DNA damage in mammalian cells and its relevance to lethality

From fourth symposium on microdosimetry; Pallanza, Italy (24 Sep 1973). Cell killing (loss of proliferative capacity) is a principal end point in all radiation effects contingent upon cell viability. DNA, the molecular carrier of the genetic inheritance, affects the affairs of a cell because the properties and characteristics of a cell are dictated by the DNA -- RNA -- protein axis of information storage, flow, and expression. Thus, the mutagenic and chromosome- breaking properties of radiation, the biological amplification available to a lesion in DNA, and the fact that DNA molecularly constitutes a very large radiation target, aH make DNA the principal target relative to many radiation effects. An indirect approach may be useful in studies of the sensitive targets in a mammalian cell. This stems from the fact that to kill cells with low LET radiation; sublethal damage must be accumulated and cells can repair this damage. Thus, focussing on DNA, and repair processes in DNA, while indirect, is supporied in the instance of cell killing by extensive experimental evidence. The status of damage registered directly in DNA may be assessed by examining changes in the sedimentation of DNA from irradiated cells. Along with measurements of cell survival, sedimentation data are discussed relative to their bearing on cell killing and their ability to help us understand the organization and replication of DNA in mammalian cells. (CH

Heat-induced changes in soil water-extractable organic matter characterized using fluorescence and FTIR spectroscopies coupled with dimensionality reduction methods

[Abstract:] Water extractable organic matter (WEOM) is a very mobile and reactive soil OM fraction, critical in the translocation of carbon (C) from soils to other environmental compartments. Transformations of WEOM due to soil heating can have implications not only at a local scale, but in places far away from the location of the event. However, their accurate characterization is costly when analyzing a large number of samples. The objectives of this work were to identify common patterns for the changes in WEOM caused by the heating of various soil types using a combination of spectroscopic and dimensionality reduction techniques. Six soils from Spain, Kenya and Israel were collected at depths 0–10 cm and analysed before and after heating in air to temperatures of 300 and 600 °C. Fluorescence EEMs were measured in soil–water extracts containing WEOM, and decomposed using parallel factor (PARAFAC) analysis. The FTIR spectra were measured in freeze-dried extracts and further analysed using non-negative matrix factorization (NMF). Total organic C and SUVA254 values of the extracts experienced changes with the heating treatments that were soil dependant. Four PARAFAC and three NMF components were sufficient to characterize WEOM changes in all soils, which showed common thermal transformation patterns irrespective of their origin and properties. Thermal transformation of fluorescent WEOM led to the increase in the proportion of a component with an emission maximum at Ex 300/Em 392 nm, and to a lower extent one with the emission maximum at Ex 300/Em 426 nm. Concomitantly, the proportion of components with emission maxima at longer excitation wavelengths was reduced. These changes occurred at the lowest heating temperature and were maintained at 600 °C, and they seem to indicate a depletion of fluorescent components more conjugated, bigger in size, and an enrichment in smaller ones. The NMF components obtained from FTIR spectra showed an increase of the proportion of compounds with Csingle bondO bonds, more oxidized. No correlations were found between the components obtained with each method, thus indicating that the information obtained from the fluorescence EEMs-PARAFAC analysis and the NMF decomposition of FTIR spectra is complementary. It can be concluded that there is a common pattern of WEOM changes induced by thermal soil transformations irrespective of the origin and properties of the soils studied, and that the combination of different spectroscopic techniques coupled with dimensionality reduction methods can be used as a simple and low-cost method to fingerprint changes in WEOM composition, in general, and those caused by soil heating, in particular

Directed avalanche processes with underlying interface dynamics

We describe a directed avalanche model; a slowly unloading sandbox driven by lowering a retaining wall. The directness of the dynamics allows us to interpret the stable sand surfaces as world sheets of fluctuating interfaces in one lower dimension. In our specific case, the interface growth dynamics belongs to the Kardar-Parisi-Zhang (KPZ) universality class. We formulate relations between the critical exponents of the various avalanche distributions and those of the roughness of the growing interface. The nonlinear nature of the underlying KPZ dynamics provides a nontrivial test of such generic exponent relations. The numerical values of the avalanche exponents are close to the conventional KPZ values, but differ sufficiently to warrant a detailed study of whether avalanche correlated Monte Carlo sampling changes the scaling exponents of KPZ interfaces. We demonstrate that the exponents remain unchanged, but that the traces left on the surface by previous avalanches give rise to unusually strong finite-size corrections to scaling. This type of slow convergence seems intrinsic to avalanche dynamics.Comment: 13 pages, 13 figure

