An extensible automated protein annotation tool: standardizing input and output using validated XML

Motivation: There is a frequent need to apply a large range of local or remote prediction and annotation tools to one or more sequences. We have created a tool able to dispatch one or more sequences to assorted services by defining a consistent XML format for data and annotations. Results: By analyzing annotation tools, we have determined that annotations can be described using one or more of the six forms of data: numeric or textual annotation of residues, domains (residue ranges) or whole sequences. With this in mind, XML DTDs have been designed to store the input and output of any server. Plug-in wrappers to a number of services have been written which are called from a master script. The resulting APATML is then formatted for display in HTML. Alternatively further tools may be written to perform post-analysis.

Influence of particle characteristics and organic matter content on the bioavailability and bioaccumulation of pyrene by clams

Hydrophobic chemicals are known to associate with sediment particles including those from both suspended particulate matter and bottom deposits. The complex and variable composition of natural particles makes it very difficult therefore, to predict the bioavailability of sediment-bound contaminants. To overcome these problems we have previously devised a test system using artificial particles, with or without humic acids, for use as an experimental model of natural sediments. In the present work we have applied this experimental technique to investigate the bioavailability and bioaccumulation of pyrene by the freshwater fingernail clam Sphaerium corneum. The uptake and accumulation of pyrene in clams exposed to the chemical in the presence of a sample of natural sediment was also investigated. According to the results obtained, particle surface properties and organic matter content are the key factors for assessing the bioavailability and bioaccumulation of pyrene by clams. (C) 2002 Elsevier Science Ltd. All rights reserved.

Mutant alleles at the rugosus loci in pea affect seed moisture sorption isotherms and the relations between seed longevity and moisture content

Pea (Pisum sativum L.) mutant near-isogenic lines (RRrbrb, rrRbRb, rrrbrb) with lower starch but higher lipid contents, brought about by lesions in the starch biosynthetic pathway, had seed moisture sorption isotherms displaced below that of the wild type (RRRbRb). The negative logarithmic relationship between seed longevity and seed storage moisture content (%, f.wt basis), determined in hermetic storage at 65 °C, also differed: longevity in the mutant near-isogenic lines was poorer and less sensitive to moisture content than in the wild type (i.e. CW was lower). The low-moisture-content limit (mc) to this relation also differed, being lower in the mutant near-isogenic lines (5.4–5.9%) than in the wild type (6.1%). In contrast, all four near-isogenic lines showed no difference (P >0.25) in the negative semi-logarithmic relationship between equilibrium relative humidity (ERH) and seed longevity. It is concluded that the effect of these alleles at the r and rb loci on seed longevity was largely indirect; a consequence of their effect on seed composition and hence on moisture sorption isotherms. However, this explanation could not be invoked at moisture contents below mc where differences in longevity remained substantial (RRRbRb double that of rrrbrb). Hence, these mutant alleles affected seed longevity directly at very low moisture contents.

Intelligent wireless web services: context-aware computing in construction-logistics supply chain

The construction industry has incurred a considerable amount of waste as a result of poor logistics supply chain network management. Therefore, managing logistics in the construction industry is critical. An effective logistic system ensures delivery of the right products and services to the right players at the right time while minimising costs and rewarding all sectors based on value added to the supply chain. This paper reports on an on-going research study on the concept of context-aware services delivery in the construction project supply chain logistics. As part of the emerging wireless technologies, an Intelligent Wireless Web (IWW) using context-aware computing capability represents the next generation ICT application to construction-logistics management. This intelligent system has the potential of serving and improving the construction logistics through access to context-specific data, information and services. Existing mobile communication deployments in the construction industry rely on static modes of information delivery and do not take into account the worker’s changing context and dynamic project conditions. The major problems in these applications are lack of context-specificity in the distribution of information, services and other project resources, and lack of cohesion with the existing desktop based ICT infrastructure. The research works focus on identifying the context dimension such as user context, environmental context and project context, selection of technologies to capture context-parameters such wireless sensors and RFID, selection of supporting technologies such as wireless communication, Semantic Web, Web Services, agents, etc. The process of integration of Context-Aware Computing and Web-Services to facilitate the creation of intelligent collaboration environment for managing construction logistics will take into account all the necessary critical parameters such as storage, transportation, distribution, assembly, etc. within off and on-site project.

