First report of the use of a saxitoxin-protein conjugate to develop a DNA aptamer to a small molecule toxin

Saxitoxin (STX) is a low molecular weight neurotoxin mainly produced by certain marine dinoflagellates that, along with its family of similarly related paralytic shellfish toxins, may cause the potentially fatal intoxication known as paralytic shellfish poisoning. Illness and fatality rates are low due to the effective monitoring programs that determine when toxins exceed the established regulatory action level and effectuate shellfish harvesting closures accordingly. Such monitoring programs rely on the ability to rapidly screen large volumes of samples. Many of the screening assays currently available employ antibodies or live animals. This research focused on developing an analytical recognition element that would eliminate the challenges associated with the limited availability of antibodies and the use of animals. Here we report the discovery of a DNA aptamer that targets STX. Concentration-dependent and selective binding of the aptamer to STX was determined using a surface plasmon resonance sensor. Not only does this work represent the first reported aptamer to STX, but also the first aptamer to any marine biotoxin. A novel strategy of using a toxin-protein conjugate for DNA aptamer selection was successfully implemented to overcome the challenges associated with aptamer selection to small molecules. Taking advantage of such an approach could lead to increased diversity and accessibility of aptamers to low molecular weight toxins, which could then be incorporated as analytical recognition elements in diagnostic assays for foodborne toxin detection. The selected STX aptamer sequence is provided here, making it available to any investigator for use in assay development for the detection of STX.

MALTS: A Tool to Simulate Lorentz Transmission Electron Microscopy From Micromagnetic Simulations

Here we describe the development of the MALTS software which is a generalized tool that simulates Lorentz Transmission Electron Microscopy (LTEM) contrast of magnetic nanostructures. Complex magnetic nanostructures typically have multiple stable domain structures. MALTS works in conjunction with the open access micromagnetic software Object Oriented Micromagnetic Framework or MuMax. Magnetically stable trial magnetization states of the object of interest are input into MALTS and simulated LTEM images are output. MALTS computes the magnetic and electric phases accrued by the transmitted electrons via the Aharonov-Bohm expressions. Transfer and envelope functions are used to simulate the progression of the electron wave through the microscope lenses. The final contrast image due to these effects is determined by Fourier Optics. Similar approaches have been used previously for simulations of specific cases of LTEM contrast. The novelty here is the integration with micromagnetic codes via a simple user interface enabling the computation of the contrast from any structure. The output from MALTS is in good agreement with both experimental data and published LTEM simulations. A widely-available generalized code for the analysis of Lorentz contrast is a much needed step towards the use of LTEM as a standardized laboratory technique.

Integrating geophysical data and upscaling techniques to support regional groundwater flow modelling: A practical example of the Lagan Valley, Northern Ireland

When studying heterogeneous aquifer systems, especially at regional scale, a degree of generalization is anticipated. This can be due to sparse sampling regimes, complex depositional environments or lack of accessibility to measure the subsurface. This can lead to an inaccurate conceptualization which can be detrimental when applied to groundwater flow models. It is important that numerical models are based on observed and accurate geological information and do not rely on the distribution of artificial aquifer properties. This can still be problematic as data will be modelled at a different scale to which it was collected. It is proposed here that integrating geophysics and upscaling techniques can assist in a more realistic and deterministic groundwater flow model. In this study, the sedimentary aquifer of the Lagan Valley in Northern Ireland is chosen due to intruding sub-vertical dolerite dykes. These dykes are of a lower permeability than the sandstone aquifer. The use of airborne magnetics allows the delineation of heterogeneities, confirmed by field analysis. Permeability measured at the field scale is then upscaled to different levels using a correlation with the geophysical data, creating equivalent parameters that can be directly imported into numerical groundwater flow models. These parameters include directional equivalent permeabilities and anisotropy. Several stages of upscaling are modelled in finite element. Initial modelling is providing promising results, especially at the intermediate scale, suggesting an accurate distribution of aquifer properties. This deterministic based methodology is being expanded to include stochastic methods of obtaining heterogeneity location based on airborne geophysical data. This is through the Direct Sample method of Multiple-Point Statistics (MPS). This method uses the magnetics as a training image to computationally determine a probabilistic occurrence of heterogeneity. There is also a need to apply the method to alternate geological contexts where the heterogeneity is of a higher permeability than the host rock.

