Continuum solvation models in the linear interaction energy method

The linear interaction energy (LIE) method in combination with two different continuum solvent models has been applied to calculate protein-ligand binding free energies for a set of inhibitors against the malarial aspartic protease plasmepsin II. Ligand-water interaction energies are calculated from both Poisson-Boltzmann (PB) and Generalized Born (GB) continuum models using snapshots from explicit solvent simulations of the ligand and protein-ligand complex. These are compared to explicit solvent calculations, and we find close agreement between the explicit water and PB solvation models. The GB model overestimates the change in solvation energy, and this is caused by consistent underestimation of the effective Born radii in the protein-ligand complex. The explicit solvent LIE calculations and LIE-PB, with our standard parametrization, reproduce absolute experimental binding free energies with an average unsigned error of 0.5 and 0.7 kcal/mol, respectively. The LIE-GB method, however, requires a constant offset to approach the same level of accuracy.     

An adeno-associated viral vector transduces the rat hypothalamus and amygdala more efficient than a lentiviral vector

Background  

This study compared the transduction efficiencies of an adeno-associated viral (AAV) vector, which was pseudotyped with an AAV1 capsid and encoded the green fluorescent protein (GFP), with a lentiviral (LV) vector, which was pseudotyped with a VSV-G envelop and encoded the discosoma red fluorescent protein (dsRed), to investigate which viral vector transduced the lateral hypothalamus or the amygdala more efficiently. The LV-dsRed and AAV1-GFP vector were mixed and injected into the lateral hypothalamus or into the amygdala of adult rats. The titers that were injected were 1 × 10⁸ or 1 × 10⁹ genomic copies of AAV1-GFP and 1 × 10⁵ transducing units of LV-dsRed.     

Backlund transformations and exact solutions for a nonlinear elliptic equation modelling isothermal magnetostatic atmosphere

The equations of magnetostatic equilibria for a plasma in agravitational field are investigated analytically. For equilibriawith an ignorable spatial coordinate, the equations reduce toa single nonlinear elliptic equation for the magnetic potentialu known as the Grad-Shafranov equation. By specifying the arbitraryfunctions in this equation, a Liouville equation is obtained.Bäcklund transformations are described and applied to obtainexact solutions for the Liouville equation modelling an isothermalmagnetostatic atmosphere, in which the current density J isproportional to the exponential of the magnetic potential andmoveover falls off exponentially with distance vertical to thebase with an e-folding distance equal to the gravitational scaleheight.     

High-K band structures in 164Er

High-spin states of the doubly-odd ¹¹²Sb were studied by in-beam spectroscopy using the ⁸⁸Sr (²⁸Si, p3n) and ⁸⁹Y (²⁹Si, α2n) fusion-evaporation reactions at beam energies of 120 and 108 MeV, respectively. γ?γ, charged particle-γ?γ coincidences, and γ?γ angular correlation analyses were employed for determining the level scheme of ¹¹²Sb. In the present work, all the levels except for low-lying states in ¹¹²Sb were newly established. Two ΔI = 1 strongly coupled bands were observed; one is a negative-parity band that is similar to those observed in the neighboring doubly-odd Sb isotopes and the other is a positive-parity band that has a new type structure not observed in the other isotopes. From the similarity of the properties of these ΔI = 1 bands to the bands built on 9/2⁺ 2p?1h states in the odd-A Sb isotopes, we suggest that these two ΔI = 1 bands should be associated with the [π(g_9/2)^?1 ? νh_11/2] and [π(g_9/2)^?1νg_7/2] configurations, respectively.     

Quantification of total fatty acids in microalgae: comparison of extraction and transesterification methods

Determination of microalgaes’ fatty acid content is often done with chloroform and methanol according to the Bligh and Dyer extraction, though faster methods exist. A number of comparisons between the Bligh and Dyer and faster methods have resulted in contradicting data, possibly due to differences in algae used and the different versions of the Bligh and Dyer method applied. Here, various forms of direct-transesterification (D-TE) and two-step transesterification (2-TE), including three versions developed in our lab, are compared with the original Bligh and Dyer (Can J Biochem Physiol 37: 911–917, 1959) extraction and two modifications thereof (Lee et al. J AOAC Int 79:487–492, 1996, and our own acidified version) on microalgae with different cell walls: Isochrysis galbana, Nannochloropsis oculata, and Phaeodactylum tricornutum. In total, fatty acid extracts from 11 methods were separated and quantified by gas chromatography with mass spectrometry. Results show that, for N. oculata and P. tricornutum, methods based on chloroform–methanol underestimated the fatty acid content compared with the 2-TE and D-TE methods, which gave similar results. Moreover, D-TE methods are faster than chloroform–methanol methods and use chemicals that are less toxic. Of the D-TE methods, the ones using hydrochloric acid and sulfuric acid recovered the most fatty acids, while boron trifluoride recovered slightly less. The main qualitative difference between the fatty acids recovered was that the chloroform–methanol methods recovered less saturated fatty acids in P. tricornutum.     

Bounded G-theory with fibred control

We use filtered modules over a Noetherian ring and fibred bounded control on homomorphisms to construct a new kind of controlled algebra with applications in geometric topology. The resulting theory can be thought of as a “pushout” of bounded K-theory with fibred control and bounded G-theory constructed and used by the authors. Bounded G-theory was geared toward constructing a G-theoretic version of assembly maps and proving the Novikov injectivity conjecture for them. The G-theory with fibred control is needed in the study of surjectivity of the assembly map. The relation between the K- and G-theories is the classical one: K-theory is meaningful, however G-theory is easier to compute, and the relationship is expressed via a Cartan map. This map turns out to be an equivalence under very mild constraints in terms of metric geometry such as finite decomposition complexity. The fibred theory is certainly more complicated than the absolute theory. This paper contains the non-equivariant theory including fibred controlled excision theorems known to be crucial for computations.     

Experimental determination of residual stresses in paperboard

A method for the experimental determination of the through-thickness residual stress distribution in paperboard is presented. The successive removal of thin layers from strips of board through surface grinding changes the stress-state and the bending stiffness resulting in a changed curvature, which is measurable. From tests of strips in both in-plane directions, stress distributions can then be evaluated using the Treuting-Read method. Geometrically nonlinear effects at the large deformations taking place are avoided through a proper choice of strip dimensions. Typical results are presented and factors influencing the accuracy of the determination are thoroughly discussed.     

On the algebraicK-theory of infinite product categories

Although theK-theory functor on the category of symmetric monoidal categories preserves finite products for essentially trivial reasons, this is not so in the case of infinite products. In this paper, we show that in factK-theory does preserve infinite products, but for non-trivial reasons.Supported in part by NSF DMS 9209714.