IR Tools: a MATLAB package of iterative regularization methods and large-scale test problems

Numerical Algorithms - This paper describes a new MATLAB software package of iterative regularization methods and test problems for large-scale linear inverse problems. The software package, called...     

Games with guaranteed scores and waiting moves

Combinatorial scoring games, with the property ‘extra pass moves for a player will do him no harm’, are characterized. The characterization involves an order embedding of Conway’s normal play games, and we call our class the universe of Guaranteed scoring games. Also, we give a theorem for comparing guaranteed games with scores (numbers) which extends Ettinger’s work on Dicot scoring games.     

High water‐content thermoresponsive hydrogels via electrostatic macrocrosslinking of cellulose nanofibrils

Atom transfer radical polymerization (ATRP) has been utilized to synthesize tri‐ and star‐block copolymers of poly(di(ethylene glycol)methyl ether methacrylate) (PDEGMA) and quaternized poly(2‐(dimethylamino)ethyl methacrylate) (qPDMAEMA). The block copolymers, all with a minimum of two cationically charged blocks, were sequentially used for electrostatic macrocrosslinking of a dilute dispersion of anionic TEMPO‐oxidized cellulose nanofibrils (CNF, 0.3 wt%), forming free‐standing hydrogels. The cationic block copolymers adsorbed irreversibly to the CNF, enabling the formation of ionically crosslinked hydrogels, with a storage modulus of up to 2.9 kPa. The ability of the block copolymers to adsorb to CNF was confirmed by quartz crystal microbalance with dissipation monitoring (QCM‐D) and infrared spectroscopy (FT‐IR), and the thermoresponsive properties of the hydrogels were investigated by rheological stress and frequency sweep, and gravimetric measurements. This method was shown to be promising for the facile production of thermoresponsive hydrogels based on CNF. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2016 , 54, 3415–3424     

Janus Face All-cis 1,2,4,5-tetrakis(trifluoromethyl)- and All-cis 1,2,3,4,5,6-hexakis(trifluoromethyl)- Cyclohexanes

We report the synthesis of all-cis 1,2,4,5-tetrakis (trifluoromethyl)- and all-cis 1,2,3,4,5,6-hexakis (trifluoromethyl)- cyclohexanes by direct hydrogenation of precursor tetrakis- or hexakis- (trifluoromethyl)benzenes. The resultant cyclohexanes have a stereochemistry such that all the CF₃ groups are on the same face of the cyclohexyl ring. All-cis 1,2,3,4,5,6-hexakis(trifluoromethyl)cyclohexane is the most sterically demanding of the all-cis hexakis substituted cyclohexanes prepared to date, with a barrier (ΔG) to ring inversion calculated at 27 kcal mol⁻¹. The X-ray structure of all-cis 1,2,3,4,5,6-hexakis(trifluoromethyl)cyclohexane displays a flattened chair conformation and the electrostatic profile of this compound reveals a large diffuse negative density on the fluorine face and a focused positive density on the hydrogen face. The electropositive hydrogen face can co-ordinate chloride (K≈10³) and to a lesser extent fluoride and iodide ions. Dehydrofluorination promoted decomposition occurs with fluoride ion acting as a base.     

Gapmer Antisense Oligonucleotides Containing 2′,3′-Dideoxy-2′-fluoro-3′-C-hydroxymethyl-β-d-lyxofuranosyl Nucleotides Display Site-Specific RNase H Cleavage and Induce Gene Silencing

Off-target effects remain a significant challenge in the therapeutic use of gapmer antisense oligonucleotides (AONs). Over the years various modifications have been synthesized and incorporated into AONs, however, precise control of RNase H-induced cleavage and target sequence selectivity has yet to be realized. Herein, the synthesis of the uracil and cytosine derivatives of a novel class of 2′-deoxy-2′-fluoro-3′-C-hydroxymethyl-β-d -lyxo-configured nucleotides has been accomplished and the target molecules have been incorporated into AONs. Experiments on exonuclease degradation showed improved nucleolytic stability relative to the unmodified control. Upon the introduction of one or two of the novel 2′-fluoro-3′-C-hydroxymethyl nucleotides as modifications in the gap region of a gapmer AON was associated with efficient RNase H-mediated cleavage of the RNA strand of the corresponding AON:RNA duplex. Notably, a tailored single cleavage event could be engineered depending on the positioning of a single modification. The effect of single mismatched base pairs was scanned along the full gap region demonstrating that the modification enables a remarkable specificity of RNase H cleavage. A cell-based model system was used to demonstrate the potential of gapmer AONs containing the novel modification to mediate gene silencing.     

Light-Responsive Elastin-Like Peptide-Based Targeted Nanoparticles for Enhanced Spheroid Penetration

We describe here a near infrared light-responsive elastin-like peptide (ELP)-based targeted nanoparticle (NP) that can rapidly switch its size from 120 to 25 nm upon photo-irradiation. Interestingly, the targeting function, which is crucial for effective cargo delivery, is preserved after transformation. The NPs are assembled from (targeted) diblock ELP micelles encapsulating photosensitizer TT1-monoblock ELP conjugates. Methionine residues in this monoblock are photo-oxidized by singlet oxygen generated from TT1, turning the ELPs hydrophilic and thus trigger NP dissociation. Phenylalanine residues from the diblocks then interact with TT1 via π-π stacking, inducing the re-formation of smaller NPs. Due to their small size and targeting function, the NPs penetrate deeper in spheroids and kill cancer cells more efficiently compared to the larger ones. This work could contribute to the design of “smart” nanomedicines with deeper penetration capacity for effective anticancer therapies.     

Absolute Asymmetric Synthesis of a Tetrahedral Silver Complex

Even though the isolation of tetrahedral stereoisomers usually presents a synthetic challenge, a highly enantioenriched tetrahedral silver complex could be easily accessed by either crystallization or Viedma ripening. The overall preparation may be regarded as an example of absolute asymmetric synthesis. Experimental results indicate that both crystallization and Viedma ripening follow a similar cluster‐controlled mechanism.     

<Emphasis Type="Italic">Gluconobacter</Emphasis> sp. cells for manufacturing of effective electrochemical biosensors and biofuel cells

Gluconobacter oxydans bacteria exhibit a unique metabolism for quick and incomplete oxidation of a wide range of different compounds (aldoses, ketoses, mono- and poly-alcohols, etc.). Such biotransformation efficiency with simple biomass production led to the industrial applications of these bacteria in the production of several important commodities. Their respiratory activity can also be successfully studied and used in the field of bioelectrochemistry. The main aim of this review is to present various strategies to improve selectivity of assays using intact/treated cells of G. oxydans, to introduce the application of G. oxydans-based biosensors in selective monitoring of analytes during biotransformation processes and to provide information about utilizable sugars in fermentation media or in biological oxygen demand value determination. The final part of the review describes potential application of G. oxydans cells in the generation of electricity from complex fuels within microbial fuel cells by advanced direct electron transfer route between bacterial cells and electrodes.