Efficiency of nonhomologous DNA end joining varies among somatic tissues, despite similarity in mechanism

Failure to repair DNA double-strand breaks (DSBs) can lead to cell death or cancer. Although nonhomologous end joining (NHEJ) has been studied extensively in mammals, little is known about it in primary tissues. Using oligomeric DNA mimicking endogenous DSBs, NHEJ in cell-free extracts of rat tissues were studied. Results show that efficiency of NHEJ is highest in lungs compared to other somatic tissues. DSBs with compatible and blunt ends joined without modifications, while noncompatible ends joined with minimal alterations in lungs and testes. Thymus exhibited elevated joining, followed by brain and spleen, which could be correlated with NHEJ gene expression. However, NHEJ efficiency was poor in terminally differentiated organs like heart, kidney and liver. Strikingly, NHEJ junctions from these tissues also showed extensive deletions and insertions. Hence, for the first time, we show that despite mode of joining being generally comparable, efficiency of NHEJ varies among primary tissues of mammals.

Identification of Local Conformational Similarity in Structurally Variable Regions of Homologous Proteins Using Protein Blocks

Structure comparison tools can be used to align related protein structures to identify structurally conserved and variable regions and to infer functional and evolutionary relationships. While the conserved regions often superimpose well, the variable regions appear non superimposable. Differences in homologous protein structures are thought to be due to evolutionary plasticity to accommodate diverged sequences during evolution. One of the kinds of differences between 3-D structures of homologous proteins is rigid body displacement. A glaring example is not well superimposed equivalent regions of homologous proteins corresponding to a-helical conformation with different spatial orientations. In a rigid body superimposition, these regions would appear variable although they may contain local similarity. Also, due to high spatial deviation in the variable region, one-to-one correspondence at the residue level cannot be determined accurately. Another kind of difference is conformational variability and the most common example is topologically equivalent loops of two homologues but with different conformations. In the current study, we present a refined view of the ``structurally variable'' regions which may contain local similarity obscured in global alignment of homologous protein structures. As structural alphabet is able to describe local structures of proteins precisely through Protein Blocks approach, conformational similarity has been identified in a substantial number of `variable' regions in a large data set of protein structural alignments; optimal residue-residue equivalences could be achieved on the basis of Protein Blocks which led to improved local alignments. Also, through an example, we have demonstrated how the additional information on local backbone structures through protein blocks can aid in comparative modeling of a loop region. In addition, understanding on sequence-structure relationships can be enhanced through our approach. This has been illustrated through examples where the equivalent regions in homologous protein structures share sequence similarity to varied extent but do not preserve local structure.

Phase relations and gibbs energies in the system Mn-Rh-O

Phase relations in the system Mn-Rh-O are established at 1273 K by equilibrating different compositions either in evacuated quartz ampules or in pure oxygen at a pressure of 1.01 x 10(5) Pa. The quenched samples are examined by optical microscopy, X-ray diffraction, and energy-dispersive X-ray analysis (EDAX). The alloys and intermetallics in the binary Mn-Rh system are found to be in equilibrium with MnO. There is only one ternary compound, MnRh2O4, with normal spinel structure in the system. The compound Mn3O4 has a tetragonal structure at 1273 K. A solid solution is formed between MnRh2O4 and Mn3O4. The solid solution has the cubic structure over a large range of composition and coexists with metallic rhodium. The partial pressure of oxygen corresponding to this two-phase equilibrium is measured as a function of the composition of the spinel solid solution and temperature. A new solid-state cell, with three separate electrode compartments, is designed to measure accurately the chemical potential of oxygen in the two-phase mixture, Rh + Mn3-2xRh2xO4, which has 1 degree of freedom at constant temperature. From the electromotive force (emf), thermodynamic mixing properties of the Mn3O4-MnRh2O4 solid solution and Gibbs energy of formation of MnRh2O4 are deduced. The activities exhibit negative deviations from Raoult's law for most of the composition range, except near Mn3O4, where a two-phase region exists. In the cubic phase, the entropy of mixing of the two Rh3+ and Mn3+ ions on the octahedral site of the spinel is ideal, and the enthalpy of mixing is positive and symmetric with respect to composition. For the formation of the spinel (sp) from component oxides with rock salt (rs) and orthorhombic (orth) structures according to the reaction, MnO (rs) + Rh2O3 (orth) --> MnRh2O4 (sp), DELTAG-degrees = -49,680 + 1.56T (+/-500) J mol-1. The oxygen potentials corresponding to MnO + Mn3O4 and Rh + Rh2O3 equilibria are also obtained from potentiometric measurements on galvanic cells incorporating yttria-stabilized zirconia as the solid electrolyte. From these results, an oxygen potential diagram for the ternary system is developed.