An Interface View of Directed Sandpile Dynamics

We present a directed unloading sand box type avalanche model, driven by slowly lowering the retaining wall at the bottom of the slope. The avalanche propagation in the two dimensional surface is related to the space-time configurations of one dimensional Kardar-Parisi-Zhang (KPZ) type interface growth dynamics. We express the scaling exponents for the avalanche cluster distributions into that framework. The numerical results agree closely with KPZ scaling, but not perfectly.Comment: 4 pages including 5 figure

A two-step learning approach for solving full and almost full cold start problems in dyadic prediction

Dyadic prediction methods operate on pairs of objects (dyads), aiming to infer labels for out-of-sample dyads. We consider the full and almost full cold start problem in dyadic prediction, a setting that occurs when both objects in an out-of-sample dyad have not been observed during training, or if one of them has been observed, but very few times. A popular approach for addressing this problem is to train a model that makes predictions based on a pairwise feature representation of the dyads, or, in case of kernel methods, based on a tensor product pairwise kernel. As an alternative to such a kernel approach, we introduce a novel two-step learning algorithm that borrows ideas from the fields of pairwise learning and spectral filtering. We show theoretically that the two-step method is very closely related to the tensor product kernel approach, and experimentally that it yields a slightly better predictive performance. Moreover, unlike existing tensor product kernel methods, the two-step method allows closed-form solutions for training and parameter selection via cross-validation estimates both in the full and almost full cold start settings, making the approach much more efficient and straightforward to implement

Scale-free energy dissipation and dynamic phase transition in stochastic sandpiles

We study numerically scaling properties of the distribution of cumulative energy dissipated in an avalanche and the dynamic phase transition in a stochastic directed cellular automaton [B. Tadi\'c and D. Dhar, Phys. Rev. Lett. {\bf 79}, 1519 (1997)] in d=1+1 dimensions. In the critical steady state occurring for the probability of toppling $p\ge p^\star$= 0.70548, the dissipated energy distribution exhibits scaling behavior with new scaling exponents $\tau_E$ and D_E for slope and cut-off energy, respectively, indicating that the sandpile surface is a fractal. In contrast to avalanche exponents, the energy exponents appear to be p- dependent in the region $p^\star \le p <1$, however the product $(\tau_E-1)D_E$ remains universal. We estimate the roughness exponent of the transverse section of the pile as $\chi =0.44\pm 0.04$. Critical exponents characterizing the dynamic phase transition at $p^\star$ are obtained by direct simulation and scaling analysis of the survival probability distribution and the average outflow current. The transition belongs to a new universality class with the critical exponents $\nu_\| =\gamma =1.22 \pm 0.02$, $\beta =0.56\pm 0.02$ and $\nu_\bot = 0.761 \pm 0.029$, with apparent violation of hyperscaling. Generalized hyperscaling relation leads to $\beta + \beta ^\prime = (d-1)\nu_\bot$, where $\beta ^\prime = 0.195 \pm 0.012$ is the exponent governed by the ultimate survival probability

Generic Sandpile Models Have Directed Percolation Exponents

We study sandpile models with stochastic toppling rules and having sticky grains so that with a non-zero probability no toppling occurs, even if the local height of pile exceeds the threshold value. Dissipation is introduced by adding a small probability of particle loss at each toppling. Generically, for models with a preferred direction, the avalanche exponents are those of critical directed percolation clusters. For undirected models, avalanche exponents are those of directed percolation clusters in one higher dimension.Comment: 4 pages, 4 figures, minor change

Local Moment Formation in the Periodic Anderson Model with Superconducting Correlations

We study local moment formation in the presence of superconducting correlations among the f-electrons in the periodic Anderson model. Local moments form if the Coulomb interaction U>U_cr. We find that U_cr is considerably stronger in the presence of superconducting correlations than in the non-superconducting system. Our study is done for various values of the f-level energy and electronic density. The smallest critical U_cr values occur for the case where the number of f- electrons per site is equal to one. In the presence of d-wave superconducting correlations we find that local moment formation presents a quantum phase transition as function of pressure. This quantum phase transition separates a region where local moments and d-wave superconductivity coexist from another region characterized by a superconducting ground state with no local moments. We discuss the possible relevance of these results to experimental studies of the competition between magnetic order and superconductivity in CeCu_2Si_2.Comment: 4 pages. accepted for publication in Phys. Rev.

Crossover phenomenon in self-organized critical sandpile models

We consider a stochastic sandpile where the sand-grains of unstable sites are randomly distributed to the nearest neighbors. Increasing the value of the threshold condition the stochastic character of the distribution is lost and a crossover to the scaling behavior of a different sandpile model takes place where the sand-grains are equally transferred to the nearest neighbors. The crossover behavior is numerically analyzed in detail, especially we consider the exponents which determine the scaling behavior.Comment: 6 pages, 9 figures, accepted for publication in Physical Review