Biocharts: a visual formalism for complex biological systems

We address one of the central issues in devising languages, methods and tools for the modelling and analysis of complex biological systems, that of linking high-level (e.g. intercellular) information with lower-level (e.g. intracellular) information. Adequate ways of dealing with this issue are crucial for understanding biological networks and pathways, which typically contain huge amounts of data that continue to grow as our knowledge and understanding of a system increases. Trying to comprehend such data using the standard methods currently in use is often virtually impossible. We propose a two-tier compound visual language, which we call Biocharts, that is geared towards building fully executable models of biological systems. One of the main goals of our approach is to enable biologists to actively participate in the computational modelling effort, in a natural way. The high-level part of our language is a version of statecharts, which have been shown to be extremely successful in software and systems engineering. The statecharts can be combined with any appropriately well-defined language (preferably a diagrammatic one) for specifying the low-level dynamics of the pathways and networks. We illustrate the language and our general modelling approach using the well-studied process of bacterial chemotaxis

Further study of the Over-Barrier Model to compute charge exchange processes

In this paper we study theoretically the process of electron capture between one-optical-electron atoms (e.g. hydrogenlike or alkali atoms) and ions at low-to-medium impact velocities ($v/v_e \approx 1$) working on a modification of an already developed classical In this work we present an improvement over the Over Barrier Model (OBM) described in a recent paper [F. Sattin, Phys. Rev. A {\bf 62}, 042711 (2000)]. We show that: i) one of the two free parameters there introduced actually comes out consistently from the starting assumptions underlying the model; ii) the modified model thus obtained is as much accurate as the former one. Furthermore, we show that OBMs are able to accurately predict some recent results of state selective electron capture, at odds with what previously supposed.Comment: RevTeX, 7 pages, 4 eps figures. To appear in Physical Review A (2001-september issue

Recovery From Monocular Deprivation Using Binocular Deprivation: Experimental Observations and Theoretical Analysis

Ocular dominance (OD) plasticity is a robust paradigm for examining the functional consequences of synaptic plasticity. Previous experimental and theoretical results have shown that OD plasticity can be accounted for by known synaptic plasticity mechanisms, using the assumption that deprivation by lid suture eliminates spatial structure in the deprived channel. Here we show that in the mouse, recovery from monocular lid suture can be obtained by subsequent binocular lid suture but not by dark rearing. This poses a significant challenge to previous theoretical results. We therefore performed simulations with a natural input environment appropriate for mouse visual cortex. In contrast to previous work we assume that lid suture causes degradation but not elimination of spatial structure, whereas dark rearing produces elimination of spatial structure. We present experimental evidence that supports this assumption, measuring responses through sutured lids in the mouse. The change in assumptions about the input environment is sufficient to account for new experimental observations, while still accounting for previous experimental results

Formal Verification Integration Approach for DSML

International audienceThe application of formal methods (especially, model check- ing and static analysis techniques) for the verification of safety critical embedded systems has produced very good results and raised the inter- est of system designers up to the application of these technologies in real size projects. However, these methods usually rely on specific verifica- tion oriented formal languages that most designers do not master. It is thus mandatory to embed the associated tools in automated verification toolchains that allow designers to rely on their usual domain-specific modeling languages (DSMLs) while enjoying the benefits of these power- ful methods. More precisely, we propose a language to formally express system requirements and interpret verification results so that system designers (DSML end-users) avoid the burden of learning some formal verification technologies. Formal verification is achieved through trans- lational semantics. This work is based on a metamodeling pattern for executable DSML that favors the definition of generative tools and thus eases the integration of tools for new DSML

A classical Over Barrier Model to compute charge exchange between ions and one-optical-electron atoms

In this paper we study theoretically the process of electron capture between one-optical-electron atoms (e.g. hydrogenlike or alkali atoms) and ions at low-to-medium impact velocities (v/v_e <= 1) working on a modification of an already developed classical Over Barrier Model (OBM) [V. Ostrovsky, J. Phys. B: At. Mol. Opt. Phys. {\bf 28} 3901 (1995)], which allows to give a semianalytical formula for the cross sections. The model is discussed and then applied to a number of test cases including experimental data as well as data coming from other sophisticated numerical simulations. It is found that the accuracy of the model, with the suggested corrections and applied to quite different situations, is rather high.Comment: 12 pages REVTEX, 5 EPSF figures, submitted to Phys Rev

Proton exchange membrane fuel cell operation and degradation in short-circuit.

