulate rocks and adakitic lavas in southeast China

description: We presented new zircon U-Pb ages and Hf isotopes of the gabbro and diorite in the southeastern edge of South China, the representative cumulate of the arc lower crust derived from hydrous magmas. Also included here are contemporaneous adakitic lavas reported in the vicinity. Bulk-rock geochemical and Sr-Nd-Pb isotopic compositions of the cumulate and adakite are reported. Meanwhile, we compiled previously published dataset of the Cretaceous adakitic rocks and A-type granites that are widespread in South China.
DOI: 10.17632/56wydw5wf5.1
title: Materials analysis applying thermodynamic (MAAT) software: A friendly and free tool to analyze the formation of solid solutions, amorphous phases and intermetallic compounds

description: Experimental thermodynamic measurements in multicomponent systems exhibit high complexity. Theoretical calculations by extrapolation of constitutive binary systems are an excellent tool to estimate the thermodynamic properties in ternary or quaternary systems. In this context, the Miedema and Bakker semi-empirical models are good to estimate the enthalpy of mixing or formation. This work presents a new software, MAAT (Materials Analysis Applying Thermodynamics), designed to calculate selected thermodynamic properties of binary and ternary systems. The MAAT is a free software that can be download from www.rpm.usm.cl. The MAAT software is a platform, written in MATLAB, which runs in 32/64 bits Windows systems. The main characteristics of the software are: i) calculation and plotting Gibbs free energy of mixing curves of random solid solutions, amorphous and intermetallic compounds, ii) calculation and plotting the activity of components in solid solutions, and iii) analysis of the effect of additional terms over the Gibbs free energy of mixing of random solid solutions, such as centrifugal field, grain size and dislocations. In this work, the thermodynamic calculations performed with MAAT are compared with experimental data in four cases: formation of solid solution (Cu-Mo-Cr system), formation of amorphous phase (Ti-Ta-Sn system), formation of intermetallic compound (Cu-Nb-Co system) and effect of centrifugal field on formation of solid solution (Cu-Cr system). For all systems analyzed, the calculations made using MAAT gave results that are comparable with experimental data.
DOI: 10.17632/dx2hmbs24b.1
title: A novel approach to reduce the application of sulfurized olefins in gear oil by synergistic action of nano-TiO2

description: Data of munuscript "A novel approach to reduce the application of sulfurized olefins in gear oil by synergistic action of nano-TiO2" Folder 1 is the raw data from figure 3 in the manuscript, which describes the size distributions of the as-prepared SA-TiO2 nanoparticles. Diameter (nm) and number (%) are used as the x and Y axes respectively. Folder 2 is the raw data from figure 5 in the manuscript, which describes the FTIR spectrum of SA-TiO2. Wavenumber (cm-1) and transmittance (%) are used as the x and Y axes respectively. Folder 3 is the raw data from figure 6a1 in the manuscript, which describes the TGA of SA-TiO2. Temperature (℃) and weight (%) are used as the x and Y axes respectively. Folder 4 is the raw data from figure 6b1 in the manuscript, which describes the DSC of SA-TiO2. Temperature (℃) and heat Flow (W/g) are used as the x and Y axes respectively. Folder 5 is the raw data from figure 7 in the manuscript, which describes the PD values of oil samples with various contents of the SA-TiO2 and SIB in base oil by four-ball tribometer.Pd (N) and SA-TiO2 content (%) are used as the x and Y axes respectively. Folder 6 is the raw data from figure 8 in the manuscript, which describes COF and WSD of GCr15 steel balls lubricated by oil samples with 1.5 wt.% SIB and various contents of the SA-TiO2 in base oil under 196 N by four-ball tribometer. Wear Scar Dameter (mm) and SA-TiO2 content (%) are used as the x and Y axes respectively. Folder 7 is the raw data from figure 9 in the manuscript, which describes the Friction coefficient curves of GCr15 steel balls lubricated by oil samples with 1.5 wt.% SIB and various contents of SA-TiO2 in base oil under 196 N by four-ball tribometer. Time (s) and Friction coefficient are used as the x and Y axes respectively. Folder 8 is the raw data from figure 10 in the manuscript, which describes the Friction coefficient curves of different oil samples under 17.9 N by UMT tester. Time (s) and Friction coefficient are used as the x and Y axes respectively. Folder 9 is the raw data from figure 12 in the manuscript, which describes the XPS spectra of C1s, O1s, Fe2p, S2p and Ti2p on the wear scar of steel ball lubricated by base oil alone and oil sample containing additives on four-ball tribometer at 196 N for 30 min. Binding energy (eV) and Counts (s) are used as the x and Y axes respectively.
DOI: 10.17632/2n7rwb2y6c.4
title: Effective Methods of Job Search for Unemployed Youth in Sri Lanka

description: This data set contains a cleaned version of the Youth Survey Database 2018 available at https://www.veriteresearch.org/publication/youth-labour-market-assessment-sri-lanka/. The data set has been cleaned and presented with the minimum requirement to help the publisher reproduce the author's work as given in his paper.
DOI: 10.17632/85x3f8r789.1
title: A novel PLOD1 gene mutation

