Amylomaltase of Pyrobaculum aerophilum IM2 produces thermoreversible starch gels

Amylomaltases are 4-α-glucanotransferases (EC 2.4.1.25) of glycoside hydrolase family 77 that transfer α-1,4-linked glucans to another acceptor, which can be the 4-OH group of an α-1,4-linked glucan or glucose. The amylomaltase-encoding gene (PAE1209) from the hyperthermophilic archaeon Pyrobaculum aerophilum IM2 was cloned and expressed in Escherichia coli, and the gene product (PyAMase) was characterized. PyAMase displays optimal activity at pH 6.7 and 95°C and is the most thermostable amylomaltase described to date. The thermostability of PyAMase was reduced in the presence of 2 mM dithiothreitol, which agreed with the identification of two possible cysteine disulfide bridges in a three-dimensional model of PyAMase. The kinetics for the disproportionation of malto-oligosaccharides, inhibition by acarbose, and binding mode of the substrates in the active site were determined. Acting on gelatinized food-grade potato starch, PyAMase produced a thermoreversible starch product with gelatin-like properties. This thermoreversible gel has potential applications in the food industry. This is the first report on an archaeal amylomaltase

III-V on-silicon sources for optical interconnect applications

Optical interconnects require efficient and flexible optical sources. This paper presents results on two technology platforms being developed for realizing these. Integration using wafer bonding technologies is well established now and the focus is on new device types including tunable lasers, multi-wavelength lasers and switching. As an alternative, we also started work on monolithic integration using heteroepitaxy directly on silicon. We here report recent results on low threshold nanowire lasers

Force balance in canonical ensembles of static granular packings

We investigate the role of local force balance in the transition from a microcanonical ensemble of static granular packings, characterized by an invariant stress, to a canonical ensemble. Packings in two dimensions admit a reciprocal tiling, and a collective effect of force balance is that the area of this tiling is also invariant in a microcanonical ensemble. We present analytical relations between stress, tiling area and tiling area fluctuations, and show that a canonical ensemble can be characterized by an intensive thermodynamic parameter conjugate to one or the other. We test the equivalence of different ensembles through the first canonical simulations of the force network ensemble, a model system.Comment: 9 pages, 9 figures, submitted to JSTA

A pilot study to evaluate the effects of C1 esterase inhibitor on the toxicity of high-dose interleukin 2.

In a pilot study six patients received 4 days' treatment with interleukin 2 (IL-2) [cumulative dose (CD) 264 +/- 26 x 10(6) IU m-2] and C1 esterase inhibitor (C1-INH) (loading dose 2,000 U, followed by 500-1,000 U twice daily). Toxicity was compared with that in patients given 4 days' treatment with standard (CD 66 +/- 12 x 10(6) IU m-2) or escalating-dose (CD 99 +/- 8 x 10(6) IU m-2) IL-2. IL-2-induced hypotension was equivalent and complement activation was less after IL-2 + C1-INH (C3a = 10.5 +/- 3.2 nmol l-1) than following standard (14.1 +/- 8.4 nmol l-1) or escalating-dose (18.3 +/- 2.9 nmol l-1) IL-2. This study demonstrates that C1-INH administration during IL-2 treatment is safe and warrants further study to evaluate its ability to ameliorate IL-2-induced toxicity

Gut colonization with methanobrevibacter smithii is associated with childhood weight development

OBJECTIVE: To prospectively investigate the presence and counts of archaea in feces of 472 children in association with weight development from 6 to 10 years of age. METHODS: Within the KOALA Birth Cohort Study, a single fecal sample from each child was analyzed by quantitative polymerase chain reaction to quantify archaea (Methanobrevibacter smithii, Methanosphera stadtmanae). Anthropometric outcomes (overweight [body mass index {BMI} >/= 85th percentile], age- and sex-standardized BMI, weight, and height z-scores) were repeatedly measured at ages (mean +/- SD) of 6.2 +/- 0.5, 6.8 +/- 0.5, 7.8 +/- 0.5, and 8.8 +/- 0.5 years. Generalized estimating equation was used for statistical analysis while controlling for confounders. RESULTS: Methanobrevibacter smithii colonization was associated with an increased risk of overweight (adjusted odds ratio [OR] = 2.69; 95% confidence interval [CI] 0.96-7.54) from 6 to 10 years of age. Children with high levels (>7 log10 copies/g feces) of this archaeon were at highest risk for overweight (OR = 3.27; 95% CI 1.09-9.83). Moreover, M. smithii colonization was associated with higher weight z-scores (adj. beta 0.18; 95% CI 0.00-0.36), but not with height. For BMI z-scores, the interaction (P = 0.008) between M. smithii and age was statistically significant, implying children colonized with M. smithii had increasing BMI z-scores with age. CONCLUSIONS: Presence and higher counts of M. smithii in the gut of children are associated with higher weight z-scores, higher BMI z-scores, and overweight

Optimally Dense Packings for Fully Asymptotic Coxeter Tilings by Horoballs of Different Types

The goal of this paper to determine the optimal horoball packing arrangements and their densities for all four fully asymptotic Coxeter tilings (Coxeter honeycombs) in hyperbolic 3-space $\mathbb{H}^3$. Centers of horoballs are required to lie at vertices of the regular polyhedral cells constituting the tiling. We allow horoballs of different types at the various vertices. Our results are derived through a generalization of the projective methodology for hyperbolic spaces. The main result states that the known B\"or\"oczky--Florian density upper bound for "congruent horoball" packings of $\mathbb{H}^3$ remains valid for the class of fully asymptotic Coxeter tilings, even if packing conditions are relaxed by allowing for horoballs of different types under prescribed symmetry groups. The consequences of this remarkable result are discussed for various Coxeter tilings.Comment: 26 pages, 10 figure

