Deposits of clastic carbonate-dominated (calciclastic) sedimentary slope systems in the rock record have been identified mostly as linearly-consistent carbonate apron deposits, even though most ancient clastic carbonate slope deposits fit the submarine fan systems better. Calciclastic submarine fans are consequently rarely described and are poorly understood. Subsequently, very little is known especially in mud-dominated calciclastic submarine fan systems. Presented in this study are a sedimentological core and petrographic characterisation of samples from eleven boreholes from the Lower Carboniferous of Bowland Basin (Northwest England) that reveals a >250 m thick calciturbidite complex deposited in a calciclastic submarine fan setting. Seven facies are recognised from core and thin section characterisation and are grouped into three carbonate turbidite sequences. They include: 1) Calciturbidites, comprising mostly of highto low-density, wavy-laminated bioclast-rich facies; 2) low-density densite mudstones which are characterised by planar laminated and unlaminated muddominated facies; and 3) Calcidebrites which are muddy or hyper-concentrated debrisflow deposits occurring as poorly-sorted, chaotic, mud-supported floatstones. These

Phd by thesis

Beginning with its discovery in 1986 and continuing through the present, the transcription factor NF-κB has attracted widespread interest based on its unusual regulation, the variety of stimuli that activate it, the diverse genes and biological responses that it controls, the striking evolutionary conservation of structure and function among family members, and its apparent involvement in a variety of human diseases (Table ​(Table1).1). Importantly, and consistent with the last point, NF-κB has been shown to be the target of several anti-inflammatory and anticancer drugs.

/pdf/series-introduction-the-transcription-factor-nf-kb-and-human-2kd3tmdia3.pdf

Series Introduction: The transcription factor NF-κB and human disease

We define a new topological summary for data that we call the persistence landscape. Since this summary lies in a vector space, it is easy to combine with tools from statistics and machine learning, in contrast to the standard topological summaries. Viewed as a random variable with values in a Banach space, this summary obeys a strong law of large numbers and a central limit theorem. We show how a number of standard statistical tests can be used for statistical inference using this summary. We also prove that this summary is stable and that it can be used to provide lower bounds for the bottleneck and Wasserstein distances.

/pdf/statistical-topological-data-analysis-using-persistence-2hbwqc96bo.pdf

Statistical topological data analysis using persistence landscapes

Transcriptional regulators of the NF-kB/IkB family promote the expression of well over 100 target genes, the majority of which participate in the host immune response (1). These proteins include a multitude of cytokines and chemokines, receptors required for immune recognition, proteins involved in antigen presentation, and adhesion receptors involved in transmigration across blood vessels walls. Because of this extensive role in immune action, NF-kB has been termed the central mediator of the immune response. Gene knockout and other studies establish roles for NF-kB in the ontogeny of the immune system but also demonstrate that NF-kB participates at multiple steps during oncogenesis (2) and the regulation of programmed cell death (3).

For several reasons, the NF-kB pathway provides an attractive target to viral pathogens. Activation of NF-kB is a rapid, immediate early (IE) event that occurs within minutes after exposure to a relevant inducer, does not require de novo protein synthesis, and results in a strong transcriptional stimulation of several early viral as well as cellular genes. In this review, we will describe strategies that viruses have evolved to modulate the NF-kB pathway, to enhance viral replication, host cell survival, and evasion of immune responses. Activation of NF-kB constitutes an obvious target because many of its target genes — growth factors, cytokines and their receptors, and proto-oncogenes — profoundly influence the host cell cycle. In addition, some viruses exploit the antiapoptotic properties of NF-kB to evade the host defense mechanisms that limit replication by killing infected cells, or conversely to trigger apoptosis as a mechanism to increase virus spread.

