Heme reactivity is uncoupled from quaternary structure in gel-encapsulated hemoglobin: a resonance Raman spectroscopic study

Encapsulation of hemoglobin (Hb) in silica gel preserves structure and function but greatly slows protein motion, thereby providing access to intermediates along the allosteric pathway that are inaccessible in solution. Resonance Raman (RR) spectroscopy with visible and ultraviolet laser excitation provides probes of heme reactivity and of key tertiary and quaternary contacts. These probes were monitored in gels after deoxygenation of oxyHb and after CO binding to deoxyHb, which initiate conformational change in the R-T and T-R directions, respectively. The spectra establish that quaternary structure change in the gel takes a week or more but that the evolution of heme reactivity, as monitored by the Fe-histidine stretching vibration, ν(FeHis), is completed within two days, and is therefore uncoupled from the quaternary structure. Within each quaternary structure, the evolving ν(FeHis) frequencies span the full range of values between those previously associated with the high- and low-affinity end states, R and T. This result supports the tertiary two-state (TTS) model, in which the Hb subunits can adopt high- and low-affinity tertiary structures, r and t, within each quaternary state. The spectra also reveal different tertiary pathways, involving the breaking and reformation of E and F interhelical contacts in the R-T direction but not the T-R direction. In the latter, tertiary motions are restricted by the T quaternary contacts.     

Measuring productivity growth under factor non-substitution: An application to US steam-electric power generation utilities

A theoretical framework is developed for decomposing partial factor productivity and measuring technical inefficiency when the underlying technology is characterized by factor non-substitution. With Farrell’s (1957) radial index of technical inefficiency being inappropriate in this case, Russell non-radial indices are adapted to measure technical inefficiency in a Leontief-type model. A system of factor demand equations with a regime specific technical inefficiency term is proposed and estimated allowing for dependence across inputs using a copula approach. Then the paper presents a complete decomposition of partial factor productivity changes using a dataset of US steam-power electric generation utilities.     

Nanocrystalline RE2O3:Tm3+ (RE: Gd3+, Y3+) Blue Phosphors Synthesized via the Combustion Method

This work reports on the preparation of a luminescent blue-emitting rare earth (RE) Tm-doped oxide phosphor. Nanocrystalline RE2O3:Tm3+ particles were prepared via the combustion method using citric acid, glycine, or urea as fuels. Samples were doped with different percentages of the activator Tm3+. The post-annealing treatment was performed in air for all the samples, at temperatures ranging from 800 to 1100 degrees C, for 4 h. The samples were characterized by X-ray diffraction (XRD), photoluminescence spectroscopy (PL) and scanning electron and transmission microscopies (SEM and TEM) in order to determine the best synthetic procedure. The post-annealed powders showed blue emission with maximum at 452 nm characteristics for Tm3+ transition 1D2 --> 3H4 (under UV excitation at 360 nm). Samples, presented a tri-dimensional porous structure (50-200 nm) formed of spheroid particles with a diameter between 20 and 60 nm. The best luminescent material was obtained when urea was used to prepare nanoparticles of Gd2O3 doped with 0.5% Tm3+, and 1100 degrees C was used as the post-annealing temperature.     

Support vector machines for predictive modeling in heterogeneous catalysis: a comprehensive introduction and overfitting investigation based on two real applications

This works provides an introduction to support vector machines (SVMs) for predictive modeling in heterogeneous catalysis, describing step by step the methodology with a highlighting of the points which make such technique an attractive approach. We first investigate linear SVMs, working in detail through a simple example based on experimental data derived from a study aiming at optimizing olefin epoxidation catalysts applying high-throughput experimentation. This case study has been chosen to underline SVM features in a visual manner because of the few catalytic variables investigated. It is shown how SVMs transform original data into another representation space of higher dimensionality. The concepts of Vapnik-Chervonenkis dimension and structural risk minimization are introduced. The SVM methodology is evaluated with a second catalytic application, that is, light paraffin isomerization. Finally, we discuss why SVMs is a strategic method, as compared to other machine learning techniques, such as neural networks or induction trees, and why emphasis is put on the problem of overfitting.     

Microsecond melting of a folding intermediate in a coiled-coil peptide, monitored by T-jump/UV Raman spectroscopy

A truncated version of the GCN4 coiled-coil peptide has been studied by ultraviolet resonance Raman (UVRR) spectroscopy with 197 nm excitation, where amide modes are optimally enhanced. Although the CD melting curve could be satisfactorily described with a two-state transition having Tm = 30 degrees C, singular value decomposition of the UVRR data yielded three principal components, whose temperature dependence implicates an intermediate form between the folded and unfolded forms, with formation and melting temperatures of 10 and 40 degrees C. Two alpha-helical amide III bands, at 1340 and 1300 cm(-1), melted out selectively at 10 and 40 degrees C, respectively, and are assigned to hydrated and unhydrated helical regions. The hydrated regions are proposed to be melted in the intermediate form, while the unhydrated regions are intact. Time-resolved UVRR spectra following laser-induced temperature jumps revealed two relaxations, with time constants of 0.2 and 15 mus. These are suggested to reflect the melting times of hydrated and unhydrated helices. The unhydrated helical region may be associated with a 14-residue "trigger" sequence that has been identified in the C-terminal half of GCN4. Dehydration of helices may be a key step in the folding of coiled-coils.     

