Fair Packing of Independent Sets
Ontology highlight
ABSTRACT:
SUBMITTER: Gasieniec L
PROVIDER: S-EPMC7254894 | biostudies-literature | 2020 Apr
REPOSITORIES: biostudies-literature
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Project description:BackgroundA major challenge in genomic research is identifying significant biological processes and generating new hypotheses from large gene sets. Gene sets often consist of multiple separate biological pathways, controlled by distinct regulatory mechanisms. Many of these pathways and the associated regulatory mechanisms might be obscured by a large number of other significant processes and thus not identified as significant by standard gene set enrichment analysis tools.ResultsWe present a novel method called Independent Enrichment Analysis (IEA) and software TAFFEL that eases the task by clustering genes to subgroups using Gene Ontology categories and transcription regulators. IEA indicates transcriptional regulators putatively controlling biological functions in studied condition.ConclusionsWe demonstrate that the developed method and TAFFEL tool give new insight to the analysis of differentially expressed genes and can generate novel hypotheses. Our comparison to other popular methods showed that the IEA method implemented in TAFFEL can find important biological phenomena, which are not reported by other methods.
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Project description:Large planetary seedlings, comets, microscale pharmaceuticals, and nanoscale soot particles are made from rigid, aggregated subunits that are compacted under low compression into larger structures spanning over 10 orders of magnitude in dimensional space. Here, we demonstrate that the packing density (?f) of compacted rigid aggregates is independent of spatial scale for systems under weak compaction. The ?f of rigid aggregated structures across six orders of magnitude were measured using nanoscale spherical soot aerosol composed of aggregates with ? 17-nm monomeric subunits and aggregates made from uniform monomeric 6-mm spherical subunits at the macroscale. We find ?f = 0.36 ± 0.02 at both dimensions. These values are remarkably similar to ?f observed for comet nuclei and measured values of other rigid aggregated systems across a wide variety of spatial and formative conditions. We present a packing model that incorporates the aggregate morphology and show that ?f is independent of both monomer and aggregate size. These observations suggest that the ?f of rigid aggregates subject to weak compaction forces is independent of spatial dimension across varied formative conditions.
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Project description:Essentials Platelet packing density in a hemostatic plug limits molecular movement to diffusion. A diffusion-dependent steep thrombin gradient forms radiating outwards from the injury site. Clot retraction affects the steepness of the gradient by increasing platelet packing density. Together, these effects promote hemostatic plug core formation and inhibit unnecessary growth.SummaryBackground Hemostasis studies performed in vivo have shown that hemostatic plugs formed after penetrating injuries are characterized by a core of highly activated, densely packed platelets near the injury site, covered by a shell of less activated and loosely packed platelets. Thrombin production occurs near the injury site, further activating platelets and starting the process of platelet mass retraction. Tightening of interplatelet gaps may then prevent the escape and exchange of solutes. Objectives To reconstruct the hemostatic plug macro- and micro-architecture and examine how platelet mass contraction regulates solute transport and solute concentration in the gaps between platelets. Methods Our approach consisted of three parts. First, platelet aggregates formed in vitro under flow were analyzed using scanning electron microscopy to extract data on porosity and gap size distribution. Second, a three-dimensional (3-D) model was constructed with features matching the platelet aggregates formed in vitro. Finally, the 3-D model was integrated with volume and morphology measurements of hemostatic plugs formed in vivo to determine how solutes move within the platelet plug microenvironment. Results The results show that the hemostatic mass is characterized by extremely narrow gaps, porosity values even smaller than previously estimated and stagnant plasma velocity. Importantly, the concentration of a chemical species released within the platelet mass increases as the gaps between platelets shrink. Conclusions Platelet mass retraction provides a physical mechanism to establish steep chemical concentration gradients that determine the extent of platelet activation and account for the core-and-shell architecture observed in vivo.
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