SQG-Differential Evolution for difficult optimization problems under a tight function evaluation budget

In the context of industrial engineering, it is important to integrate efficient computational optimization methods in the product development process. Some of the most challenging simulation-based engineering design optimization problems are characterized by: a large number of design variables, the absence of analytical gradients, highly non-linear objectives and a limited function evaluation budget. Although a huge variety of different optimization algorithms is available, the development and selection of efficient algorithms for problems with these industrial relevant characteristics, remains a challenge. In this communication, a hybrid variant of Differential Evolution (DE) is introduced which combines aspects of Stochastic Quasi-Gradient (SQG) methods within the framework of DE, in order to improve optimization efficiency on problems with the previously mentioned characteristics. The performance of the resulting derivative-free algorithm is compared with other state-of-the-art DE variants on 25 commonly used benchmark functions, under tight function evaluation budget constraints of 1000 evaluations. The experimental results indicate that the new algorithm performs excellent on the 'difficult' (high dimensional, multi-modal, inseparable) test functions. The operations used in the proposed mutation scheme, are computationally inexpensive, and can be easily implemented in existing differential evolution variants or other population-based optimization algorithms by a few lines of program code as an non-invasive optional setting. Besides the applicability of the presented algorithm by itself, the described concepts can serve as a useful and interesting addition to the algorithmic operators in the frameworks of heuristics and evolutionary optimization and computing

Electrically Tunable Scattering from Devitrite–Liquid Crystal Hybrid Devices

Devitrite is normally an unwanted crystalline impurity in the soda-lime-silica glass making process. Thin needles formed by heterogeneous nucleation of devitrite on the glass surface provide unique birefringence properties for potential applications in tunable optical devices. Here, devitrite and a liquid crystal are combined to create an electrically variable optical diffuser. The magnitude and scattering angle of the transmitted light propagating through the diffuser are tuned by varying the voltage between the graphene and indium tin oxide electrodes on either side of the liquid crystal. The threshold voltage to switch the transmitted light from a predominantly horizontal diffusion to a random order is 3.5 V. Angle-resolved measurements show broad diffusion angles of transmitted light with a maximum deflection of ±60°. The dynamically tunable devitrite-liquid crystal hybrid devices may advance the development of currently less viable technologies including beam shaping and automatic light transmission control.Leverhulme Trust, Royal Society, Engineering and Physical Sciences Research Council (IAA Follow on Fund

Electrically Tunable Scattering from Devitrite–Liquid Crystal Hybrid Devices

Devitrite is normally an unwanted crystalline impurity in the soda-lime-silica glass making process. Thin needles formed by heterogeneous nucleation of devitrite on the glass surface provide unique birefringence properties for potential applications in tunable optical devices. Here, devitrite and a liquid crystal are combined to create an electrically variable optical diffuser. The magnitude and scattering angle of the transmitted light propagating through the diffuser are tuned by varying the voltage between the graphene and indium tin oxide electrodes on either side of the liquid crystal. The threshold voltage to switch the transmitted light from a predominantly horizontal diffusion to a random order is 3.5 V. Angle-resolved measurements show broad diffusion angles of transmitted light with a maximum deflection of ±60°. The dynamically tunable devitrite-liquid crystal hybrid devices may advance the development of currently less viable technologies including beam shaping and automatic light transmission control.Leverhulme Trust, Royal Society, Engineering and Physical Sciences Research Council (IAA Follow on Fund

Influence of specific HSP70 domains on fibril formation of the yeast prion protein Ure2.

Ure2p is the protein determinant of the Saccharomyces cerevisiae prion state [URE3]. Constitutive overexpression of the HSP70 family member SSA1 cures cells of [URE3]. Here, we show that Ssa1p increases the lag time of Ure2p fibril formation in vitro in the presence or absence of nucleotide. The presence of the HSP40 co-chaperone Ydj1p has an additive effect on the inhibition of Ure2p fibril formation, whereas the Ydj1p H34Q mutant shows reduced inhibition alone and in combination with Ssa1p. In order to investigate the structural basis of these effects, we constructed and tested an Ssa1p mutant lacking the ATPase domain, as well as a series of C-terminal truncation mutants. The results indicate that Ssa1p can bind to Ure2p and delay fibril formation even in the absence of the ATPase domain, but interaction of Ure2p with the substrate-binding domain is strongly influenced by the C-terminal lid region. Dynamic light scattering, quartz crystal microbalance assays, pull-down assays and kinetic analysis indicate that Ssa1p interacts with both native Ure2p and fibril seeds, and reduces the rate of Ure2p fibril elongation in a concentration-dependent manner. These results provide new insights into the structural and mechanistic basis for inhibition of Ure2p fibril formation by Ssa1p and Ydj1p

Secondary nucleation of monomers on fibril surface dominates α\alpha-synuclein aggregation and provides autocatalytic amyloid amplification