Extraction and determination of ellagic acid content in chestnut bark and fruit

Chestnuts are an important economic resource in the chestnut growing regions, not only for the fruit, but also for the wood. The content of ellagic acid (EA), a naturally occurring inhibitor of carcinogenesis, was determined in chestnut fruits and bark. EA was extracted with methanol and free ellagic acid was determined by HPLC with UV detection, both in the crude extract and after hydrolysis. The concentration of EA was generally increased after hydrolysis due to the presence of ellagitannins in the crude extract. The concentration varied between 0.71 and 21.6 ing g(-1) (d.w.) in un-hydrolyzed samples, and between 2.83 and 18.4 mg g(-1) (d.w.) ill hydrolyzed samples. In chestnut fruits, traces of EA were present in the seed, with higher concentrations in the pellicle and pericarp. However, all fruit tissues had lower concentrations of EA than had the bark. The concentration of EA in the hydrolyzed samples showed a non-linear correlation with the concentration in the unhydrolyzed extracts. (C) 2008 Elsevier Ltd. All rights reserved.

Effect of dietary fish oil on biohydrogenation of fatty acids and milk fatty acid content in cows

Mechanisms underlying milk fat conjugated linoleic acid (CLA) responses to supplements of fish oil were investigated using five lactating cows each fitted with a rumen cannula in a simple experiment consisting of two consecutive 14-day experimental periods. During the first period cows were offered 18 kg dry matter (DM) per day of a basal (B) diet formulated from grass silage and a cereal based-concentrate (0.6 : 0.4; forage : concentrate ratio, on a DM basis) followed by the same diet supplemented with 250 g fish oil per day (FO) in the second period. The flow of non-esterified fatty acids leaving the rumen was measured using the omasal sampling technique in combination with a triple indigestible marker method based on Li-Co-EDTA, Yb-acetate and Cr-mordanted straw. Fish oil decreased DM intake and milk yield, but had no effect on milk constituent content. Milk fat trans-11C(18:1), total trans-C-18:1, cis-9 trans-11 CLA, total CLA, C-18 :2 (n- 6) and total C-18:2 content were increased in response to fish oil from 1.80, 4.51, 0.39, 0. 56, 0.90 and 1.41 to 9.39, 14.39, 1.66, 1.85, 1.25 and 4.00 g/100 g total fatty acids, respectively. Increases in the cis-9, trans-11 isomer accounted for proportionately 0.89 of the CLA response to fish oil. Furthermore, fish oil decreased the flow of C-18:0 (283 and 47 g/day for B and FO, respectively) and increased that of trans-C-18:1 fatty acids entering the omasal canal (38 and 182 g/day). Omasal flows of trans-C-18:1 acids with double bonds in positions from delta-4 to -15 inclusive were enhanced, but the effects were isomer dependent and primarily associated with an increase in trans-11C(18:1) leaving the rumen (17.1 and 121.1 g/day for B and FO, respectively). Fish oil had no effect on total (4.36 and 3.50 g/day) or cis-9, trans-11 CLA (2.86 and 2.08 g/day) entering the omasal canal. Flows of cis-9, trans-11 CLA were lower than the secretion of this isomer in milk. Comparison with the transfer of the trans-9, trans-11 isomer synthesized in the rumen suggested that proportionately 0.66 and 0.97 of cis-9, trans-11 CLA was derived from endogenous conversion of trans-11 C-18:1 in the mammary gland for B and FO, respectively. It is concluded that fish oil enhances milk fat cis-9, trans-11 CLA content in response to increased supply of trans-11 C-18:1 that arises from an inhibition of trans C-18:1 reduction in the rumen.

