Linked Environment Data for the Life Sciences
Environment Agencies from Europe and the US are setting up a network of Linked Environment Data and are looking to crosslink it with Linked Data contributions from the life sciences.
cs.OH↗
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Results for “q-bio.OT”
Search indexed arXiv papers on artificial intelligence, large language models, computer vision and robotics. Read source abstracts and follow links to arXiv.
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The differences between natural and artificial life. Towards a definition of life
It is high time to openly and without finalism define the dangerous but needed term 'purposeful information', whose quantity is an Eigen information value. Using the term 'biological information' in its stead forces one into an uncomfortable detour. I propose such a definition based on the generalized notions of 'information' and 'encoding'. Next, the properties of the spontaneous process of collecting purposeful information are investigated. In effect, the properties of this process: the goal 'continuation of existence', reproduction and Darwinian mechanism are derived which suggest, that it is the natural life process. A 'natural identity criterion' appears in this process for an evolving object, that is connected to a 'small change tendency'. Likewise, 'hereditary information' is defined. Artificial life is constructed by living objects, is a part of natural life process and its properties are not an effect of its internal restrictions but of external assumptions.
nlin.AO↗
Characterization of the norepinephrine-activation of adenylate cyclase suggests a role in memory affirmation pathways. Overexposure to epinephrine inactivates adenylate-cyclase,a causal pathway for stress-pathologies
Incubation with noradrenaline (norepinephrine) of isolated membranes of rat's brain corpus striatum and cortex, showed that ionic-magnesium (Mg2+) is required for the neurotransmitter activatory response of Adenylate Cyclase [ATP pyrophosphate-lyase (cyclizing), (EC 4.6.1.1)], AC.An Mg2+-dependent response to the activatory effects of adrenaline, and subsequent inhibition by calcium, suggest capability for a turnover, associated with cyclic changes in membrane potential and participation in a short term-memory pathway.In the cell, the neurotransmitter by activating AC generates intracellular cyclic AMP. Calcium entrance in the cell inhibits the enzyme. The increment of cyclic AMP activates kinaseA and their protein phosphorylating activity, allowing a long term memory pathway. Hence, consolidating neuronal circuits, related to emotional learning and memory affirmation.The activatory effect relates to an enzyme-noradrenaline complex which may participate on the physiology of the fight or flight response, by prolonged exposure. However, the persistence of an unstable enzyme complex turns the enzyme inactive. Effect concordant, with the observation that prolonged exposure to adrenaline, participate in the etiology of stress triggered pathologies. At the cell physiological level AC responsiveness to hormones could be modulated by the concentration of Chelating Metabolites. These ones produce the release of free ATP4-, a negative modulator of AC and the Mg2+ activated insulin receptor tyrosine kinase (IRTK). Thus, allowing an integration of the hormonal response of both enzymes by ionic controls. This effect could supersede the metabolic feedback control by energy-charge. Accordingly, maximum hormonal response of both enzymes, to high Mg2+ and low free ATP4-, allows a correlation with the known effects of low caloric intake increasing average life expectancy.
q-bio.OT↗
The Virtual Institute for Integrative Biology (VIIB)
The Virtual Institute for Integrative Biology (VIIB) is a Latin American initiative for achieving global collaborative e-Science in the areas of bioinformatics, genome biology, systems biology, metagenomics, medical applications and nanobiotechnolgy. The scientific agenda of VIIB includes: construction of databases for comparative genomics, the AlterORF database for alternate open reading frames discovery in genomes, bioinformatics services and protein simulations for biotechnological and medical applications. Human resource development has been promoted through co-sponsored students and shared teaching and seminars via video conferencing. E-Science challenges include: interoperability and connectivity concerns, high performance computing limitations, and the development of customized computational frameworks and flexible workflows to efficiently exploit shared resources without causing impediments to the user. Outreach programs include training workshops and classes for high school teachers and students and the new Adopt-a-Gene initiative. The VIIB has proved an effective way for small teams to transcend the critical mass problem, to overcome geographic limitations, to harness the power of large scale, collaborative science and improve the visibility of Latin American science It may provide a useful paradigm for developing further e-Science initiatives in Latin America and other emerging regions.
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PhyloGrid: a development for a workflow in Phylogeny
In this work we present the development of a workflow based on Taverna which is going to be implemented for calculations in Phylogeny by means of the MrBayes tool. It has a friendly interface developed with the Gridsphere framework. The user is able to define the parameters for doing the Bayesian calculation, determine the model of evolution, check the accuracy of the results in the intermediate stages as well as do a multiple alignment of the sequences previously to the final result. To do this, no knowledge from his/her side about the computational procedure is required.
cs.CE↗
Advances in the Biomedical Applications of the EELA Project
In the last years an increasing demand for Grid Infrastructures has resulted in several international collaborations. This is the case of the EELA Project, which has brought together collaborating groups of Latin America and Europe. One year ago we presented this e-infrastructure used, among others, by the Biomedical groups for the studies of oncological analysis, neglected diseases, sequence alignments and computation phylogenetics. After this period, the achieved advances are summarised in this paper.
