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The crystal structures for the three perovskites, CaSnO(3), YAlO(3), and LaAlO(3), were geometry optimized at the density functional theory level for a wide range of simulated isotropic pressures up to 80 GPa. The connections between the geometry optimized bond lengths, R(M-O), the values of the electron density, ρ(r(c)), the local kinetic, G(r(c)), potential, V(r(c)), energy densities, H(r(c)), and the Laplacian, ∇(2)(r(c)), at the bond critical points, r(c), for the M-O nonequivalent bonded interactions were examined. With increasing pressure, ρ(r(c)) increases along four distinct trends when plotted in terms of the Al-O, Ca-O, Sn-O, Y-O, and La-O bond lengths, but when the bond lengths were plotted in terms of ρ(r(c))/r where r is the periodic table row number of the M atoms, the data scatter along a single trend modeled by the power law regression expression R(M-O) = 1.41(ρ(r(c))/r)(-0.21), an expression that is comparable with that obtained for the bonded interactions for a large number of silicate and oxides crystals, R(M-O) = 1.46(ρ(r(c))/r)(-0.19) and that obtained for a relatively large number of hydroxyacid molecules R(M-O) = 1.39(s/r)(-0.22) where s is the Pauling bond strength of a bonded interaction. The similarity of the expressions determined for the perovskites, silicate and oxides crystals, and hydroxyacid molecules suggest that the bonded interactions in molecules and crystal are not only similar and comparable. The close correspondence of the expressions for the perovskites, the silicate and oxide crystals, and the molecules indicates that Pauling bond strength and ρ(r(c)) are comparable measures of the bonded interactions, the larger the accumulation of the electron density between the bonded atoms the larger the value of s, the shorter the bond lengths. It also indicates that the bonded interactions that govern the bond length variations behave as if largely short ranged. Like ρ(r(c))/r, the values of G(r(c))/r, V(r(c))/r, ∇(2)(r(c))/r likewise correlate in terms of R(M-O) in a single trend. With increasing pressure, the value of V(r(c)) decreases at a faster rate than G(r(c)) increases consistent with the observation that ρ(r(c)) increases with increasing pressure thereby stabilizing the structures at high pressures. As evinced by the well-developed power law trends between R(M-O) and the bond critical point properties, the bulk of the bonded interactions for the perovskites are concluded to change progressively from closed-shell to intermediate polar covalent interactions with increasing pressure. A well-developed trend between the ratios ∣V(r(c))∣ /G(r(c)) and H(r(c))/ρ(r(c)) is consistent with this conclusion. The employment of a positive value for the Laplacian alone in distinguishing between closed shell and polar covalent bonded interactions is unsatisfactory when 2G(r(c)) > ∣V(r(c))∣ > G(r(c)).

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PURPOSE: To describe an efficient method for verifying the size and centering of the radiation field from the Cyberknife IRIS variable collimator with sub-millimeter accuracy using a general purpose commercially available diode array. METHODS: We present a technique using a conventional diode array (Sun Nuclear Profiler) with the array at an extended distance of 320 cm. The projection of the 4 mm diode spacing back to the 80 cm field definition distance gives an effective spacing of 1 mm, sufficient to confirm proper operation of the IRIS. We describe the data acquisition process and present data comparing the Profiler measurements to scanned measurements for both profile and FWHM analysis and reproducibility of the technique over repeated measurements. RESULTS: Average difference between original water scanner measurements and diode array measurements over the 12 aperture sizes) from 5 mm to 60 mm) were - 0.14 mm (range 0.03 mm to 0.83 mm). Reproducibility and centering measurements had a similar range of accuracy. CONCLUSIONS: A general purpose commercially available diode array can be used to quickly and accurately characterize the field size and centering of the Cyberknife IRIS variable collimator system with sub-millimeter accuracy subsequent to service, software recalibration, software upgrades or associated with routine QA. This technique avoids the time consuming and cumbersome water tank scanning with a diode and the difficulties associated with image based measurements (CR or radiochromic film) that require time consuming and careful calibration and choice of threshold values.