In Vitro Photodynamic Activity of 5,15-bis(3-Hydroxyphenyl)porphyrin and Its Halogenated Derivatives Against Cancer Cells

5,15-Diarylporphyrins ( 1-5 ) with hydroxyl groups and halogens as substituents were prepared by condensation between unsubstituted dipyrromethane and halogenated m -hydroxybenzaldehydes. Photophysical properties show that the nonhalogenated porphyrin 1 has higher fluorescence yield but lower singlet oxygen formation quantum yield than the halogenated derivatives due to the heavy atom effect. The in vitro activity of these derivatives was tested against WiDr colorectal adenocarcinoma and A375 melanoma cancer cells. All porphyrins present a much higher phototoxicity than Photofrin^® with IC ₅₀ values lower than the 50 n m level for WiDr cells and 25 n m level for A375 cancer cells. The most photoactive compound is the nonhalogenated porphyrin 1 which also presents the highest uptake. Halogenated derivatives present much lower uptakes than 1 . However, their photoactivity is similar to compound 1 showing that their intrinsic photoactivity (ISP) is very high. Iodinated compound 4 presents the highest ISP. The greater ability of these porphyrins to destroy cancer cells could be related to their photophysical and photochemical properties.     

Drilling rate of five metals with picosecond laser pulses at 355, 532, and 1064 nm

Experimental results on picosecond laser processing of aluminum, nickel, stainless steel, molybdenum, and tungsten are described. Hole drilling is employed for comparative analysis of processing rates in an air environment. Drilling rates are measured over a wide range of laser fluences (0.05–20?J/cm²). Experiments with picosecond pulses at 355?nm are carried out for all five metals and in addition at 532?nm, and 1064?nm for nickel. A comparison of drilling rate with 6-ps and 6-ns pulses at 355?nm is performed. The dependence of drilling rate on laser fluence measured with picosecond pulses demonstrates two logarithmic regimes for all five metals. To determine the transition from one regime to another, a critical fluence is measured and correlated with the thermal properties of the metals. The logarithmic regime at high-fluence range with UV picosecond pulses is reported for the first time. The energy efficiency of material removal for the different regimes is evaluated. The results demonstrate that UV picosecond pulses can provide comparable quality and higher processing rate compared with literature data on ablation with near-IR femtosecond lasers. A significant contribution of two-photon absorption to the ablation process is suggested to explain high processing rate with powerful UV picosecond pulses.     

On the correlation between droplet volume and irradiation conditions in the laser forward transfer of liquids

The analysis of the morphology of droplets printed through laser-induced forward transfer (LIFT) of liquid films shows that: (i)?the droplet volume is linearly related with the energy of the laser pulse that originated it, (ii)?the liquid ejection process is activated by an energy density threshold?F ₀, and (iii)?the droplet volume can be correlated with a dimensional parameter of the laser beam through an oversimple model that states that the amount of printed liquid equals the liquid contained in the cylindrical portion of an irradiated film whose base corresponds to the cross-sectional area of the beam with energy density higher than?F ₀. Although these issues seem to describe correctly the LIFT process, some problematic instances arise from them. Thus, the linear relation between droplet volume and laser pulse energy seems to be inconsistent with the existence of the threshold?F ₀. On the other hand, the compatibility between the model and the aforementioned linear relation requires to be explained. Finally, the model is based on the idea that transfer takes place in a way analogous to the LIFT of solid films, but time-resolved imaging studies have demonstrated that liquid ejection follows a dynamics which seems quite unsuited with that idea. In this work previous results are re-analyzed and new experiments are performed in an attempt to clarify these questions. It is then shown that the inconsistencies pointed out are only apparent, and that the validity of the model is limited to irradiation conditions where the beam dimensions are significantly larger than the thickness of the liquid film. Furthermore, an explanation is provided for the dependence of the success and failure of the model on those irradiation conditions in terms of the diverse liquid ejection dynamics taking place.     

New calibrations and time stability of the response of the INTERCAST CR-39

We present new calibrations of different production batches (from 1989 to 1999) of the INTERCAST CR-39, using the BNL-AGS 1 A GeV iron beam. The comparison with previous results, obtained with the 158 A GeV lead beam from the CERN-SPS shows that, while each production batch has a different calibration curve (mainly due to minor differences in the production conditions), the aging effect is negligible. We also tested the dependence of the CR-39 response from the time elapsed between exposure and analysis (fading effect). The fading effect, if present, is less then 10%. It may be compatible with the experimental uncertainties on the bulk etching rate v_B.     

Fast Algorithms to Generate Necklaces, Unlabeled Necklaces, and Irreducible Polynomials over GF(2)

Many applications call for exhaustive lists of strings subject to various constraints, such as inequivalence under group actions. A k-ary necklace is an equivalence class of k-ary strings under rotation (the cyclic group). A k-ary unlabeled necklace is an equivalence class of k-ary strings under rotation and permutation of alphabet symbols. We present new, fast, simple, recursive algorithms for generating (i.e., listing) all necklaces and binary unlabeled necklaces. These algorithms have optimal running times in the sense that their running times are proportional to the number of necklaces produced. The algorithm for generating necklaces can be used as the basis for efficiently generating many other equivalence classes of strings under rotation and has been applied to generating bracelets, fixed density necklaces, and chord diagrams. As another application, we describe the implementation of a fast algorithm for listing all degree n irreducible and primitive polynomials over GF(2).