Mass singularity and confining property in QED3QED_3

We discuss the properties of the position space fermion propagator in three dimensional QED which has been found previouly based on Ward-Takahashi-identity for soft-photon emission vertex and spectral representation.There is a new type of mass singularity which governs the long distance behaviour.It leads the propagator vanish at large distance.This term corresponds to dynamical mass in position space.Our model shows confining property and dynamical mass generation for arbitrary coupling constant.Since we used dispersion retation in deriving spectral function there is a physical mass which sets a mass scale.For finite cut off we obtain the full propagator in the dispersion integral as a superposition of different massses.Low energy behaviour of the proagator is modified to decrease by position dependent mass.In the limit of zero infrared cut-off the propagator vanishes with a new kind of infrared behaviour.Comment: 22pages,4figures,revtex4,Notational sloppiness are crrected.Submitted to JHE

Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualization

Motivation: Biological systems are complex and challenging to model and therefore model reuse is highly desirable. To promote model reuse, models should include both information about the specifics of simulations and the underlying biology in the form of metadata. The availability of computationally tractable metadata is especially important for the effective automated interpretation and processing of models. Metadata are typically represented as machine-readable annotations which enhance programmatic access to information about models. Rule-based languages have emerged as a modelling framework to represent the complexity of biological systems. Annotation approaches have been widely used for reaction-based formalisms such as SBML. However, rule-based languages still lack a rich annotation framework to add semantic information, such as machine-readable descriptions, to the components of a model. Results: We present an annotation framework and guidelines for annotating rule-based models, encoded in the commonly used Kappa and BioNetGen languages. We adapt widely adopted annotation approaches to rule-based models. We initially propose a syntax to store machine-readable annotations and describe a mapping between rule-based modelling entities, such as agents and rules, and their annotations. We then describe an ontology to both annotate these models and capture the information contained therein, and demonstrate annotating these models using examples. Finally, we present a proof of concept tool for extracting annotations from a model that can be queried and analyzed in a uniform way. The uniform representation of the annotations can be used to facilitate the creation, analysis, reuse and visualization of rule-based models. Although examples are given, using specific implementations the proposed techniques can be applied to rule-based models in general

Task-Related Effects on the Temporal and Spatial Dynamics of Resting-State Functional Connectivity in the Default Network

Recent evidence points to two potentially fundamental aspects of the default network (DN), which have been relatively understudied. One is the temporal nature of the functional interactions among nodes of the network in the resting-state, usually assumed to be static. The second is possible influences of previous brain states on the spatial patterns (i.e., the brain regions involved) of functional connectivity (FC) in the DN at rest. The goal of the current study was to investigate modulations in both the spatial and temporal domains. We compared the resting-state FC of the DN in two runs that were separated by a 45 minute interval containing cognitive task execution. We used partial least squares (PLS), which allowed us to identify FC spatiotemporal patterns in the two runs and to determine differences between them. Our results revealed two primary modes of FC, assessed using a posterior cingulate seed – a robust correlation among DN regions that is stable both spatially and temporally, and a second pattern that is reduced in spatial extent and more variable temporally after cognitive tasks, showing switching between connectivity with certain DN regions and connectivity with other areas, including some task-related regions. Therefore, the DN seems to exhibit two simultaneous FC dynamics at rest. The first is spatially invariant and insensitive to previous brain states, suggesting that the DN maintains some temporally stable functional connections. The second dynamic is more variable and is seen more strongly when the resting-state follows a period of task execution, suggesting an after-effect of the cognitive activity engaged during task that carries over into resting-state periods

Asymmetric leaves1 mediates leaf patterning and stem cell function in Arabidopsis

Meristem function in plants requires both the maintenance of stem cells and the specification of founder cells from which lateral organs arise. Lateral organs are patterned along proximodistal, dorsoventral and mediolateral axes (1,2). Here we show that the Arabidopsis mutant asymmetric leaves1 (as1) disrupts this process. AS1 encodes a myb domain protein, closely related to PHANTASTICA in Antirrhinum and ROUGH SHEATH2 in maize, both of which negatively regulate knotted-class homeobox genes. AS1 negatively regulates the homeobox genes KNAT1 and KNAT2 and is, in turn, negatively regulated by the meristematic homeobox gene SHOOT MERISTEMLESS. This genetic pathway defines a mechanism for differentiating between stem cells and organ founder cells within the shoot apical meristem and demonstrates that genes expressed in organ primordia interact with meristematic genes to regulate shoot morphogenesi