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An understanding of the role played by intermolecular forces in terms of the electron density distribution is fundamental to the understanding of the self-assembly of molecules in the formation of a molecular crystal. Using ab initio methods capable of describing both short-range intramolecular interactions and long-range London dispersion interactions arising from electron correlation, analyses of inorganic dimers of As(4)S(4) and As(4)O(6) molecules cut from the structures of realgar and arsenolite, respectively, reveal that the molecules adopt a configuration that closely matches that observed for the crystal. Decomposition of the interaction energies using symmetry-adapted perturbation theory reveals that both model dimers feature significant stabilization from electrostatic forces as anticipated by a Lewis acid/Lewis base picture of the interaction. London dispersion forces also contribute significantly to the interaction, although they play a greater role in the realgar structure near equilibrium than in arsenolite.

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The calculated electron density distribution for orpiment, As(2)S(3), reveals that As-S, S-S, and As-As bond paths are associated with the experimental interlayer directed bonded interactions detected in a combined infrared and Raman study. The successful modeling of the infrared- and Raman-determined interlayer bonded interactions together with bond paths and the structuralization of a variety of inorganic molecules in terms of "key-lock" bond path mainstays support the argument that van der Waals forces in inorganic molecular crystals are directional.

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Previous studies show the demineralization of biogenic, amorphous, and crystalline forms of silica is enhanced in the presence of alkali and alkaline earth cations. The origins of this effect are difficult to explain in light of work suggesting predominantly weak outer-sphere type interactions between these ions and silica. Here we investigate the ability of M(II) aqua ions to promote the hydrolysis of Si-O bonded interactions relative to ion-free water using electronic structure methods. Reaction pathways for Si-O hydrolysis are calculated with the B3LYP and PBE1PBE density functionals at the 6-31G(d) and 6-311+G(d,p) levels in the presence of water, and both inner- and outer-sphere adsorption complexes of Mg(2+)(6H(2)O) and Ca(2+)(6H(2)O). All reaction trajectories involving hydrated ions are characterized by one or more surmountable barriers associated with the rearrangement of ion-associated water molecules, and a single formidable barrier corresponding to hydrolysis of the Si-O bonded interaction. The hydrolysis step for outer-sphere adsorption is slightly less favorable than the water-induced reaction. In contrast, the barrier opposing Si-O hydrolysis in the presence of inner-sphere species is generally reduced relative to the water-induced pathway, indicating that the formation of inner-sphere complexes may be prerequisite to the detachment of Si species from highly coordinated surface sites. The results suggest a two-part physical model for ion-promoted Si-O hydrolysis that is consistent with experimental rate measurements. First, a bond path is formed between the cation and a bridging oxygen site on the silica surface that weakens the surrounding Si-O interactions, making them more susceptible to attack by water. Second, Si-O hydrolysis occurs adjacent to these inner-sphere species in proportion to the frequency of ion-associated solvent reorganization events. Both processes are dependent upon the particular ion hydration environment, which suggests measured cation-specific demineralization rates arise from differential barriers opposing reorganization of ion-associated solvent molecules at the silica-water interface.

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OBJECTIVES: To estimate the exposure-response function associating polycyclic aromatic hydrocarbon (PAH) exposure and lung cancer, with consideration of smoking. METHODS: Mortality, occupational exposure and smoking histories were ascertained for a cohort of 16,431 persons (15,703 men and 728 women) who had worked in one of four aluminium smelters in Quebec from 1950 to 1999. A variety of exposure-response functions were fitted to the cohort data using generalised relative risk models. RESULTS: In 677 lung cancer cases there was a clear trend of increasing risk with increasing cumulative exposure to PAH measured as benzo(a)pyrene (BaP). A linear model predicted a relative risk of 1.35 (95% CI 1.22 to 1.51) at 100 microg/m(-3) BaP years, but there was a significant departure from linearity in the direction of decreasing slope with increasing exposures. Among the models tried, the best fitting were a two-knot cubic spline and a power curve (RR = (1+bx)(p)), the latter predicting a relative risk of 2.68 at 100 microg/m(-3) BaP years. Additive models and multiplicative models for combining risks from occupational PAH and smoking fitted almost equally well, with a slight advantage to the additive. CONCLUSION: Despite the large cohort with long follow-up, the shape of the exposure-response function and the mode of combination of risks due to occupational PAH and smoking remains uncertain. If a linear exposure-response function is assumed, the estimated slope is broadly in line with the estimate from a previous follow-up of the same cohort, and somewhat higher than the average found in a recent meta-analysis of lung cancer studies.

