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Code and Dataset for Thesis "Bayesian Analysis of Spatial Log-Gaussian Cox Processes"
Get PDFThese files contain the relevant code and data to produce the results presented in the thesis titled "Bayesian Analysis of Spatial Log-Gaussian Cox Processes" by Nadeen Khaleel.
These files contain the input data and the output results for the implementation of the models and exploratory analysis as well as the implementation of the Grid Mesh Optimisation method and the INLA within MCMC algorithms. Some of the input data corresponds to the processed crime data in US cities, in particular incidences of homicide and motor vehicle theft in Los Angeles, New York and Portland, aggregated to census-tract level or discretisation grids. The raw third party data is not included; however, a document detailing how to access the relevant data is provided and all of the code used to clean and extract the necessary data from the raw data is included.
These files additionally contain the relevant code for the data tidying, manipulation and simulation as well as the code to implement the Grid Mesh Optimisation method and the INLA within MCMC algorithms.R Software was solely used within the data tidying/manipulation and simulation as well as for the code and any results output. Any tidied or simulated data is stored under the .rda or .rds format and any code is available in the .R or .Rmd format with output from the latter in the form .html
Data for Brønsted Acid-Catalyzed Desilylative Heterocyclization to form Substituted Furans
No full textOriginal, unprocessed data for all novel compounds in the associated paper. Data available includes 1H, 13C, and 19F Nuclear Magnetic Resonance (NMR) data, copies of mass spectrometry data, and copies of infra-red (IR) spectra.Full experimental details for the preparation of each compound can be found in the Supplementary Information of the associated paper.
Infrared spectra were recorded on a Perkin-Elmer PerkinElmer Spectrum 100 ATR-FTIR spectrometer. Spectra were recorded of either thin films or solids, with characteristic absorption wavenumbers (νmax) reported in cm–1.
1H, 13C{1H}, 19F{1H}, and 31P{H} NMR spectra were acquired on either a Bruker AV300 (1H 300 MHz; 13C{1H} 75 MHz; 19F{1H} 282 MHz, 31P{H} 162Hz), a Bruker AV400 (1H 400 MHz; 13C{1H} 101 MHz; 19F{1H} 376 MHz, 31P{H} 162Hz), or an Agilent ProPulse 500 (1H 500 MHz, 13C{1H} 126 MHz, 19F{1H} 470 MHz) in the deuterated solvent stated. All chemical shifts are quoted in parts per million (ppm) relative to the residual solvent peak. All coupling constants, J, are quoted in Hz. Multiplicities are indicated as s (singlet), d (doublet), t (triplet), q (quartet), m (multiplet), and multiples thereof. The abbreviation Ar denotes aromatic and app denotes apparent. NMR peak assignments were confirmed using 2D 1H correlated spectroscopy (COSY), 2D 1H nuclear Overhauser effect spectroscopy (NOESY), 2D 1H−13C heteronuclear multiple-bond correlation spectroscopy (HMBC), and 2D 1H−13C heteronuclear single quantum coherence (HSQC) where necessary.
Mass spectrometry (m/z) data were acquired by either electrospray ionisation (ESI), chemical ionisation (CI), electron impact (EI), atmospheric solids analysis probe (ASAP), atmospheric pressure chemical ionization (APCI) or nanospray ionisation (NSI) at the University of Bath ([A]+ or [A]– quoted).IR spectra were processed using Perkin-Elmer PerkinElmer Spectrum FTIR control software. Final processed spectra are available as PDF files.
NMR data were processed using MestReNova (v.11.0.2) available from Mestrelab Research S.L. Original unprocessed FID files and processed MestReNova files are available.
