L(2,1)-labeling of the strong product of paths and cycles.
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ABSTRACT:
SUBMITTER: Shao Z
PROVIDER: S-EPMC3953572 | biostudies-other | 2014
REPOSITORIES: biostudies-other
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Project description:BackgroundInteraction graphs (signed directed graphs) provide an important qualitative modeling approach for Systems Biology. They enable the analysis of causal relationships in cellular networks and can even be useful for predicting qualitative aspects of systems dynamics. Fundamental issues in the analysis of interaction graphs are the enumeration of paths and cycles (feedback loops) and the calculation of shortest positive/negative paths. These computational problems have been discussed only to a minor extent in the context of Systems Biology and in particular the shortest signed paths problem requires algorithmic developments.ResultsWe first review algorithms for the enumeration of paths and cycles and show that these algorithms are superior to a recently proposed enumeration approach based on elementary-modes computation. The main part of this work deals with the computation of shortest positive/negative paths, an NP-complete problem for which only very few algorithms are described in the literature. We propose extensions and several new algorithm variants for computing either exact results or approximations. Benchmarks with various concrete biological networks show that exact results can sometimes be obtained in networks with several hundred nodes. A class of even larger graphs can still be treated exactly by a new algorithm combining exhaustive and simple search strategies. For graphs, where the computation of exact solutions becomes time-consuming or infeasible, we devised an approximative algorithm with polynomial complexity. Strikingly, in realistic networks (where a comparison with exact results was possible) this algorithm delivered results that are very close or equal to the exact values. This phenomenon can probably be attributed to the particular topology of cellular signaling and regulatory networks which contain a relatively low number of negative feedback loops.ConclusionThe calculation of shortest positive/negative paths and cycles in interaction graphs is an important method for network analysis in Systems Biology. This contribution draws the attention of the community to this important computational problem and provides a number of new algorithms, partially specifically tailored for biological interaction graphs. All algorithms have been implemented in the CellNetAnalyzer framework which can be downloaded for academic use at http://www.mpi-magdeburg.mpg.de/projects/cna/cna.html.
| S-EPMC2708159 | biostudies-literature
Project description:Although standards have identified temporary carbon storage as an important element to consider in wood product LCAs, there has been no consensus on a methodology for its accounting. This work aims to improve the accounting of carbon storage and fluxes in long-life wood products in LCA. Biogenic carbon from harvested roundwood logs were tracked using the Carbon Budget Model Framework for Harvested Wood Products (CBMF-HWP). Carbon flows through wood product manufacturing, building life and end-of-life phases, and carbon stocks and fluxes from harvest to the atmosphere were estimated. To cover the products commonly used in the Canadian building industry, a range of softwood products types, provinces and territories and building lifetimes were considered. In addition, policy scenarios were considered in order to model the effects of dynamic parameters through time as a policy target is reached. Most wood products have similar emissions profiles, though cross-laminated timber has higher sawmill emissions and oriented-strand board has higher initial post-demolition emissions. The region of construction is also predictive of the initial post-demolition emissions. Higher recycling rates shift materials from landfills into subsequent product systems, thus avoiding landfill emissions. Landfill decay rates are affected by climate and results in a large range of landfill emissions. The degree of postponement of end-of-life emissions is highly dependent upon the wood product type, region and building lifespan parameters. This work develops biogenic carbon profiles that allows for modelling dynamic cradle-to-grave LCAs of Canadian wood products.Supplementary informationThe online version of this article (doi:10.1007/s42452-020-03979-2) contains supplementary material, which is available to authorized users.
| S-EPMC7799381 | biostudies-literature
Project description:BackgroundViral tracers are important tools for mapping brain connectomes. The feature of predominant anterograde transneuronal transmission offers herpes simplex virus-1 (HSV-1) strain H129 (HSV1-H129) as a promising candidate to be developed as anterograde viral tracers. In our earlier studies, we developed H129-derived anterograde polysynaptic tracers and TK deficient (H129-dTK) monosynaptic tracers. However, their broad application is limited by some intrinsic drawbacks of the H129-dTK tracers, such as low labeling intensity due to TK deficiency and potential retrograde labeling caused by axon terminal invasion. The glycoprotein K (gK) of HSV-1 plays important roles in virus entry, egress, and virus-induced cell fusion. Its deficiency severely disables virus egress and spread, while only slightly limits viral genome replication and expression of viral proteins. Therefore, we created a novel H129-derived anterograde monosynaptic tracer (H129-dgK) by targeting gK, which overcomes the limitations of H129-dTK.MethodsUsing our established platform and pipeline for developing viral tracers, we generated a novel tracer by deleting the gK gene from the H129-G4. The gK-deleted virus (H129-dgK-G4) was reconstituted and propagated in the Vero cell expressing wildtype H129 gK (gKwt) or the mutant gK (gKmut, A40V, C82S, M223I, L224V, V309M), respectively. Then the obtained viral tracers of gKmut pseudotyped and gKwt coated H129-dgK-G4 were tested in vitro and in vivo to characterize their tracing properties.ResultsH129-dgK-G4 expresses high levels of fluorescent proteins, eliminating the requirement of immunostaining for imaging detection. Compared to the TK deficient monosynaptic tracer H129-dTK-G4, H129-dgK-G4 labeled neurons with 1.76-fold stronger fluorescence intensity, and visualized 2.00-fold more postsynaptic neurons in the downstream brain regions. gKmut pseudotyping leads to a 77% decrease in retrograde labeling by reducing axon terminal invasion, and thus dramatically improves the anterograde-specific tracing of H129-dgK-G4. In addition, assisted by the AAV helper trans-complementarily expressing gKwt, H129-dgK-G4 allows for mapping monosynaptic connections and quantifying the circuit connectivity difference in the Alzheimer's disease and control mouse brains.ConclusionsgKmut pseudotyped H129-dgK-G4, a novel anterograde monosynaptic tracer, overcomes the limitations of H129-dTK tracers, and demonstrates desirable features of strong labeling intensity, high tracing efficiency, and improved anterograde specificity.