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Bond paths, local energy density properties, and Laplacian, L(r) = -wedge(2)rho(r), composite isosurfaces of the electron density distributions were calculated for the intramolecular and intermolecular bonded interactions for molecular solids of As(2)O(3) and AsO(2) composition, an As(2)O(5) crystal, a number of arsenate molecules, and the arsenic metalloid, arsenolamprite. The directed intermolecular van der Waals As-O, O-O, and As-As bonded interactions are believed to serve as mainstays between the individual molecules in each of the molecular solids. As-O bond paths between the bonded atoms connect Lewis base charge concentrations and Lewis acid charge depletion domains, whereas the O-O and As-As paths connect Lewis base pair and Lewis acid pair domains, respectively, giving rise to sets of intermolecular directed bond paths. The alignment of the directed bond paths results in the periodic structures adopted by the arsenates. The arrangements of the As atoms in the claudetite polymorphs of As(2)O(3) and the As atoms in arsenolamprite are similar. Like the As(2)O(3) polymorphs, arsenolamprite is a molecular solid connected by relatively weak As-As intermolecular directed van der Waals bond paths between the layers of stronger As-As intramolecular bonded interactions. The bond critical point and local energy density properties of the intermolecular As-As bonded interactions in arsenolamprite are comparable with the As-As interactions in claudetite I. As such, the structure of claudetite I can be viewed as a stuffed derivative of the arsenolamprite structure with O atoms between pairs of As atoms comprising the layers of the structure. The cubic structure adopted by the arsenolite polymorph can be understood in terms of sets of directed acid-base As-O and base-base O-O pair domains and bond paths that radiate from the tetrahedral faces of its constituent molecules, serving as face-to-face key-lock mainstays in forming a periodic tetrahedral array of molecules rather than one based on some variant of close packing. The relatively dense structure and the corrugation of the layers in claudetite I can also be understood in terms of directed van der Waals As-O bonded interactions. Our study not only provides a new basis for understanding the crystal chemistry and the structures of the arsenates, but it also calls for a reappraisal of the concept of van der Waals bonded interactions, how the structures of molecular solids are viewed, and how the molecules in these solids are bonded in a periodic structure.

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Bond critical point (bcp) and local energy density properties for the electron density (ED) distributions, calculated with first-principle quantum mechanical methods for divalent transition metal Mn-, Co-, and Fe-containing silicates and oxides are compared with experimental model ED properties for tephroite, Mn 2SiO 4, fayalite, Fe 2SiO 4, and Co 2SiO 4 olivine, each determined with high-energy synchrotron single-crystal X-ray diffraction data. Trends between the experimental bond lengths, R(M-O), (M = Mn, Fe, Co), and the calculated bcp properties are comparable with those observed for non-transition M-O bonded interactions. The bcp properties, local total energy density, H( r c), and bond length trends determined for the Mn-O, Co-O, and Fe-O interactions are also comparable. A comparison is also made with model experimental bcp properties determined for several Mn-O, Fe-O, and Co-O bonded interactions for selected organometallic complexes and several oxides. Despite the complexities of the structures of the organometallic complexes, the agreement between the calculated and model experimental bcp properties is fair to good in several cases. The G( r c)/rho( r c) versus R(M-O) trends established for non-transition metal M-O bonded interactions hold for the transition metal M-O bonded interactions with G( r c)/rho( r c) increasing in value as H( r c) becomes progressively more negative in value, indicating an increasing shared character of the interaction as G( r c)/rho( r c) increases in value. As observed for the non-transition metal M-O bonded interactions, the Laplacian, nabla (2)rho( r c), increases in value as rho( r c) increases and as H( r c) decreases and becomes progressive more negative in value. The Mn-O, Fe-O, and Co-O bonded interactions are indicated to be of intermediate character with a substantial component of closed-shell character compared with Fe-S and Ni-S bonded interactions, which show greater shared character based on the | V( r c)|/ G( r c) bond character indicator. The atomic charges conferred on the transition metal atoms for the three olivines decrease with increasing atomic number from Mn to Fe to Co as the average M-O bond lengths decrease from 2.219 to 2.168 to 2.128 A, respectively.

