Time-resolved fluorescence spectra using time-correlated photon counting: Picosecond fluorescence in aqueous solutions of Cr(III) complexes at room temperature

A new procedure for measuring time-resolved emission spectra has been implemented. This technique has subnanosecond time resolution combined with the sensitivity and dynamic range needed to cope with extremely weak luminescence. Using this method the emissions of Cr(NH₃)₂ (NCS)₄^? and Cr(NCS)₆^3- in aqueous solution at room temperature have each been analyzed into two components. The fast component has a broad spectrum and is assigned to prompt fluorescence with lifetime below 100 ps. The slow component is dominated by phosphorescence but may include some delayed fluorescence. The phosphorescence lifetime is 5.5 ± 0.5 ns in Cr(NH₃)₂ (NCS)₄^? and 1.65 ± 0.1 ns in Cr(NCS)₆^3-. Order of magnitude estimates have been derived for other photophysical parameters.     

Novel Methods to Manipulate Autolysis in Sparkling Wine: Effects on Yeast

Sparkling wine made by the traditional method (Méthode Traditionelle) develops a distinct and desirable flavour and aroma profile attributed to proteolytic processes during prolonged ageing on lees. Microwave, ultrasound and addition of β-glucanase enzymes were applied to accelerate the disruption of Saccharomyces cerevisiae, and added to the tirage solution for secondary fermentation in traditional sparkling winemaking. Scanning electron microscopy and flow cytometry analyses were used to observe and describe yeast whole-cell anatomy, and cell integrity and structure via propidium iodide (PI) permeability after 6-, 12- and 18-months post-tirage. Treatments applied produced features on lees that were distinct from that of the untreated control yeast. Whilst control yeast displayed budding cells (growth features) with smooth, cavitated and flat external cell appearances; microwave treated yeast cells exhibited modifications like ‘doughnut’ shapes immediately after treatment (time 0). Similar ‘doughnut’-shaped and ‘pitted/porous’ cell features were observed on progressively older lees from the control. Flow cytometry was used to discriminate yeast populations; features consistent with cell disruption were observed in the microwave, ultrasound and enzyme treatments, as evidenced by up to 4-fold increase in PI signal in the microwave treatment. Forward and side scatter signals reflected changes in size and structure of yeast cells, in all treatments applied. When flow cytometry was interpreted alongside the scanning electron microscopy images, bimodal populations of yeast cells with low and high PI intensities were revealed and distinctive ‘doughnut’-shaped cell features observed in association with the microwave treatment only at tirage, that were not observed until 12 months wine ageing in older lees from the control. This work offers both a rapid approach to visualise alterations to yeast cell surfaces and a better understanding of the mechanisms of yeast lysis. Microwave, ultrasound or β-glucanase enzymes are tools that could potentially initiate the release of yeast cell compounds into wine. Further investigation into the impact of such treatments on the flavour and aroma profiles of the wines through sensory evaluation is warranted.     

Cobalt(II) and cobalt(III) dipicolinate complexes: solid state,solution, and in vivo insulin-like properties

The synthesis and characterization of Co(II) and Co(III) 2,6-pyridinedicarboxylate (dipic(2-)) complexes are reported. Solid-state X-ray characterizations were performed on [Co(H(2)dipic)(dipic)].3H(2)O and [Co(dipic)(mu-dipic)Co(H(2)O)(5)].2H(2)O. Two coordination modes not previously observed in dipicolinate transition metal complexes were observed in these complexes; one involves metal coordination to the short C-O (C=O) bond, and the other involves metal coordination to a protonated oxygen atom. Solution studies, including paramagnetic NMR and UV-vis spectroscopy, were done showing the high stability and low lability of the Co(III) complex, whereas the Co(II) complexes exhibited ligand exchange in the presence of excess ligand. The [Co(dipic)(2)](2-) complex has pH dependent lability and in this regard is most similar to the [VO(2)dipic](-) complex. The [Co(dipic)(2)](2-) was found to be effective in reducing the hyperlipidemia of diabetes using oral administration in drinking water in rats with STZ-induced diabetes. Oral administration of VOSO(4) was used as a positive control for metal efficacy against diabetes. In addition to providing a framework to evaluate structure-function relationships of various transition metal complexes in alleviating the symptoms of diabetes, this work describes novel aspects of structural and solution cobalt chemistry.     