Perhaps not surprisingly, the persistent activation of the NF-kB pathway maintained by certain viruses contributes to oncogenic transformation (2). In addition to the classic studies with the avian REV-T retrovirus which contains the v-Rel oncoprotein and induces a rapid and fatal B-cell lymphoma in young birds (4), several lines of evidence demonstrate that NF-kB family members contribute to human oncogenesis. Localization of NF-kB–encoding genes at sites of chromosomal translocations and genomic rearrangements in cancer, high levels of NF-kB activity in many breast cancer cells, and constitutive nuclear NF-kB complexes in Hodgkin’s lymphoma cells all support this view (2). Furthermore, as discussed below, viral oncogene products, including human T-cell leukemia virus type 1 (HTLV-1) Tax protein and Epstein-Barr virus latent infection membrane protein 1 (EBV LMP1), each act by unique mechanisms to disrupt NF-kB regulation and initiate viral transformation.

/pdf/hostile-takeovers-viral-appropriation-of-the-nf-kb-pathway-27gm6gflxs.pdf

Hostile takeovers: viral appropriation of the NF-kB pathway

Virus infections induce a proinflammatory response including expression of cytokines and chemokines. The subsequent leukocyte recruitment and antiviral effector functions contribute to the first line of defense against viruses. The molecular virus-cell interactions initiating these events have been studied intensively, and it appears that viral surface glycoproteins, double-stranded RNA, and intracellular viral proteins all have the capacity to activate signal transduction pathways leading to the expression of cytokines and chemokines. The signaling pathways activated by viral infections include the major proinflammatory pathways, with the transcription factor NF-κB having received special attention. These transcription factors in turn promote the expression of specific inducible host proteins and participate in the expression of some viral genes. Here we review the current knowledge of virus-induced signal transduction by seven human pathogenic viruses and the most widely used experimental models for viral infections. The molecular mechanisms of virus-induced expression of cytokines and chemokines is also analyzed.

https://mmbr.asm.org/content/mmbr/65/1/131.full.pdf

Molecular Pathways in Virus-Induced Cytokine Production

Herpes Simplex Virus Type 1 Induction of Persistent NF-κB Nuclear Translocation Increases the Efficiency of Virus Replication

Generalizing the concept of a Reeb graph, the Reeb space of a multivariate continuous mapping identifies points of the domain that belong to a common component of the preimage of a point in the range. We study the local and global structure of this space for generic, piecewise linear mappings on a combinatorial manifold.

Reeb spaces of piecewise linear mappings

The Reeb graph is a construction which originated in Morse theory to study a real valued function defined on a topological space. More recently, it has been used in various applications to study noisy data which creates a desire to define a measure of similarity between these structures. Here, we exploit the fact that the category of Reeb graphs is equivalent to the category of a particular class of cosheaf. Using this equivalency, we can define an `interleaving' distance between Reeb graphs which is stable under the perturbation of a function. Along the way, we obtain a natural construction for smoothing a Reeb graph to reduce its topological complexity. The smoothed Reeb graph can be constructed in polynomial time.

Categorified Reeb Graphs

The Reeb graph is a construction which originated in Morse theory to study a real-valued function defined on a topological space. More recently, it has been used in various applications to study noisy data which creates a desire to define a measure of similarity between these structures. Here, we exploit the fact that the category of Reeb graphs is equivalent to the category of a particular class of cosheaf. Using this equivalency, we can define an `interleaving' distance between Reeb graphs which is stable under the perturbation of a function. Along the way, we obtain a natural construction for smoothing a Reeb graph to reduce its topological complexity. The smoothed Reeb graph can be constructed in polynomial time.

Given a continuous function $f\colon \mathbb{X} \to \mathbb{R}$ on a topological space, we consider the preimages of intervals and their homology groups and show how to read the ranks of these groups from the extended persistence diagram of $f$. In addition, we quantify the robustness of the homology classes under perturbations of $f$ using well groups, and we show how to read the ranks of these groups from the same extended persistence diagram. The special case $\mathbb{X} = \mathbb{R}^3$ has ramifications in the fields of medical imaging and scientific visualization.

/pdf/homology-and-robustness-of-level-and-interlevel-sets-22anbsawoe.pdf

Amit Patel

Papers

Herpes Simplex Virus Type 1 Induction of Persistent NF-κB Nuclear Translocation Increases the Efficiency of Virus Replication

Reeb spaces of piecewise linear mappings

Categorified Reeb Graphs

Categorified Reeb Graphs

Homology and robustness of level and interlevel sets