Linked disambiguated distributional semantic networks

We present a new hybrid lexical knowledge base that combines the contextual information of distributional models with the conciseness and precision of manually constructed lexical networks. The computation of our count-based distributional model includes the induction of word senses for single-word and multi-word terms, the disambiguation of word similarity lists, taxonomic relations extracted by patterns and context clues for disambiguation in context. In contrast to dense vector representations, our resource is human readable and interpretable, and thus can be easily embedded within the Semantic Web ecosystem

The site of attachment of retinal in bacteriorhodopsin. The epsilon-amino group in Lys-41 is not required for proton translocation

Chymotryptic fragments C-1 (amino acids 72-248) and C-2 (amino acids 1-71) of bacteriorhodopsin have been shown previously to reassociate so as to regenerate the native bacteriorhodopsin chromophore in lipid/detergent mixtures and to form functional proton-translocating vesicles. The fragment C-2 has now been selectively methylated with formaldehyde and sodium cyanoborohydride to give the epsilon-dimethylamino derivatives of Lys-30, 40, and 41 in 96-99% average yield. The methylated and unmethylated C-2 fragments were identical in their ability to reassociate with fragment C-1 and retinal to regenerate the bacteriorhodopsin chromophore and to form functional proton-translocating vesicles. In contrast, dimethylation of the lysine residues of the C-1 fragment gave a derivative which did not form an active complex with unmethylated C-2. We conclude that the epsilon-amino group in Lys-41 is not required for Schiff's base formation with retinal at any step in the light-driven proton-translocation cycle

Determination of nutrient salts by automatic methods both in seawater and brackish water: the phosphate blank

9 páginas, 2 tablas, 2 figurasThe main inconvenience in determining nutrients in seawater by automatic methods is simply solved: the preparation of a suitable blank which corrects the effect of the refractive index change on the recorded signal. Two procedures are proposed, one physical (a simple equation to estimate the effect) and the other chemical (removal of the dissolved phosphorus with ferric hydroxide).Support for this work came from CICYT (MAR88-0245 project) and Conselleria de Pesca de la Xunta de GaliciaPeer reviewe

Oligodendrocytes Do Not Export NAA-Derived Aspartate In Vitro.

Oligodendroglial cells are known to de-acetylate the N-acetylaspartate (NAA) synthesized and released by neurons and use it for lipid synthesis. However, the role of NAA regarding their intermediary metabolism remains poorly understood. Two hypotheses were proposed regarding the fate of aspartate after being released by de-acetylation: (1) aspartate is metabolized in the mitochondria of oligodendrocyte lineage cells; (2) aspartate is released to the medium. We report here that aspartoacylase mRNA expression increases when primary rat oligodendrocyte progenitor cells (OPCs) differentiate into mature cells in culture. Moreover, characterising metabolic functions of acetyl coenzyme A and aspartate from NAA catabolism in mature oligodendrocyte cultures after 5 days using isotope-labelled glucose after 5-days of differentiation we found evidence of extensive NAA metabolism. Incubation with [1,6-13C]glucose followed by gas chromatography-mass spectrometry and high performance liquid chromatography analyses of cell extracts and media in the presence and absence of NAA established that the acetate moiety produced by hydrolysis of NAA does not enter mitochondrial metabolism in the form of acetyl coenzyme A. We also resolved the controversy concerning the possible release of aspartate to the medium: aspartate is not released to the medium by oligodendrocytes in amounts detectable by our methods. Therefore we propose that: aspartate released from NAA joins the cytosolic aspartate pool rapidly and takes part in the malate-aspartate shuttle, which transports reducing equivalents from glycolysis into the mitochondria for ATP production and enters the tricarboxylic acid cycle at a slow rate.This work was supported by grants from the UK Multiple Sclerosis Society and from Qatar Foundation. The work was further supported by core funding from the Wellcome Trust and MRC to the Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute. The authors acknowledge the excellent technical support in GC-MS and HPLC analysis from Lars Evje (NTNU, Norway).This is the final version of the article. It first appeared from Springer at http://dx.doi.org/10.1007/s11064-016-1985-y

Circulating omentin as a novel biomarker for colorectal cancer risk: Data from the EPIC - Potsdam cohort study

Omentin is a novel biomarker shown to exert metabolic, inflammatory and immune-related properties, and thereby could be implicated in the risk of colorectal cancer (CRC). So far, the association between omentin and CRC risk has not been evaluated in prospective cohort studies. We investigated the association between pre-diagnostic plasma omentin concentrations and risk of CRC in a case-cohort comprising 251 incident CRC cases diagnosed over a mean follow-up time of 10.4 years and 2,295 persons who remained free of cancer in the European Prospective Investigation into Cancer and Nutrition-Potsdam study. Hazard ratios as a measure of relative risk (RR) and 95% confidence intervals (CI-s) were computed using a Prentice modified Cox regression. In a model adjusted for established CRC risk factors, age, sex, education, dietary and lifestyle factors, body mass index (BMI) and waist circumference, higher omentin concentrations were associated with a higher CRC risk (RRcontinuously per doubling of omentin concentrations=1.98, 95%CI: 1.45-2.73). Additional adjustment for metabolic biomarkers, including glycated hemoglobin, high-density lipoprotein cholesterol and C-reactive protein, did not alter the results. In stratified analyses, the positive association between omentin and CRC risk was retained in participants with BMI< 30 (RRcontinuously per doubling of omentin concentrations=2.26; 95%CI: 1.57-3.27), whereas among participants with BMI{greater than or equal to} 30 no association was revealed (RRcontinuously per doubling of omentin concentrations =1.07; 95%CI: 0.63-1.83; Pinteraction= 0.005). These novel findings provide the first lines of evidence for an independent association between pre-diagnostic omentin concentrations and CRC risk and suggest a potential interaction with the adiposity state of the individual

