QSAR with experimental and predictive distributions: an information theoretic approach for assessing model quality

We propose that quantitative structure–activity relationship (QSAR) predictions should be explicitly represented as predictive (probability) distributions. If both predictions and experimental measurements are treated as probability distributions, the quality of a set of predictive distributions output by a model can be assessed with Kullback–Leibler (KL) divergence: a widely used information theoretic measure of the distance between two probability distributions. We have assessed a range of different machine learning algorithms and error estimation methods for producing predictive distributions with an analysis against three of AstraZeneca’s global DMPK datasets. Using the KL-divergence framework, we have identified a few combinations of algorithms that produce accurate and valid compound-specific predictive distributions. These methods use reliability indices to assign predictive distributions to the predictions output by QSAR models so that reliable predictions have tight distributions and vice versa. Finally we show how valid predictive distributions can be used to estimate the probability that a test compound has properties that hit single- or multi- objective target profiles.     

Reproducibility of serum protein profiling by systematic assessment using solid-phase extraction and matrix-assisted laser desorption/ionization mass spectrometry

Protein profiling of human serum by matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) is potentially a new diagnostic tool for early detection of human diseases, including cancer. Sample preparation is a key issue in MALDI MS and the analysis of complex samples such as serum requires optimized, reproducible methods for handling and deposition of protein samples. Data acquisition in MALDI MS is also a critical issue, since heterogeneity of sample deposits leads to attenuation of ion signals in MALDI MS. In order to improve the robustness and reproducibility of MALDI MS for serum protein profiling we investigated a range of sample preparation techniques and developed a statistical method based on repeated analyses for evaluation of protein-profiling performance of MALDI MS. Two different solid-phase extraction (SPE) methods were investigated, namely custom-made microcolumns and commercially available magnetic beads. Using these two methods, nineteen different sample preparation methods for serum profiling by MALDI MS were systematically tested with regard to matrix selection, stationary phase, selectivity, and reproducibility. Microcolumns were tested with regard to chromatographic properties; reversed phase (C8, C18, SDB-XC), ion-exchange (anion, weak cation, mixed-phase (SDB-RPS)) and magnetic beads were tested with regard to chromatographic properties; reversed phase (C8) or affinity chromatography (Cu-IMAC). The reproducibility of each sample preparation method was determined by enumeration and analysis of protein signals that were detected in at least six out of nine spectra obtained by three triplicate analyses of one serum sample.A candidate for best overall performance as evaluated by the number of peaks generated and the reproducibility of mass spectra was found among the tested methods. Up to 418 reproducible peaks were detected in one cancer serum sample. These protein peaks can be part of a possible diagnostic profile, suggesting that this sample preparation method and data acquisition approach is suitable for large-scale analysis of serum samples for protein profiling.     

Picosecond passively mode-locked GaSb-based semiconductor disk laser operating at 2 μm

We report on a passively mode-locked optically pumped GaSb-based semiconductor disk laser producing stable picosecond optical pulses at a 1.95 μm wavelength. The gain mirror was comprised of a 15 quantum well InGaSb/GaSb structure. A fast semiconductor saturable absorber mirror with three InGaSb/GaSb quantum wells was used to attain self-starting mode-locked operation at a fundamental repetition rate of 881.2 MHz. The laser produced pulses with 30 pJ energy and a duration of 1.1 ps within a factor of 2 of the Fourier limit.     

A regular decomposition of the edge-product space of phylogenetic trees

We investigate the topology and combinatorics of a topological space called the edge-product space that is generated by the set of edge-weighted finite labelled trees. This space arises by multiplying the weights of edges on paths in trees, and is closely connected to tree-indexed Markov processes in molecular evolutionary biology. In particular, by considering combinatorial properties of the Tuffley poset of labelled forests, we show that the edge-product space has a regular cell decomposition with face poset equal to the Tuffley poset.     

