Papers by Daniela Gerovska
Molecular Human Reproduction, 2016
Does primordial germ cell (PGC) activation start before mouse embryo implantation, and does the p... more Does primordial germ cell (PGC) activation start before mouse embryo implantation, and does the possible regulation of the DNA (cytosine-5-)-methyltransferase 3-like (Dnmt3l) by transcription factor AP-2, gamma (TCFAP2C) have a role in this activation and in the primitive endoderm (PE)-epiblast (EPI) lineage specification? A burst of expression of PGC markers, such as Dppa3/Stella, Ifitm2/Fragilis, Fkbp6 and Prdm4, is observed from embryonic day (E) 3.25, and some of them, together with the late germ cell markers Zp3, Mcf2 and Morc1, become restricted to the EPI subpopulation at E4.5, while the dynamics analysis of the PE-EPI transitions in the single-cell data suggests that TCFAP2C transitorily represses Dnmt3l in EPI cells at E3.5 and such repression is withdrawn with reactivation of Dnmt3l expression in PE and EPI cells at E4.5. In the mouse preimplantation embryo, cells with the same phenotype take different fates based on the orchestration between topological clues (cell polarity, positional history and division orientation) and gene regulatory rules (at transcriptomics and epigenomics level), prompting the proposal of positional, stochastic and combined models explaining the specification mechanism. PGC specification starts at E6.0-6.5 post-implantation. In view of the important role of DNA methylation in developmental events, the cross-talk between some transcription factors and DNA methyltransferases is of particular relevance. TCFAP2C has a CpG DNA methylation motif that is not methylated in pluripotent cells and that could potentially bind on DNMT3L, the stimulatory DNA methyltransferase co-factor that assists in the process of de novo DNA methylation. Chromatin-immunoprecipitation analysis has demonstrated that Dnmt3l is indeed a target of TCFAP2C. We aimed to assess the timing of early preimplantation events and to understand better the segregation of the inner cell mass (ICM) into PE and EPI. We designed a single-cell transcriptomics dynamics computational study to identify markers of the PE-EPI bifurcation in ICM cells through searching for statistically significant (using the Student's t-test method) differently expressed genes (DEGs) between PE and EPI cells from E3.5 to E4.5. The DEGs common for E3.5 and E4.5 were used as the markers defining the steady states. We collected microarray and next-generation sequencing transcriptomics data from public databases from bulk populations and single cells from mice at E3.25, E3.5 and E4.5. The results are based on three independent single-cell transcriptomics data sets, with a fold change of 3 and P-value <0.01 for the DEG selection. The dynamics analysis revealed new transitory E3.5 and steady PE and EPI markers. Among the transitory E3.5 PE markers (Dnmt3l, Dusp4, Cpne8, Akap13, Dcaf12l1, Aaed1, B4galt6, BC100530, Rnpc3, Tfpi, Lgalsl, Ckap4 and Fbxl20), several (Dusp4, Akap13, Cpn8, Dcaf12l1 and Tfpi) are related to the extracellular regulated kinase pathway. We also identified new transitory E3.5 EPI markers (Sgk1, Mal, Ubxn2a, Atg16l2, Gm13102, Tcfap2c, Hexb, Slc1a1, Svip, Liph and Mier3), six new stable PE markers (Sdc4, Cpn1, Dkk1, Havcr1, F2r/Par1 and Slc7a6os) as well as three new stable EPI markers (Zp3, Mcf2 and Hexb), which are known to be late stage germ cell markers. We found that mouse PGC marker activation starts at least at E3.25 preimplantation. The transcriptomics dynamics analyses support the regulation of Dnmt3l expression by TCFAP2C. Since the regulation of Dnmt3l by TCFAP2C is based on computational prediction of DNA methylation motifs, Chip-Seq and transcriptomics data, functional studies are required to validate this result. We identified a collection of previously undescribed E3.5-specific PE and EPI markers, and new steady PE and EPI markers. Identification of these genes, many of which encode cell membrane proteins, will facilitate the isolation and characterization of early PE and EPI populations. Since it is so well established in the literature that mouse PGC specification is a post-implantation event, it was surprising for us to see activation of PGC markers as early as E3.25 preimplantation, and identify the newly found steady EPI markers as late germ cell markers. The discovery of such early activation of PGC markers has important implications in the derivation of germ cells from pluripotent cells (embryonic stem cells or induced pluripotent stem cells), since the initial stages of such derivation resemble early development. The early activation of PGC markers points out the difficulty of separating PGC cells from pluripotent populations. Collectively, our results suggest that the combining of the precision of single-cell omics data with dynamic analysis of time-series data can establish the timing of some developmental stages as earlier than previously thought. LARGE-SCALE DATA: Not applicable. This work was supported by grants DFG15/14 and DFG15/020 from Diputación…