A gap analysis on modelling of sea lice infection pressure from salmonid farms. I. A structured knowledge review

Sustainability of aquaculture, an important component of the blue economy, relies in part on ensuring assessment of environmental impact and interactions relating to sea lice dispersing from open pen salmon and trout farms. We review research underpinning the key stages in the sea lice infection process to support modelling of lice on wild salmon in relation to those on farms. The review is split into 5 stages: larval production; larval transport and survival; exposure and infestation of new hosts; development and survival of the attached stages; and impact on host populations. This modular structure allows the existing published data to be reviewed and assessed to identify data gaps in modelling sea lice impacts in a systematic way. Model parameterisation and parameter variation is discussed for each stage, providing an overview of knowledge strength and gaps. We conclude that a combination of literature review, empirical data collection and modelling studies are required on an iterative basis to ensure best practice is applied for sustainable aquaculture. The knowledge gained can then be optimised and applied at regional scales, with the most suitable modelling frameworks applied for the system, given regional limitations

A gap analysis on modelling of sea lice infection pressure from salmonid farms. II. Identifying and ranking knowledge gaps: output of an international workshop

Sea lice are a major health hazard for farmed Atlantic salmon in Europe, and their impact is felt globally. Given the breadth of ongoing research in sea lice dispersal and population modelling, and focus on research-led adaptive management, we brought experts together to discuss research knowledge gaps. Gaps for salmon lice infection pressure from fish farms were identified and scored by experts in sea lice-aquaculture-environment interactions, at an international workshop in 2021. The contributors included experts based in Scotland, Norway, Ireland, Iceland, Canada, the Faroe Islands, England and Australia, employed by governments, industry, universities and non-government organisations. The workshop focused on knowledge gaps underpinning 5 key stages in salmon lice infection pressure from fish farms: larval production; larval transport and survival; exposure and infestation of new hosts; development and survival of the attached stages; and impact on host populations. A total of 47 research gaps were identified; 5 broad themes emerged with 13 priority research gaps highlighted as important across multiple sectors. The highest-ranking gap called for higher quality and frequency of on-farm lice count data, along with better sharing of information across sectors. We highlight the need for synergistic international collaboration to maximise transferable knowledge. Round table discussions through collaborative workshops provide an important forum for experts to discuss and agree research priorities

4D Super-Resolution Microscopy with Conventional Fluorophores and Single Wavelength Excitation in Optically Thick Cells and Tissues

Optical super-resolution imaging of fluorescently stained biological samples is rapidly becoming an important tool to investigate protein distribution at the molecular scale. It is therefore important to develop practical super-resolution methods that allow capturing the full three-dimensional nature of biological systems and also can visualize multiple protein species in the same sample

Heterogeneous Nuclear Ribonucleoprotein K Interacts with Abi-1 at Postsynaptic Sites and Modulates Dendritic Spine Morphology

BACKGROUND: Abelson-interacting protein 1 (Abi-1) plays an important role for dendritic branching and synapse formation in the central nervous system. It is localized at the postsynaptic density (PSD) and rapidly translocates to the nucleus upon synaptic stimulation. At PSDs Abi-1 is in a complex with several other proteins including WASP/WAVE or cortactin thereby regulating the actin cytoskeleton via the Arp 2/3 complex. PRINCIPAL FINDINGS: We identified heterogeneous nuclear ribonucleoprotein K (hnRNPK), a 65 kDa ssDNA/RNA-binding-protein that is involved in multiple intracellular signaling cascades, as a binding partner of Abi-1 at postsynaptic sites. The interaction with the Abi-1 SH3 domain is mediated by the hnRNPK-interaction (KI) domain. We further show that during brain development, hnRNPK expression becomes more and more restricted to granule cells of the cerebellum and hippocampal neurons where it localizes in the cell nucleus as well as in the spine/dendritic compartment. The downregulation of hnRNPK in cultured hippocampal neurons by RNAi results in an enlarged dendritic tree and a significant increase in filopodia formation. This is accompanied by a decrease in the number of mature synapses. Both effects therefore mimic the neuronal morphology after downregulation of Abi-1 mRNA in neurons. CONCLUSIONS: Our findings demonstrate a novel interplay between hnRNPK and Abi-1 in the nucleus and at synaptic sites and show obvious similarities regarding both protein knockdown phenotypes. This indicates that hnRNPK and Abi-1 act synergistic in a multiprotein complex that regulates the crucial balance between filopodia formation and synaptic maturation in neurons