Information-theoretic approaches to SVM feature selection for metagenome read classification

Analysis of DNA sequences isolated directly from the environment, known as metagenomics, produces a large quantity of genome fragments that need to be classified into specific taxa. Most composition-based classification methods use all features instead of a subset of features that may maximize classifier accuracy. We show that feature selection methods can boost performance of taxonomic classifiers. This work proposes three different filter-based feature selection methods that stem from information theory: (1) a technique that combines Kullback-Leibler, Mutual Information, and distance information, (2) a text mining technique, TF-IDF, and (3) minimum redundancy-maximum-relevance (mRMR). The feature selection methods are compared by how well they improve support vector machine classification of genomic reads. Overall, the 6mer mRMR method performs well, especially on the phyla-level. If the number of total features is very large, feature selection becomes difficult because a small subset of features that captures a majority of the data variance is less likely to exist. Therefore, we conclude that there is a trade-off between feature set size and feature selection method to optimize classification performance. For larger feature set sizes, TF-IDF works better for finer-resolutions while mRMR performs the best out of any method for N=6 for all taxonomic levels.     

The d'--d--d' vertical triad is less discriminating than the a'--a--a' vertical triad in the antiparallel coiled-coil dimer motif

Elucidating relationships between the amino-acid sequences of proteins and their three-dimensional structures, and uncovering non-covalent interactions that underlie polypeptide folding, are major goals in protein science. One approach toward these goals is to study interactions between selected residues, or among constellations of residues, in small folding motifs. The α-helical coiled coil has served as a platform for such studies because this folding unit is relatively simple in terms of both sequence and structure. Amino acid side chains at the helix-helix interface of a coiled coil participate in so-called "knobs-into-holes" (KIH) packing whereby a side chain (the knob) on one helix inserts into a space (the hole) generated by four side chains on a partner helix. The vast majority of sequence-stability studies on coiled-coil dimers have focused on lateral interactions within these KIH arrangements, for example, between an a position on one helix and an a' position of the partner in a parallel coiled-coil dimer, or between a--d' pairs in an antiparallel dimer. More recently, it has been shown that vertical triads (specifically, a'--a--a' triads) in antiparallel dimers exert a significant impact on pairing preferences. This observation provides impetus for analysis of other complex networks of side-chain interactions at the helix-helix interface. Here, we describe a combination of experimental and bioinformatics studies that show that d'--d--d' triads have much less impact on pairing preference than do a'--a--a' triads in a small, designed antiparallel coiled-coil dimer. However, the influence of the d'--d--d' triad depends on the lateral a'--d interaction. Taken together, these results strengthen the emerging understanding that simple pairwise interactions are not sufficient to describe side-chain interactions and overall stability in antiparallel coiled-coil dimers; higher-order interactions must be considered as well.     

Variational multirate integration in multi-body dynamics

For systems that contain slow and fast dynamics, variational multirate integration schemes are used. These schemes split the system into parts which are simulated using two time grids consisting of micro and macro nodes. This formulation can be extended for multi-body systems. The rigid multi-body system is described by the so called director formulation and constraints describing the joints connecting the bodies. With the Lagrange multiplier method, the constraints are introduced into the equations of motion. A way to implement the null space method into the variational multirate framework is shown and the influence on the number of unknowns is investigated. (© 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim)     

Synthesis of Benzofurans by the Action of Copper on Terminal Alkynes and O-Halophenols

Cuprous acetylides react with aryl halides to yield aryl acetylenes and with o-halophenols to give benzofurans.^1,2 The broad scope of this latter reaction for the synthesis of benzofuran natural products is shown by application inter alia to norlignans,³ euparinoids,⁴ phytoalexins,⁵ furanocoumarins,⁶ fomannoxin,⁷ isotubaic acid⁸ and machicendiol.     