pure and applied geophysics PAGEOPH, 2005
Here, we propose a new, finite-difference algorithm for Euler deconvolution, based on the Euler's... more Here, we propose a new, finite-difference algorithm for Euler deconvolution, based on the Euler's homogeneity equation accounting for a constant background field which allows simultaneous depth and shape estimation. The algorithm uses as input data the measured anomalous field and its firstorder derivatives, in contrast to methods based on the input of higher order field derivatives. The test of the algorithm on a model of interfering fields of elementary sources with different field fall-off rates, resulting in background close to a linear one, shows that it can give a good estimation of both the depth to the sources singular points and their respective structural indices. A set of tests was carried out on column-like models with shapes ranging from the elementary model of a dipole to that of a point pole, and of models of arbitrary shape with two singular points in between. It showed that when the ratio of the distance between the observation plane and the source's top and the length of the body allows classification of it as a dipole or a point pole, the value of the estimated structural index is close to the integer value, typical for the respective elementary source. In such cases the estimated depth value refers to that of the special internal point of the respective type of source. This can facilitate in certain situations the interpretation of noninteger structural indices and their associated depth estimates obtained with the new Euler deconvolution algorithm. Inversion of a set of magnetic data from northern Bulgaria, caused by basaltic bodies of different shape, with the proposed method confirmed that the most intense anomalies are caused by column-like bodies outcropping on the surface and with considerable depth extent.
Egu General Assembly Conference Abstracts, May 1, 2010
Harmonic splines (HS) are global basis functions concentrated in localised regions that can be us... more Harmonic splines (HS) are global basis functions concentrated in localised regions that can be used to model geopotential data without loss of resolution. Here, we apply HS modelling to produce a global model of the Earth's lithospheric anomaly field from satellite data. Shure et al. (1982) developed a minimum norm algorithm applicable to global datasets, which involves solving a data-by-data system of equations. This approach cannot be applied directly to large satellite dataset owing to the computational burden involved, but because the satellite 'footprint' is small, most of the matrix elements are negligibly small. We therefore use sparse iterative matrix methods, with Jacobi preconditioning to improve convergence, to downward continue the lithospheric anomaly field measured by satellite. We use the dataset of Stockman et al. (2009) which allows a direct comparison with the results of their spherical tesselation modelling method, including the fit to the data. We produce equivalent spherical harmonic coefficients of the HS model for comparison with more conventional methods. Originally developed for vector component data, scalar data are incorporated into the HS model using the method of Langel and Whaler (1996). Regional high resolution near-surface (e.g. aeromagnetic) data are combined with the global satellite dataset in a joint HS model, though the number of such data and the lack of matrix sparseness means modifications to the method (e.g. the depleted basis method of Parker and Shure (1982)) resulting in some loss of resolution are necessary. The best prospects for the method are therefore to resolve the spectrum at intermediate wavelengths given the appropriate large-scale or long flight/marine line surveys, avoiding artefacts that can be introduced by compiling multiple near-surface datasets without exercising the longer wavelength control that satellite data bring.