Evaluation of Serpa cheese proteolysis by nitrogen content and capillary zone electrophoresis

Proteolysis of Serpa cheese produced traditionally (B) and semi-industrially (C) was evaluated for the first time by determination of nitrogen content and capillary zone electrophoresis (CZE). A citrate dispersion of cheese was fractionated to determine the nitrogen in pH 4.4, trichloroacetic and phosphotungstic acid soluble fractions (pH 4.4-SN, TCA-SN and PTA-SN, respectively). The pH 4.4-SN was significantly higher for B ( P < 0.001), while TCA-SN was significantly higher for C ( P < 0.001). PTA-SN was also higher for C but at 60 days ripening no significant difference was found between B and C. Degradation of alpha(s1) - and beta-caseins evaluated by CZE was in good agreement with the maturation index (pH 4.4-SN/TN).

Selenium supplementation of lactating dairy cows: effects on milk production and total selenium content and speciation in blood, milk and cheese

Forty multiparous Holstein cows were used in a 16-week continuous design study to determine the effects of either selenium (Se) source, selenised yeast (SY) (derived from a specific strain of Saccharomyces cerevisiae CNCM 1-3060) or sodium selenite (SS), or Se inclusion rate in the form of SY in the diets of lactating dairy cows on the Se concentration and speciation in blood, milk and cheese. Cows received ad libitum a total mixed ration (TMR) with a 1 : 1 forage: concentrate ratio on a dry matter (DM) basis. There were four diets (T-1 to T-4), which differed only in either source or dose of Se additive. Estimated total dietary Se for T, (no supplement), T-2 (SS), T-3 (SY) and T-4 (SY) was 0.16, 0.30, 0.30 and 0.45 mg/kg DM, respectively. Blood and milk samples were taken at 28-day intervals and at each time point there were positive linear effects of Se in the form of SY on the Se concentration in blood and milk. At day 112 blood and milk Se values for T-1 to T-4 were 177, 208, 248 and 279 +/- 6.6 and 24, 38, 57 and 72 +/- 3.7 ng/g fresh material, respectively, and indicate improved uptake and incorporation of Se from SY. In whole blood, selenocysteine (SeCys) was the main selenised amino acid and the concentration of selenomethionine (SeMet) increased with the increasing inclusion rate of SY In milk, there were no marked treatment effects on the SeCys content, but Se source had a marked effect on the concentration of SeMet. At day 112 replacing SS (T-2) with SY (T-3) increased the SeMet concentration of milk from 36 to 111 ng Se/g and its concentration increased further to 157ng Se/g dried sample as the inclusion rate of SY increased further (T-4) to provide 0.45 mg Se/kg TMR. Neither Se source nor inclusion rate affected the keeping quality of milk. At day 112 milk from T-1, T-2 and T-3 was made into a hard cheese and Se source had a marked effect on total Se and the concentration of total Se comprised as either SeMet or SeCys. Replacing SS (T-2) with SY (T-3) increased total Se, SeMet and SeCys content in cheese from 180 to 340 ng Se/g, 57 to 153 ng Se/g and 52 to 92 ng Se/g dried sample, respectively. The use of SY to produce food products with enhanced Se content as a means of meeting the Se requirements is discussed

The effects of low-temperature potato storage and washing and soaking pre-treatments on the acrylamide content of French fries

BACKGROUND: Since the discovery in 2002 of acrylamide in a wide range of foods, there has been much work done to explore mechanisms of formation and to reduce acrylamide in commercial products. This study aimed to investigate simple measures which could be used to reduce acrylamide formation in home-cooked French fries, using potatoes from three cultivars stored under controlled conditions and sampled at three time points. RESULTS: The reducing sugar content for all three cultivars increased during storage, which led to increased acrylamide levels in the French fries. Washing and soaking (30 min or 2 h) raw French fries before cooking led to reductions in acrylamide of up to 23, 38 and 48% respectively. Pre-treated fries were lighter in colour after cooking than the corresponding controls. CONCLUSION: Pre-treatments such as soaking or washing raw French fries in water reduce acrylamide and colour formation in the final product when cooking is stopped at a texture-determined endpoint. (c) 2008 Society of Chemical Industry.

