Deformation of sand in plane strain and oxisymmetric compression

Small scale laboratory experiments, in which the specimen is considered to represent an element of soil in the soil mass, are essential to the evolution of fundamental theories of mechanical behaviour. In this thesis, plane strain and axisymmetric compression tests, performed on a fine sand, are reported and the results are compared with various theoretical predictions. A new apparatus is described in which cuboidal samples can be tested in either axisymmetric compression or plane strain. The plane strain condition is simulated either by rigid side platens, in the conventional manner, or by flexible side platens which also measure the intermediate principal stress. Close control of the initial porosity of the specimens is achieved by a vibratory method of sample preparation. The strength of sand is higher in plane strain than in axisymmetric compression, and the strains required to mobilize peak strength are much smaller. The difference between plane strain and axisymmetric compression behaviour is attributed to the restrictions on particle movement enforced by the plane strain condition; this results in an increase in the frictional component of shear strength. The stress conditions at failure in plane strain, including the intermediate principal stress, are accurately predicted by a theory based on the stress- dilatancy interpretation of Mohr's circles. Detailed observations of rupture modes are presented and measured rupture plane inclinations are predicted by the stress-dilatancy theory. Although good correlation with the stress-dilatancy theory is obtained during virgin loading, in both axisymmetric compression and plane strain, the stress-dilatancy rule is only obeyed during reloading if the specimen has been unloaded to approximate ambient stress conditions. The shape of the stress-strain curves during pre-peak deformation, in both plane strain and axisymmetric compression, is accurately described bv a combined parabolic-hyperbolic specification.

Shaping acoustic fields as a toolset for microfluidic manipulations in diagnostic technologies

Ultrasonics offers the possibility of developing sophisticated fluid manipulation tools in lab-on-a-chip technologies. Here we demonstrate the ability to shape ultrasonic fields by using phononic lattices, patterned on a disposable chip, to carry out the complex sequence of fluidic manipulations required to detect the rodent malaria parasite Plasmodium berghei in blood. To illustrate the different tools that are available to us, we used acoustic fields to produce the required rotational vortices that mechanically lyse both the red blood cells and the parasitic cells present in a drop of blood. This procedure was followed by the amplification of parasitic genomic sequences using different acoustic fields and frequencies to heat the sample and perform a real-time PCR amplification. The system does not require the use of lytic reagents nor enrichment steps, making it suitable for further integration into lab-on-a-chip point-of-care devices. This acoustic sample preparation and PCR enables us to detect ca. 30 parasites in a microliter-sized blood sample, which is the same order of magnitude in sensitivity as lab-based PCR tests. Unlike other lab-on-a-chip methods, where the sample moves through channels, here we use our ability to shape the acoustic fields in a frequency-dependent manner to provide different analytical functions. The methods also provide a clear route toward the integration of PCR to detect pathogens in a single handheld system.

Detection of phospholipid oxidation in oxidatively stressed cells by reversed-phase HPLC coupled with positive-ionization electrospray MS

Measurement of lipid peroxidation is a commonly used method of detecting oxidative damage to biological tissues, but the most frequently used methods, including MS, measure breakdown products and are therefore indirect. We have coupled reversed-phase HPLC with positive-ionization electrospray MS (LC-MS) to provide a method for separating and detecting intact oxidized phospholipids in oxidatively stressed mammalian cells without extensive sample preparation. The elution profile of phospholipid hydroperoxides and chlorohydrins was first characterized using individual phospholipids or a defined phospholipid mixture as a model system. The facility of detection of the oxidized species in complex mixtures was greatly improved compared with direct-injection MS analysis, as they eluted earlier than the native lipids, owing to the decrease in hydrophobicity. In U937 and HL60 cells treated in vitro with t-butylhydroperoxide plus Fe2+, lipid oxidation could not be observed by direct injection, but LC-MS allowed the detection of monohydroperoxides of palmitoyl-linoleoyl and stearoyl-linoleoyl phosphatidylcholines. The levels of hydroperoxides observed in U937 cells were found to depend on the duration and severity of the oxidative stress. In cells treated with HOCl, chlorohydrins of palmitoyloleoyl phosphatidylcholine were observed by LC-MS. The method was able to detect very small amounts of oxidized lipids compared with the levels of native lipids present. The membrane-lipid profiles of these cells were found to be quite resistant to damage until high concentrations of oxidants were used. This is the first report of direct detection by LC-MS of intact oxidized phospholipids induced in cultured cells subjected to oxidative stress.