A differential technique was implemented for the calculation of the low sensitive to the sources ... more A differential technique was implemented for the calculation of the low sensitive to the sources magnetisation vector direction and showing high centricity T transform of the total anomalous magnetic field over large areas, where the changes in the values
SEG Technical Program Expanded Abstracts 2004, 2004
pure and applied geophysics PAGEOPH, 2005
Here, we propose a new, finite-difference algorithm for Euler deconvolution, based on the Euler's... more Here, we propose a new, finite-difference algorithm for Euler deconvolution, based on the Euler's homogeneity equation accounting for a constant background field which allows simultaneous depth and shape estimation. The algorithm uses as input data the measured anomalous field and its firstorder derivatives, in contrast to methods based on the input of higher order field derivatives. The test of the algorithm on a model of interfering fields of elementary sources with different field fall-off rates, resulting in background close to a linear one, shows that it can give a good estimation of both the depth to the sources singular points and their respective structural indices. A set of tests was carried out on column-like models with shapes ranging from the elementary model of a dipole to that of a point pole, and of models of arbitrary shape with two singular points in between. It showed that when the ratio of the distance between the observation plane and the source's top and the length of the body allows classification of it as a dipole or a point pole, the value of the estimated structural index is close to the integer value, typical for the respective elementary source. In such cases the estimated depth value refers to that of the special internal point of the respective type of source. This can facilitate in certain situations the interpretation of noninteger structural indices and their associated depth estimates obtained with the new Euler deconvolution algorithm. Inversion of a set of magnetic data from northern Bulgaria, caused by basaltic bodies of different shape, with the proposed method confirmed that the most intense anomalies are caused by column-like bodies outcropping on the surface and with considerable depth extent.
Journal of Applied Geophysics, 2004
The transforms based on magnitude of the magnetic anomaly (MMA), or absolute value of anomalous m... more The transforms based on magnitude of the magnetic anomaly (MMA), or absolute value of anomalous magnetic intensity, are relatively insensitive to the direction of the source magnetisation vector and show high centricity. Obtaining them requires calculation of only first-order horizontal derivatives of the component magnetic anomalies X, Y and Z, obtained through transformation of total magnetic anomalies DT (TMA). We studied the use of the magnetic transforms based on the MMA of a dipole source and that of their ratios for determining the geometric and physical parameters of compact environmental ferrometallic sources. Analytical formulas for all the parameters of the magnetic dipole based on calculation of MMAs, their gradients and Laplacian, and their ratios were obtained. The horizontal position of the dipole source is determined by the maximum of the Laplacian of the MMA, which is the transform with the highest centricity. We applied the approach on model data and on magnetic anomalies over environmental sources, represented by unexploded ordnance (UXO) and clutter from the Badlands Bombing Range, USA. The obtained parameter values were compared with those estimated through Euler deconvolution using unprescribed structural index and linear model of the background, and through inversion. The comparison showed that the proposed method produced similar depth results to that of the Euler deconvolution method for the objects with estimated structural index over and around 2.5, i.e., for the sources, which to a great extent can be approximated with a dipole. The inversion for the dipole parameters using as initial parameters the estimated with the MMA transform method ones confirmed the results of the MMA transform method for the dipole coordinates and magnetisation for all items. D
GEOPHYSICS, 2006
We solve the inverse magnetic problem for the depth and shape of simple sources in the presence o... more We solve the inverse magnetic problem for the depth and shape of simple sources in the presence of a regional field and truly random noise. We do not use noise-generating derivatives nor are we forced to solve complex systems of equations. Our inverse operator applies a new geometric type of field transform, the finite-difference similarity transform ͑FDST͒, that is based on a postulated degree of homogeneity in the potential field. Magnetic data from two height levels are required for the calculation of the FDSTs. The FDSTs are generated for an assumed central point of similarity ͑CPS͒ and a trial value ͑index͒ for the coefficient of similarity, and they are sensitive to the distance between the source and the CPS and to the agreement between the index and the degree of homogeneity in the data. When the CPS converges to a singular point in the potential field, say, the center or the top edge of the source, and when the trial index converges on the degree of homogeneity present in the data, the FDST drops in amplitude and its plot approaches a straight line, thereby signaling an interpretation for the source position and type. All inverse operations are fully automated and applicable to the interpretation of large data sets. The necessary data for the second level can be obtained by actual measurement or, alternatively, by deriving them from the data at the first level by an upward, analytical continuation. Upward continuation suppresses high-wavenumber random noise and thus contributes to a stable inversion. Model tests show that a suitable height for the second level is less than the expected depth of the source below the first level, while a suitable window length is about twice that depth. Examples show that the proposed inversion is effective on both model and field data. Note that this approach can be extended to the inversion of any component or derivative of the 2D or 3D magnetic or gravity fields from simple sources.
