Evaluation and comparison of mammalian subcellular localization prediction methods

BACKGROUND: Determination of the subcellular location of a protein is essential to understanding its biochemical function. This information can provide insight into the function of hypothetical or novel proteins. These data are difficult to obtain experimentally but have become especially important since many whole genome sequencing projects have been finished and many resulting protein sequences are still lacking detailed functional information. In order to address this paucity of data, many computational prediction methods have been developed. However, these methods have varying levels of accuracy and perform differently based on the sequences that are presented to the underlying algorithm. It is therefore useful to compare these methods and monitor their performance. RESULTS: In order to perform a comprehensive survey of prediction methods, we selected only methods that accepted large batches of protein sequences, were publicly available, and were able to predict localization to at least nine of the major subcellular locations (nucleus, cytosol, mitochondrion, extracellular region, plasma membrane, Golgi apparatus, endoplasmic reticulum (ER), peroxisome, and lysosome). The selected methods were CELLO, MultiLoc, Proteome Analyst, pTarget and WoLF PSORT. These methods were evaluated using 3763 mouse proteins from SwissProt that represent the source of the training sets used in development of the individual methods. In addition, an independent evaluation set of 2145 mouse proteins from LOCATE with a bias towards the subcellular localization underrepresented in SwissProt was used. The sensitivity and specificity were calculated for each method and compared to a theoretical value based on what might be observed by random chance. CONCLUSION: No individual method had a sufficient level of sensitivity across both evaluation sets that would enable reliable application to hypothetical proteins. All methods showed lower performance on the LOCATE dataset and variable performance on individual subcellular localizations was observed. Proteins localized to the secretory pathway were the most difficult to predict, while nuclear and extracellular proteins were predicted with the highest sensitivity

Extracting Proofs from Tabled Proof Search

We consider the problem of model checking specifications involving co-inductive definitions such as are available for bisimulation. A proof search approach to model checking with such specifications often involves state exploration. We consider four different tabling strategies that can minimize such exploration significantly. In general, tabling involves storing previously proved subgoals and reusing (instead of reproving) them in proof search. In the case of co-inductive proof search, tables allow a limited form of loop checking, which is often necessary for, say, checking bisimulation of non-terminating processes. We enhance the notion of tabled proof search by allowing a limited deduction from tabled entries when performing table lookup. The main problem with this enhanced tabling method is that it is generally unsound when co-inductive definitions are involved and when tabled entries contain unproved entries. We design a proof system with tables and show that by managing tabled entries carefully, one would still be able to obtain a sound proof system. That is, we show how one can extract a post-fixed point from a tabled proof for a co-inductive goal. We then apply this idea to the technique of bisimulation ''up-to'' commonly used in process algebra

The Influence of Active Phase Loading on the Hydrodeoxygenation (HDO) of Ethylene Glycol over Promoted MoS2_{2}/MgAl2_{2}O4_{4} Catalysts

The hydrodeoxygenation (HDO) of ethylene glycol over MgAl$_{2}$O$_{4}$ supported NiMo and CoMo catalysts with around 0.8 and 3 wt% Mo loading was studied in a continuous flow reactor setup operated at 27 bar H$_{2}$ and 400 °C. A co-feed of H2S of typically 550 ppm was beneficial for both deoxygenation and hydrogenation and for enhancing catalyst stability. With 2.8-3.3 wt% Mo, a total carbon based gas yield of 80-100 % was obtained with an ethane yield of 36-50 % at up to 118 h on stream. No ethylene was detected. A moderate selectivity towards HDO was obtained, but cracking and HDO were generally catalyzed to the same extent by the active phase. Thus, the C2/C1 ratio of gaseous products was 1.1-1.5 for all prepared catalysts independent on Mo loading (0.8-3.3 wt%), but higher yields of C1-C3 gas products were obtained with higher loading catalysts. Similar activities were obtained from Ni and Co promoted catalysts. For the low loading catalysts (0.83-0.88 wt% Mo), a slightly higher hydrogenation activity was observed over NiMo compared to CoMo, giving a relatively higher yield of ethane compared to ethylene. Addition of 30 wt% water to the ethylene glycol feed did not result in significant deactivation. Instead, the main source of deactivation was carbon deposition, which was favored at limited hydrogenation activity and thus, was more severe for the low loading catalysts

Toughening mechanisms in novel nano-silica epoxy polymers

A crosslinked epoxy polymer has been modified by the addition of nano-silica particles. The particles were introduced via a sol-gel technique which gave a very well dispersed phase of nanosilica particles which were about 20 nm in diameter. The glass transition temperature was unchanged by the addition of the nano-particles, but both the modulus and toughness were increased. The fracture energy increased from 100 J/m2 for the unmodified epoxy to 460 J/m2 for the epoxy with 13 vol% of nano-silica. The microscopy studies showed evidence of debonding of the nano-particles and subsequent plastic void growth of the epoxy polymer. A theoretical model of plastic void growth was used to confirm this mechanism