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Biological Concepts Instrument (BCI): A diagnostic tool for revealing student thinking
A key to effective teaching is an awareness and accurate understanding of the thinking and implicit assumptions that students bring to the subject to be learned. In the absence of extensive Socratic interactions with students, one strategy to assess student thinking involves the use of concept inventories (CIs). CIs are typically multiple-choice assessments, constructed based on research into student thinking and language, and designed to reveal the presence of common misconceptions and implicit assumptions pertaining to a particular facet of a subject. Here we describe the open-source Biological Concepts Instrument (BCI), a diagnostic, multiple-choice instrument designed to provide instructors with a preliminary map of a number of basic ideas in molecular level biology. We describe the strategy behind its design, the research upon which it is based, item construction, and its possible uses as a means to reveal and address persistent and often unrecognized conceptual obstacles.
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Chem2Bio2RDF: A Linked Open Data Portal for Chemical Biology
The Chem2Bio2RDF portal is a Linked Open Data (LOD) portal for systems chemical biology aiming for facilitating drug discovery. It converts around 25 different datasets on genes, compounds, drugs, pathways, side effects, diseases, and MEDLINE/PubMed documents into RDF triples and links them to other LOD bubbles, such as Bio2RDF, LODD and DBPedia. The portal is based on D2R server and provides a SPARQL endpoint, but adds on few unique features like RDF faceted browser, user-friendly SPARQL query generator, MEDLINE/PubMed cross validation service, and Cytoscape visualization plugin. Three use cases demonstrate the functionality and usability of this portal.
cs.IR↗
The multiplet structure of the genetic code, in one and small number
In this short paper, it is shown that the multiplet structure of the standard genetic code is derivable from the total number of nucleotides contained in 64 codons, 192, a small number. The degeneracy class-number is derived as the number of numbers coprime to the number of Family-Boxes involved for the quartets, the doublets and the singlets. Those for the triplet and the sextets are computed as simple linear combinations of the preceeding ones. Some interesting consequences are also presented.
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Rate distortion coevolutionary dynamics and the flow nature of cognitive epigenetic systems
We outline a model for a cognitive epigenetic system based on elements of the Shannon theory of information and the statistical physics of the generalized Onsager relations. Particular attention is paid to the concept of the rate distortion function and from another direction as motivated by the thermodynamics of computing, the fundamental homology with the free energy density of a physical system. A unifying aspect of the dynamic framework involves the concept of a groupoid and of a groupoid atlas. From a stochastic differential equation we postulate a multidimensional Ito process for an epigenetic system from which a stochastic flow may permeate through components of this atlas.
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Consciousness: A Direct Link with Life's Origin?
Inspired by the Penrose-Hameroff thesis, we are intuitively led to examine an intriguing correspondence of 'induction' (by fields), with the complex phenomenon of (metabolism-sustained) consciousness: Did sequences of associated induction patterns in field-susceptible biomatter have simpler beginnings?
physics.hist-ph↗
The genetic code, 8-dimensional hypercomplex numbers and dyadic shifts
Matrix forms of the representation of the multi-level system of molecular-genetic alphabets have revealed algebraic properties of this system. Families of genetic (4*4)- and (8*8)-matrices show unexpected connections of the genetic system with Walsh functions and Hadamard matrices, which are known in theory of noise-immunity coding, digital communication and digital holography. Dyadic-shift decompositions of such genetic matrices lead to sets of sparse matrices. Each of these sets is closed in relation to multiplication and defines relevant algebra of hypercomplex numbers. It is shown that genetic Hadamard matrices are identical to matrix representations of Hamilton quaternions and its complexification in the case of unit coordinates. The diversity of known dialects of the genetic code is analyzed from the viewpoint of the genetic algebras. An algebraic analogy with Punnett squares for inherited traits is shown. Our results are used in analyzing genetic phenomena. The statement about existence of the geno-logic code in DNA and epigenetics on the base of the spectral logic of systems of Boolean functions is put forward. Our results show promising ways to develop algebraic-logical biology, in particular, in connection with the logic holography on Walsh functions.
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Length, Weight, and Yield in Channel Catfish, Lake Diane, MI
Background: Channel catfish (Ictalurus punctatus) are important to both commercial aquaculture and recreational fisheries. Little published data is available on length-weight relationships of channel catfish in Michigan. Though there is no record of public or private stocking, channel catfish appeared in Lake Diane between 1984 and 1995 and it has developed into an excellent fishery. Results: NLLS regression yields parameter estimates of b = 3.2293 and a = 0.00522. The improved model yields the same estimate for the exponent, b, and a length estimate (parameter L1) of 45.23 cm. Estimates of uncertainty and covariance are smaller for the improved model, but the correlation coefficient is r = 0.995 in both cases. LLS regression produced different parameter values, a = 0.01356 and b = 2.9726, and a smaller correlation coefficient, r = 0.980. On average, catfish in the sample weighed 106.0% of the standard weight, (Brown et al.) and the linear regression (no slope) of fillet yield vs. total weight suggests a typical fillet yield of 28.1% with r = 0.989. Conclusion: Most of the fish in the sample were above the standard weight, heavier than the 75th percentile for their length. Channel catfish are doing well in Lake Diane and the population is well matched to the food supply. Management should attempt to maintain current population levels. In this case, the improved length-weight model, W(L) = (L/L1)^b, provided lower uncertainties in parameter estimates and smaller covariance than the traditional model.
