The ups and downs of protein topology; rapid comparison of protein structure

Protein topology can be described at different levels. At themost fundamental level, it is a sequence of secondary structureelements (a `primary topology string'). Searching predictedprimary topology strings against a library of strings from knownprotein structures is the basis of some protein fold recognitionmethods. Here a method known as TOPSCAN is presented for rapidcomparison of protein structures. Rather than a simple two-letteralphabet (encoding strand and helix), more complex alphabetsare used encoding direction, proximity, accessibility and lengthof secondary elements and loops in addition to secondary structure.Comparisons are made between the structural information contentof primary topology strings and encodings which contain additionalinformation (`secondary topology strings'). The algorithm isextremely fast, with a scan of a large domain against a libraryof more than 2000 secondary structure strings completing in     

Increased α-linolenic acid intake increases tissue α-linolenic acid content and apparent oxidation with little effect on tissue docosahexaenoic acid in the guinea pig

The essential fatty acids do not have identical roles in nutrition. Linoleic acid (LA) accumulates throughout the body of most mammals, whereas α-linolenic acid (ALA) is rarely found in tissue lipids to the same extent as LA. It has been argued that this is the result of metabolism of ALA to docosahexaenoic acid (DHA) or that ALA is rapidly β-oxidized to acetyl CoA and CO₂. In this study, we consider the effect of high and low ALA levels on the tissue distribution of ALA and other n-3 polyunsaturated fatty acids (PUFA) in all tissues. Guinea pigs were fed one of two defined diets for 3 wk from wearning with both diets containing 1.8% (by weight) of LA and either 1.7% ALA or 0.03% ALA. The high ALA diet was associated with significantly increased ALA levels in all tissues except the brain and significantly increased levels of long-chain n-3 PUFA in all tissues except intestines, brain, carcass, and skin. The long-chain n-3 PUFA content of the whole body was less than 5% of that of the ALA content in both diet groups, and the major long-chain n-3 PUFA (>66% of total) in the body was 22∶5n−3. The brain was the only tissue where the DHA content exceeded that of 22∶5n−3. On the low ALA diet, there appeared to be conservation of ALA based on a comparison of the ratio of LA to ALA in the tissues compared with that in the diet. On the high ALA diet there was a loss of ALA relative to LA in the tissues compared with the diet. These studies suggest that the low levels of tissue ALA in the guinea pig are likely the result of β-oxidation or excretion via the skin and fur rather than metabolism to DHA.     

Perceiving,learning, and exploiting object affordances for autonomous pile manipulation

Autonomous manipulation in unstructured environments will enable a large variety of exciting and important applications. Despite its promise, autonomous manipulation remains largely unsolved. Even the most rudimentary manipulation task—such as removing objects from a pile—remains challenging for robots. We identify three major challenges that must be addressed to enable autonomous manipulation: object segmentation, action selection, and motion generation. These challenges become more pronounced when unknown man-made or natural objects are cluttered together in a pile. We present a system capable of manipulating unknown objects in such an environment. Our robot is tasked with clearing a table by removing objects from a pile and placing them into a bin. To that end, we address the three aforementioned challenges. Our robot perceives the environment with an RGB-D sensor, segmenting the pile into object hypotheses using non-parametric surface models. Our system then computes the affordances of each object, and selects the best affordance and its associated action to execute. Finally, our robot instantiates the proper compliant motion primitive to safely execute the desired action. For efficient and reliable action selection, we developed a framework for supervised learning of manipulation expertise. To verify the performance of our system, we conducted dozens of trials and report on several hours of experiments involving more than 1,500 interactions. The results show that our learning-based approach for pile manipulation outperforms a common sense heuristic as well as a random strategy, and is on par with human action selection.     

