cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.2621996
title: Hyperparameter tuning and performance assessment of statistical and machine-learning algorithms using spatial data

description: This is a research compendium (RC) for the publication "Hyperparameter tuning and performance assessment of statistical and machine-learning algorithms using spatial data".

The code (including figures, appendices and the manuscript) is packed in <strong>pathogen-modeling-master.zip </strong>or can be found directly in the Github repository.


	<strong>Publication figures</strong>: analysis/paper/submission/3/latex-source-files/
	<strong>Appendices</strong>: analysis/paper/submission/3/


This RC represents a static snapshot at the time of submission. The Github repository will receive changes after the publication was published.

<strong>Data sources</strong>


	Atlas Climatico: http://opengis.uab.es/wms/iberia/index.htm
	DEM: ftp://ftp.geo.euskadi.eus/lidar/MDE_LIDAR_2016_ETRS89/
	Lithology: http://www.geo.euskadi.eus/geonetwork/srv/spa/main.home
	pH: https://esdac.jrc.ec.europa.eu/content/soil-ph-europe#tabs-0-description=0
	soil: https://www.isric.org/explore/soilgrids


<strong>Licenses</strong>

All files are shared via the given license with the exception of "soil.tif" which is shared via the <strong>ODbL </strong>license<strong>.</strong>
DOI: 10.17632/kdr8wk63h6.1
title: Data for: Modal abundance, density and chemistry of micrometer-sized assemblages by advanced electron microscopy: application to chondrites

description: Here is an example of what it is possible to do using the ACADEMY methodology (Based on Hyperspy). This code is also available here: https://github.com/ZanettaPM/Demo-ACADEMY The github repository will be kept up to date
DOI: 10.5286/isis.e.rb1610145
title: Lipodepsipeptides and Brown Blotch Disease in Mushrooms (ii) the role of tolaasin

description: Tolaasin is a lipodepsipeptide (lipo = hydrophobic side chain, depsipeptide is an amino acid ring closed in a particular way) produced by strains of Pseudomonas tolaasii, and it causes Brown Blotch disease in mushrooms. This is a major problem in commercial mushroom growing. The role of tolaasin is not understood. The protective coating of mushrooms is largely built of hydrophobin, an amphiphile that forms very hydrophobic surfaces. Tolaasin is surface active but phase separates and does not appear to self-assemble in solution. It may therefore solubilize or weaken the hydrophobin layer. Tolaasin is detected by the formation of a "white line" when it comes into contact with some other lipodepsipeptides, which are evidently antagonistic to tolaasin but the mechanism is not understood. These two aspects of the interfacial behaviour of tolaasin will be explored.
DOI: 10.5286/isis.e.rb1610158
title: Understanding Chemical Expansion in Perovskite Oxides: Impact of Long-Range Defect Ordering

description: "Chemical expansion" occurs when some ceramics expand upon releasing oxygen. Their ability to effectively "breathe" oxygen makes them of use in sustainable energy conversion/storage devices like solid oxide cells. However, chemical expansion during use causes cracks in these brittle materials, a problem for durability. Therefore chemical expansion must be better understood so that materials with minimal chemical expansion can be designed. In this work neutron diffraction will be applied in realistic operating conditions to perovskite-structured oxides to investigate how a particular structural aspect (long-range oxygen ordering) impacts the chemical expansion behavior. Lattice expansion, changes in atomic positions, and oxygen content during oxygen loss will be monitored and compared to prior simulations and overall (bulk) expansion measurements when oxygen is ordered vs. disordered.
DOI: 10.5286/isis.e.rb1620374
title: Textured magnetic phases at a ferromagnetic quantum phase transition

description: Quantum critically is a unifying theme across correlated electron physics.  Classical or thermal phase transitions occur at nonzero temperature and are driven by thermal fluctuations, quantum phase transitions occur at T=0 as a function of a non-thermal control parameter (e.g. pressure, composition, magnetic field). They are driven by quantum fluctuations. At a mean-field level the description of quantum and classical phase transitions is similar. However, when order parameter fluctuations are taken into account, they are different. The quantum fluctuations allow the system to explore additional configuration phase space and stabilize new phases or change the nature of the transition. Here we will search for a new spiral magnetic phase which is created by suppressing the ferromagnetic behavior of a metal with hydrostatic pressure at very low temperature.
DOI: 10.5286/isis.e.rb1710336
title: Binding behaviour of PAMAMs G5 and G4.5 to zwitterionic and anionic lipid bilayers

