Archetypes of open-source business models

Electronic Markets - The open-source paradigm offers a plethora of opportunities for innovative business models (BMs) as the underlying codebase of the technology is accessible and extendable by...     

Methods and Applications of In Silico Aptamer Design and Modeling

Aptamers are nucleic acid analogues of antibodies with high affinity to different targets, such as cells, viruses, proteins, inorganic materials, and coenzymes. Empirical approaches allow the design of in vitro aptamers that bind particularly to a target molecule with high affinity and selectivity. Theoretical methods allow significant expansion of the possibilities of aptamer design. In this study, we review theoretical and joint theoretical-experimental studies dedicated to aptamer design and modeling. We consider aptamers with different targets, such as proteins, antibiotics, organophosphates, nucleobases, amino acids, and drugs. During nucleic acid modeling and in silico design, a full set of in silico methods can be applied, such as docking, molecular dynamics (MD), and statistical analysis. The typical modeling workflow starts with structure prediction. Then, docking of target and aptamer is performed. Next, MD simulations are performed, which allows for an evaluation of the stability of aptamer/ligand complexes and determination of the binding energies with higher accuracy. Then, aptamer/ligand interactions are analyzed, and mutations of studied aptamers made. Subsequently, the whole procedure of molecular modeling can be reiterated. Thus, the interactions between aptamers and their ligands are complex and difficult to understand using only experimental approaches. Docking and MD are irreplaceable when aptamers are studied in silico.     

Pulsed laser reshaping and fragmentation of upconversion nanoparticles — from hexagonal prisms to 1D nanorods through “Medusa”-like structures

One dimensional (1D) nanostructures attract considerable attention, enabling a broad application owing to their unique properties. However, the precise mechanism of 1D morphology attainment remains a matter of debate. In this study, ultrafast picosecond (ps) laser-induced treatment on upconversion nanoparticles (UCNPs) is offered as a tool for 1D-nanostructures formation. Fragmentation, reshaping through recrystallization process and bioadaptation of initially hydrophobic (β-Na_1.5Y_1.5F₆: Yb³⁺, Tm³⁺/β-Na_1.5Y_1.5F₆) core/shell nanoparticles by means of one-step laser treatment in water are demonstrated. “True” 1D nanostructures through “Medusa”-like structures can be obtained, maintaining anti-Stokes luminescence functionalities. A matter of the one-dimensional UCNPs based on direction of energy migration processes is debated. The proposed laser treatment approach is suitable for fast UCNP surface modification and nano-to-nano transformation, that open unique opportunities to expand UCNP applications in industry and biomedicine.

     

Cell-Based Optimization of Covalent Reversible Ketoamide Inhibitors Bridging the Unprimed to the Primed Site of the Proteasome β5 Subunit

The ubiquitin-proteasome system (UPS) is an established therapeutic target for approved drugs to treat selected hematologic malignancies. While drug discovery targeting the UPS focuses on irreversibly binding epoxyketones and slowly-reversibly binding boronates, optimization of novel covalent-reversibly binding warheads remains largely unattended. We previously reported α-ketoamides to be a promising reversible lead motif, yet the cytotoxic activity required further optimization. This work focuses on the lead optimization of phenoxy-substituted α-ketoamides combining the structure-activity relationships from the primed and the non-primed site of the proteasome β5 subunit. Our optimization strategy is accompanied by molecular modeling, suggesting occupation of P1′ by a 3-phenoxy group to increase β5 inhibition and cytotoxic activity in leukemia cell lines. Key compounds were further profiled for time-dependent inhibition of cellular substrate conversion. Furthermore, the α-ketoamide lead structure 27 does not affect escape response behavior in Danio rerio embryos, in contrast to bortezomib, which suggests increased target specificity.     

Microstructure and mechanical properties of Mg-5Li-1Al sheets prepared by accumulative roll bonding

Ultrafine-grain and high-strength Mg-5Li-1Al sheets were prepared by accumulative roll bonding (ARB) process. Evolution of microstructure and mechanical properties of ARB-processed Mg-5Li-1Al sheets was investigated.Results show that, during ARB process, the evolution of deformation mechanism of t Mg-5Li-1Al alloy is as follows: twinning deformation, shear deformation, forming macro shear zone, and finally dynamic recrystallization (DRX). The grain refining mechanism changes from twin DRX to rotation DRX. With the increase in ARB cycles, strength of the Mg-5Li-1Al sheets is enhanced, whilst elongation varies slightly. With the increase in rolling cycles, anisotropy of mechanical properties decreases. It is conclusive that strain hardening and grain refinement dominate the strengthening mechanism of Mg-5Li-1Al alloy.     