GEOPHYSICS, 2006
We present a Matlab tool that calculates five magnitude magnetic transforms ͑MMTs͒ from an input ... more We present a Matlab tool that calculates five magnitude magnetic transforms ͑MMTs͒ from an input measured anomalous magnetic field. The MMTs are all based on the total magnitude anomaly ͑TMA͒, and consist of the TMA itself, the modulus of the gradient of the TMA, the Laplacian of the TMA, half of the square root of the Laplacian of the square of the TMA, and the square root of the product of the TMA plus the Laplacian of the TMA. These MMTs produce anomalies that are closer to the magnetic source's true horizontal position and are simpler to interpret than the measured anomalous magnetic field itself. While the conventional magnetic transforms of reduction-to-the-pole ͑RTP͒, the pseudogravity field, and the analytic signal ͑AS͒ also have these properties, these MMTs have several additional advantages. They require only first-order, horizontal derivatives for their calculation. They are also more stable at low magnetic latitudes than the RTP, and have a pattern that is independent of the geomagnetic-field vector direction, in contrast to the AS.
GEOPHYSICS, 2010
We present an automatic procedure -Magnetic And Gravity SOUNDing Differential Similarity Transfor... more We present an automatic procedure -Magnetic And Gravity SOUNDing Differential Similarity Transform ͑MaGSoundDST͒ -for inversion of regular or irregular magnetic-and gravitygrid data measured on even or uneven surfaces. It solves for horizontal position, depth, and structural index of simple sources and is independent of a linear background. In addition, it estimates the shape of sources consisting of several singular points and lines. The method uses the property of the differential similarity transform ͑DST͒ of a magnetic or a gravity anomaly to become zero or linear at all observation points when the central point of similarity of the transform, which we refer to as the probing point, coincides with a source's singular point. It uses a measured anomalous field and its calculated or measured ͑gradiometry͒ first-order derivatives. The method is independent of the magnetization-vector direction in the magnetic data case and does not require reduction-to-the-pole transformed data as input. With MaGSoundDST, we provide an important alternative interpretation technique to the Euler deconvolution procedures, combining a moving-window method, whereby the solutions are linked to singular points of causative bodies, with an approach in which the solutions are linked to the real sources. The procedure involves calculating a 3D function that evaluates the linearity of the DST for different integer or noninteger structural indices, using a moving window. We sound the subsurface along a vertical line under each window center. Then we combine the 3D results for different structural indices and present them in three easy-tointerpret maps, avoiding the need for clustering techniques. We deduce only one solution for location and type of simple sources, which is a major advantage over Euler deconvolution. Application to different cases of synthetic and real data shows the method's applicability to various types of magnetic and gravity field investigations.
Geophysical Prospecting, 2006
ABSTRACT Magnitude transforms include magnitude magnetic anomalies (MMA), their gradients and Lap... more ABSTRACT Magnitude transforms include magnitude magnetic anomalies (MMA), their gradients and Laplacians. They can be calculated from the total magnetic anomalies or other component anomalies. Magnitude magnetic anomalies have a space distribution different from that of the component anomalies. Their values are non-negative and their respective patterns are similar to the positive gravity anomalies. Magnitude transforms are an effective tool for magnetic data analysis due to their simplified pattern and direct correlation with the space location of the source. They have advantages over the traditionally used reduction-to-the-pole (RTP) transform, especially at low magnetic latitudes. The calculation of magnitudes of the anomalous field requires the total field data to be transformed into the component anomalies, while the reduction-to-the-pole transform also includes a rotation of the magnetization vector, the orientation of which is usually assumed. For equal latitudes, the transfer functions of component-component transforms in the frequency domain show better stability than the component-component-rotation transfer function. This is illustrated by a comparison of analytical expressions, and synthetic models of magnetic fields. The Dixon seamount case shows the possibilities for an improved data analysis and more confident source recognition at low latitudes using magnetic transforms.
Geophysical Prospecting, 2009
The differential similarity transform of a magnetic anomaly is a linear combination of its intens... more The differential similarity transform of a magnetic anomaly is a linear combination of its intensity and gradient components. This transform is sensitive to the distance between a chosen central point of similarity and the source and depends on the degree of homogeneity of the field. Taking advantage of this property, a new field inversion method resulting in the evaluation of source position and shape type is proposed and implemented. The field gradient components are measured directly in magnetic gradiometry, or they can be calculated from the measured field data. Regional and local linear backgrounds are accounted for by the method. The method can be applied on either regularly or irregularly-spaced data sets, on even or uneven surfaces of observation. The solving of the systems of equations is not necessary. A semi-automated inversion for both location and shape of the sources is implemented. Model and field tests illustrate the effectiveness of the proposed inversion technique for depth and shape estimates.