| S-EPMC8744342 | biostudies-literature
Project description:With the ongoing globalization of the pharmaceutical industry, efforts to harmonize technical requirements of registering drugs and biologics, including vaccines, have produced a number of useful guidelines utilized around the world. However, such efforts have not been extended to the regulatory review process or product labeling. Prescribing information and patient information leaflet are two types of such product labeling documents. This study examined the differences in the languages of these documents between the United States (US) and European Union (EU). The key documents examined were the U.S. Food & Drug Administration's (FDA) Package Inserts (PIs), U.S. Centers for Disease Control and Prevention's (CDC) Vaccine Information Statements (VISs), and the European Medicines Agency's (EMA) Summary of Product Characteristics (SmPCs) and Package Leaflets (PLs). Prescribing information and patient information leaflet languages were subsequently organized into ten and seven categories, respectively. Comparison of FDA PIs to EMA SmPCs showed little harmonization between the two regions, and CDC VISs to EMA PLs revealed even less.
| S-EPMC7550305 | biostudies-literature
Project description:The Late Miocene paleogeography of central Europe and its climatic history are well studied with a resolution of c. 106 years. Small-scale climatic variations are yet unresolved. Observing past climatic change of short periods, however, would encourage the understanding of the modern climatic system. Therefore, past climate archives require a resolution on a decadal to millennial scale. To detect such a short-term evolution, a continuous 6-m-core of the Paleo-Lake Pannon was analyzed in 1-cm-sample distance to provide information as precise and regular as possible. Measurements of the natural gamma radiation and magnetic susceptibility combined with the total abundance of ostracod shells were used as proxies to estimate millennial- to centennial scale environmental changes during the mid-Tortonian warm period. Patterns emerged, but no indisputable age model can be provided for the core, due to the lack of paleomagnetic reversals and the lack of minerals suitable for absolute dating. Therefore, herein we propose another method to determine a hypothetic time frame for these deposits. Based on statistical processes, including Lomb-Scargle and REDFIT periodograms along with Wavelet spectra, several distinct cyclicities could be detected. Calculations considering established off-shore sedimentation rates of the Tortonian Vienna Basin revealed patterns resembling Holocene solar-cycle-records well. The comparison of filtered data of Miocene and Holocene records displays highly similar patterns and comparable modulations. A best-fit adjustment of sedimentation rate results in signals which fit to the lower and upper Gleissberg cycle, the de Vries cycle, the unnamed 500-year- and 1000-year-cycles, as well as the Hallstatt cycle. Each of these cycles has a distinct and unique expression in the investigated environmental proxies, reflecting a complex forcing-system. Hence, a single-proxy-analysis, as often performed on Holocene records, should be considered cautiously as it might fail to capture the full range of solar cycles.
| S-EPMC3617729 | biostudies-literature
Project description:Unlike their B-alkyl counterparts, brominated N-alkyl B-aryl 2,1-borazaronaphthalenes undergo a self-arylation reaction in the presence of a catalytic amount of palladium and base, in which the azaborine serves as both the electrophile and the nucleophile. The products of the self-arylation are air- and moisture-stable 2,1-borazaronaphthols, previously only observed in basic alcoholic solvents. The steric encumbrance of the azaborine appears to prevent formation of the corresponding boron acid anhydride, allowing access to a family of 2,1-borazaronaphthol derivatives.
| S-EPMC4156240 | biostudies-literature
Project description:Carbanions of phenylacetonitriles, benzyl sulfones, and dialkyl benzylphosphonates add nitroarenes at the ortho-position to the nitro group to form [Formula: see text]-adducts that, upon treatment with trialkylchlorosilane and additional base (t-BuOK or DBU), transform into 3-aryl-2,1-benzisoxazoles in moderate-to-good yields.
| S-EPMC4591207 | biostudies-literature
Project description:In 17 patients with rapid cycling bipolar disorder, time-series analyses detected synchronies between mood cycles and three lunar cycles that modulate the amplitude of the moon's semi-diurnal gravimetric tides: the 14.8-day spring-neap cycle, the 13.7-day declination cycle and the 206-day cycle of perigee-syzygies ('supermoons'). The analyses also revealed shifts among 1:2, 1:3, 2:3 and other modes of coupling of mood cycles to the two bi-weekly lunar cycles. These shifts appear to be responses to the conflicting demands of the mood cycles' being entrained simultaneously to two different bi-weekly lunar cycles with slightly different periods. Measurements of circadian rhythms in body temperature suggest a biological mechanism through which transits of one of the moon's semi-diurnal gravimetric tides might have driven the patients' bipolar cycles, by periodically entraining the circadian pacemaker to its 24.84-h rhythm and altering the pacemaker's phase-relationship to sleep in a manner that is known to cause switches from depression to mania.
| S-EPMC5524624 | biostudies-literature