Application and use of isothermal calorimetry in pharmaceutical development

There are many steps involved in developing a drug candidate into a formulated medicine and many involve analysis of chemical interaction or physical change. Calorimetry is particularly suited to such analyses as it offers the capacity to observe and quantify both chemical and physical changes in virtually any sample. Differential scanning calorimetry (DSC) is ubiquitous in pharmaceutical development, but the related technique of isothermal calorimetry (IC) is complementary and can be used to investigate a range of processes not amenable to analysis by DSC. Typically, IC is used for longer-term stability indicating or excipient compatibility assays because both the temperature and relative humidity (RH) in the sample ampoule can be controlled. However, instrument design and configuration, such as titration, gas perfusion or ampoule-breaking (solution) calorimetry, allow quantification of more specific values, such as binding enthalpies, heats of solution and quantification of amorphous content. As ever, instrument selection, experiment design and sample preparation are critical to ensuring the relevance of any data recorded. This article reviews the use of isothermal, titration, gas-perfusion and solution calorimetry in the context of pharmaceutical development, with a focus on instrument and experimental design factors, highlighted with examples from the recent literature. © 2011 Elsevier B.V.

Accurate estimation of isoelectric point of protein and peptide based on amino acid sequences

Motivation: In any macromolecular polyprotic system - for example protein, DNA or RNA - the isoelectric point - commonly referred to as the pI - can be defined as the point of singularity in a titration curve, corresponding to the solution pH value at which the net overall surface charge - and thus the electrophoretic mobility - of the ampholyte sums to zero. Different modern analytical biochemistry and proteomics methods depend on the isoelectric point as a principal feature for protein and peptide characterization. Protein separation by isoelectric point is a critical part of 2-D gel electrophoresis, a key precursor of proteomics, where discrete spots can be digested in-gel, and proteins subsequently identified by analytical mass spectrometry. Peptide fractionation according to their pI is also widely used in current proteomics sample preparation procedures previous to the LC-MS/MS analysis. Therefore accurate theoretical prediction of pI would expedite such analysis. While such pI calculation is widely used, it remains largely untested, motivating our efforts to benchmark pI prediction methods. Results: Using data from the database PIP-DB and one publically available dataset as our reference gold standard, we have undertaken the benchmarking of pI calculation methods. We find that methods vary in their accuracy and are highly sensitive to the choice of basis set. The machine-learning algorithms, especially the SVM-based algorithm, showed a superior performance when studying peptide mixtures. In general, learning-based pI prediction methods (such as Cofactor, SVM and Branca) require a large training dataset and their resulting performance will strongly depend of the quality of that data. In contrast with Iterative methods, machine-learning algorithms have the advantage of being able to add new features to improve the accuracy of prediction. Contact: yperez@ebi.ac.uk Availability and Implementation: The software and data are freely available at https://github.com/ypriverol/pIR. Supplementary information: Supplementary data are available at Bioinformatics online.