description: Polymers are commonly used in drug delivery to create dosage forms that enable delivery of the active ingredient to the site of action within the body. Towards controlled drug delivery polymers enable the development of systems that help to minimise side effects. There are a variety of ways in which polymers can interact with cell membranes, via specific receptors and also via disruption of the lipid membrane itself. We have been investigating the role of different properties of polymers on their ability to interact with lipid membranes. PAMAM is a highly branched polymer with either cationic (G5) or anionic (G4.5) end groups. In this proposal we ask for neutron reflectometry INTER beam time to investigate the interfacial structure of lipid layers in the presence of PAMAM G4.5 and G5.
DOI: 10.5286/isis.e.rb1720006
title: Investigating the Mechanism of Cooperative Melting in Metal-Organic Frameworks

description: Zeolitic imidazolate frameworks (ZIFs) are formed from inorganic nodes connected by organic ligands, and share structural features with zeolites. They have recently been observed to melt to a molten state, which curiously retains the chemical composition of the crystalline phase. Whilst ZIF-62 [Zn(Im)1.75(bIm)0.25] (Im = imidazolate C3H3N2- and bIm = benzimidazolate C7H5N2-) has been observed to melt at 410 ºC, ZIF-8 [M(mIm)2] (M = Co, Zn and mIm = 2-methylimidazolate C4H5N2-) does not melt before decomposing at ~550 ºC. Curiously, when the two are heated together to only 410 ºC and then cooled, glass is formed whereas Bragg peaks belonging to ZIF-8 would be expected. This highly unusual result paves the way for multiple MOFs to be included within the same liquid/glass state. We wish to gain mechanistic insight into this behaviour by performing an in-situ neutron diffraction experiment.
DOI: 10.5286/isis.e.rb1720011
title: Glassy dynamics as seen by neutron Compton scattering: the case of amorphous alloy Zr40Be60.

description: The thermal stability and structure of binary amorphous Zr - Be alloys have been studied by us previously using differential scanning calorimetry and ND over a wide concentration range (30 &lt; x&lt;65). The studied amorphous system involved the composition range around the eutectic composition with boundary phases. It has been found that the crystallization of alloys with low beryllium contents (hypoeutectic alloys with x&lt;40) proceeds in two stages. At higher beryllium contents (hypereutectic alloys), one phase transition of the amorphous phase to a mixture of the alpha-Zr and ZrBe phases has been observed. This proposal seeks MANSE and neutron diffraction signs of thermal stability, vitrification and crystallisation of Zr40Be60 system by obtaining Zr and Be kinetic energies at temperatures T=1000 and 1200K below, 1600 at, and 1700K, above the crystalisation temperature.
DOI: 10.5286/isis.e.rb1720012
title: How chemical interaction scale affects the dynamics of dense metallic liquids

description: Using deep inelastic neutron scattering, we plan to investigate chemical short range order on a quantitative level in liquid alloys and its correlation with the long range mass transport in the melt. We chose two alloy melts, Zr34Ni36 and Hf35Ni65, where Zr and Hf exhibit identical valence electron shell configurations and very similar chemical properties. However, the atomic dynamics in the alloy melts differ by a factor of 2. By measuring the mass-resolved, atom-projected vibrational density of states, we intend to quantify the chemical interaction in the melt in terms of the chemical interaction scale. This allows us to gain deeper insight on the interaction potentials and the electronic origin of chemical short range order in the liquid alloys, in order to understand the structure-property relation in the disordered systems.
DOI: 10.17632/dsd4jmmpt5.1
title: Data for: Endowments and Risky Choice

description: Experiment data from the paper, Endowments and Risky Choice.
DOI: 10.17632/gtctw5t8jg.1
title: Data for: Endowments and Risky Choice

description: Experiment data for "Endowments and Risky Choice."
DOI: 10.17632/wxtvzbwj8m.1
title: Data for: A Novel approach to Risk-Informed Decision-Making under non-ideal Instrumentation and Control conditions through the Application of Bayes' Theorem