Preventive Support for Kindergarteners Most At-Risk for Mathematics Difficulties: Computer-Assisted Intervention

Weaknesses in early number skills have been found to be a risk factor for later difficulties in mathematical performance. Nevertheless, only a few intervention studies with young children have been published. In this study, the responsiveness to early support in kindergarteners with most severe difficulties was examined with two different computer programs. Two intervention groups were matched by age, visuo-spatial, and phonological working memory, as well as early number skills. After a short and intensive computerized intervention, the results indicated significant intervention effects for verbal counting Wilcoxon ES (r) = 0.46, and dot counting fluency, r = 0.52, when practiced with GraphoGame Math, as well as for basic arithmetic, r = 0.63, when practiced with Number Race. The findings suggest that a targeted computerized practice can produce specific training effects in kindergarteners most at-risk for mathematics difficulties. The results are discussed with regard to practical implications for educational game development.     

Additive‐like amounts of HDPE prevent creep of molten LDPE: Phase‐behavior and thermo‐mechanical properties of a melt‐miscible blend

Low‐density polyethylene (LDPE) is the preferred type of polyolefin for many medical and electrical applications because of its superior purity and cleanliness. However, the inferior thermo‐mechanical properties as compared to, for example, high‐density polyethylene (HDPE), which arise because of the lower melting temperature of LDPE, constitute a significant drawback. Here, we demonstrate that the addition of minute amounts of HDPE to a LDPE resin considerably improves the mechanical integrity above the melting temperature of LDPE. A combination of dynamic mechanical analysis and creep experiments reveals that the addition of as little as 1 to 2 wt% HDPE leads to complete form stability above the melting temperature of LDPE. The investigated LDPE/HDPE blend is found to be miscible in the melt, which facilitates the formation of a solid‐state microstructure that features a fine distribution of HDPE‐rich lamellae. The absence of creep above the melting temperature of LDPE is rationalized with the presence of tie chains and trapped entanglements that connect the few remaining crystallites. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2017 , 55, 146–156     

Poly[(acetone)tetraaqua[μ6‐ethyl (dichloromethylene)diphosphonato][μ5‐ethyl (dichloromethylene)diphosphonato]tribarium(II)]

The novel title compound, [Ba₃(C₃H₅Cl₂O₆P₂)₂(C₃H₆O)(H₂O)₄]_n, has a polymeric two‐dimensional network structure which lies parallel to the (10) plane. The asymmetric unit consists of three independent Ba²⁺ ions, two of them eight‐coordinated and the third nine‐coordinated, and two independent ethyl (dichloromethylene)diphosphonate(3−) ligands, one acetone ligand and four aqua ligands. The coordination environments around the BaO₈ polyhedra are best described as bicapped trigonal prismatic, while the BaO₉ polyhedron is in a distorted tricapped trigonal prismatic geometry. The two diphosphonate ligands adopt different coordination modes. Both ligands chelate three metal cations, but one is coordinated to six metal cations in total and forms two six‐membered and one four‐membered chelate ring, while the other is coordinated to five metal cations in total and forms one six‐membered and two four‐membered chelate rings, the fifth unsubstituted O atom remaining uncoordinated.     

Sustainable stabilization of oil in water emulsions by cellulose nanocrystals synthesized from deep eutectic solvents

There is an urgent global need to develop novel types of environmentally safe dispersing chemicals from renewable resources in order to reduce the environmental impact of oil spills. For this goal, cellulose, the most abundant natural polymeric source, is a promising green, nontoxic alternative that could replace the current synthetic surfactants. In this study, cellulose nanocrystals (CNC) synthesized using a deep eutectic solvent (DES) and two commercially available cellulose nanocrystals were used as marine diesel oil–water Pickering emulsion stabilizers. In particular, oil in water (o/w) emulsion formation and stability of emulsified oil during storing were addressed using a laser diffraction particle size analyzer, image analysis, and oil emulsion volume examination. The particle size of the o/w reference without CNCs after dispersing was over 50 µm and coalescence occurred only a few minutes after the emulsifying mixing procedure. All three investigated CNCs were effective stabilizers for the o/w system (oil droplets size under 10 µm) by preventing the oil droplet coalescence over time (6 weeks) and resulting in a stable creaming layer. The CNCs prepared using green DES systems boasted performance comparable to that of commercial CNCs, and they showed effectiveness at 0.1% dispersant dosage.