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BACKGROUND: Cysteine-rich secretory protein 2 (CRISP2) is localized to the human sperm acrosome and tail. It can regulate ryanodine receptors Ca(2+) gating and binds to mitogen-activated protein kinase kinase kinase 11 in the acrosome and gametogenetin 1 (GGN1) in the tail. METHODS AND RESULTS: In order to test the hypothesis that CRISP2 variations contribute to male infertility, we screened coding and flanking intronic regions in 92 infertile men with asthenozoo- and/or teratozoospermia and 176 control men using denaturing HPLC and sequencing. There were 21 polymorphisms identified, including 13 unreported variations. Three SNPs resulted in amino acid substitutions: L59V, M176I and C196R. All were only present in a heterozygous state and found in fertile men. However, the C196R polymorphism was of particular interest as it resulted in the loss of a strictly conserved cysteine involved in intramolecular disulphide bonding. Screening of an additional 637 infertile men identified 23 heterozygous C196R men to give an overall frequency of 3.6%, compared with 3.4% in control men. The functional significance of the C196R polymorphism was defined using a yeast two-hybrid assay. The C196R substitution resulted in the loss of CRISP2-GGN1 binding. CONCLUSIONS: Although none of the many polymorphisms identified herein showed a significant association with male infertility, functional studies suggested that the C196R polymorphism may compromise CRISP2 function.

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Bond paths of maximum electron density spanning O-O edges shared between equivalent or quasiequivalent MOn (n > 4) coordination polyhedra are not uncommon electron density features displayed by silicates. On the basis of the positive values for the local electronic energy density, H(rc), at the bond critical points, rc, they qualify as weak "closed-shell" interactions. As observed for M-O bonded interactions (M = first and second row metal atoms), the electron density, rho(rc), and the Laplacian of the electron density increase in a regular way as the separation between the O atoms, R(O-O), decreases. A simple model, based on R(O-O) and the distances of the Si atoms from the midpoint between adjacent pairs of O atoms, partitions the O-O bond paths in the high-pressure silica polymorph coesite into two largely disjoint domains, one with and one without bond paths. The occurrence of O-O bond paths shared in common between equivalent coordination polyhedra suggests that they may be grounded in some cases on factors other than bonded interactions, particularly since they are often displayed by inert procrystal representations of the electron density. In these cases, it can be argued that the accumulation of the electron density along the paths has its origin, at least in part, in the superposition of the peripheral electron density distributions of the metal M atoms occupying the edge-sharing polyhedra. On the other hand, the accumulation of electron density along the paths may stabilize a structure by shielding the adjacent M atoms in the edge-sharing polyhedra. For closed-shell Li-O, Na-O, and Mg-O interactions, H(rc) is positive and increases as the value of rho(rc) increases, unlike the "shared" Be-O, B-O, C-O, Al-O, Si-O, P-O, and S-O interactions, where H(rc) is negative and decreases as rho(rc) increases. The H(rc) values for the weak closed-shell O-O interactions also increase as rho(rc) increases, as observed for the closed-shell M-O interactions. On the basis of the bond critical point properties and the negative H(rc) value, the O-O interaction comprising the O2 molecule in silica III qualifies as a shared interaction.