description: This dataset contains supporting data for the paper titled: A Novel approach to Risk-Informed Decision-Making under non-ideal Instrumentation and Control conditions through the Application of Bayes' Theorem.
DOI: 10.25345/c5g90z
title: MassIVE MSV000083653 - Atg16L1 deficiency induces insulin resistance through KLHL9-KLHL13-CUL3 complex-mediated IRS1 degradation
title: Data contains LC-MS data of proximity-based biotin labeling assay (BioID) to generate the protein interaction network of KLHL9 and KLHL13 proteins fused to FlagBirA (N-terminal tag) and expressed in T-REx HEK293 cells.
DOI: 10.5286/isis.e.rb1610193
title: Biological membrane mimics made of deuterated lipids extracted from E. coli

description: Biological membrane mimics are a bottle neck in biophysical studies today. The need to develop advanced models that actually represent the properties of specific cellular membranes is imperative in order to advance the understanding of for example their role as barriers and for affinity studies with biomolecules in solution. Recently, there has been a boost in the development of complex membranes for models of bacterial membranes among others. In this work we would like to further contribute at the advancing of this field by creating mimics of mammalian membranes using deuterated lipid species extracted from various strains of E. coli: a genetically modified strain that produces PC and regular strains producing PE, PG and cardiolipin.
DOI: 10.5286/isis.e.rb1620052
title: Hydrogen Insertion into Zirconium- and Vanadium-Substituted Substoichiometric Titanium Carbides: a Neutron Compton Scattering View

description: Despite the insight provided by the ab initio approach, there still remain some important questions concerning the hydrogen insertion in new hydrogen storage systems, Ti0.9V0.1C0.6 and Ti0.9Zr0.1C0.6. It is still largely unknown whether H is located in these materials, in octahedral and-or tetrahedral sites of the fcc structure or elsewhere. Secondly and more importantly for the future development of the hydrogen storage technology, ab initio calculation and electrochemistry results from Ti0.9V0.1C0.6 and Ti0.9Zr0.1C0.6 show that hydrogen storage is drastically increased in presence of Zr, but strongly decreased in presence of V. The main goal of the proposed experiment is to verify if zirconium attracts more hydrogen atoms around the Zr-C vacancy in Ti0.9Zr0.1C0.6Hx. This question will be addressed using perform mass-resolved neutron spectroscopy and simultaneous neutron diffraction
DOI: 10.5286/isis.e.rb1670519
title: Clarification of superconducting mechanism and electronic phase diagram of FeSe from Co impurity doping studied by muon spin relaxation
DOI: 10.5286/isis.e.rb1720116
title: Temperature Dependence of the Magnetic Excitations in Ni-doped NaFeAs

description: In a recent work by Jun Zhao's group [Nature Communications 7, 12182 (2016)], they show that FeSe exhibits both stripe (1,0) and Néel (1,1) antiferromagnetic order, with the low-temperature state (and SC) favoring the stripe order. This result is very important in understanding the competing instabilities in iron based superconductors. The (1,1) excitation is not often seen with neutron scattering, but we have also recently seen it in the NaFeAs system, and our preliminary results suggest it may be temperature dependent as in the FeSe paper. By repeating the FeSe experiment with Ni-underdoped, superconducting NaFeAs, we have an excellent opportunity to compare the iron pnictide and chalcogenide families.
DOI: 10.5286/isis.e.rb1720140
title: Measurement of the hydration of B-DNA

description: Water is intimately entwined structurally with DNA. Depending on its hydration state, DNA can form several forms: A, B, C, D and Z. In addition water bound in the grooves of the double helix is essential for helix stability. The naturally forming B-form of DNA as originally defined by Crick and Watson has a helical pitch of 10 base pairs every 34 angstroms, where the bases are in a flat planar conformation perpendicular to the helical axis. This form has been the subject of extensive structural, modelling and biochemical studies, as such a large body of literature exists on this form of DNA.We wish to use wide angle neutron scattering on the NIMROD beamline at ISIS to probe the role of hydration water in DNA stability. This will be a pilot study with a synthetic construct that contains a cognate and non-cognate site for the restriction endonuclease EcoRI.
DOI: 10.5286/isis.e.rb1720163
title: Spinwaves excitations in the zigzag spin chain compound beta-CaCr2O4