Online solid phase extraction liquid chromatography tandem mass spectrometry (SPE-LC-MS/MS) method for the determination of sucralose in reclaimed and drinking waters and its photo degradation in natural waters from South Florida

Background Sucralose has gained popularity as a low calorie artificial sweetener worldwide. Due to its high stability and persistence, sucralose has shown widespread occurrence in environmental waters, at concentrations that could reach up to several μg/L. Previous studies have used time consuming sample preparation methods (offline solid phase extraction/derivatization) or methods with rather high detection limits (direct injection) for sucralose analysis. This study described a faster and sensitive analytical method for the determination of sucralose in environmental samples. Results An online SPE-LC–MS/MS method was developed, being capable to quantify sucralose in 12 minutes using only 10 mL of sample, with method detection limits (MDLs) of 4.5 ng/L, 8.5 ng/L and 45 ng/L for deionized water, drinking and reclaimed waters (1:10 diluted with deionized water), respectively. Sucralose was detected in 82% of the reclaimed water samples at concentrations reaching up to 18 μg/L. The monthly average for a period of one year was 9.1 ± 2.9 μg/L. The calculated mass loads per capita of sucralose discharged through WWTP effluents based on the concentrations detected in wastewaters in the U. S. is 5.0 mg/day/person. As expected, the concentrations observed in drinking water were much lower but still relevant reaching as high as 465 ng/L. In order to evaluate the stability of sucralose, photodegradation experiments were performed in natural waters. Significant photodegradation of sucralose was observed only in freshwater at 254 nm. Minimal degradation (<20%) was observed for all matrices under more natural conditions (350 nm or solar simulator). The only photolysis product of sucralose identified by high resolution mass spectrometry was a de-chlorinated molecule at m/z 362.0535, with molecular formula C12H20Cl2O8. Conclusions Online SPE LC-APCI/MS/MS developed in the study was applied to more than 100 environmental samples. Sucralose was frequently detected (>80%) indicating that the conventional treatment process employed in the sewage treatment plants is not efficient for its removal. Detection of sucralose in drinking waters suggests potential contamination of surface and ground waters sources with anthropogenic wastewater streams. Its high resistance to photodegradation, minimal sorption and high solubility indicate that sucralose could be a good tracer of anthropogenic wastewater intrusion into the environment.

Elemental analysis and forensic comparison of soils by laser-induced breakdown spectroscopy (LIBS) and laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS)

The elemental analysis of soil is useful in forensic and environmental sciences. Methods were developed and optimized for two laser-based multi-element analysis techniques: laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) and laser-induced breakdown spectroscopy (LIBS). This work represents the first use of a 266 nm laser for forensic soil analysis by LIBS. Sample preparation methods were developed and optimized for a variety of sample types, including pellets for large bulk soil specimens (470 mg) and sediment-laden filters (47 mg), and tape-mounting for small transfer evidence specimens (10 mg). Analytical performance for sediment filter pellets and tape-mounted soils was similar to that achieved with bulk pellets. An inter-laboratory comparison exercise was designed to evaluate the performance of the LA-ICP-MS and LIBS methods, as well as for micro X-ray fluorescence (μXRF), across multiple laboratories. Limits of detection (LODs) were 0.01-23 ppm for LA-ICP-MS, 0.25-574 ppm for LIBS, 16-4400 ppm for μXRF, and well below the levels normally seen in soils. Good intra-laboratory precision (≤ 6 % relative standard deviation (RSD) for LA-ICP-MS; ≤ 8 % for μXRF; ≤ 17 % for LIBS) and inter-laboratory precision (≤ 19 % for LA-ICP-MS; ≤ 25 % for μXRF) were achieved for most elements, which is encouraging for a first inter-laboratory exercise. While LIBS generally has higher LODs and RSDs than LA-ICP-MS, both were capable of generating good quality multi-element data sufficient for discrimination purposes. Multivariate methods using principal components analysis (PCA) and linear discriminant analysis (LDA) were developed for discriminations of soils from different sources. Specimens from different sites that were indistinguishable by color alone were discriminated by elemental analysis. Correct classification rates of 94.5 % or better were achieved in a simulated forensic discrimination of three similar sites for both LIBS and LA-ICP-MS. Results for tape-mounted specimens were nearly identical to those achieved with pellets. Methods were tested on soils from USA, Canada and Tanzania. Within-site heterogeneity was site-specific. Elemental differences were greatest for specimens separated by large distances, even within the same lithology. Elemental profiles can be used to discriminate soils from different locations and narrow down locations even when mineralogy is similar.