A memetic algorithm for the capacitated m-ring-star problem

The Capacitated m-Ring-Star Problem (CmRSP) models a network topology design problem in the telecommunications industry. In this paper, we propose to solve this problem using a memetic algorithm that includes a crossover operation, a mutation operation, a local search involving three neighborhood operators, and a population selection strategy that maintains population diversity. Our approach generates the best known solutions for 131 out of 138 benchmark instances, improving on the previous best solutions for 24 of them, and exhibits more advantages on large benchmark instances when compared with the best existing approach. Additionally, all existing algorithms for this problem in literature assume that the underlying graph of the problem instance satisfies the triangle inequality rule; our approach does not require this assumption. We also generated a new set of 36 larger test instances based on a digital data service network price structure to serve as a new benchmark data set for future researchers.     

Methanol oxidation on Au/TiO2 catalysts

We have investigated the adsorption and reaction of methanol with Au/TiO₂ catalysts using a pulsed flow reactor, DRIFTS and TPD. The TiO₂ (P25) surface adsorbed a full monolayer of methanol, much of it in a dissociative manner, forming methoxy groups associated with the cationic sites, and hydroxyl groups at the anions. The methoxy is relatively stable until 250 °C, at which point decomposition occurs, producing mainly dimethyl ether by a bimolecular surface reaction. As the concentration of methoxy on the surface diminishes, so the mechanism reverts to a de-oxygenation pathway, producing mainly methane and water (at ~330 °C in TPD), but also with some coincident CO and hydrogen. Au catalysts were prepared by the deposition-precipitation method to give Au loadings between 0.5–3 wt %. The effect of low levels of Au on the reactivity is marked. The pathway which gives methane, which is characteristic of titania, remains, but a new feature of the reaction is the evolution of CO₂ and H₂ at lower temperature (a peak is seen in TPD at 220 °C), and the elimination of the DME-producing state. Clearly this is associated with the presence of Au and appears to be due to the production of a formate species on the surface of the Au component. This formate species is mainly involved in the reaction of methanol with the Au/TiO₂ catalysts which results in a combustion pathway being followed, with complete conversion occurring by ~130 °C.     

Potassium sorbate solutions as copper chemical mechanical planarization (CMP) based slurries

Copper depassivation and repassivation characteristics in potassium sorbate solutions, subsequent to mechanical abrading are reported. The identification of copper repassivation kinetics obtained subsequent to mechanical damage of copper protective films formed in sorbate based solutions is discussed. The repassivation rate of copper in sorbate based solutions was measured by means of a slurryjet system capable of measuring single particle impingments on microelectrodes. Copper repassivation rates measured by this slurryjet system in sulfate solutions containing 10 g L⁻¹ potassium sorbate were found to be in the range of 0.5-1.5 ms. An increase in the potassium sorbate concentration leads to a decrease in copper repassivation time at potentials ranging from 200 to 600 mV_Ag/AgCl. The impingement angle between the copper surface and a single abrasive particle has no impact on copper repassivation time nor peak current (I_max) values. XPS studies revealed that copper passivation in potassium based solution was due to the formation of a thin film which is constituted of: Cu₂O, Cu(OH)₂ and Cu(II)-sorbate, while copper(II)-sorbate is mainly present at the top levels of the passive film. It is therefore recommended that the use of potassium sorbate as a passivating component in conjunction with the addition of strong oxidizing agents in chemical mechanical planarization (CMP) slurry design should be considered.     

Kinetics of the hydroformylation of soybean oil by ligand-modified homogeneous rhodium catalysis

The kinetics and mechanism of the hydroformylation of soybean oil by homogeneous ligand-modified rhodium catalysts were investigated at 70–130°C and 4000–11,000 kPa. The effects of reaction rates on systematic variations in reaction parameters were evaluated in order to develop an industrial process to convert vegetable oils to polyaldehydes. The activation energies in the presence of triphenylphosphine (Ph₃P) (61.1±0.8 kJ/mol) (mean±SD) and triphenyl phosphite [(PhO)₃P] (77.4±5.0 kJ/mol) were determined. The catalyst was deactivated at temperatures higher than 100°C. An evaluation of the effects of the reaction parameters on initial rates yielded the rate laws for Ph₃P {rate=k [olefin][Rh(CO)₂Acac]^1.1 [Ph₃P]^−0.5 (pH₂+pCO)^1.4, where Rh(CO)₂Acac is (acetylacetonato)dicarbonylrhodium (I)} and (PhO)₃P {rate=[olefin] [Rh(CO)₂Acac]^1.2 [(PhO)₃P]^−0.8 (pH₂+pCO)^0.9 at total pressures lower than 7000 kPa, and rate =[olefin] [Rh(CO)₂Acac]^1.2 [(PhO)₃P]^−0.8(pH₂+pCO)^1.7 at total pressures higher than 7000 kPa}.     