International audienceThis paper presents an experimental study dealing with operation and degradation during an electrical short circuit of a proton exchange membrane fuel cell stack. The physical quantities in the fuel cell (electrical voltage and current, gas stoichiometry, pressures, temperatures and gas humidity) are studied before, during and after the failure. After a short circuit occurs, a high peak of current appears but decreases to stabilize in a much lower value. The voltage drops in all the cells and even some cells presents reversal potentials. The degradation is quantified by using electrochemical impedance spectroscopy

Control dependence for extended finite state machines

Though there has been nearly three decades of work on program slicing, there has been comparatively little work on slicing for state machines. One of the primary challenges that currently presents a barrier to wider application of state machine slicing is the problem of determining control dependence. We survey existing related definitions, introducing a new definition that subsumes one and extends another. We illustrate that by using this new definition our slices respect Weiser slicing’s termination behaviour. We prove results that clarify the relationships between our definition and older ones, following this up with examples to motivate the need for these differences

New onset or relapsing neuromyelitis optica temporally associated with SARS-CoV-2 infection and COVID-19 vaccination: a systematic review

BackgroundNeuromyelitis optica spectrum disorder (NMOSD) is a rare chronic neuroinflammatory autoimmune condition. Since the onset of the COVID-19 pandemic, there have been reports of NMOSD clinical manifestations following both SARS-CoV-2 infections and COVID-19 vaccinations.ObjectiveThis study aims to systematically review the published literature of NMOSD clinical manifestations associated with SARS-CoV-2 infections and COVID-19 vaccinations.MethodsA Boolean search of the medical literature was conducted between December 1, 2019 to September 1, 2022, utilizing Medline, Cochrane Library, Embase, Trip Database, Clinicaltrials.gov, Scopus, and Web of Science databases. Articles were collated and managed on Covidence® software. The authors independently appraised the articles for meeting study criteria and followed PRISMA guidelines. The literature search included all case reports and case series that met study criteria and involved NMOSD following either the SARS-CoV-2 infection or the COVID-19 vaccination.ResultsA total of 702 articles were imported for screening. After removing 352 duplicates and 313 articles based on exclusion criteria, 34 articles were analyzed. A total of 41 cases were selected, including 15 patients that developed new onset NMOSD following a SARS-CoV-2 infection, 21 patients that developed de novo NMOSD following COVID-19 vaccination, 3 patients with known NMOSD that experienced a relapse following vaccination, and 2 patients with presumed Multiple Sclerosis (MS) that was unmasked as NMOSD post-vaccination. There was a female preponderance of 76% among all NMOSD cases. The median time interval between the initial SARS-CoV-2 infection symptoms and NMOSD symptom onset was 14  days (range 3–120  days) and the median interval between COVID-19 vaccination and onset of NMO symptoms was 10  days (range 1 to 97  days). Transverse myelitis was the most common neurological manifestation in all patient groups (27/41). Management encompassed acute treatments such as high dose intravenous methylprednisolone, plasmapheresis, and intravenous immunoglobulin (IVIG) and maintenance immunotherapies. The majority of patients experienced a favorable outcome with complete or partial recovery, but 3 patients died.ConclusionThis systematic review suggests that there is an association between NMOSD and SARS-CoV-2 infections and COVID-19 vaccinations. This association requires further study using quantitative epidemiological assessments in a large population to better quantify the risk

Distribution of entanglement in light-harvesting complexes and their quantum efficiency

Recent evidence of electronic coherence during energy transfer in photosynthetic antenna complexes has reinvigorated the discussion of whether coherence and/or entanglement has any practical functionality for these molecular systems. Here we investigate quantitative relationships between the quantum yield of a light-harvesting complex and the distribution of entanglement among its components. Our study focusses on the entanglement yield or average entanglement surviving a time scale comparable to the average excitation trapping time. As a prototype system we consider the Fenna-Matthews-Olson (FMO) protein of green sulphur bacteria and show that there is an inverse relationship between the quantum efficiency and the average entanglement between distant donor sites. Our results suggest that longlasting electronic coherence among distant donors might help modulation of the lightharvesting function.Comment: Version accepted for publication in NJ