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Bond critical point and local energy density properties together with net atomic charges were calculated for theoretical electron density distributions, rho(r), generated for a variety of Fe and Cu metal-sulfide materials with high- and low-spin Fe atoms in octahedral coordination and high-spin Fe atoms in tetrahedral coordination. The electron density, rho(rc), the Laplacian, triangle down2rho(rc), the local kinetic energy, G(rc), and the oxidation state of Fe increase as the local potential energy density, V(rc), the Fe-S bond lengths, and the coordination numbers of the Fe atoms decrease. The properties of the bonded interactions for the octahedrally coordinated low-spin Fe atoms for pyrite and marcasite are distinct from those for high-spin Fe atoms for troilite, smythite, and greigite. The Fe-S bond lengths are shorter and the values of rho(rc) and triangle down2rho(rc) are larger for pyrite and marcasite, indicating that the accumulation and local concentration of rho(r) in the internuclear region are greater than those involving the longer, high-spin Fe-S bonded interactions. The net atomic charges and the bonded radii calculated for the Fe and S atoms in pyrite and marcasite are also smaller than those for sulfides with high-spin octahedrally coordinated Fe atoms. Collectively, the Fe-S interactions are indicated to be intermediate in character with the low-spin Fe-S interactions having greater shared character than the high-spin interactions. The bond lengths observed for chalcopyrite together with the calculated bond critical point properties are consistent with the formula Cu+Fe3+S2. The bond length is shorter and the rho(rc) value is larger for the FeS4 tetrahedron displayed by metastable greigite than those displayed by chalcopyrite and cubanite, consistent with a proposal that the Fe atom in greigite is tetravalent. S-S bond paths exist between each of the surface S atoms of adjacent slabs of FeS6 octahedra comprising the layer sulfide smythite, suggesting that the neutral Fe3S4 slabs are linked together and stabilized by the pathways of electron density comprising S-S bonded interactions. Such interactions not only exist between the S atoms for adjacent S8 rings in native sulfur, but their bond critical point properties are similar to those displayed by the metal sulfides.

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For a variety of molecules and earth materials, the theoretical local kinetic energy density, G(r(c)), increases and the local potential energy density, V(r(c)), decreases as the M-O bond lengths (M = first- and second-row metal atoms bonded to O) decrease and the electron density, rho(r(c)), accumulates at the bond critical points, r(c). Despite the claim that the local kinetic energy density per electronic charge, G(r(c))/rho(r(c)), classifies bonded interactions as shared interactions when less than unity and closed-shell when greater, the ratio was found to increase from 0.5 to 2.5 au as the local electronic energy density, H(r(c)) = G(r(c)) + V(r(c)), decreases and becomes progressively more negative. The ratio appears to be a measure of the character of a given M-O bonded interaction, the greater the ratio, the larger the value of rho(r(c)), the smaller the coordination number of the M atom and the more shared the bonded interaction. H(r(c))/rho(r(c)) versus G(r(c))/rho(r(c)) scatter diagrams categorize the M-O bonded interactions into domains with the local electronic energy density per electron charge, H(r(c))/rho(r(c)), tending to decrease as the electronegativity differences for the bonded pairs of atoms decrease. The values of G(r(c)) and V(r(c)), estimated with a gradient-corrected electron gas theory expression and the local virial theorem, are in good agreement with theoretical values, particularly for the bonded interactions involving second-row M atoms. The agreement is poorer for shared C-O and N-O bonded interactions.

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Bond critical point, local kinetic energy density, G(rc), and local potential energy density, V(rc), properties of the electron density distributions, rho(r), calculated for silicates such as quartz and gas-phase molecules such as disiloxane are similar, indicating that the forces that govern the Si-O bonded interactions in silica are short-ranged and molecular-like. Using the G(rc)/rho(rc) ratio as a measure of bond character, the ratio increases as the Si-O bond length, the local electronic energy density, H(rc)= G(rc) + V(rc), and the coordination number of the Si atom decrease and as the accumulation of the electron density at the bond critical point, rho(rc), and the Laplacian, inverted Delta2 rho(rc), increase. The G(rc)/rho(rc) and H(rc)/rho(rc) ratios categorize the bonded interaction as observed for other second row atom M-O bonds into discrete categories with the covalent character of each of the M-O bonds increasing with the H(rc)/rho(rc) ratio. The character of the bond is examined in terms of the large net atomic charges conferred on the Si atoms comprising disiloxane, stishovite, quartz, and forsterite and the domains of localized electron density along the Si-O bond vectors and on the reflex side of the Si-O-Si angle together with the close similarity of the Si-O bonded interactions observed for a variety of hydroxyacid silicate molecules and a large number of silicate crystals. The bond critical point and local energy density properties of the electron density distribution indicate that the bond is an intermediate interaction between Al-O and P-O bonded interactions rather than being a closed-shell or a shared interaction.

