Feedbacks from the metabolic network to the genetic network reveal regulatory modules in E. coli and B. subtilis

The genetic regulatory network (GRN) plays a key role in controlling the response of the cell to changes in the environment. Although the structure of GRNs has been the subject of many studies, their large scale structure in the light of feedbacks from the metabolic network (MN) has received relatively little attention. Here we study the causal structure of the GRNs, namely the chain of influence of one component on the other, taking into account feedback from the MN. First we consider the GRNs of E. coli and B. subtilis without feedback from MN and illustrate their causal structure. Next we augment the GRNs with feedback from their respective MNs by including (a) links from genes coding for enzymes to metabolites produced or consumed in reactions catalyzed by those enzymes and (b) links from metabolites to genes coding for transcription factors whose transcriptional activity the metabolites alter by binding to them. We find that the inclusion of feedback from MN into GRN significantly affects its causal structure, in particular the number of levels and relative positions of nodes in the hierarchy, and the number and size of the strongly connected components (SCCs). We then study the functional significance of the SCCs. For this we identify condition specific feedbacks from the MN into the GRN by retaining only those enzymes that are essential for growth in specific environmental conditions simulated via the technique of flux balance analysis (FBA). We find that the SCCs of the GRN augmented by these feedbacks can be ascribed specific functional roles in the organism. Our algorithmic approach thus reveals relatively autonomous subsystems with specific functionality, or regulatory modules in the organism. This automated approach could be useful in identifying biologically relevant modules in other organisms for which network data is available, but whose biology is less well studied.Comment: 15 figure

Genetic Algorithm Based Charge Optimization of Lithium-Ion Batteries in Small Satellites

Small spacecraft that are powered by solar energy have limitations because of the size of their solar panels. With the limitations on the solar panel size, it is generally hard to comply with the demands from all the satellite subsystems, payloads and batteries at the same time. To overcome these problems we have developed and adopted a power management optimization scheme that runs in real time in the satellite. The proposed power management scheme primarily involves scheduling of loads (various subsystem operations, payload experimentation, battery charging, etc.) so that power utilization and thereby the charge of the batteries is at its optimum. We have developed a genetic algorithm based schedule optimizer and propose an FPGA based fitness evaluation function for it

Conduit Companies, Beneficial Ownership, and the Test of Substantive Business Activity in Claims for Relief under Double Tax Treaties

If interpreted in a strict legal sense, beneficial ownership rules in tax treaties would have no effect on conduit companies because companies at law own their property and income beneficially. Conversely, a company can never own anything in a substantive sense because economically a company is no more than a congeries of arrangements that represents the people behind it. Faced with these contradictory considerations, people have adopted surrogate tests that they attempt to employ in place of the treaty test of beneficial ownership. An example is that treaty benefits should be limited to companies that are both resident in the states that are parties to the treaty and that carry on substantive business activity. The test is inherently illogical. The origins of the substantive business activity test appear to lie in analogies drawn with straw company and base company cases. Because there is no necessary relationship between ownership and activity, the test of substantive business activity can never provide a coherent surrogate for the test of beneficial ownership. The article finishes with a Coda that summarises suggestions for reform to be made in work that is to follow. (authors' abstract)Series: WU International Taxation Research Paper Serie

Beyond the obvious: unveiling primary effusion lymphoma in a 76-year-old female with multifaceted clinical presentation

Primary effusion lymphoma (PEL) is an exceptionally rare and challenging entity to diagnose, characterized by the development of lymphomatous effusions in body cavities without a solid tumour mass. Here, we present a case of PEL in a 76-year-old retired professor with a complex medical history including diabetes, hypertension, and bilateral total knee replacement surgery. The patient initially presented with dry cough and breathlessness, which led to the discovery of a right pleural effusion exhibiting lymphocytic predominance with high ADA but lacking malignant cells. Prompt initiation of empiric anti-tubercular therapy (ATT) resulted in symptomatic improvement and resolution of the effusion. However, subsequent admission to the emergency room due to vomiting, weakness, and walking difficulties unveiled a positive rapid antigen test for COVID-19 and identified moderate right-sided pleural effusion. Additional investigations including positron emission tomography–computed tomography (PET-CT), magnetic resonance imaging (MRI) brain, and cell block analysis unveiled intriguing findings, prompting further evaluation and immunohistochemical (IHC) analysis. IHC markers revealed CD20+, Ki-67 proliferation index of 80%, CD79a+, CD 3 -, CD138-, CD30-, and CD10-, indicative of atypical B cell proliferation. Importantly, the presence of human herpes virus-8 (HHV-8) was confirmed through LANA1 staining, solidifying the diagnosis of primary effusion lymphoma. This case highlights the diagnostic challenges encountered and emphasizes the importance of comprehensive evaluation and IHC profiling confirmation in establishing an accurate diagnosis of PEL

Placental thickness: an important parameter in determining gestational age and fetal growth during ANC scan

Background: Gestational Age (GA) is one of the most imperative parameters required for proper management in pregnancy. Routinely GA is estimated by sonography utilising Biparietal Diameter (BPD), Femur Length (FL), Abdominal Circumference (AC) and Head Circumference (HC). In any case, these parameters have some limitations. Hence, there is need to find other parameters that may complement the established fetal biometric parameters in predicting GA. The objective of the present study was to assess placental thickness in second and third trimester pregnancies and its relationship with fetal gestational age and its role in detecting LBW and IUGRMethods: A cross sectional prospective study was carried out in three hundred pregnant women between 13 to 40 weeks of gestation, who came for routine antenatal sonography. Placental thickness was measured along with routine parameters. Placental thickness was measured at the level of umbilical cord insertion by two-dimensional ultrasonography.Results: Correlation between the GA by LMP and Placental thickness by ultrasound was done by using Karl Pearson's Correlation(r). The values were expressed as mean + standard deviation. Correlation between placental thickness and gestational age was statistically significant as p value is <0.01. Placental thickness measured in millimetres increases with gestational age in second and third trimester.Conclusions: The correlation between the placental thickness and gestational age was linear and direct. Therefore, Placental thickness is used as a predictor for estimation of gestational age of the fetus in cases where LMP is not known and in detecting developing IUGR and low birth weight

How to assign volunteers to tasks compatibly ? A graph theoretic and parameterized approach

In this paper we study a resource allocation problem that encodes correlation between items in terms of \conflict and maximizes the minimum utility of the agents under a conflict free allocation. Admittedly, the problem is computationally hard even under stringent restrictions because it encodes a variant of the {\sc Maximum Weight Independent Set} problem which is one of the canonical hard problems in both classical and parameterized complexity. Recently, this subject was explored by Chiarelli et al.~[Algorithmica'22] from the classical complexity perspective to draw the boundary between {\sf NP}-hardness and tractability for a constant number of agents. The problem was shown to be hard even for small constant number of agents and various other restrictions on the underlying graph. Notwithstanding this computational barrier, we notice that there are several parameters that are worth studying: number of agents, number of items, combinatorial structure that defines the conflict among the items, all of which could well be small under specific circumstancs. Our search rules out several parameters (even when taken together) and takes us towards a characterization of families of input instances that are amenable to polynomial time algorithms when the parameters are constant. In addition to this we give a superior 2^{m}|I|^{\Co{O}(1)} algorithm for our problem where $m$ denotes the number of items that significantly beats the exhaustive \Oh(m^{m}) algorithm by cleverly using ideas from FFT based fast polynomial multiplication; and we identify simple graph classes relevant to our problem's motivation that admit efficient algorithms