LOCATE: a mammalian protein subcellular localization database

LOCATE is a curated, web-accessible database that houses data describing the membrane organization and subcellular localization of mouse and human proteins. Over the past 2 years, the data in LOCATE have grown substantially. The database now contains high-quality localization data for 20% of the mouse proteome and general localization annotation for nearly 36% of the mouse proteome. The proteome annotated in LOCATE is from the RIKEN FANTOM Consortium Isoform Protein Sequence sets which contains 58 128 mouse and 64 637 human protein isoforms. Other additions include computational subcellular localization predictions, automated computational classification of experimental localization image data, prediction of protein sorting signals and third party submission of literature data. Collectively, this database provides localization proteome for individual subcellular compartments that will underpin future systematic investigations of these regions. It is available at http://locate.imb.uq.edu.au

Population density and group size effects on reproductive behavior in a simultaneous hermaphrodite

<p>Abstract</p> <p>Background</p> <p>Despite growing evidence that population dynamic processes can have substantial effects on mating system evolution, little is known about their effect on mating rates in simultaneous hermaphrodites. According to theory, mating rate is expected to increase with mate availability because mating activity is primarily controlled by the male sexual function. A different scenario appears plausible in the hermaphroditic opisthobranch <it>Chelidonura sandrana</it>. Here, field mating rates are close to the female fitness optimum, suggesting that mating activity remains unresponsive to variation in mate availability.</p> <p>Results</p> <p>Applying an experimental design that aims at independent experimental manipulation of density and social group size, we find substantial increases in mate encounter rate with both factors, but no statistically detectable effects on mating rate in <it>C. sandrana</it>. Instead, mating rate remained close to the earlier determined female fitness optimum.</p> <p>Conclusions</p> <p>We demonstrate that mating rate in <it>C. sandrana </it>is largely unresponsive to variation in mate availability and is maintained close to the female fitness optimum. These findings challenge the prevailing notion of male driven mating rates in simultaneous hermaphrodites and call for complementary investigations of mating rate effects on fitness through the male sexual function.</p

Quadrupole Susceptibility and Elastic Softening due to a Vacancy in Silicon Crystal

We investigate the electronic states around a single vacancy in silicon crystal by using the Green's function approach. The triply degenerate vacancy states within the band gap are found to be extended over a large distance $\sim20 {\rm \AA}$ from the vacancy site and contribute to the reciprocal temperature dependence of the quadrupole susceptibility resulting in the elastic softening at low temperture. The Curie constant of the quadrupole susceptibility for the trigonal mode ($O_{yz},O_{zx},O_{xy}$) is largely enhanced as compared to that for the tetragonal mode ($O_{2}^{0},O_{2}^{2}$). The obtained results are consistent with the recent ultrasonic experiments in silicon crystal down to 20 mK. We also calculate the dipole and octupole susceptibilities and find that the octupole susceptibilities are extremely enhannced for a specific mode.Comment: 6 pages, with 5 figure

A comparative investigation of the efficacy of CO2 and high power diode lasers for the forming of EN3 mild steel sheets

A comparative investigation of the effectiveness of a high power diode laser (HPDL) and a CO2 laser for the forming of thin section EN3 mild steel sheet has been conducted. The buckling mechanism was identified as the laser forming mechanism responsible for the induced bending. For both lasers it was found that the induced bending angles increased with an increasing number of irradiations and high laser powers, whilst decreasing as the traverse speed was increased. Also, it was apparent from the experimental results that the laser bending angle was only linearly proportional to the number of irradiations when the latter was small due to local material thickening along the bend edge with a high number of irradiations. Owing to the mild steel’s greater beam absorption at the HPDL wavelength, larger bending angles were induced when using the HPDL. However, under certain conditions the performance of the CO2 laser in terms of induced bending angle was seen to approach that of the HPDL. Nevertheless, similar results between the two lasers were only achieved with increasing irradiations, thus it was concluded that the efficacy of the HPDL was higher than that of the CO2 laser insofar as it was more efficient. From graphical results and the employment of an analytical procedure, the laser line energy range in which accurate control of the HPDL bending of the mild steel sheets could be exercised efficiently was found to be 53 J mm-1 < P/v < 78 J mm-1, whilst for the CO2 laser the range was 61 J mm-1 < P/v < 85 J mm-1

Parton distributions in the chiral quark model: a continuum computation

We compute the parton distributions for the chiral quark model. We present a new technique for performing such computations based on Green functions. This approach avoids a discretization of the spectrum. It therefore does not need any smoothing procedures. The results are similar to those of other groups, however the distributions peak at smaller $x$.Comment: 19 pages, 8 Figures, LaTeX, some typos corrected, some additional comments in the conclusion