An effective and simple heuristic for the set covering problem

This paper investigates the development of an effective heuristic to solve the set covering problem (SCP) by applying the meta-heuristic Meta-RaPS (Meta-heuristic for Randomized Priority Search). In Meta-RaPS, a feasible solution is generated by introducing random factors into a construction method. Then the feasible solutions can be improved by an improvement heuristic. In addition to applying the basic Meta-RaPS, the heuristic developed herein integrates the elements of randomizing the selection of priority rules, penalizing the worst columns when the searching space is highly condensed, and defining the core problem to speedup the algorithm. This heuristic has been tested on 80 SCP instances from the OR-Library. The sizes of the problems are up to 1000 rows × 10,000 columns for non-unicost SCP, and 28,160 rows × 11,264 columns for the unicost SCP. This heuristic is only one of two known SCP heuristics to find all optimal/best known solutions for those non-unicost instances. In addition, this heuristic is the best for unicost problems among the heuristics in terms of solution quality. Furthermore, evolving from a simple greedy heuristic, it is simple and easy to code. This heuristic enriches the options of practitioners in the optimization area.     

Psychophysical recovery from pulse-train forward masking in electric hearing

Psychophysical pulse-train forward-masking (PTFM) recovery functions were measured in fifteen subjects with the Nucleus mini-22 cochlear implant and six subjects with the Clarion cochlear implant. Masker and probe stimuli were 500-Hz trains of 200- or 77-micros/phase biphasic current pulses. Electrode configurations were bipolar for Nucleus subjects and monopolar for Clarion subjects. Masker duration was 320 ms. Probe duration was either 10 ms or 30 ms. Recovery functions were measured for a high-level masker on a middle electrode in all 21 subjects, on apical and basal electrodes in 7 of the Nucleus and 3 of the Clarion subjects, and for multiple masker levels on the middle electrode in 8 Nucleus subjects and 6 Clarion subjects. Recovery functions were described by an exponential process in which threshold shift (in microA) decreased exponentially with increasing time delay between the offset of the masker pulse train and the offset of the probe pulse train. All but 3 of the 21 subjects demonstrated recovery time constants on a middle electrode that were less than 95 ms. The mean time constant for these 18 subjects was 54 ms (s.d. 17 ms). Three other subjects tested on three electrodes exhibited time constants larger than 95 ms from an apical electrode only. Growth-of-masking slopes depended upon time delay, as expected from an exponential recovery process, i.e., progressively shallower slopes were observed at time delays of 10 ms and 50 ms. Recovery of threshold shift (in microA) for PTFM in electrical hearing behaves inthe same way as recovery of threshold shift (in dB) for pure-tone forward masking in acoustic hearing. This supports the concept that linear microamps are the electrical equivalent of acoustic decibels. Recovery from PTFM was not related to speech recognition in a simple manner. Three subjects with prolonged PTFM recovery demonstrated poor speech scores. The remaining subjects with apparently normal PTFM recovery demonstrated speech scores ranging from poor to excellent. Findings suggest that normal PTFM recovery is only one of several factors associated with good speech recognition in cochlear-implant listeners. Comparisons of recovery curves for 10- and 30-ms probe durations in two subjects showed little or no temporal integration at time delays less than 95 ms where recovery functions have steep slopes. The same subjects exhibited large amounts of temporal integration at longer time delays where recovery slopes are more gradual. This suggests that probe detection depends primarily on detection of the final pulses in the probe stimulus and supports the use of offset-to-offset time delays for characterizing PTFM recovery in electric hearing.