Feeding response of Ips paraconfusus to phloem and phloem metabolites of Heterobasidion annosum-inoculated ponderosa pine,Pinus ponderosa

In studies of feeding by the bark beetle, Ips paraconfusus, two pine stilbenes (pinosylvin and pinosylvin methyl ether), ferulic acid glucoside, and enantiomers of the four most common sugars present in ponderosa pine phloem (sucrose, glucose, fructose, and raffinose) did not stimulate or reduce male feeding when assayed on wet -cellulose with or without stimulatory phloem extractives present. When allowed to feed on wet -cellulose containing sequential extracts (hexane, methanol, and water) of ponderosa pine phloem, methanol and water extractives stimulated feeding, but hexane extractives did not. Males confined in wet -cellulose containing aqueous or organic extracts of culture broths derived from phloem tissue and containing the root pathogen, Heterobasidion annosum, ingested less substrate than beetles confined to control preparations. In an assay using logs from uninoculated ponderosa pines, the mean lengths of phloem in the digestive tracts increased as time spent feeding increased. Males confined to the phloem of basal logs cut from ponderosa pines artificially inoculated with H. annosum ingested significantly less phloem than beetles in logs cut from trees that were (combined) mock-inoculated or uninoculated and did not contain the pathogen. However, individual pathogen-containing treatments were not significantly different from uninoculated controls. It was concluded that altered feeding rates are not a major factor which may explain why diseased ponderosa pines are colonized by I. paraconfusus.     

Are quantum dots ready for in vivo imaging in human subjects?

Nanotechnology has the potential to profoundly transform the nature of cancer diagnosis and cancer patient management in the future. Over the past decade, quantum dots (QDs) have become one of the fastest growing areas of research in nanotechnology. QDs are fluorescent semiconductor nanoparticles suitable for multiplexed in vitro and in vivo imaging. Numerous studies on QDs have resulted in major advancements in QD surface modification, coating, biocompatibility, sensitivity, multiplexing, targeting specificity, as well as important findings regarding toxicity and applicability. For in vitro applications, QDs can be used in place of traditional organic fluorescent dyes in virtually any system, outperforming organic dyes in the majority of cases. In vivo targeted tumor imaging with biocompatible QDs has recently become possible in mouse models. With new advances in QD technology such as bioluminescence resonance energy transfer, synthesis of smaller size non-Cd based QDs, improved surface coating and conjugation, and multifunctional probes for multimodality imaging, it is likely that human applications of QDs will soon be possible in a clinical setting.     

Lipid hydrolysis and oxidation on the surface of milled rice

The changes in milled rice FFA content and composition and in conjugated diene (CD) content and bacterial, yeast, and mold counts were determined at 24, 37, and 50°C and 70% RH over 50 d. There was a rapid rate of FFA formation during the first few days of storage, which was optimal at 37°C, but that slowed after 2, 4, and 5 d at 37, 24, and 50°C, respectively. There was a second increase in FFA after about day 12 that increased with increasing temperature, indicating nonlipase hydrolysis. Linoleic and oleic acids were the main components of the total FFA produced on the surface of milled rice. The pattern of CD development followed that of FFA increase. Bacterial growth correlated with increased FFA levels after 12 d of storage, suggesting that bacterial lipase rather than bran lipase may be responsible for rice lipid hydrolysis