Mass spectroscopy data was used as received from the managed facilities. The spectra are available as PDF files.The numbers of individual folders correspond to the compound numbers in the associated manuscript
Dataset for "Transition metal migration and O2 formation underpin voltage hysteresis in oxygen-redox disordered rocksalt cathodes"
No full textThis dataset contains the computational data and analysis for the paper "Transition metal migration and O2 formation underpin voltage hysteresis in oxygen-redox disordered rocksalt cathodes". It includes input and output files for the density functional theory (DFT) calculations, performed using VASP and CRYSTAL.All calculations were performed using the VASP and CRYSTAL codes. Input files for each calculation are contained within the dataset. Further details may be found in the associated manuscript
Dataset for Second harmonic Rayleigh scattering optical activity of single Ag nanohelices in a liquid
No full textThis dataset contains raw data for the associated scientific paper. The data relate to samples made of metal nanohelices with nominal dimensions of length = 110 nm, loop diameter = 50 nm, loop pitch = 55 nm and wire diameter = 25 nm. The composition is Ag 97% and Ti 3%, with a 10 nm Au nanoparticle attached at one end of the helix. More details can be found in the experimental section of the research paper. The data include images of the samples, numeric data values for the curves and numerical simulation data. Specifically, there are 4 folders.
– Lumerical Data: this folder contains the numerical simulations performed on the samples. Simulations are provided for electric (E) and magnetic (H) fields. The metadata text file provides all the details.
– Pulse length emission: this folder contains 4 sub-folders with data acquired on different days. For each sub-folder, the raw data files are provided and a plain text file provides technical details.
– SHRS power dependence: provides 2 raw data files and a ReadMe text file specifying details.
– SHRS rotating analyser: provides 76 raw data files and a ReadMe text file with all the technical details.The methodology is available in the associated paper
TIEGCM November Experiment – November full state (c)
No full textThis dataset contains the model run for the period between 16 and 17 November 2003, with all model fields replaced with the corresponding fields from the storm time run (20 to 21 November 2003) at 6 a.m. on 16 November.Full details of the methodology may be found in the 'Method' section of the associated paper.Details about this dataset are available from the main record: https://doi.org/10.15125/BATH-0057
Supplementary materials for "Exercising body but not mind: A qualitative exploration of attitudes to combining physical activity and mindfulness practice for mental health promotion"
Get PDFSupplementary materials for a study of the attitudes of a UK-wide sample of university students towards combining physical activity and mindfulness practice in order to maintain good mental health. Recruitment of participants was conducted over social media (Twitter). The materials in this set include the recruitment flyer, screening survey content, interview schedule and full interview transcripts. The set also includes full ethics documentation (available on request).
This study is part of a doctoral research project aiming to investigate the potential of combining physical activity and mindfulness practice for maintaining good mental health, and to create a digital intervention supporting people with their combined practice
Data sets for "Structural Investigation of Sulfobetaines and Phospholipid Monolayers at the air-water interface"
No full textNormalized neutron and X-ray reflectivity data for Langmuir monolayers composed of mixtures of dimyristoylphosphatidylcholine, DMPC and a single 18-carbon tailed sulfobetaine, SB3-18 on pure water at room temperature and at surface pressures of 15 mN/m and 35 mN/m.
Neutron measurements are carried out on D2O and air contrast matched water. Measurements were carried out with deuterated and hydrogenated lipids.Neutron reflectivity measurements were carried out on Inter at the ISIS Pulsed Neutron and Muon source at room temperature. Mixtures of DMPC and SB3-18 were investigates on D2O and air contrast matched water, ACMW. Deuterated phospholipid and sulfobetaine were used along with hydrogenated samples.
X-Ray reflectivity measurements were carried out on I07 at The Diamond Light Source. As above mixtures of DMPC and SB3-18 were carried out on a water subphase at room temperature under a helium atmosphere.
For both data sets are carried out at two surface pressures, the surface pressure in both cases is controlled by a Nima Langmuir trough.Neutron reflectivity data was stitched together and normalised using Mantid software.