Integrating Multiple Point Statistics with Aerial Geophysical Data to assist Groundwater Flow Models

The process of accounting for heterogeneity has made significant advances in statistical research, primarily in the framework of stochastic analysis and the development of multiple-point statistics (MPS). Among MPS techniques, the direct sampling (DS) method is tested to determine its ability to delineate heterogeneity from aerial magnetics data in a regional sandstone aquifer intruded by low-permeability volcanic dykes in Northern Ireland, UK. The use of two two-dimensional bivariate training images aids in creating spatial probability distributions of heterogeneities of hydrogeological interest, despite relatively ‘noisy’ magnetics data (i.e. including hydrogeologically irrelevant urban noise and regional geologic effects). These distributions are incorporated into a hierarchy system where previously published density function and upscaling methods are applied to derive regional distributions of equivalent hydraulic conductivity tensor K. Several K models, as determined by several stochastic realisations of MPS dyke locations, are computed within groundwater flow models and evaluated by comparing modelled heads with field observations. Results show a significant improvement in model calibration when compared to a simplistic homogeneous and isotropic aquifer model that does not account for the dyke occurrence evidenced by airborne magnetic data. The best model is obtained when normal and reverse polarity dykes are computed separately within MPS simulations and when a probability threshold of 0.7 is applied. The presented stochastic approach also provides improvement when compared to a previously published deterministic anisotropic model based on the unprocessed (i.e. noisy) airborne magnetics. This demonstrates the potential of coupling MPS to airborne geophysical data for regional groundwater modelling.

Air pollutant contamination and acidification of surface waters in the North York Moors, UK: Multi-proxy evidence from the sediments of a moorland pool

Despite the extensive geographical range of palaeolimnological studies designed to assess the extent of surface water acidification in the United Kingdom during the 1980s, little attention was paid to the status of surface waters in the North York Moors (NYM). In this paper, we present sediment core data from a moorland pool in the NYM that provide a record of air pollution contamination and surface water acidification. The 41-cm-long core was divided into three lithostratigraphic units. The lower two comprise peaty soils and peats, respectively, that date to between approximately 8080 and 6740 cal. BP. The uppermost unit comprises peaty lake muds dating from between approximately ad 1790 and the present day (ad 2006). The lower two units contain pollen dominated by forest taxa, whereas the uppermost unit contains pollen indicative of open landscape conditions similar to those of the present. Heavy metal, spheroidal carbonaceous particle, mineral magnetics and stable isotope analysis of the upper sediments show clear evidence of contamination by air pollutants derived from fossil-fuel combustion over the last c. 150years, and diatom analysis indicates that the naturally acidic pool became more acidic during the 20th century. We conclude that the exceptionally acidic surface waters of the pool at present (pH=c. 4.1) are the result of a long history of air pollution and not because of naturally acidic local conditions. We argue that the highly acidic surface waters elsewhere in the NYM are similarly acidified and that the lack of evidence of significant recovery from acidification, despite major reductions in the emissions of acidic gases that have taken place over the last c. 30years, indicates the continuing influence of pollutant sulphur stored in catchment peats, a legacy of over 150years of acid deposition.

