Mining sequences with exceptional transition behaviour of varying order using quality measures based on information-theoretic scoring functions

Data Mining and Knowledge Discovery - Discrete Markov chains are frequently used to analyse transition behaviour in sequential data. Here, the transition probabilities can be estimated using...     

Solid state NMR study of segmented polymer networks: fine-tuning of phase morphology via their molecular design

Segmented polymer networks (SPNs) based on thermo-sensitive poly(N-isopropyl acryl amide) (PNIPAA) and poly(tetrahydrofuran) (PTHF) have been synthesized by free radical copolymerization of PTHF bis-macromonomers with N-isopropyl acrylamide. The nature of the polymerizable end group on the bis-macromonomer has been varied, respectively from acrylate to acrylamide end groups. The multiphase behaviour of the corresponding SPNs has been examined as a function of the nature of the end group by making use of solid-state ¹³C CP/MAS NMR relaxometry, ¹H wideline NMR relaxometry and dynamic mechanical analysis (DMA). When PTHF with acrylate end groups was used during the SPN formation, analysis of proton spin-lattice relaxation times (T_1H) and proton spin-lattice relaxation times in the rotating frame (T_1ρH) revealed phase separation with domain sizes larger than 5 nm when the PTHF fraction exceeds 10 wt%. Only for lower PTHF-amounts, the SPNs were homogeneous on the nanometer scale. On the other hand, when PTHF with acrylamide end groups was used as macromolecular cross-linker, the NMR results showed the absence of any domain formation for SPNs with PTHF fractions up to 50 wt%. The major impact of the molecular design on the ultimate phase morphology of bicomponent polymer networks has been confirmed in all cases by DMA-analysis.     

Improving accuracy in detecting acoustic onsets.

In current cognitive psychology, naming latencies are commonly measured by electronic voice keys that detect when sound exceeds a certain amplitude threshold. However, recent research (e.g., K. Rastle & M. H. Davis, 2002) has shown that these devices are particularly inaccurate in precisely detecting acoustic onsets. In this article, the authors discuss the various problems and solutions that have been put forward with respect to this issue and show that classical voice keys may trigger several tens of milliseconds later than acoustic onset. The authors argue that a solution to this problem may come from voice keys that use a combination of analogue and digital noise (nonspeech sound) detection. It is shown that the acoustic onsets detected by such a device are only a few milliseconds delayed and correlate highly (up to .99) with reaction time values obtained by visual waveform inspection. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Role of nitrogen lewis basicity in boronate affinity chromatography of nucleosides

Urinary modified nucleosides have a potential role as cancer biomarkers, and most of the methods used in their study have utilized low-pressure phenylboronate affinity chromatography materials for the purification of the cis-diol-containing nucleosides. In this study, a boronate HPLC column was surprisingly shown not to trap the nucleosides as would be expected from experience with the classic Affigel 601 resin but showed only partial selectivity toward cis-diol groups while other groups exhibited better retention. In aprotic conditions, trapping of nucleosides was possible; however, the selectivity toward cis-diol-containing compounds was lost with the Lewis basicity of available nitrogens being the main determinant of retention. The experimental findings are compared to and confirmed by DFT calculations.     

The Progress of Intestinal Epithelial Models from Cell Lines to Gut-On-Chip

Over the past years, several preclinical in vitro and ex vivo models have been developed that helped to understand some of the critical aspects of intestinal functions in health and disease such as inflammatory bowel disease (IBD). However, the translation to the human in vivo situation remains problematic. The main reason for this is that these approaches fail to fully reflect the multifactorial and complex in vivo environment (e.g., including microbiota, nutrition, and immune response) in the gut system. Although conventional models such as cell lines, Ussing chamber, and the everted sac are still used, increasingly more sophisticated intestinal models have been developed over the past years including organoids, InTESTine™ and microfluidic gut-on-chip. In this review, we gathered the most recent insights on the setup, advantages, limitations, and future perspectives of most frequently used in vitro and ex vivo models to study intestinal physiology and functions in health and disease.     

Life cycle assessment of Jatropha biodiesel as transportation fuel in rural India

Since 2003 India has been actively promoting the cultivation of Jatropha on unproductive and degraded lands (wastelands) for the production of biodiesel suitable as transportation fuel. In this paper the life cycle energy balance, global warming potential, acidification potential, eutrophication potential and land use impact on ecosystem quality is evaluated for a small scale, low-input Jatropha biodiesel system established on wasteland in rural India. In addition to the life cycle assessment of the case at hand, the environmental performance of the same system expanded with a biogas installation digesting seed cake was quantified. The environmental impacts were compared to the life cycle impacts of a fossil fuel reference system delivering the same amount of products and functions as the Jatropha biodiesel system under research. The results show that the production and use of Jatropha biodiesel triggers an 82% decrease in non-renewable energy requirement (Net Energy Ratio, NER = 1.85) and a 55% reduction in global warming potential (GWP) compared to the reference fossil-fuel based system. However, there is an increase in acidification (49%) and eutrophication (430%) from the Jatropha system relative to the reference case. Although adding biogas production to the system boosts the energy efficiency of the system (NER = 3.40), the GWP reduction would not increase (51%) due to additional CH₄ emissions. For the land use impact, Jatropha improved the structural ecosystem quality when planted on wasteland, but reduced the functional ecosystem quality. Fertilizer application (mainly N) is an important contributor to most negative impact categories. Optimizing fertilization, agronomic practices and genetics are the major system improvement options.     

Secreted production of a custom-designed, highly hydrophilic gelatin in Pichia pastoris

A custom-designed, highly hydrophilic gelatin was produced inPichia pastoris. Secreted production levels in single-copytransformants were in the range 3–6 g/l of clarified brothand purification to near homogeneity could be accomplished bydifferential ammonium sulfate precipitation. Despite the factthat gelatins are highly susceptible to proteolysis becauseof their unfolded structure, the recombinant protein was shownto be fully intact by SDS–PAGE, N-terminal sequencing,gel filtration chromatography and mass spectrometry. Owing toits highly hydrophilic nature, the migration of the syntheticgelatin in SDS–PAGE was severely delayed. Esterificationof the carboxylic amino acid side chains resulted in normalmigration. The high polarity of the synthetic gelatin also accountsfor its negligible surface activity in water at concentrationsup to 5% (w/v), as determined by tensiometry. Circular dichroismspectrometry showed that the non-hydroxylated gelatin did notform triple helices at 4°C. The spectrum was even more representativeof the random coil conformation than the spectrum of naturalnon-hydroxylated gelatins.     

Nonhydrolyzable Heptose Bis- and Monophosphate Analogues Modulate Pro-inflammatory TIFA-NF-κB Signaling

d -Glycero-d -manno-heptose-1β,7-bisphosphate (HBP) and d -glycero-d -manno-heptose-1β-phosphate (H1P) are bacterial metabolites that were recently shown to stimulate inflammatory responses in host cells through the activation of the TIFA-dependent NF-κB pathway. To better understand structure-based activity in relation to this process, a family of nonhydrolyzable phosphonate analogues of HBP and H1P was synthesized. The inflammation modulation by which these molecules induce the TIFA-NF-κB signal axis was evaluated in vivo at a low-nanomolar concentration (6 nM) and compared to that of the natural metabolites. Our data showed that three phosphonate analogues had similar stimulatory activity to HBP, whereas two phosphonates antagonized HBP-induced TIFA-NF-κB signaling. These results open new horizons for the design of pro-inflammatory and innate immune modulators that could be used as vaccine adjuvant.