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PHQ-9 and GAD-7 Coded Dataset
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An arboreal lifestyle is thought to be central to primate origins, and most extant primate species still live in the trees. Nonetheless, terrestrial locomotion is a widespread adaptation which has arisen repeatedly within the primate lineage. The absence of terrestriality among the New World monkeys (Platyrrhini) is thus notable and raises questions about the ecological pressures that constrain the expansion of platyrrhines into terrestrial niches. Here, we report the results of a natural experiment, comparing patterns of terrestrial behavior in white-faced capuchin monkeys (Cebus capucinus imitator) living on two islands off of the Pacific coast of Panama that lack mammalian predators (island sites) with the behavior of capuchins at three sites in central Panama with more intact predator communities (mainland sites). Surveys with camera traps revealed increased terrestriality in island vs. mainland sites. Capuchin detection rates were higher, the range of party sizes observed was larger, and individuals engaged in a wider range of terrestrial behaviors on the islands lacking mammalian predators. Further, females carrying infants were frequently photographed on the ground at the island sites, but never at the mainland sites. These findings support the longstanding hypothesis that predators constrain the exploitation of terrestrial niches by primates. These results are also consistent with the hypothesis that arboreal locomotion imposes costs that primates will avoid by walking on the ground when predation risk is low.
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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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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
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Raw data of HIGD2A-BioID2 experiment. Total spectrum count for 3 independent experiments for HIGD2A-BioID2 and 3 independent experiments for the control BioID targeted to the mitochondria (MTS-BioID2).
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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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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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Hardware design for build a Step Width System Capture
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Open data and R analysis scripts for the paper as submitted for publication: "Poppelaars, E. S., Klackl, J., Scheepers, DT, Mühlberger, C., & Jonas, E. (2019). Reflecting on existential threats elicits self-reported negative affect but no physiological arousal." A dataset of 171 undergraduate students were randomly allocated to one of four existential threat conditions: mortality salience, freedom restriction, uncontrollability, and uncertainty; or to the non-existential threat condition: social-evaluative threat; or to a control condition (TV salience). Three facets of arousal were measured: positive and negative affect before and after reflection, subjective arousal during baseline and reflection, and physiological activation during baseline and reflection (electrodermal, cardiovascular, and respiratory), as well as personality traits (e.g. trait avoidance and approach, self-esteem). Description of files: - File 'README.txt' contains the description of the files (metadata). - File '20191024_IJMData_brief.sav' contains the raw data. - Files 'EXI.outl.del.RData' contains the complete dataset with missing values, with extra variables calculated, and with outliers deleted. - File 'Codebook_EXI.outl.del.csv' contains a description of all variables in the 'EXI.outl.del.RData' file (metadata). - Files 'EXI.outl.del.imp.RData' and 'EXI.outl.del.imp.extra.RData' contain multiple imputed datasets (without missing values) that can be used to reproduce results from the paper. - File '01_CalculationOfData.R' is an R analysis script that imports the raw data, calculates new variables, and imputes missing data via multiple imputation using the 'predictorMatrixAdj.xlsx' file. - File '02_AnalysisOfImputedData.R' is an R analysis script that calculates descriptive statistics, creates plots, and tests hypotheses using t-tests, Bayesian statistics, and multiple lineair regressions. Also uses the custom functions: 'BF.evidence.R', 'cohen.d.magnitude.R' and 'p.value.sig.R'.
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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.
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