Development of advanced capillary electrophoresis techniques with UV and mass spectrometry detection for forensic, pharmaceutical and environmental applications

Capillary electrophoresis (CE) is a modern analytical technique, which is electrokinetic separation generated by high voltage and taken place inside the small capillaries. In this dissertation, several advanced capillary electrophoresis methods are presented using different approaches of CE and UV and mass spectrometry are utilized as the detection methods. ^ Capillary electrochromatography (CEC), as one of the CE modes, is a recent developed technique which is a hybrid of capillary electrophoresis and high performance liquid chromatography (HPLC). Capillary electrochromatography exhibits advantages of both techniques. In Chapter 2, monolithic capillary column are fabricated using in situ photoinitiation polymerization method. The column was then applied for the separation of six antidepressant compounds. ^ Meanwhile, a simple chiral separation method is developed and presented in Chapter 3. Beta cycodextrin was utilized to achieve the goal of chiral separation. Not only twelve cathinone analytes were separated, but also isomers of several analytes were enantiomerically separated. To better understand the molecular information on the analytes, the TOF-MS system was coupled with the CE. A sheath liquid and a partial filling technique (PFT) were employed to reduce the contamination of MS ionization source. Accurate molecular information was obtained. ^ It is necessary to propose, develop, and optimize new techniques that are suitable for trace-level analysis of samples in forensic, pharmaceutical, and environmental applications. Capillary electrophoresis (CE) was selected for this task, as it requires lower amounts of samples, it simplifies sample preparation, and it has the flexibility to perform separations of neutral and charged molecules as well as enantiomers. ^ Overall, the study demonstrates the versatility of capillary electrophoresis methods in forensic, pharmaceutical, and environmental applications.^

Absolute abundances of dinoflagellate cysts in surface sediment samples from four sites: Lycopodium marker-grain method

Absolute abundances (concentrations) of dinoflagellate cysts are often determined through the addition of Lycopodium clavatum marker-grains as a spike to a sample before palynological processing. An inter-laboratory calibration exercise was set up in order to test the comparability of results obtained in different laboratories, each using its own preparation method. Each of the 23 laboratories received the same amount of homogenized splits of four Quaternary sediment samples. The samples originate from different localities and consisted of a variety of lithologies. Dinoflagellate cysts were extracted and counted, and relative and absolute abundances were calculated. The relative abundances proved to be fairly reproducible, notwithstanding a need for taxonomic calibration. By contrast, excessive loss of Lycopodium spores during sample preparation resulted in non-reproducibility of absolute abundances. Use of oxidation, KOH, warm acids, acetolysis, mesh sizes larger than 15 µm and long ultrasonication (> 1 min) must be avoided to determine reproducible absolute abundances. The results of this work therefore indicate that the dinoflagellate cyst worker should make a choice between using the proposed standard method which circumvents critical steps, adding Lycopodium tablets at the end of the preparation and using an alternative method.

Trissoralen um medicamento de baixa dosagem: estudos termoanalíticos da compatibilidade do fármaco-excipientes e determinação de parâmetros de qualidade para cápsulas magistrais