Parkinson’s disease (PD) is characterized by proteinaceous aggregates named Lewy Bodies and Lewy Neurites containing $\alpha$-synuclein fibrils. The underlying aggregation mechanism of this protein is dominated by a secondary process at mildly acidic pH, as in endosomes and other organelles. This effect manifests as a strong acceleration of the aggregation in the presence of seeds and a weak dependence of the aggregation rate on monomer concentration. The molecular mechanism underlying this process could be nucleation of monomers on fibril surfaces or fibril fragmentation. Here, we aim to distinguish between these mechanisms. The nature of the secondary processes was investigated using differential sedimentation analysis, trap and seed experiments, quartz crystal microbalance experiments and super-resolution microscopy. The results identify secondary nucleation of monomers on the fibril surface as the dominant secondary process leading to rapid generation of new aggregates, while no significant contribution from fragmentation was found. The newly generated oligomeric species quickly elongate to further serve as templates for secondary nucleation and this may have important implications in the spreading of PD.This work was supported by the Swedish Research Council and its Linneaus Centers for Organizing Molecular Matter (E. Sparr and S. Linse), the European Research Council (S. Linse), Nanolund (S. Linse), Multipark (S. Linse and R. Gaspar), the Leverhulme Trust (A. Buell), Magdalene College, Cambridge (A. Buell), the Parkinson’s and Movement Disorder Foundation (A. Buell), EPSRC (C.F. Kaminski), MRC (C.F. Kaminski) and Wellcome Trust UK (C.F. Kaminski)

Historical geography II: Digital imaginations

In my second report discussing the state of historical geography, I review some of the ways historical geographers have made use of digital technologies and digital media. I also highlight how digital data, research, and presentation are affecting related humanities disciplines and inspiring their practitioners to engage more fully with geographic concepts of space, place, and cartography. I argue that information technologies and digital media can deepen the place of historical geography in the academy and in the public’s eye.Yeshttps://us.sagepub.com/en-us/nam/manuscript-submission-guideline

Nanobodies raised against monomeric alpha-synuclein inhibit fibril formation and destabilize toxic oligomeric species

BACKGROUND: The aggregation of the protein ɑ-synuclein (ɑS) underlies a range of increasingly common neurodegenerative disorders including Parkinson’s disease. One widely explored therapeutic strategy for these conditions is the use of antibodies to target aggregated ɑS, although a detailed molecular-level mechanism of the action of such species remains elusive. Here, we characterize ɑS aggregation in vitro in the presence of two ɑS-specific single-domain antibodies (nanobodies), NbSyn2 and NbSyn87, which bind to the highly accessible C-terminal region of ɑS. RESULTS: We show that both nanobodies inhibit the formation of ɑS fibrils. Furthermore, using single-molecule fluorescence techniques, we demonstrate that nanobody binding promotes a rapid conformational conversion from more stable oligomers to less stable oligomers of ɑS, leading to a dramatic reduction in oligomer-induced cellular toxicity. CONCLUSIONS: The results indicate a novel mechanism by which diseases associated with protein aggregation can be inhibited, and suggest that NbSyn2 and NbSyn87 could have significant therapeutic potential

Integrative analyses identify modulators of response to neoadjuvant aromatase inhibitors in patients with early breast cancer

Introduction Aromatase inhibitors (AIs) are a vital component of estrogen receptor positive (ER+) breast cancer treatment. De novo and acquired resistance, however, is common. The aims of this study were to relate patterns of copy number aberrations to molecular and proliferative response to AIs, to study differences in the patterns of copy number aberrations between breast cancer samples pre- and post-AI neoadjuvant therapy, and to identify putative biomarkers for resistance to neoadjuvant AI therapy using an integrative analysis approach. Methods Samples from 84 patients derived from two neoadjuvant AI therapy trials were subjected to copy number profiling by microarray-based comparative genomic hybridisation (aCGH, n = 84), gene expression profiling (n = 47), matched pre- and post-AI aCGH (n = 19 pairs) and Ki67-based AI-response analysis (n = 39). Results Integrative analysis of these datasets identified a set of nine genes that, when amplified, were associated with a poor response to AIs, and were significantly overexpressed when amplified, including CHKA, LRP5 and SAPS3. Functional validation in vitro, using cell lines with and without amplification of these genes (SUM44, MDA-MB134-VI, T47D and MCF7) and a model of acquired AI-resistance (MCF7-LTED) identified CHKA as a gene that when amplified modulates estrogen receptor (ER)-driven proliferation, ER/estrogen response element (ERE) transactivation, expression of ER-regulated genes and phosphorylation of V-AKT murine thymoma viral oncogene homolog 1 (AKT1). Conclusions These data provide a rationale for investigation of the role of CHKA in further models of de novo and acquired resistance to AIs, and provide proof of concept that integrative genomic analyses can identify biologically relevant modulators of AI response

Distinct thermodynamic signatures of oligomer generation in the aggregation of the amyloid-beta peptide

Mapping free-energy landscapes has proved to be a powerful tool for studying reaction mechanisms. Many complex biomolecular assembly processes, however, have remained challenging to access using this approach, including the aggregation of peptides and proteins into amyloid fibrils implicated in a range of disorders. Here, we generalize the strategy used to probe free-energy landscapes in protein folding to determine the activation energies and entropies that characterize each of the molecular steps in the aggregation of the amyloid-β peptide (Aβ42), which is associated with Alzheimer’s disease. Our results reveal that interactions between monomeric Aβ42 and amyloid fibrils during fibril-dependent secondary nucleation fundamentally reverse the thermodynamic signature of this process relative to primary nucleation, even though both processes generate aggregates from soluble peptides. By mapping the energetic and entropic contributions along the reaction trajectories, we show that the catalytic efficiency of Aβ42 fibril surfaces results from the enthalpic stabilization of adsorbing peptides in conformations amenable to nucleation, resulting in a dramatic lowering of the activation energy for nucleation