Biosorbents based on pine sawdust and malt sprouts for preconcentration and ICP-OES determination of nonferrous,heavy, and precious metals in the environmental samples

Pine sawdust and malt sprouts modified with orthophosphoric acid and carbamide have been proposed for solid-phase extraction (SPE) of nonferrous, heavy, and precious metals and their subsequent determination in the environmental samples by inductively coupled plasma optical emission spectrometry (ICP-OES). Modified adsorbents were characterized by SEM, TGA, and FT-IR and compared with native matrixes. SPE of some nonferrous and precious metal ions by biosorbents was studied. Depending on the SPE conditions, it was possible to separate nonferrous and heavy metals from alkali and alkaline earth metals. The proposed adsorbents are effective for preconcentration of nonferrous and heavy metals from natural waters and precious metals from solutions after digestion of geological samples.     

Statistical hierarchical clustering algorithm for outlier detection in evolving data streams

Machine Learning - Anomaly detection is a hard data analysis process that requires constant creation and improvement of data analysis algorithms. Using traditional clustering algorithms to analyse...     

A Comprehensive Review of Genetically Engineered Mouse Models for Prader-Willi Syndrome Research

Prader-Willi syndrome (PWS) is a neurogenetic multifactorial disorder caused by the deletion or inactivation of paternally imprinted genes on human chromosome 15q11-q13. The affected homologous locus is on mouse chromosome 7C. The positional conservation and organization of genes including the imprinting pattern between mice and men implies similar physiological functions of this locus. Therefore, considerable efforts to recreate the pathogenesis of PWS have been accomplished in mouse models. We provide a summary of different mouse models that were generated for the analysis of PWS and discuss their impact on our current understanding of corresponding genes, their putative functions and the pathogenesis of PWS. Murine models of PWS unveiled the contribution of each affected gene to this multi-facetted disease, and also enabled the establishment of the minimal critical genomic region (PWScr) responsible for core symptoms, highlighting the importance of non-protein coding genes in the PWS locus. Although the underlying disease-causing mechanisms of PWS remain widely unresolved and existing mouse models do not fully capture the entire spectrum of the human PWS disorder, continuous improvements of genetically engineered mouse models have proven to be very powerful and valuable tools in PWS research.     

Body Odors of Parasitized Caterpillars Give Away the Presence of Parasitoid Larvae to Their Primary Hyperparasitoid Enemies

Foraging success of parasitoids depends on the utilization of reliable information on the presence of their often, inconspicuous hosts. These parasitic wasps use herbivore-induced plant volatiles (HIPVs) that provide reliable cues on host presence. However, host searching of hyperparasitoids, a group of parasitoids that parasitize the larvae and pupae of other parasitoids, is more constrained. Their hosts do not feed on plants, and often are even concealed inside the body of the herbivore host. Hyperparasitoids recently have been found to use HIPVs of plants damaged by herbivore hosts in which the parasitoid larvae develop. However, hyperparasitoids that search for these parasitoid larvae may be confronted with healthy and parasitized caterpillars on the same plant, further complicating their host location. In this study, we addressed whether the primary hyperparasitoid Baryscapus galactopus uses caterpillar body odors to discriminate between unparasitized herbivores and herbivores carrying larvae of parasitoid hosts. We show that the hyperparasitoids made faster first contact and spent a longer mounting time with parasitized caterpillars. Moreover, although the three parasitoid hosts conferred different fitness values for the development of B. galactopus, the hyperparasitoids showed similar behavioral responses to caterpillar hosts carrying different primary parasitoid hosts. In addition, a two-chamber olfactometer assay revealed that volatiles emitted by parasitized caterpillars were more attractive to the hyperparasitoids than those emitted by unparasitized caterpillars. Analysis of volatiles revealed that body odors of parasitized caterpillars differ from unparasitized caterpillars, allowing the hyperparasitoids to detect their parasitoid host.