Novel model of neuronal bioenergetics: postsynaptic utilization of glucose but not lactate correlates positively with Ca2+ signalling in cultured mouse glutamatergic neurons

We have previously investigated the relative roles of extracellular glucose and lactate as fuels for glutamatergic neurons during synaptic activity. The conclusion from these studies was that cultured glutamatergic neurons utilize glucose rather than lactate during NMDA (N-methyl-d-aspartate)-induced synaptic activity and that lactate alone is not able to support neurotransmitter glutamate homoeostasis. Subsequently, a model was proposed to explain these results at the cellular level. In brief, the intermittent rises in intracellular Ca2+ during activation cause influx of Ca2+ into the mitochondrial matrix thus activating the tricarboxylic acid cycle dehydrogenases. This will lead to a lower activity of the MASH (malate–aspartate shuttle), which in turn will result in anaerobic glycolysis and lactate production rather than lactate utilization. In the present work, we have investigated the effect of an ionomycin-induced increase in intracellular Ca2+ (i.e. independent of synaptic activity) on neuronal energy metabolism employing 13C-labelled glucose and lactate and subsequent mass spectrometric analysis of labelling in glutamate, alanine and lactate. The results demonstrate that glucose utilization is positively correlated with intracellular Ca2+ whereas lactate utilization is not. This result lends further support for a significant role of glucose in neuronal bioenergetics and that Ca2+ signalling may control the switch between glucose and lactate utilization during synaptic activity. Based on the results, we propose a compartmentalized CiMASH (Ca2+-induced limitation of the MASH) model that includes intracellular compartmentation of glucose and lactate metabolism. We define pre- and post-synaptic compartments metabolizing glucose and glucose plus lactate respectively in which the latter displays a positive correlation between oxidative metabolism of glucose and Ca2+ signalling

Mapping migrant territories as topological deformations of space

Our research uses the concept of “territories” to describe the production of migrant space. The article describes a project based in London where the everyday practice of walking is used to map migrant territories, which are conceptualized as dispersed and overlapping, causing topological deformations to the actual lived space. We interrogate these deformations through focusing on the micro-scale and the everyday, mapping them as “scapes” and “spheres.” Using specific computational techniques, we transform the original walks into an architectural tool for investigating the fluctuations and flows of the contemporary city. In doing so, we approach territories from two distinct angles: from the geopolitical perspective of territories seen as the product of the interplay of politics, power, and space and from the biological perspective of territories seen as the primal need of all animals, including humans, for space and a certain distinction from their environment and from others

Tandem mass spectrometry data quality assessment by self-convolution

<p>Abstract</p> <p>Background</p> <p>Many algorithms have been developed for deciphering the tandem mass spectrometry (MS) data sets. They can be essentially clustered into two classes. The first performs searches on theoretical mass spectrum database, while the second based itself on <it>de novo </it>sequencing from raw mass spectrometry data. It was noted that the quality of mass spectra affects significantly the protein identification processes in both instances. This prompted the authors to explore ways to measure the quality of MS data sets before subjecting them to the protein identification algorithms, thus allowing for more meaningful searches and increased confidence level of proteins identified.</p> <p>Results</p> <p>The proposed method measures the qualities of MS data sets based on the symmetric property of b- and y-ion peaks present in a MS spectrum. Self-convolution on MS data and its time-reversal copy was employed. Due to the symmetric nature of b-ions and y-ions peaks, the self-convolution result of a good spectrum would produce a highest mid point intensity peak. To reduce processing time, self-convolution was achieved using Fast Fourier Transform and its inverse transform, followed by the removal of the "DC" (Direct Current) component and the normalisation of the data set. The quality score was defined as the ratio of the intensity at the mid point to the remaining peaks of the convolution result. The method was validated using both theoretical mass spectra, with various permutations, and several real MS data sets. The results were encouraging, revealing a high percentage of positive prediction rates for spectra with good quality scores.</p> <p>Conclusion</p> <p>We have demonstrated in this work a method for determining the quality of tandem MS data set. By pre-determining the quality of tandem MS data before subjecting them to protein identification algorithms, spurious protein predictions due to poor tandem MS data are avoided, giving scientists greater confidence in the predicted results. We conclude that the algorithm performs well and could potentially be used as a pre-processing for all mass spectrometry based protein identification tools.</p

Multispecies justice:Climate-just futures with, for and beyond humans

In 2019, the climate emergency entered mainstream debates. The normative frame of climate justice as conceived in academia, policy arenas, and grassroots action, although imperative and growing in popularity across climate movements, is no longer adequate to address this emergency. This is for two reasons: first, as a framing for the problem, current notions of climate justice are insufficient to overcome the persistent silencing of voices belonging to multiple “others”; and second, they do not question, and thus implicitly condone, human exceptionalism and the violence it enacts, historically and in this era of the Anthropocene. Therefore, we advocate for the concept of multispecies justice to enrich climate justice in order to more effectively confront the climate crisis. The advantage of reconceptualizing climate justice in this way is that it becomes more inclusive; it acknowledges the differential histories and practices of social, environmental, and ecological harm, while opening just pathways into uncertain futures. A multispecies justice lens expands climate justice by decentering the human and by recognizing the everyday interactions that bind individuals and societies to networks of close and distant others, including other people and more‐than‐human beings. Such a relational lens provides a vital scientific, practical, material, and ethical road map for navigating the complex responsibilities and politics in the climate crisis. Most importantly, it delineates what genuine flourishing could mean, what systemic transformations may involve (and with whom), how to live with inevitable and possibly intolerable losses, and how to prefigure and enact alternative and just futures