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PHQ-9 and GAD-7 Coded Dataset
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Radiogrammetric parameters of the femur were assessed in an adult sample (N=98) from the Coimbra Identified Skeletal Collection (Portugal). Anteroposterior radiographs of the midshaft area of the left femur of each individual were taken using a mammogram film with an exposure time of mAseg 80-50,exposure of Kv 30-35 and focal distance of 1.0 m. Maximum length of the femur, as defined by Martin and Saller (1957), was determined. Measurements of diaphysis total width (DTW) and medullary width (MW) were taken following a standardized guide. Radiogrammetry was used to establish cortical index (FEMCI) in the femoral mid-shaft. Diaphysis total width (DTW) and femoral cortical index (FEMCI) are significantly higher in males, while medullary width (MW) is not statistically different between sexes. The evaluation of femoral cortical bone reveals sex-specific trajectories of endosteal bone loss and periosteal apposition, stemming from sexual differences in the rate and pattern of bone loss, and in bone size. In females, endocortical bone loss rises with age, particularly in peri- and postmenopausal years, decelerating later in life. Concomitantly, accretion of bone in the subperiosteal surface persists throughout adulthood — partially offsetting bone fragility in women. Strength in the femoral mid-diaphysis appears to be preserved throughout most of the life course in both sexes.
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Provides all origin files used in simulation of impact energy using sigmoidal models.
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  • File Set
Distinguishing between bull Y- and X-bearing sperm populations is advantageous for techniques with sexed bull semen. The aim of this study was to produce a single-chain fragment variable (scFv) antibody against plasma membrane epitopes on bull Y-bearing sperm to distinguish between Y- and X- sperm. Variable heavy (VH) and variable light (VL) region genes generated from a hybridoma cell secreting a specific Y-bearing sperm monoclonal antibody (mAb-1F9) were cloned and expressed. The expected sizes of the DNA bands were ~350 bp for the VH gene and ~318 bp for the VL gene. The VH and VL genes were generated and used to construct an scFv gene (~650 bp) and express the corresponding soluble scFv antibody. Compared with the parent mAb-1F9, the scFv antibodies presented a high affinity for Y-bearing sperm and low cross-reactivity with X-bearing sperm. An immunofluorescence analysis confirmed that the scFv antibodies and mAb-1F9 recognize epitopes on the Y-bearing sperm surface. The fluorescence signal was strong on the plasma membrane of Y-bearing sperm but very weak for X-bearing sperm. This study helps the application and production of engineered scFv antibodies specific to Y-bearing sperm to distinguish between Y- and X-bearing sperm populations for techniques involving sexed bull semen
Data Types:
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1H-NMR spectroscopy data from 24-hr urine samples from Diets 1 and 4, Dietary Metabotype Score (DMS), blood glucose measurement and urinary calorific value. Data contains quantified values for identified metabolites (in mmol/ml) of 24-hr urine samples for 19 volunteers for the two reference diets in Excel format. For each sample, the DMS, area-under-the-curve (AUC) glucose and calorific value (in J/g) are also given. This data accompanies Garcia-Perez et al. (2020) "Dietary metabotype modelling predicts individual responses to dietary interventions: A feasibility study" Nature Food (submitted, ref.: NATFOOD-19060125C)
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Mesenchymal stem/stromal cells (MSC) have immunomodulatory properties, studied in a wide range of diseases. Validated Quality Controls must be able to confirm this activity in the context of clinical trials. This study presents the validation of a method, quantifying the ability of MSC to inhibit T cell proliferation according to the ICH Q2 standard. Peripheral blood mononuclear cells (PBMC) from a bank of ten donors, labeled with CellTrace Violet (CTV), were co-cultured with MSC at seven different ratios for seven days. Flow cytometry analysis was used to obtain the percentage of division (PD) of T cells. Two parameters were calculated: the percentage of inhibition (PI) of T cell proliferation, for each ratio X, determined using the following formula PI ratio X = (PD control – PD ratio X) / PD control, and the corresponding area under the curve (AUC). The validation of two different CTV-PBMC banks did not show any statistical difference and demonstrated stability over 509 days of storage. Analysis of repeatability and reproducibility showed a standard deviation (SD) of 6.1% and 4.6%, respectively. Robustness analysis, corresponding to the ability of a method to resist small but deliberate variations in its parameters, for PBMC, and MSC, did not present any difference. The assay was linear on the exploited range and permitted to distinguish MSC presenting different ranges of inhibition activity. This quantification method of MSC immunomodulatory activity displayed low analytical variability, sufficient robustness, and no inter-bank variability of PBMC. Therefore, it could be used for MSC manufacturing batch qualification.