Influence of fruit ripening process on the natural antioxidant content of Hojiblanca virgin olive oils

The effect of fruit ripeness on the antioxidant content of 'Hojiblanca' virgin olive oils was studied. Seasonal changes were monitored at bi-weekly intervals for three consecutive crop years. Phenolic content, tocopherol composition, bitterness index, carotenoid and chlorophyllic pigments and oxidative stability were analysed. In general, the antioxidants and the related parameters decreased as olive fruit ripened. The phenolics and bitterness, closely related parameters, did not present significant differences among years. Although in general, the tocopherols decreased during olive ripening gamma-tocopherol increased. Differences between crop years were found only for total tocopherols and alpha-tocopherol, which showed higher content in low rainfall year oils. The pigment content decreased during ripening, chlorophyll changing faster. For low rainfall years, the level of pigments was higher, reaching significant differences between yields. Significant differences among years were found for oil oxidative stability; higher values were obtained for drought years. A highly significant prediction model for oxidative stability has been obtained. (C) 2004 Elsevier Ltd. All rights reserved.

The human thalamus processes syntactic and semantic language violations

Numerous linguistic operations have been assigned to cortical brain areas, but the contributions of subcortical structures to human language processing are still being discussed. Using simultaneous EEG recordings directly from deep brain structures and the scalp, we show that the human thalamus systematically reacts to syntactic and semantic parameters of auditorily presented language in a temporally interleaved manner in coordination with cortical regions. In contrast, two key structures of the basal ganglia, the globus pallidus internus and the subthalamic nucleus, were not found to be engaged in these processes. We therefore propose that syntactic and semantic language analysis is primarily realized within cortico-thalamic networks, whereas a cohesive basal ganglia network is not involved in these essential operations of language analysis.

Neural mechanisms of visual object priming: evidence for perceptual and semantic distinctions in fusiform cortex

Previous functional imaging studies have shown that facilitated processing of a visual object on repeated, relative to initial, presentation (i.e., repetition priming) is associated with reductions in neural activity in multiple regions, including fusiforin/lateral occipital cortex. Moreover, activity reductions have been found, at diminished levels, when a different exemplar of an object is presented on repetition. In one previous study, the magnitude of diminished priming across exemplars was greater in the right relative to the left fusiform, suggesting greater exemplar specificity in the right. Another previous study, however, observed fusiform lateralization modulated by object viewpoint, but not object exemplar. The present fMRI study sought to determine whether the result of differential fusiform responses for perceptually different exemplars could be replicated. Furthermore, the role of the left fusiform cortex in object recognition was investigated via the inclusion of a lexical/semantic manipulation. Right fusiform cortex showed a significantly greater effect of exemplar change than left fusiform, replicating the previous result of exemplar-specific fusiform lateralization. Right fusiform and lateral occipital cortex were not differentially engaged by the lexical/semantic manipulation, suggesting that their role in visual object recognition is predominantly in the. C visual discrimination of specific objects. Activation in left fusiform cortex, but not left lateral occipital cortex, was modulated by both exemplar change and lexical/semantic manipulation, with further analysis suggesting a posterior-to-anterior progression between regions involved in processing visuoperceptual and lexical/semantic information about objects. The results are consistent with the view that the right fusiform plays a greater role in processing specific visual form information about objects, whereas the left fusiform is also involved in lexical/semantic processing. (C) 2003 Elsevier Science (USA). All rights reserved.