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Anthropogenic Renourishment Feedback on Shorebirds: a Multispecies Bayesian Perspective
In this paper the realized niche of the Snowy Plover (Charadrius alexandrinus), a primarily resident Florida shorebird, is described as a function of the scenopoetic and bionomic variables at the nest-, landscape-, and regional-scale. We identified some pos- sible geomorphological controls that influence nest-site selection and survival using data collected along the Florida Gulf coast. In particular we focused on the effects of beach replenishment interventions on the Snowy Plover (SP), and on the migratory Piping Plover (PP) (Charadrius melodus) and Red Knot (RK) (Calidris canutus). To quantify the relationship between past renourishment projects and shorebird species we used a Monte Carlo procedure to sample from the posterior distribution of the binomial probabilities that a region is not a nesting or a wintering ground conditional on the occurrence of a beach replenishment intervention in the same and the previous year. The results indicate that it was 2.3, 3.1, and 0.8 times more likely that a region was not a wintering ground following a year with a renourishment intervention for the SP, PP and RK respectively. For the SP it was 2.5. times more likely that a region was not a breeding ground after a renourishment event. Through a maximum entropy principle model we observed small differences in the habitat use of the SP during the breeding and the wintering season. However the habitats where RK was observed ap- peared quite different. Maintaining and creating optimal suitable habitats for SP characterized by sparse low vegetation in the foredunes areas, and uneven/low-slope beach surfaces, is the proposed conservation scenario to convert anthropic beach restorations and SP populations into a positive feedback without impacting other threatened shorebird species.
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Randomness and Multi-level Interactions in Biology
The dynamic instability of the living systems and the "superposition" of different forms of randomness are viewed as a component of the contingently increasing organization of life along evolution. We briefly survey how classical and quantum physics define randomness differently. We then discuss why this requires, in our view, an enrichment of the understanding of the effects of their concurrent presence in biological systems' dynamics. Biological randomness is then presented as an essential component of the heterogeneous determination and intrinsic unpredictability proper to life phenomena, due to the nesting and interaction of many levels of organization. Even increasing organization itself induces growing disorder, by energy dispersal effects of course, but also by variability and differentiation. Co-operation between diverse components in networks implies at the same time the presence of constraints due to the peculiar forms of (bio-)resonance and (bio-)entanglement we discuss.
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What does photon energy tell us about cellphone safety?
It has been argued that cellphones are safe because a single microwave photon does not have enough energy to break a chemical bond. We show that cellphone technology operates in the classical wave limit, not the single photon limit. Based on energy densities relative to thermal energy, we estimate thresholds at which effects might be expected. These seem to correspond somewhat with many experimental observations. Revised with appendix responding to critique published by B. Leikind.
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Application in the Ethanol Fermentation of Immobilized Yeast Cells in Matrix of Alginate/Magnetic Nanoparticles, on Chitosan-Magnetite Microparticles and Cellulose-coated Magnetic Nanoparticles
Saccharomyces cerevisiae cells were entrapped in matrix of alginate and magnetic nanoparticles and covalently immobilized on magnetite-containing chitosan and cellulose-coated magnetic nanoparticles. Cellulose-coated magnetic nanoparticles with covalently immobilized thermostable α-amylase and chitosan particles with immobilized glucoamylase were also prepared. The immobilized cells and enzymes were applied in column reactors - 1/for simultaneous corn starch saccharification with the immobilized glucoamylase and production of ethanol with the entrapped or covalently immobilized yeast cells, 2/ for separate ethanol fermentation of the starch hydrolysates with the fixed yeasts. Hydrolysis of corn starch with the immobilized α-amylase and glucoamylase, and separate hydrolysis with the immobilized α-amylase were also examined. In the first reactor the ethanol yield reached approx. 91% of the theoretical; the yield was approx. 86% in the second. The ethanol fermentation was affected by the type of immobilization, the initial particle loading, feed sugar concentration and the dilution rate. The ethanol productivity with entrapped cells reached 264.0 g/L.h at particle loading rate 70% and dilution rate 3.0 h-1 with reducing sugar concentration of 200.0 g/L. The prepared magnetic particles with fixed yeast cells were stable at 4oC in saline for more than 1 month. .
physics.chem-ph↗
DNA Circuits Based on Isothermal Constrained Loop Extension DNA Amplification
In this paper, we first describe the isothermal constrained loop extension DNA amplification (ICLEDA), which is a new variant of amplification combining the advantages of rolling circle amplification (RCA) and of strand displacement amplification (SDA). Then, we formalize this process in terms of the theory of formal languages and show, on the basis of this formulation, how to manage OR and AND gates. We then explain how to introduce negation, which allows us to prove that, in principle, it is possible to implement the computation of any boolean function on DNA strands using ICLEDA.
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