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The Excel File and Mat File contain the raw and transformed data that we used in our paper 'Financial Wealth, Investment and Sentiment in a Bayesian DSGE Model'.
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  • Software/Code
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Data and code files for manuscript submitted to the Journal of Theoretical Biology.
Data Types:
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  • Software/Code
  • Dataset
SVR-LSM Code and Results for Wiesen, Karnath & Sperber: Disconnection somewhere down the line: Multivariate lesion-symptom mapping of the line bisection error.
Data Types:
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  • File Set
Different human linker histone (H1) variants are expected to have distinct binding modes to the nucleosome. The position and orientation of a number of different H1 globular domains on the nucleosome were investigated through molecular docking using MGLTools and HADDOCK. The nucleosome core and linker DNA in the GH5-chromatosome structure (PDB: 4QLC) were used as a docking template. GH5 (in PDB: 4QLC) was re-docked to this template to test the docking algorithm. Docked and re-docked GH5 compared well. The docking algorithm was further tested by docking the NMR solution structure of the globular domain of chicken H1 (GH1, PDB: 1GHC) to the nucleosome template. The position of docked GH1 on the nucleosome agreed with literature. 
The N-terminal - and globular domain H1x hybrid (NGH1x) was studied using solution NMR in both low (20 mM sodium phosphate, pH 7.0) and high (20 mM sodium phosphate, 1 M sodium perchlorate, pH 7.0) ionic strength conditions (de Wit, H., Vallet, A., Brutscher, B. et al. Biomol NMR Assign (2019) 13: 249. https://doi.org/10.1007/s12104-019-09886-x). These low and high ionic strength structures were docked to the nucleosome template. 
Homology (MODELLER) and ab initio modeling (CS-ROSETTA) were employed to model structures for other human H1 globular domains: GH1.0, GH1.4, GH1oo, and GH1t. The modeled structures were also docked to the nucleosome template.
 All the docking procedures listed above produced 100 models of different energies. In each case, the lowest energy docked model was chosen. The structures of all the H1 globular domains that were docked to the template are given as PDB files (1GHC_lowest_energy.pdb; 2LSO_lowest_energy.pdb; GH5_re-docked_position.pdb; NGH1x_high_salt_NTD.pdb; NGH1x_low_salt_NTD.pdb; modeled_GH1_0_lowest_energy.pdb; modeled_GH1_4_lowest_energy.pdb; modeled_GH1oo_lowest_energy.pdb; modelled_GH1t_lowest_energy.pdb) in the data file. The nucleosome template structure is also given in PDB file format (4QLC_nucleosome_without_GH5.pdb). Finally, the docked models are also given (GH5-chromatosome.pdb; 1GHC-chromatosome.pdb; 2LSO-chromatosome.pdb; GH1_0-chromatosome.pdb; GH1_4-chromatosome.pdb; GH1oo-chromatosome.pdb; GH1t-chromatosome.pdb; NGH1x_no_salt-chromatosome.pdb; NGH1x_salt-chromatosome.pdb). The files are compatible with most molecular graphics software. The file Dockings_modelling_test_and_results.pdf provides the modeling and docking results in figures and tables. A short description of each figure and table is given within the PDF file.
Data Types:
  • Sequencing Data
  • Dataset
  • Document