Compositional data-driven alternatives to single geochemical component maps

Conventional practice in Regional Geochemistry includes as a final step of any geochemical campaign the generation of a series of maps, to show the spatial distribution of each of the components considered. Such maps, though necessary, do not comply with the compositional, relative nature of the data, which unfortunately make any conclusion based on them sensitive
to spurious correlation problems. This is one of the reasons why these maps are never interpreted isolated. This contribution aims at gathering a series of statistical methods to produce individual maps of multiplicative combinations of components (logcontrasts), much in the flavor of equilibrium constants, which are designed on purpose to capture certain aspects of the data.
We distinguish between supervised and unsupervised methods, where the first require an external, non-compositional variable (besides the compositional geochemical information) available in an analogous training set. This external variable can be a quantity (soil density, collocated magnetics, collocated ratio of Th/U spectral gamma counts, proportion of clay particle fraction, etc) or a category (rock type, land use type, etc). In the supervised methods, a regression-like model between the external variable and the geochemical composition is derived in the training set, and then this model is mapped on the whole region. This case is illustrated with the Tellus dataset, covering Northern Ireland at a density of 1 soil sample per 2 square km, where we map the presence of blanket peat and the underlying geology. The unsupervised methods considered include principal components and principal balances
(Pawlowsky-Glahn et al., CoDaWork2013), i.e. logcontrasts of the data that are devised to capture very large variability or else be quasi-constant. Using the Tellus dataset again, it is found that geological features are highlighted by the quasi-constant ratios Hf/Nb and their ratio against SiO2; Rb/K2O and Zr/Na2O and the balance between these two groups of two variables; the balance of Al2O3 and TiO2 vs. MgO; or the balance of Cr, Ni and Co vs. V and Fe2O3. The largest variability appears to be related to the presence/absence of peat.

Sediment magnetic properties of glacial till deposited since the Little Ice Age maximum for selected glaciers at Svartisen and Okstindan, northern Norway

Samples of glacial till deposited since the Little Ice Age (LIA) maximum by two glaciers, North Bogbre at Svartisen and Corneliussen-breen at Okstindan, northern Norway, were obtained from transects running from the current glacier snout to the LIA (c. AD 1750) limit. The samples were analysed to determine their sediment magnetic properties, which display considerable variability. Significant trends in some magnetic parameters are evident with distance from the glacier margin and hence length of subaerial exposure. Magnetic susceptibility (X) decreases away from the contemporary snout, perhaps due to the weathering of ferrimagnetic minerals into antiferromagnetic forms, although this trend is generally not statistically significant. Trends in the ratios of soft IRM/hard IRM which are statistically significant support this hypothesis, suggesting that antiferromagnetic minerals are increasing relative to ferrimagnetic minerals towards the LIA maximum. Backfield ratios (IRM -100 mT/SIRM) also display a significant and strong trend towards magnetically harder behaviour with proximity to the LIA maximum. Thus, by employing a chronosequence approach, it may be possible to use sediment magnetics data as a tool for reconstructing glacier retreat in areas where more traditional techniques, such as lichenometry, are not applicable.

Effect of Ti-C and Cr Additions on Magnetic Properties of Nanocrystalline (Pr,Nd)-Fe-B Alloys

The addition of both Ti-C and Cr as grain refiners in Nd-Fe-B nanocomposites substantially increases the coercive field Hc. This motived our investigation of the effect of Ti-C and Cr on Pr-Fe-B nanocomposites. Melt-spun ribbons of composition (Pr(9.5)Fe(84.5)B(6))(0.97-x)Cr(x)(TiC)(0.03)(x = 0; 0.25; 0.5; 0.75; 1) and (Nd(9.5)Fe(84.5)B(6))(0.97-x)Cr(x)(TiC)(0.03)(x = 0.5 and 1) were produced for study. For a Pr nanocomposite with 1% Cr, Hc = 12.5 kOe. However, the energy product was limited to 13.6 MGOe by the remanence value. Rietveld analysis of X-ray spectra showed the ribbons to consist of predominantly hard (similar to 70 wt%) R(2)Fe(14)B, the soft phase being (similar to 30 wt%) alpha-Fe. Mossbauer measurements at 300 K are consistent with a reduced hyperfine field for the hard magnetic phase due to the Cr addition. Analysis of transmission electron microscopy images showed the Pr nanocomposite with 1% Cr to have an increased average grain size.

Magnetic Hyperthermia With Fe(3)O(4) Nanoparticles: The Influence of Particle Size on Energy Absorption

We have studied the magnetic and power absorption properties of a series of magnetic nanoparticles (MNPs) of Fe(3)O(4) with average sizes < d > ranging from 3 to 26 rim. Heating experiments as a function of particle size revealed a strong increase in the specific power absorption (SPA) values for particles with < d > = 25-30 mn. On the other side saturation magnetization M(s) values of these MNPs remain essentially constant for particles with < d > above 10 rim, suggesting that the absorption mechanism is not determined by Ms. The largest SPA value obtained was 130 W/g, corresponding to a bimodal particle distribution with average size values of 17 and 26 nm.