Phase-relations in the system CAO-SIO2-ZRO2 AT 1573-K

Zirconia-based solid electrolytes with zircon (ZrSiO4) as the auxiliary electrode have been suggested of sensing silicon concentrations in iron and steel melts. A knowledge of phase relations in the ternary system MO-SiO2-ZrO2 (M = Ca, Mg) is useful for selecting an appropriate auxiliary electrode. In this investigation, an isothermal section for the phase diagram of the system CaO-SiO2ZrO2 at 1573 K has been established by equilibrating mixtures of component oxides in air, followed by quenching and phase identification by optical miroscopy, energy disperse analysis of X-rays (EDAX) and X-ray diffraction analysis (XRD). The equilibrium phase relations have also been confirmed by computation using the available thermodynamic data on condensed phases in the system. The results indicate that zircon is not in thermodynamic equilibrium with calcia-stabilized zirconia or calcium zirconate. The silica containing phase in equilibrium with stabilized zirconia is Ca3ZrSi2O9. Calcium zirconate can coexist with Ca3ZrSi2O9 and Ca2SiO4.

Phase relations in the system Cu─Ho─O and stability of Cu2Ho2O5

The phase relations in the system Cu-Ho-O have been determined at 1300 K using X-ray diffraction, optical microscopy, and electron microprobe analysis of samples equilibrated in evacuated quartz ampules and in pure oxygen. Only one ternary compound, Cu2Ho2O5, was found to be stable. The Gibbs free energy of formation of this compound has been measured using the solid-state cell Pt,Cu2O + Cu2Ho2O5 + Ho2O3/(Y2O3)ZrO2/CuO + Cu2O,Pt in the temperature range of 973 to 1350 K. For the formation of Cu2Ho2O5 from its binary component oxides, 2CuO(s) + Ho2O3(S) --> Cu2Ho2O5(s) DELTAG-degrees = 11190 - 13.8T(+/- 120) J-mol-1 Since the formation is endothermic, CU2Ho2O5 becomes thermodynamically unstable with respect to CuO and Ho2O3 below 810 K. When the oxygen partial pressure over Cu2Ho2O5 is lowered, it decomposes according to the reaction 2Cu2Ho2O5(s) --> 2Ho2O3(s) + 2Cu2O(S) + O2(g) for which the equilibrium oxygen potential is given by DELTAmu(O2) = - 238510 + 160.2T(+/- 450) J.mol-1 The decomposition temperature at an oxygen partial pressure of 1.52 x 10(4) Pa was measured using a combined DTA-TGA apparatus. Based on these results, an oxygen potential diagram for the system Cu-Ho-O at 1300 K is presented.

Stress-state-permeability relations for overconsolidated clays

Analysis of experimental data of soils in both the normally consolidated and overconsolidated states reveal that the proposed relationships are tenable. Preconsolidation stress level influences the level of permeability.

Phase Relations in the System La-Rh-O and Thermodynamic Properties of LaRhO3

Phase relations in the system La-Rh-O at 1223 Ii have been determined by examination of equilibrated samples by optical and scanning electron microscopy, powder X-ray diffraction (XRD), and energy-dispersive analysis of X-rays (EDAX). Only one ternary oxide, LaRhO3, with distorted orthorhombic perovskite structure (Pbnm, a = 0.5525, b = 0.5680, and c = 0.7901 nm) was identified. The alloys and intermetallics along the La-Rh binary are in equilibrium with La2O3. The thermodynamic properties of LaRhO3 were determined in the temperature range 890 to 1310 K, using a solid-state cell incorporating yttria-stabilized zirconia as the electrolyte. A new four-compartment design of the emf cell was used to enhance the accuracy of measurement. For the reaction 1/2La(2)O(3) + 1/2Rh(2)O(3) --> LaRhO3, Delta G degrees = - 70 780 + 4.89T (+/- 90) J.mol(-1) The compound decomposes on heating to a mixture of La2O3, Ph and O-2. The calculated decomposition temperatures are 1843 (+/- 5) K in pure O-2 and 1728 (+/- 5) K in air at a pressure of 1.01 x 10(5) Pa. The phase diagrams for the system La-Rh-O at different partial pressures of oxygen are calculated from the thermodynamic information.

Metastable phase relations and europium(II) luminescence of barium hexa-aluminates prepared by gel to crystallite conversion

Wet chemical reaction of hydrated alumina gels, Al2O3.yH(2)O(80relations in Ba-hexa-aluminates can be attributed to preparative route dependent metastability.