description: yphoscoliotic Ehlers-Danlos syndrome (kEDS) is a rare autosomal recessive connective tissue disorder characterized by progressive kyphoscoliosis, congenital muscular hypotonia, marked joint hypermobility, and severe skin hyperextensibility and fragility. Deficiency of lysyl hydroxylase 1 (LH1) due to mutations of PLOD1 (procollagen-lysine, 2-oxoglutarate 5-dioxygenase 1) gene has been identified as the pathogenic cause of kEDS (kEDS-PLOD1). Up to now, kEDS-PLOD1 has not been reported among Chinese population. We reported a 17-year-old Chinese male patient presenting with hypotonia, joint hypermobility and scoliosis was referred to our hospital. After birth, he was found to have severe hypotonia leading to delayed motor development. Subsequently, joint hypermobility, kyphoscoliosis and amblyopia were found. Inguinal hernia was found at age 5 years and closed by surgery. At the same time, he presented with hyperextensible and bruisable velvety skin with widened atrophic scarring after minor trauma. Dislocation of elbow joint was noted at age of 6 years. Orthopedic surgery for correction of kyphoscoliosis was performed at age 10 years. His family history was unremarkable. Physical examination revealed elevated blood pressure. Slight facial dysmorphologies including high palate, epicanthal folds, and down-slanting palpebral fissures were found. He also had blue sclerae with normal hearing. X-rays revealed severe degree of scoliosis and osteopenia. The Echocardiography findings were normal. Laboratory examination revealed a slightly elevated bone turnover. Based on the clinical manifestations presented by our patient, kEDS was suspected. Genetic analysis revealed a novel homozygous missense mutation of PLOD1 (c.1697 G&gt;A, p.C566Y) (NM_000302.4), confirming the diagnosis of kEDS-PLOD1. Corresponding heterozygous mutation was detected in his parents. This variant is possibly causative for kEDS because it was predicted to be “PROBABLY DAMAGING” with a score 0.999 by Polyphen‐2, “AFFECT PROTEIN FUNCTION” with a score 0.00 by SIFT, and “disease causing” by Mutation Taster.
DOI: 10.17632/tjm38bb88y.1
title: Table S2 A study of Nonstructural protein 1 of SARS-CoV-2 is a potent pathogenicity factor redirecting host protein synthesis machinery toward viral RNA. Yuan et al

description: Source data and summary statistics of cellular viability effect by introduction of SARS-CoV-2 viral proteins and mutants
DOI: 10.17632/jwy6h942j3.1
title: Table S1 A study of Nonstructural protein 1 of SARS-CoV-2 is a potent pathogenicity factor redirecting host protein synthesis machinery toward viral RNA. Yuan et al

description: Oligo sequences used in this study
DOI: 10.17632/32mmm3xk3v.1
title: Table S4 A study of Nonstructural protein 1 of SARS-CoV-2 is a potent pathogenicity factor redirecting host protein synthesis machinery toward viral RNA. Yuan et al

description: . DAVID pathway analysis of Nsp1 differentially expressed gene sets Sup table 4.1 Functional clustering of Nsp1 vs Vector Control highly downregulated genes (q &lt; 1e-30) Sup table 4.2 Functional clustering of Nsp1 vs Nsp1 Mutant highly downregulated genes (q &lt; 1e-30) Sup table 4.3 Functional clustering of Nsp1 vs Vector Control highly upregulated genes (q &lt; 1e-30) Sup table 4.4 Functional clustering of Nsp1 vs Nsp1 Mutant highly upregulated genes (q &lt; 1e-30) Sup table 4.5 Biological processes enrichment of Nsp1 vs Vector Control highly downregulated genes (q &lt; 1e-30) Sup table 4.6 Biological processes enrichment of Nsp1 vs Nsp1 Mutant highly downregulated genes (q &lt; 1e-30) Sup table 4.7 Biological processes enrichment of Nsp1 vs Vector Control highly upregulated genes (q &lt; 1e-30) Sup table 4.8 Biological processes enrichment of Nsp1 vs Nsp1 Mutant highly upregulated genes (q &lt; 1e-30) Sup table 4.9 Gene list of Nsp1 vs Vector Control highly downregulated genes (q &lt; 1e-30) Sup table 4.10 Gene list enrichment of Nsp1 vs Nsp1 Mutant highly downregulated genes (q &lt; 1e-30) Sup table 4.11 Gene list enrichment of Nsp1 vs Vector Control highly upregulated genes (q &lt; 1e-30) Sup table 4.12 Gene list enrichment of Nsp1 vs Nsp1 Mutant highly upregulated genes (q &lt; 1e-30) Sup table 4.13 Gene list of Nsp1 vs Vector Control all downregulated genes (q &lt; 0.01) Sup table 4.14 Gene list of Nsp1 vs Vector Control all upregulated genes (q &lt; 0.01)