description: The S=3/2 zigzag chain antiferromagnet beta-CaCr2O4 exhibits broad spinwave excitations at low temperature, related to an incommensurate magnetic order that sets at TN = 21K. However, an excitation spectrum characterized by an unusual broad signal persists well above TN, and is thought to arise from the contribution of a two-spinon continuum. Recently, a large single crystal was successfully synthesized and we would like to study and fully characterize the spin dynamics, especially in the low temperature regime, in order to determine the spin Hamiltonian of this system.
DOI: 10.5286/isis.e.rb1720334
title: SAXS and SANS measurements on chocolate surfactants in triglyceride oils

description: Molten chocolate is a dense suspension of solids (mainly sugar) in oil, to which surfactants have been added to improve the flow properties, either during manufacture or in the consumers mouth ('mouth feel'). The two surfactants are lecithin, which is a lipid molecule derived from soya or egg, and a polymeric surfactant (PGPR) with a comb-like structure, the tynes of which resemble polymerised versions of the lecithin tails, and the backbone of which resembles a polymerised version of the lecithin head group. Used in combination these surfactants make it much easier for the suspension to flow. We have a model that explains this in terms of lamellar layers of lecithin incorporating PGPR at the sugar oil interface. To complete the model of how these form, we will perform small angle scattering of the surfactants individually and combined in the oils used to form our model molten chocolate.
DOI: 10.5286/isis.e.rb1720383
title: Copper precipitates in nuclear power plant pressuriser weld after 29 years of operation

description: The pressuriser is a vital part of a pressurised water reactor (PWR). We are now investigating a weld of a pressuriser that has been in operation for 29 years. The long time at about 345C has degraded the material properties. Studies using atom probe tomography (APT) have shown that Cu-particles have formed (at dislocations). The particles are unevenly distributed on the sub-micron scale studied by APT. By using SANS it will be possible to obtain statistically relevant data on the Cu particle size distribution and number density. In addition, it will be possible to measure variations through the thickness of the weld and observe the influence of the slight temperature gradient from the inside to the outside of the pressuriser. Such information is practically impossible to obtain with other methods, and is important for understanding ageing and embrittlement of reactor components.
DOI: 10.5286/isis.e.rb1810710
title: Effect of pressure-transmitting medium on the phase transformation of para-aminobenzoic acid

description: The pressure-transmitting medium in a high-pressure experiment is usually thought of as an inert medium that allows the sample to be compresses rather than crushed.  In organic materials, the choice of medium can alter the crystal structure of the sample depending on the solubility.  P-aminobenzoic acid is a well-known organic substance that is used extensively to explore polymorphism and crystallisation.  In this experiment we will investigate the pressure-transmission medium and the way in which the material reacts to compression in the medium.  Our Raman studies have shown that in water, ethanol and a 50% mixture of each, p-aminobenzoic acid can either undergo a phase transition to a new high-pressure phase or remain in the known form. We will follow these experimental observations with diffraction measurements so that structural information can be elucidated.
DOI: 10.5286/isis.e.rb1620302
title: Crystal and Magnetic Structure of Two New Frustrated quantum Magnets

description: Frustration in Heisenberg spin systems originates from antiferromagnetic networks of triangles or tetrahedra. Of the possible model systems, the 3-dimensional network of corner-shared triangles (known as the hyperkagome lattice) has not been explored experimentally despite predictions that it should give rise novel ground states. We have successfully synthesized powder samples of two new cuprates. The 1st, 2nd and 3rd neighbour interactions couple the Cu ions into isolated triangles, a hyperkagome lattice and uniform chains respectively. Our magnetic susceptibility reveals a broad maximum in both samples while long-range magnetic order occurs at a much lower temperature as is typical of quantum magnets. Here we wish to determine the crystal and magnetic structure. The nature of the magnetic ordering will reflect the exchange interactions and provide insights into the underlying physics.
DOI: 10.5286/isis.e.rb1710450
title: Micro-Metagenomics: Characterising Virus-Surface Interactions for Microfluidic Diagnosis