Similarity solution of unsteady boundary layer equations with a magnetic field

The unsteady laminar incompressible boundary layer flow of an electrically conducting fluid in the stagnation region of two-dimensional and axisymmetric bodies with an applied magnetic field has been studied. The boundary layer equations which are parabolic partial differential equations with three independent variables have been reduced to a system of ordinary differential equations by using suitable transformations and then solved numerically using a shooting method. Here, we have obtained new solutions which are solutions of both the boundary layer and Navier-Stokes equations.

Efficient algorithms for learning kernels from multiple similarity matrices with general convex loss functions

In this paper we consider the problem of learning an n × n kernel matrix from m(1) similarity matrices under general convex loss. Past research have extensively studied the m = 1 case and have derived several algorithms which require sophisticated techniques like ACCP, SOCP, etc. The existing algorithms do not apply if one uses arbitrary losses and often can not handle m > 1 case. We present several provably convergent iterative algorithms, where each iteration requires either an SVM or a Multiple Kernel Learning (MKL) solver for m > 1 case. One of the major contributions of the paper is to extend the well knownMirror Descent(MD) framework to handle Cartesian product of psd matrices. This novel extension leads to an algorithm, called EMKL, which solves the problem in O(m2 log n 2) iterations; in each iteration one solves an MKL involving m kernels and m eigen-decomposition of n × n matrices. By suitably defining a restriction on the objective function, a faster version of EMKL is proposed, called REKL,which avoids the eigen-decomposition. An alternative to both EMKL and REKL is also suggested which requires only an SVMsolver. Experimental results on real world protein data set involving several similarity matrices illustrate the efficacy of the proposed algorithms.

Phase relations in the Fe Ni Cr S system and the sulfidation of an austenitic stainless steel

The stability fields of various sulfide phases that form on Fe-Cr, Fe-Ni, Ni-Cr, and Fe-Cr-Ni alloys have been developed as a function of temperature and the partial pressure of sulfur. The calculated stability fields in the ternary A-B-S system are displayed on plots of log \textpS2 pS2 vs. the conjugate extensive variable (nA/nA–nB), which provides a better framework for following the sulfidation of Fe-Cr-Ni alloys at high temperatures. Experimental and estimated thermodynamic data were used in developing the sulfur potential diagrams. Current models and correlations were employed to estimate the unknown thermodynamic behavior of solid solutions of sulfides and to supplement the incomplete phase-diagram data of geophysical literature. These constructed stability field diagrams are in excellent agreement with the sulfide phases and compositions determined experimentally during the sulfidation of SAE 310 stainless steel. The sulfur potential plots appear to be very useful in predicting and correlating the sulfidation of commercial alloys.

Phase relations and activities in the Co Ni O system at 1373 K

The tie-lines delineating equilibria between CoO-NiO and Co-Ni solid solutions in the ternary Co-Ni-O system at 1373 K have been determined by electron microprobe andedax point count analysis of the oxide phase equilibrated with the alloy. The oxygen potentials corresponding to the tie-line compositions have been measured using a solid oxide galvanic cell with calcia-stabilized zirconia electrolyte and Ni + NiO reference electrode. Activities in the metallic and oxide solid solution have been derived using a new Gibbs-Duhem integration technique. Both phases exhibit small positive deviations from ideality; the values ofG E/X 1 X 2 are 2640 J mol−1 for the metallic phase and 2870 J mol−1 for the oxide solid solution.

Gibbs energy of formation of CuCrO4 and phase relations in the system Cu-Cr-O below 735 K

A solid state galvanic cell incorporating yttria-stabilized zirconia electrolyte and ruthenium(IV) oxide electrodes has been used to measure the equilibrium chemical potential of oxygen corresponding to the decomposition of CuCrO4 in the range 590–760 K. For the reaction CuO(tenorite) + CuCr2O4(spinel) + 1.5O2(g)→2CuCrO4(orth), ΔGXXX = −183540 + 249.6T(±900) J mol−1. The decomposition temperature of CuCrO4 in pure oxygen at a pressure of 1.01 × 105 Pa is 735(±1) K. By combining the results obtained in this study with data on the Gibbs energy of formation of CuCr2O4 and CuCrO2 reported earlier, the standard Gibbs energy of formation of CuCrO4 and the phase relations in the system Cu-Cr-O at temperatures below 735 K have been deduced. Electron microscopic studies have indicated that the decomposition of CuCrO4 to CuCr2O4 is topotactic.