Absolute Free Energy of Binding Calculations for Macrophage Migration Inhibitory Factor in Complex with a Druglike Inhibitor

Calculation of the absolute free energy of binding (ΔGbind) for a complex in solution is challenging owing to the need for adequate configurational sampling and an accurate energetic description, typically with a force field (FF). In this study, Monte Carlo (MC) simulations with improved side-chain and backbone sampling are used to assess ΔGbind for the complex of a druglike inhibitor (MIF180) with the protein macrophage migration inhibitory factor (MIF) using free energy perturbation (FEP) calculations. For comparison, molecular dynamics (MD) simulations were employed as an alternative sampling method for the same system. With the OPLS-AA/M FF and CM5 atomic charges for the inhibitor, the ΔGbind results from the MC/FEP and MD/FEP simulations, −8.80 ± 0.74 and −8.46 ± 0.85 kcal/mol, agree well with each other and with the experimental value of −8.98 ± 0.28 kcal/mol. The convergence of the results and analysis of the trajectories indicate that sufficient sampling was achieved for both approaches. Repeating the MD/FEP calculations using current versions of the CHARMM and AMBER FFs led to a 6 kcal/mol range of computed ΔGbind. These results show that calculation of accurate ΔGbind for large ligands is both feasible and numerically equivalent, within error limits, using either methodology

Exploiting Term Hiding to Reduce Run-time Checking Overhead

One of the most attractive features of untyped languages is the flexibility in term creation and manipulation. However, with such power comes the responsibility of ensuring the correctness of these operations. A solution is adding run-time checks to the program via assertions, but this can introduce overheads that are in many cases impractical. While static analysis can greatly reduce such overheads, the gains depend strongly on the quality of the information inferred. Reusable libraries, i.e., library modules that are pre-compiled independently of the client, pose special challenges in this context. We propose a technique which takes advantage of module systems which can hide a selected set of functor symbols to significantly enrich the shape information that can be inferred for reusable libraries, as well as an improved run-time checking approach that leverages the proposed mechanisms to achieve large reductions in overhead, closer to those of static languages, even in the reusable-library context. While the approach is general and system-independent, we present it for concreteness in the context of the Ciao assertion language and combined static/dynamic checking framework. Our method maintains the full expressiveness of the assertion language in this context. In contrast to other approaches it does not introduce the need to switch the language to a (static) type system, which is known to change the semantics in languages like Prolog. We also study the approach experimentally and evaluate the overhead reduction achieved in the run-time checks.Comment: 26 pages, 10 figures, 2 tables; an extension of the paper version accepted to PADL'18 (includes proofs, extra figures and examples omitted due to space reasons

Progressive multifocal leukoencephalopathy following fludarabine treatment in a chronic lymphocytic leukemia patient

Progressive multifocal leukoencephalopathy (PML) is a neurological disease caused by infection of the central nervous system (CNS) with the JC polyomavirus (JCV). JCV is endemic and infects a large proportion (70–90%) of healthy individuals worldwide, but infection is latent. JCV reactivation may occur, if the immune function is compromised. Aim: To present a PML case in a CLL patient after a long course of disease and treatment with fludarabine. JCV virus infection in this patient was proven both in brain biopsy material and blood. Methods: Patient with a nine-year history of CLL was hospitalized with the weakness in the right leg and left hand, tremors, speech difficulties. An MRI diagnosed infiltrative glial tumor of the left hemisphere, proliferating predominantly in the frontal lobe, more in the gyrus frontalis superior region. CNS tumor biopsy performed. Results: Morphology and immunoprofile of the lesion consistent with progressive multifocal leukoencephalopathy. The material from biopsy was diagnosed as positive for JCV DNA. JCV and HHV-7 genomic sequences were found in patient’s PBL DNA sample. In a plasma DNA sample, only genomic sequences were detected. Conclusion: The present case draws attention to the fact that the use of fludarabine and its combinations in CLL therapy increases the risk of JCV infection reactivation and development of serious complications like PML

Secondary forest regeneration benefits old-growth specialist bats in a fragmented tropical landscape

Tropical forest loss and fragmentation are due to increase in coming decades. Understanding how matrix dynamics, especially secondary forest regrowth, can lessen fragmentation impacts is key to understanding species persistence in modified landscapes. Here, we use a whole-ecosystem fragmentation experiment to investigate how bat assemblages are influenced by the regeneration of the secondary forest matrix. We surveyed bats in continuous forest, forest fragments and secondary forest matrix habitats, similar to 15 and similar to 30 years after forest clearance, to investigate temporal changes in the occupancy and abundance of old-growth specialist and habitat generalist species. The regeneration of the second growth matrix had overall positive effects on the occupancy and abundance of specialists across all sampled habitats. Conversely, effects on generalist species were negligible for forest fragments and negative for secondary forest. Our results show that the conservation potential of secondary forests for reverting faunal declines in fragmented tropical landscapes increases with secondary forest age and that old-growth specialists, which are often of most conservation concern, are the greatest beneficiaries of secondary forest maturation. Our findings emphasize that the transposition of patterns of biodiversity persistence in island ecosystems to fragmented terrestrial settings can be hampered by the dynamic nature of human-dominated landscapes.Peer reviewe

Synthesis and characterization of new aromatic esters based on 4,16-pregnadiene-6,20-dione skeleton