X-Ray reflectivity data was also normalised to the critical edge and by the incident flux at the Diamond light source.Reflectivity data, here given as .dat files, can be fitted and plotted using a range of programs, the Motofit package for Igor Pro, the Motofit GUI or RASCAL are some examples
Far-infrared magnetospectroscopy (FIRMS) simulation tool
No full textThe firms_sim code and its associated scripts and programs may be used to simulate far-infrared magnetospectroscopy spectra.This record relates to V1.1 (commit 80b8202d) in the GitLab repository.
Please cite the associated paper in preference to citing this software directly
Dataset for "Is depression associated with reduced optimistic belief updating?"
Get PDFWe evaluated optimistic belief updating (the finding that healthy individuals update their beliefs more following good news than bad) for positive and negative life events in individuals experiencing depression (n = 54) and healthy controls (n = 56). We have provided the raw questionnaire data (depression, anxiety, optimism) and belief updating task, as well as the cleaned data used for analysis. Code for cleaning and analysing data is available for use in R.
Based on this data we found that whereas healthy participants updated their beliefs more following good news than bad, individuals experiencing depression lacked this bias. Our findings for positive life events were inconclusive, but on balance suggested that reduced optimistic belief updating in depression did not occur.Due to the COVID-19 pandemic, recruitment took place online using the participant recruitment platform ‘Prolific’. Screening surveys were completed online using ‘Qualtrics’. Two groups of participants were screened and recruited on the basis of Patient Health Questionnaire (PHQ-9) scores according to recommended clinical guidelines. A moderately severe to severely depressed sample was recruited with PHQ-9 scores ≥ 15. A healthy control sample was recruited with PHQ-9 scores ≤ 4.
Participants in both groups were aged 18 and over, fluent in written and spoken English, with normal or corrected to normal vision, and were current residents of the United Kingdom. Participants were included irrespective of any comorbid psychiatric disorders, or current treatment for depression. To ensure high quality of data, custom pre-screening was used on Prolific to identify participants that had previously completed ≥ 5 studies with a 98% acceptance rate.
Testing took place online, self-report measures were completed using ‘Qualtrics’ and the Belief Updating Task was completed using ‘Inquisit’. Participants completed questionnaire measures of depression, anxiety, trait optimism, state positive and negative affect and demographics. They then completed a belief updating task. In this task, participants are asked to estimate the probability of experiencing an event within their lifetime, before being presented with the actual probability. After completing a number of trials they are then asked again what their likelihood is of experiencing the event. We are interested in the extent to which participants change their original belief depending on whether they were given good news or bad news about the probability of experiencing the life event.Data was anonymised prior to cleaning, through random re-assignment of unique IDs and removal of potentially identifying variables. Aside from the anonymisation changes, the raw data is provided as well as the code used to clean data to produce the aggregate data used for analysis.The data was cleaned and analysed using R version 4.0.5.
Data is provided in .CSV, .XLSX and .R filesA data dictionary is provided outlining the organisation of data and describing individual variables
Heat Transfer Calculations for "Engineering aspects of FlowNMR spectroscopy setups for online analysis of solution-phase processes"
No full textTo explore the importance of heat transfer in flow analytical systems a basic model was created from first principles. This model (detailed within the excel file) was used to generate temperature profiles along lengths of 1/16” or 1/32” polymer tubing, containing a range of different solvents, with solvents flowing through at 4 mL/min. These tubing materials are often used in analytical flow setups to transfer reaction mixtures between instruments and reaction vessels, where precipitation can cause blockages on mixture cooling it is important to ensure the mixture is effectively heated throughout the flow apparatus. The data produced showed that the temperature of a heated mixture can reduce by 50% (relative to ambient temperature), if flowed without thermal regulation. While passive insulation is not as effective as active thermal regulation, the data modelled illustrated its importance in preventing heat loss in areas which are not easily temperature regulated such as pump heads and unions. The excel spreadsheet was constructed and labelled such that different tubing materials, thickness, solvents, and temperatures could be modelled for a fixed length of straight tubing.Full details of the methodology may be found in the supplementary information of the associated paper.The interpretation and derivation of the model can be found in the associated thesis and paper
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