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A classification of the hydrogen fluoride H-F-bonded interactions comprising a large number of molecules has been proposed by Espinosa et al. [J. Chem. Phys. 117, 5529 (2002)] based on the ratio /Vr(c)/ / Gr(c) where /Vr(c)/ is the magnitude of the local potential-energy density and Gr(c) is the local kinetic-energy density, each evaluated at a bond critical point r(c). A calculation of the ratio for the M-O bonded interactions comprising a relatively large number of oxide molecules and earth materials, together with the constraints imposed by the values of inverted Delta2rho r(c) and the local electronic energy density, Hr(c) = Gr(c) + Vr(c), in the H-F study, yielded practically the same classification for the oxides. This is true despite the different trends that hold between the bond critical point and local energy density properties with the bond lengths displayed by the H-F and M-O bonded interactions. On the basis of the ratio, Li-O, Na-O, and Mg-O bonded interactions classify as closed-shell ionic bonds, Be-O, Al-O, Si-O, B-O, and P-O interactions classify as bonds of intermediate character with the covalent character increasing from Be-O to P-O. N-O interactions classify as shared covalent bonds. C-O and S-O bonded interactions classify as both intermediate and covalent bonded interactions. The C-O double- and triple-bonded interactions classify as intermediate-bonded interactions, each with a substantial component of covalent character and the C-O single-bonded interaction classifies as a covalent bond whereas their local electronic energy density values indicate that they are each covalent bonded interactions. The ratios for the Be-O, Al-O, and Si-O bonded interactions indicate that they have a substantial component of ionic character despite their classification as bonds of intermediate character. The trend between the ratio and the character of the bonded interactions is consistent with trends expected from electronegativity considerations. The ratio increases as the net charges and the coordination numbers for the atoms for several Ni-sulfides decrease. On the contrary, the ratio for the Si-O bonded interactions for the orthosilicate, forsterite, Mg2SiO4, and the high-pressure silica polymorph, stishovite, decreases as the observed net atomic charges and the coordination numbers of Si and O increase in value. The ratio for the Ni-Ni bonded interactions for the Ni-sulfides and bulk Ni metal indicate that the interactions are intermediate in character with a substantial component of ionic character.

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Chronic lymphocytic leukaemia (CLL) follows a variable clinical course with patient survival ranging from only a few years despite treatment, to several decades in patients who may never require clinical intervention. Determination of the mutational status of a patient's immunoglobulin heavy chain variable region (Ig V(H)) gene has been used to provide prognostic information, but this assay is not available in most laboratories. The discovery of the expression of the protein tyrosine kinase zeta-associated protein (ZAP)-70 in V(H)-unmutated CLL cases led to its proposal as a surrogate marker for V(H) status. This study investigated the measurement of ZAP-70 expression in CLL using different flow cytometric protocols. Two different antibodies and two different staining methods were compared. The Caltag ZAP-70 antibody and Fix & Perm kit were the easiest to use and were the most sensitive and specific combination, with 91% concordance between ZAP-70 expression and V(H) status. Three patients (9%) were discordant (two V(H) mutated/ZAP-70 positive, and one V(H) unmutated/ZAP-70 negative). No correlation existed between CD38 and either ZAP-70 expression or V(H) status. Measurement of ZAP-70 expression using the Caltag antibody/kit combination provides a standardized flow cytometric method that could be introduced into a routine CLL immunophenotyping panel in a clinical diagnostic laboratory.

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