description: Traditional methods of viral detection are based on the isolation and culture of viral pathogens, but often viruses cannot be cultivated under laboratory conditions, constituting a substantial barrier to viral diagnostics and discovery. Microfluidics is a multidisciplinary field in which low volumes of fluids are used in high-throughput screening. Therefore, when combined with appropriate system and filter designs, microfluidics could make the ideal technology for the filtering, detection and quantification of viruses within a sample. This proposal is an integral part of a one year pump-prime project to analyse the properties of viruses which differ substantially in size, shape & deformability on different microfluidic surfaces. This information from neutron reflectivity and scattering will be used to inform mathematical modelling leading to initial trial microfluidic devices.
DOI: 10.5286/isis.e.rb1720227
title: Antimicrobial Mechanisms of Model Biocides via Their Interaction with Lipopolysaccharides Studied by Neutron Reflection

description: The global increase of bacterial resistance to antibiotics has led to increasing interest in research focusing on the development and characterization of new antimicrobial agents. One class of promising antimicrobials found in nature are Antimicrobial Peptides (AMPs). In contrast to most existing biocides, it is thought that AMPs would share broadly similar modes of membrane disruption. We have designed a novel class of AMPs with the general sequence G(IIKK)nI-NH2, with n = 3-4, denoted as G3 and G4. We propose to compare the binding of these peptides to the spread LPS monolayer with the performance from model biocides SDS, DTAB and trichosan, to identify any structural differences in their membrane attacking processes.
DOI: 10.5286/isis.e.rb1720257
title: Effect of Pressure on the Structure and Dynamics of Titanium Tetrachloride

description: At ambient pressure TiCl4 forms a molecular solid consisting of isolated TiCl4 molecules (phase-I). At 0.5 GPa this structure undergoes a transition to phase-II, which is polymeric with 6-coordinate Ti. We have tried in the past to collect INS spectra on phase-II on TOSCA and MAPS, with the aim of (1) detecting premonitory behaviour in phase-I and (2) identifying the thermodynamic factors which drive the transformation.   While excellent quality data were collected for phase-I, the spectra of phase-II were weak on account of the low sample volume available in the gas pressure cell.  The recent upgrade on TOSCA has resulted in an enhancement of sensitivity in the relevant energy region of at least 20-fold, providing an excellent opportunity to attempt recollection of INS data on phase-II at 0.5 GPa.
DOI: 10.5286/isis.e.rb1720431
title: High-Pressure Studies of CL-20/Hydrogen Peroxide Solvates

description: This proposal will explore the effect of elevated pressure on the behaviour of two important hydrogen peroxide solvates of the explosive CL-20.  We will use neutron diffraction to investigate changes in hydrogen bonding as a function of pressure for both solvates; (ii) follow the structural evolution of the solvates as a function of pressure; (iii) investigate whether the solvates desolvate at elevated pressures, and (iv) explore whether new forms can be obtained at elevated pressures and if so whether they can be recovered to ambient conditions.   The high-quality structural data that will be obtained, including the effects of pressure on hydrogen-bonding motifs, will provide insight into molecular energy transfer, detonation mechanisms and, particularly the sensitivities to initiation.
DOI: 10.5286/isis.e.rb1770002
title: Hydrogen trapped sites in aluminum alloys studied by muon spin relaxation method

description: Hydrogen can be a main energy resource in near future.  Al-Mg-Si-Cu alloys have been used as an inner materials for a high-pressure hydrogen container.  There are plenty of studies investigating hydrogen trapping sites in Al alloys, but hydrogen behavior has been still unknown, especially their kinetic properties of atomic states.  For safer use of aluminum alloys in hydrogen gas/liquid tanks and other hydrogen atmosphere, we are interested in hydrogen trapped sites in aluminum alloys.  For this purpose, we would like to establish a new technique to study the kinetic property of hydrogen atoms in commercial aluminum alloys using a muon spin relaxation method.
DOI: 10.5286/isis.e.rb1810181
title: Investigating Lead Halide Perovskite Solar cells using ALCs

description: The research and development of Lead Halide perovskite solar cells is one of the most rapidly growing research areas. Since the discovery of these organic-inorganic metal halide perovskite solar cells in 2009, the devices have shown great promise, with efficiency up to over 20%. This efficiency is a factor 4 greater than organic semiconductor solar cells and the materials are cheaper compared to the traditional inorganic semiconductors such as silicon. Due to the rapid development of devices with the aim to get them to market, less work has been done on understanding the fundamental science, such that there are issues with the lifetime, the reliability and reproducibility of the materials and devices. This proposal looks to investigate these materials using the avoided level crossing technique, to provide further information on the underlying mechanisms, hence help bring them to market.