The trioxsalen (Tri) is a low-dose drug used in the treatment of psoriasis and other skin diseases. The aim of the study was applying the thermal analysis and complementary techniques for characterization, evaluation of the trioxsalen stability and components of manipulated pharmaceutical formulations. The thermal behavior of the Tri by TG/DTG-DTA in dynamic atmosphere of synthetic air and nitrogen showed the same profile with a melting peak followed by a volatilization-related event. From the curves TG / DTG is observed a single stage of mass loss. By heating the drug in the stove at temperatures of 80, 240 and 260 °C, it had no change in chemical structure through the techniques of XRD, HPLC, MIR, OM and SEM. From the non-isothermal and isothermal TG kinetic studies was possible to calculate the activation energy and reaction order for the Tri. The drug showed good thermal stability. Studies on drug-excipient compatibility showed interaction of trissoralen with sodium lauryl sulfate 1:1. There was no interaction with aerosol, pregelatinized starch, sodium starch glycolate, cellulose, croscarmellose sodium, magnesium stearate, lactose and mannitol.The characterization of three trioxsalen formulations at concentrations of 2.5, 5, 7.5, 10, 12.5 and 15 mg was performed by DSC, TG / DTG, XRD, NIR and MIR. The PCA classification method based on spectral data from the NIR and MIR of trissoralen formulations allows successful differentiation into three groups. The formulation 3 was the one that best showed analytical profile with the following composition of aerosil excipients, pre-gelatinized starch and cellulose. The activation energy of the volatilization process of the drug was determined in binary mixtures and formulation 3 through fitting and isoconversional methods. The binary mixture with sodium starch glycolate and lactose showed differences in kinetic parameters compared to the drug isolated. The thermoanalytical techniques (DSC and TG / DTG) were shown to be promising methodologies for quantifying trioxsalen obtained by the linearity, selectivity, no use solvents, without sample preparation, speed and practicality.

Analysis of bio-derived platform chemicals in ionic liquid media by desorption/ionization mass spectrometry

In this work, desorption/ionization mass spectrometry was employed for the analysis of sugars and small platform chemicals that are common intermediates in biomass transformation reactions. Specifically, matrix-assisted laser desorption/ionization (MALDI) and desorption electrospray ionization (DESI) mass spectrometric techniques were employed as alternatives to traditional chromatographic methods. Ionic liquid matrices (ILMs) were designed based on traditional solid MALDI matrices (2,5-dihydroxybenzoic acid (DHB) and α-cyano-4-hydroxycinnamic acid (CHCA)) and 1,3-dialkylimidazolium ionic liquids ([BMIM]Cl, [EMIM]Cl, and [EMIM]OAc) that have been employed as reaction media for biomass transformation reactions such as the conversion of carbohydrates to valuable platform chemicals. Although two new ILMs were synthesized ([EMIM][DHB] and [EMIM][CHCA] from [EMIM]OAc), chloride-containing ILs did not react with matrices and resulted in mixtures of IL and matrix in solution. Compared to the parent solid matrices, much less matrix interference was observed in the low mass region of the mass spectrum (< 500 Da) using each of the IL-matrices. Furthermore, the formation of a true ILM (i.e. a new ion pair) does not appear to be necessary for analyte ionization. MALDI sample preparation techniques were optimized based on the compatibility with analyte, IL and matrix. ILMs and IL-matrix mixtures of DHB allowed for qualitative analysis of glucose, fructose, sucrose and N-acetyl-D-glucosamine. Analogous CHCA-containing ILMs did not result in appreciable analyte signals under similar conditions. Small platform compounds such as 5-hydroxymethylfurfural (HMF) and levulinic acid were not detected by direct analysis using MALDI-MS. Furthermore, sugar analyte signals were only detected at relatively high matrix:IL:analyte ratios (1:1:1) due to significant matrix and analyte suppression by the IL ions. Therefore, chemical modification of analytes with glycidyltrimethylammonium chloride (GTMA) was employed to extend this method to quantitative applications. Derivatization was accomplished in aqueous IL solutions with fair reaction efficiencies (36.9 – 48.4 % glucose conversion). Calibration curves of derivatized glucose-GTMA yielded good linearity in all solvent systems tested, with decreased % RSDs of analyte ion signals in IL solutions as compared to purely aqueous systems (1.2 – 7.2 % and 4.2 – 8.7 %, respectively). Derivatization resulted in a substantial increase in sensitivity for MALDI-MS analyses: glucose was reliably detected at IL:analyte ratios of 100:1 (as compared to 1:1 prior to derivatization). Screening of all test analytes resulted in appreciable analyte signals in MALDI-MS spectra, including both HMF and levulinic acid. Using appropriate internal standards, calibration curves were constructed and this method was employed for monitoring a model dehydration reaction of fructose to HMF in [BMIM]Cl. Calibration curves showed wide dynamic ranges (LOD – 100 ng fructose/μg [BMIM]Cl, LOD – 75 ng HMF/μg [BMIM]Cl) with correlation coefficients of 0.9973 (fructose) and 0.9931 (HMF). LODs were estimated from the calibration data to be 7.2 ng fructose/μg [BMIM]Cl and 7.5 ng HMF/μg [BMIM]Cl, however relatively high S/N ratios at these concentrations indicate that these values are likely overestimated. Application of this method allowed for the rapid acquisition of quantitative data without the need for prior separation of analyte and IL. Finally, small molecule platform chemicals HMF and levulinic acid were qualitatively analyzed by DESI-MS. Both HMF and levulinic acid were easily ionized and the corresponding molecular ions were easily detected in the presence of 10 – 100 times IL, without the need for chemical modification prior to analysis. DESI-MS analysis of ILs in positive and negative ion modes resulted in few ions in the low mass region, showing great potential for the analysis of small molecules in IL media.