A series of new aromatic esters based on 4,16-pregnadiene-6,20-dione skeleton, namely 3β-benzoyloxy-4,16-pregnadiene-6,20-dione and 3β-furoyloxy-4,16-pregnadiene- 6,20-dione, which may be good inhibitors for the 5α-reductase enzyme and show high antiandrogenic activity, were synthesized starting from diosgenin. The structures of the steroids were characterized by elemental analysis, 1H NMR, 13C NMR, IR and mass spectrum. Single crystal X-ray diffraction measurement on one of the new compounds, 3β-(p-methoxybenzoyloxy)-4,16-pregnadiene-6,20-dione revealed that the A, B, C, and D ring adopted half chair, distorted chair, distorted chair, and distorted envelope conformation, respectively. The molecules in the crystal were packed face-to-face at the normal van der Waals distances

Interplay of superexchange and orbital degeneracy in Cr-doped LaMnO3

We report on structural, magnetic and Electron Spin Resonance (ESR) investigations in the manganite system LaMn_{1-x}Cr_{x}O_{3} (x<=0.5). Upon Cr-doping we observe a reduction of the Jahn-Teller distortion yielding less distorted orthorhombic structures. A transition from the Jahn-Teller distorted O' to the pseudocubic O phase occurs between 0.3<x<0.4. A clear connection between this transition and the doping dependence of the magnetic and ESR properties has been observed. The effective moments determined by ESR seem reduced with respect to the spin-only value of both Mn^{3+} and Cr^{3+} ions

Photodegradation of Phenol over a Hybrid Organo-Inorganic Material: Iron(II) Hydroxyphosphonoacetate

Water treatment is a hot topic, and it will become much more important in the decades ahead. Advanced oxidation processes are being increasingly used for organic contaminant removal, for example using photo-Fenton reactions. Here we report the use of an organo-inorganic hybrid, Fe[HO3PCH(OH)COO]·2H2O, as Fenton photocatalyst for phenol oxidation with H2O2 under UVA radiation. Preactivation, catalyst content, and particle size parameters have been studied/optimized for increasing phenol mineralization. Upon reaction, iron species are leached from the catalyst making a homogeneous catalysis contribution to the overall phenol photo-oxidation. Under optimized conditions, the mineralization degree was slightly larger than 90% after 80 min of irradiation. Analysis by X-ray photoelectron spectroscopy revealed important chemical modifications occurring on the surface of the catalyst after activation and phenol photodegradation. The sustained slow delivery of iron species upon phenol photoreaction is advantageous as the mixed heterogeneous−homogeneous catalytic processes result in very high phenol mineralization.Proyecto nacional MAT2010-1517

Divalent Metal Vinylphosphonate Layered Materials: Compositional Variability, Structural Peculiarities, Dehydration Behavior, and Photoluminescent Properties

A family of M-VP (M = Ni, Co, Cd, Mn, Zn, Fe, Cu, Pb; VP = vinylphosphonate) and M-PVP (M = Co, Cd; PVP = phenylvinylphosphonate) materials have been synthesized by hydrothermal methods and characterized by FTIR, elemental analysis, and thermogravimetric analysis (TGA). Their structures were determined either by single crystal X-ray crystallography or from laboratory X-ray powder diffraction data. The crystal structure of some M-VP and M-PVP materials is two-dimensional (2D) layered, with the organic groups (vinyl or phenylvinyl) protruding into the interlamellar space. However, the Pb-VP and Cu-VP materials show dramatically different structural features. The porous, three-dimensional (3D) structure of Pb-VP contains the Pb center in a pentagonal pyramid. A Cu-VP variant of the common 2D layered structure shows a very peculiar structure. The structure of the material is 2D with the layers based upon three crystallographically distinct Cu atoms; an octahedrally coordinated Cu2+ atom, a square planar Cu2+ atom and a Cu+ atom. The latter has an unusual co-ordination environment as it is 3-coordinated to two oxygen atoms with the third bond across the double bond of the vinyl group. Metal-coordinated water loss was studied by TGA and thermodiffractometry. The rehydration of the anhydrous phases to give the initial phase takes place rapidly for Cd-PVP but it takes several days for Co-PVP. The M-VP materials exhibit variable dehydration-rehydration behavior, with most of them losing crystallinity during the process.Proyecto nacional MAT2010-15175 (MICINN, España

Symbolic analysis of analog circuits containing voltage mirrors

7 páginas, 7 figuras, 2 tablas, 4 imágenes.-- Open Access: This article is distributed under the terms of the Creative Commons Attribution Noncommercial License.The pathological elements voltage mirror (VM) and current mirror (CM) have shown advantages in analog behavioral modeling and circuit synthesis, where many nullor-mirror equivalences have been explored to design and to transform voltage-mode circuits to current-mode ones and viceversa. However, both the VM and CM have not equivalents to perform automatic symbolic circuit analysis. In this manner, we introduce nullor-equivalents for these pathological elements allowing to include parasitics and to perform only symbolic nodal analysis. The nullor-equivalent of the CM is extended to provide multiple-outpus (MO-CM). Finally, two active filters containing VMs, CMs and MO-CMs are analysed to show the usefulness of the models.This work is supported by: UC-MEXUS and CONACyT under grants CN-09-310 and 48396-Y; by Promep-Mexico under grant UATLX-PTC-088; by Consejeria de Innovacion, Ciencia y Empresa, Junta de Andalucia-Spain TIC-2532; and by the JAE-Doc program of CSIC co-funded by FSE, Spain.Peer reviewe