Geophysical Prospecting, 2009
We present a new method to estimate the direction of the magnetization vector of geological bodie... more We present a new method to estimate the direction of the magnetization vector of geological bodies based upon the correlation between the reduced-to-the-pole field for tentative values of the magnetization direction and the total magnitude anomaly, obtained by a transform of the measured magnetic field. The reduced-to-the-pole and the total magnitude anomaly are centred over the sources in the case of 2D anomalies or well-centred in the case of compact 3D sources and have similar patterns for the same source. The method has several important advantages over similar transformcorrelation methods for estimation of the magnetization direction. It calculates only one transform for many tentative values of the magnetization direction. The method does not use derivatives of any order and relies on confident isolation of the target anomalies based on one of the compared transforms, the total magnitude anomaly. We studied the performance of the method on five 2.5D and compact 3D sources. We analysed possible inherent to the method errors, as well as errors due to interference from neighbouring sources. Finally, we estimated the magnetization-vector direction of the main sources causing the magnetic field in the Burgas region and the adjoining southeast Bulgarian Black Sea shelf. The sources in the Black Sea shelf show prevalently reverse magnetization, while the sources on land have normal or reverse magnetization.
Geophysical Prospecting, 2000
Magnetic data interpretation faces dif®culties due to the various shapes of magnetic anomalies an... more Magnetic data interpretation faces dif®culties due to the various shapes of magnetic anomalies and the positions of their extrema with respect to the causative bodies for different directions of the source magnetization. The well-known transforms ± reduction to the pole, pseudogravity ®eld, and analytic signal (total gradient) ± help in reducing the problem. Another way to achieve the required effect is the transformation of magnetic data, DT or Z, into values of the anomalous magnetic intensity T. In this respect, we have found some transforms based on differential operators such as the gradient of T and its modulus R |=T|, the Laplacian L = 2 T, the product T = 2 T and its square root Q, and the Laplacian = 2 (T 2 ) and its square root E, to be useful. They are slightly sensitive to the magnetization orientation and their extrema occur above the sources.
Computers & Geosciences, 2003
A tool for fully automatic magnetic data interpretation, solving Euler's homogeneity equation wit... more A tool for fully automatic magnetic data interpretation, solving Euler's homogeneity equation with unprescribed structural index and for a linear background in each moving window, is presented here. The implemented Euler deconvolution algorithm is based on the properties of the differential similarity transformation, which decouples the coordinates and the structural index of the singular point and the parameters of the linear background field. Since the deconvolution algorithm resolves the singular point locations well, this allows the application of a two stage clustering technique, focusing the estimated singular point coordinates and structural indices, followed by a statistical analysis of the final solutions. The automatic technique was tested on simple and complex 3D model magnetic anomalies. Finally, the technique was applied to real magnetic anomaly data from the Burgas region and the adjoining Black Sea shelf of Bulgaria. The tool consists of two main functions, written in Matlab v.5.3, requiring Matlab's SPLINE and STATISTICS toolkits. r
Harmonic splines (HS) are global basis functions concentrated in localised regions that can be us... more Harmonic splines (HS) are global basis functions concentrated in localised regions that can be used to model geopotential data without loss of resolution. Here, we apply HS modelling to produce a global model of the Earth's lithospheric anomaly field from satellite data. Shure et al. (1982) developed a minimum norm algorithm applicable to global datasets, which involves solving a data-by-data
Euler deconvolution of magnetic anomalies over basaltic bodies along the Suhindol-Svishtov line i... more Euler deconvolution of magnetic anomalies over basaltic bodies along the Suhindol-Svishtov line in Northern Bulgaria was implemented. Original algorithms and programs for 3D Euler deconvolution using differential similarity transformations of the magnetic field was applied. This allowed simultaneous estimation of the singular point coordinates and the structural index, without requiring input data about the magnetization vector and the shape of the causative bodies. Thus, estimates of the depth range and the main features of the morphology of a number of basaltic bodies along the line of the paleovulcanic centers and their periphery were obtained. Most of the sources are vertical pipelike intrusions (volcanic necks) to the south and lenticular bodies to the north and along the periphery. The depth range of the massive bodies varies from several hundred meters to two kilometers.
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Papers by Daniela Gerovska