Using high resolution tracer data to constrain water storage, flux and age estimates in a spatially distributed rainfall-runoff model

Acknowledgements The authors would like to thank Jonathan Dick, Josie Geris, Jason Lessels, and Claire Tunaley for data collection and Audrey Innes for lab sample preparation. We also thank Christian Birkel for discussions about the model structure and comments on an earlier draft of the paper. Climatic data were provided by Iain Malcolm and Marine Scotland Fisheries at the Freshwater Lab, Pitlochry. Additional precipitation data were provided by the UK Meteorological Office and the British Atmospheric Data Centre (BADC).We thank the European Research Council ERC (project GA 335910 VEWA) for funding the VeWa project.

Resistance and resilience to droughts : hydropedological controls on catchment storage and run-off response

Acknowledgements The authors would like to thank Jonathan Dick, Maria Blumstock, Claire Tunaley and Jason Lessels for assistance with the field work and Audrey Innes for lab sample preparation. Climatic data were provided by Iain Malcolm and Marine Scotland Fisheries at the Freshwater Lab, Pitlochry. Additional precipitation and temperature data were provided by the UK Meteorological Office and the British Atmospheric Data Centre (BADC). We are grateful for the careful and constructive comments of two anonymous reviewers that helped to improve an earlier version of this manuscript. The European Research Council ERC (project GA 335910) is thanked for funding.

Resistance and resilience to droughts : hydropedological controls on catchment storage and run-off response

Acknowledgements The authors would like to thank Jonathan Dick, Maria Blumstock, Claire Tunaley and Jason Lessels for assistance with the field work and Audrey Innes for lab sample preparation. Climatic data were provided by Iain Malcolm and Marine Scotland Fisheries at the Freshwater Lab, Pitlochry. Additional precipitation and temperature data were provided by the UK Meteorological Office and the British Atmospheric Data Centre (BADC). We are grateful for the careful and constructive comments of two anonymous reviewers that helped to improve an earlier version of this manuscript. The European Research Council ERC (project GA 335910) is thanked for funding.

Growing spherulitic calcite grains in saline, hyperalkaline lakes : Experimental evaluation of the effects of Mg-clays and organic acids

Acknowledgements BP Exploration Co. is thanked for funding, and particularly the Carbonate Team (Anna Matthews, Teresa Sabato Ceraldi, and Darryl G. Green) for supporting this research and for fruitful discussions. Mark Anderson, Kim Rosewell, and Tony Sinclair (University of Hull) are thanked for laboratory assistance, and for SEM sample preparation and set-up respectively. The technical and human support from Prof. Jörg Hardege and Maggy A. Harley (University of Hull) was key to perform these experiments. We would like to acknowledge an anonymous reviewer for the detailed and constructive comments, and Brian Jones's editorial handling of the manuscript which is greatly appreciated.