The learning curve of laparoscopic, robot-assisted and transanal total mesorectal excisions:a systematic review

Background The standard treatment of rectal carcinoma is surgical resection according to the total mesorectal excision principle, either by open, laparoscopic, robot-assisted or transanal technique. No clear consensus exists regarding the length of the learning curve for the minimal invasive techniques. This systematic review aims to provide an overview of the current literature regarding the learning curve of minimal invasive TME. Methods A systematic literature search was performed. PubMed, Embase and Cochrane Library were searched for studies with the primary or secondary aim to assess the learning curve of either laparoscopic, robot-assisted or transanal TME for rectal cancer. The primary outcome was length of the learning curve per minimal invasive technique. Descriptive statistics were used to present results and the MINORS tool was used to assess risk of bias. Results 45 studies, with 7562 patients, were included in this systematic review. Length of the learning curve based on intraoperative complications, postoperative complications, pathological outcomes, or a composite endpoint using a risk-adjusted CUSUM analysis was 50 procedures for the laparoscopic technique, 32-75 procedures for the robot-assisted technique and 36-54 procedures for the transanal technique. Due to the low quality of studies and a high level of heterogeneity a meta-analysis could not be performed. Heterogeneity was caused by patient-related factors, surgeon-related factors and differences in statistical methods. Conclusion Current high-quality literature regarding length of the learning curve of minimal invasive TME techniques is scarce. Available literature suggests equal lengths of the learning curves of laparoscopic, robot-assisted and transanal TME. Well-designed studies, using adequate statistical methods are required to properly assess the learning curve, while taking into account patient-related and surgeon-related factors

Bayesian Centroid Estimation for Motif Discovery

Biological sequences may contain patterns that are signal important biomolecular functions; a classical example is regulation of gene expression by transcription factors that bind to specific patterns in genomic promoter regions. In motif discovery we are given a set of sequences that share a common motif and aim to identify not only the motif composition, but also the binding sites in each sequence of the set. We present a Bayesian model that is an extended version of the model adopted by the Gibbs motif sampler, and propose a new centroid estimator that arises from a refined and meaningful loss function for binding site inference. We discuss the main advantages of centroid estimation for motif discovery, including computational convenience, and how its principled derivation offers further insights about the posterior distribution of binding site configurations. We also illustrate, using simulated and real datasets, that the centroid estimator can differ from the maximum a posteriori estimator.Comment: 24 pages, 9 figure

On the combustion of fine iron particles beyond FeO stoichiometry: Insights gained from molecular dynamics simulations

Molecular dynamics (MD) simulations are performed to investigate the thermal and mass accommodation coefficients (TAC and MAC, respectively) for the combination of iron(-oxide) and air. The obtained values of TAC and MAC are then used in a point-particle Knudsen model to investigate the effect on the combustion behavior of (fine) iron particles. The thermal accommodation for the interactions of $\mathrm{Fe}$ with $\mathrm{N_2}$ and $\mathrm{Fe_xO_y}$ with $\mathrm{O_2}$ is investigated for different surface temperature, while the mass accommodation coefficient for iron(-oxide) with oxygen is investigated for different initial oxidation stages $Z_\mathrm{O}$, which represents the molar ratio of $\mathrm{O}/\left(\mathrm{O} + \mathrm{Fe}\right)$, and different surface temperatures. The MAC decreases almost linearly as a function of $Z_\mathrm{O}$, with a steeper slope when $Z_\mathrm{O} < 0.5$ and a gentler slope when $0.5 < Z_\mathrm{O} < 0.57$. By incorporating the MD-informed accommodation coefficients into the single iron particle model, the oxidation beyond $Z_\mathrm{O} = 0.5$ (from stoichiometric $\mathrm{FeO}$ to $\mathrm{Fe_3O_4}$) is modeled. A new temperature evolution for single iron particles is observed compared to results obtained with previously developed continuum models. Specifically, results of the present simulations show that the oxidation process continues after the particle reaching the peak temperature, while previous models predicting a maximum temperature was attained when the particle is fully oxidized to $Z_\mathrm{O} = 0.5$. Since the rate of formation slows down as the MAC decreases with an increasing oxidation stage, the rate of heat loss exceeds the rate of heat release upon reaching the maximum temperature. Finally, the effect of transition-regime heat and mass transfer on the combustion behavior of fine iron particles is investigated and discussed

Observational Validation of The Compensating Mass Flux Through The Shell Around Cumulus Clouds

The existence of a subsiding shell around cumulus clouds has been observed before in several aircraft measurement campaigns. Recent results from large-eddy simulations (LES) showed that the downward mass flux through the shell compensates for a significant fraction of the upward mass flux through the cloud. In this study, aeroplane measurements from the Rain In Cumulus over the Ocean (RICO) field campaign are used to verify the existence of this compensating mass flux. Just as in the LES results, the in-shell downward mass flux is found to be significant. However, a few differences were found in comparison with the LES results; most of them were explained by taking into account the difference between the two-dimensional slabs in LES and the one-dimensional lines from aeroplane observations