Caracterização geológico-geofísica do meio aqüífero fissural : uma contribuição aos modelos de fluxo e armazenamento de água subterrânea

Northeastern Brazil is mainly formed by crystalline terrains (around 60% in area). Moreover, this region presents a semi-arid climate so that it is periodically subject to drought seasons. Furthermore, ground water quality extracted fromwells usually presents poor quality because of their high salinity contents. Nevertheless, ground water is still a very important source of water for human and animal consumption in this region. Well sitting in hard rocks terrains in Northeastern Brazil offers a mean success index of aboul 60%, given that a successful siting is defined by a well producing at least 0.5 m³/h. This low index reveals lack of knowledga about the true conditions of storage and percolation of ground water in crystalline rocks. Two models for structures storing and producing ground water in crystalline rocks in Northeastem Brazil have been proposed in the literature. The first model,tradnionally used for well sitting since the sixties are controlled by faults or fractures zones. This model is commonly referred, in Brazilian hydrogeological literature, as the "creek-crack" model (riacho-fenda in Portuguese). Sites appearing to present dense drainage network are preferred for water well siting - particularly at points where the drainages cross-cul each other. Field follow up work is usually based only on geological criteria. The second model is the "eluvio-alluvial through" (calha eluvio-aluvionar in Portuguese); it is also described in the literature but it is not yet incorporated in well sitting practice. This model is based on the hypothesis that reclilinear drainages can also be controlled by the folietion of the rock. Eventually, depending upon the degree of weathering, a through-shaped structure filled with sediments (alluvium and regolith) can be developed which can store and water can be produced from. Using severalfield case studies, this Thesis presents a thorough analysis ofthe two above cited models and proposes a new model. The analysis is based on an integrated methodological approach using geophysics and structural geology. Both land (Resitiviy and Ground Penetrating Radar- GPR) and aerogeophysical (magnetics and frequency domain eletromagnetics) surveys were used. Slructural analysis emphasized neolectonic aspects; in general, itwas found that fractures in the E-W direction are relatively open, as compared to fracturas inthe N-S direction, probably because E-W fractures were opened by the neotectonic stress regime in Northeastern Brazil, which is controlled by E-W compression and N-S extension. The riacho-fenda model is valid where drainages are controlled by fractures. The degree of fracturing and associated weathering dictale the hydrogeological potential of the structure. Field work in structural analogues reveals that subvertical fractures show consistent directions both in outcrop and aerophotograph scales. Geophysical surveys reveal subvertical conductive anomalies associated to the fracture network controlling the drainage; one of the borders of the conductive anomaly usually coincide wih the drainage. An aspect of particular importance to the validation of fracture control are the possible presence of relalively deep conductive anomalies wihoul continuation or propagalion to the surface. The conductive nature of lhe anomaly is due to the presence of wealhered rock and sedirnenls (alluvium and/or regolilh) storing ground waler which occur associated to the fracture network. Magnetic surveys are not very sensisnive to these structures.lf soil or covering sedirnents are resislive (> 100 Ohm.m), GPR can ba used to image precisely lhe fracture network. A major limialion of riacho-fenda model, revealed by GPR images, is associated to the fact thal subhorizontal fractures do play a very important role in connecting the fracture network, besides connect shallow recharge zones to relalively deep subvertical frecture zones. Iffractures play just a secondary control on the drainage, however, r/acho-fenda model may have a very limiled validny; in these cases, large portions oflhe drainage do nol coincide wilh frectures and mosl oflhewells localed in lhe drainage surrounding would resull dry. Usually, a secondary conlrol on lhe drainage by Ihefraclure networkcan be revealed only wilh detailed geophysical survey. The calha elClv1o-aluvlonarmodel is valid where drainages are conlrolled by folialion. The degree 01 wealhering 01 lhe lolialion planes dictales lhe hydrogeological polenlial 01 lhe slruclure. Outcrop analysis reveals Ihal lolialion and drainage direclions are parallel and Ihal no Iraclures, orfraclures wilh diflerent directions 01 lhe drainage direclion occur. Geophysical surveys reveal conduclive anomalies in a slab lorm associaled 10 lhe Ihrough 01 lhe wealhered rock and sedimenls (alluvium and/or regolith). Magnelic surveys can ofler a very good conlrol on lolialion direclion. An importanl aspect 10 validale lolialion conlrol are lhe presence 01 conductive anomalies showing shallow and deep portions area which are linked. Illhere is an exlensive soil cover, r/acho-fenda and calha eIClv1o-aluv/onar conlrols can be easily misinlerpreled in lhe absence 01 geophysical conlrol. Certainly, Ihis lacl could explain at leasl a part of lhe failure index in well sitting. The model wealhering sack (bolsllo de Intempertsmo in Portuguese) is proposed to explain cases where a very inlensive wealhering occur over lhe crystalline rock so Ihal a secondary inlerslilial porosity is crealed. The waler is Ihen stored in lhe porous of lhe regolilh in a similar mannerlo sedimentary rocks. A possible example ofthis model was delecled by using land geophysical survey where a relalivelyvery deep isolaled conduclive anomaly, in a slab form, was delected. Iflhis structure does store ground waler, certainly Ihere must be a link 01 lhe deep slructure wilh lhe surface in orderlo provide walerfeeding. This model mighl explain anomalous waler yields as greal as 50 m³/h Ihalsomelimescan occur in crystalline rocks in Northeaslern Brazil