How does the brain mediate interpretation of incongruent auditory emotions? The neural response to prosody in the presence of conflicting lexico-semantic cues

We frequently encounter conflicting emotion cues. This study examined how the neural response to emotional prosody differed in the presence of congruent and incongruent lexico-semantic cues. Two hypotheses were assessed: (i) decoding emotional prosody with conflicting lexico-semantic cues would activate brain regions associated with cognitive conflict (anterior cingulate and dorsolateral prefrontal cortex) or (ii) the increased attentional load of incongruent cues would modulate the activity of regions that decode emotional prosody (right lateral temporal cortex). While the participants indicated the emotion conveyed by prosody, functional magnetic resonance imaging data were acquired on a 3T scanner using blood oxygenation level-dependent contrast. Using SPM5, the response to congruent cues was contrasted with that to emotional prosody alone, as was the response to incongruent lexico-semantic cues (for the 'cognitive conflict' hypothesis). The right lateral temporal lobe region of interest analyses examined modulation of activity in this brain region between these two contrasts (for the 'prosody cortex' hypothesis). Dorsolateral prefrontal and anterior cingulate cortex activity was not observed, and neither was attentional modulation of activity in right lateral temporal cortex activity. However, decoding emotional prosody with incongruent lexico-semantic cues was strongly associated with left inferior frontal gyrus activity. This specialist form of conflict is therefore not processed by the brain using the same neural resources as non-affective cognitive conflict and neither can it be handled by associated sensory cortex alone. The recruitment of inferior frontal cortex may indicate increased semantic processing demands but other contributory functions of this region should be explored.

False recognition of abstract versus common objects in older and younger adults: testing the semantic categorization account

Older adults often demonstrate higher levels of false recognition than do younger adults. However, in experiments using novel shapes without preexisting semantic representations, this age-related elevation in false recognition was found to be greatly attenuated. Two experiments tested a semantic categorization account of these findings, examining whether older adults show especially heightened false recognition if the stimuli have preexisting semantic representations, such that semantic category information attenuates or truncates the encoding or retrieval of item-specific perceptual information. In Experiment 1, ambiguous shapes were presented with or without disambiguating semantic labels. Older adults showed higher false recognition when labels were present but not when labels were never presented. In Experiment 2, older adults showed higher false recognition for concrete but not abstract objects. The semantic categorization account was supported.

Motor brain regions are involved in the encoding of delayed intentions: a fMRI study

In studies of prospective memory, recall of the content of delayed intentions is normally excellent, probably because they contain actions that have to be enacted at a later time. Action words encoded for later enactment are more accessible from memory than those encoded for later verbal report [Freeman, J.E., and Ellis, J.A. 2003a. The representation of delayed intentions: A prospective subject-performed task? Journal of Experimental Psychology: Learning, Memory, and Cognition, 29, 976-992.]. As this higher assessibility is lost when the intended actions have to be enacted during encoding, or when a motor interference task is introduced concurrent to intention encoding, Freeman and Ellis suggested that the advantage of to-be-enacted actions is due to additional preparatory motor operations during encoding. Accordingly, in a fMRI study with 10 healthy young participants, we investigated whether motor brain regions are differentially activated during verbal encoding of actions for later enactment with the right hand in contrast to verbal encoding of actions for later verbal report. We included an additional condition of verbal encoding of abstract verbs for later verbal report to investigate whether the semantic motor information inherent in action verbs in contrast to abstract verbs activates motor brain regions different from those involved in the verbal encoding of actions for later enactment. Differential activation for the verbal encoding of to-be-enacted actions in contrast to to-be-reported actions was found in brain regions known to be involved in covert motor preparation for hand movements, i.e. the postcentral gyrus, the precuneus, the dorsal and ventral premotor cortex, the posterior middle temporal gyrus and the inferior parietal lobule. There was no overlap between these brain regions and those differentially activated during the verbal encoding of actions in contrast to abstract verbs for later verbal report. Consequently, the results of this fMRI study suggest the presence of preparatory motor operations during the encoding of delayed intentions requiring a future motor response, which cannot be attributed to semantic information inherent to action verbs. (c) 2006 Elsevier B.V. All rights reserved.