analise da dispersao de ondas de superficie na provincia borborema, Nordeste do Brasil

The Borborema Province, Northeastern Brazil, had its internal structure investigated by different geophysical methods like gravity, magnetics and seismics. Additionally, many geological studies were also carried out to define the structural domains of this province. Despite the plethora of studies, there are still many important open aspects about its evolution. Here, we study the velocity structure of S-wave in the crust using dispersion of surface waves. The dispersion of surface waves allows an estimate of the average thickness of the crust across the region between the stations. The inversion of the velocity structure was carried out using the inter-station dispersion of surface waves of Rayleigh and Love types. The teleseismic events are mainly from the edges of the South and North American plates. The period of data collection occurred between 2007 and 2010 and we selected 7 events with magnitude above 5.0 MW and up to 40 km depth. The difference between the events back-azimuths and the interstation path was not greater than 10. We also know the depth of the Moho, results from Receiver Functions (Novo Barbosa, 2008), and use those as constrains in inversion. Even using different parameterizations of models for the inversion, our results were very similar the mean profiles velocity structure of S-wave. In pairs of stations located in the Cear´a Central Domain Borborema the province, there are ranges of depths for which the velocities of S are very close. Most of the results in the profile near the Moho complicate their interpretation at that depth, coinciding with the geology of the region, where there are many shear zones. In particular, the profile that have the route Potiguar Bacia in inter-station, had low velocities in the crust. We combine these results to the results of gravimetry and magnetometry (Oliveira, 2008) and receptor function (Novo Barbosa, 2008). We finally, the first results on the behavior of the velocity structure of S-wave with depth in the Province Borborema

Modal analysis of anisotropic diffused-channel waveguide by a scalar finite element method

A procedure to model optical diffused-channel waveguides is presented in this work. The dielectric waveguides present anisotropic refractive indexes which are calculated from the proton concentration. The proton concentration inside the channel is calculated by the anisotropic 2D-linear diffusion equation and converted to the refractive indexes using mathematical relations obtained from experimental data, the arbitrary refractive index profile is modeled by a. nodal expansion in the base functions. The TE and TM-like propagation properties (effective index) and the electromagnetic fields for well-annealed proton-exchanged (APE) LiNbO3 waveguides are computed by the finite element method.

MATHEMATICA notebook for computing tetrahedral finite element shape functions and matrices for the Helmholtz equation

A MATHEMATICA notebook to compute the elements of the matrices which arise in the solution of the Helmholtz equation by the finite element method (nodal approximation) for tetrahedral elements of any approximation order is presented. The results of the notebook enable a fast computational implementation of finite element codes for high order simplex 3D elements reducing the overheads due to implementation and test of the complex mathematical expressions obtained from the analytical integrations. These matrices can be used in a large number of applications related to physical phenomena described by the Poisson, Laplace and Schrodinger equations with anisotropic physical properties.

Nucleon magnetic moments in light-front models with quark mass asymmetries

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)