Edge Ratchet and Simulated Annealing to Improve RF Score of the Supertree of Life

Constructing the Supertree of Life can provide crucially valuable knowledge to address many critical contemporary challenges such as fighting diseases, improving global agriculture, and protecting ecosystems to name a few. However, building such a tree is among the most complicated and challenging scientific problems. In the case of biological data, the true species tree is not available. Hence, the accuracy of the supertree is usually evaluated based on its similarity to the given source input trees. In this work, we aim at improving the accuracy of the supertree in terms of its cumulative Robinson Foulds (RF) distance to the source trees. This problem is NP-hard. Therefore, we have to resort to heuristic algorithms. We have two main contributions in this work. First, we propose a new technique, Edge Ratchet, which is used in a hill-climbing based algorithm to deal with local optimum problem. Second, we develop a Simulated Annealing algorithm to minimize total RF distance of the supertree to the source trees. Our results demonstrate that these two algorithms are able to improve the accuracy of the best existing supertree algorithms with regard to RF distance

Edge Ratchet and Simulated Annealing to Improve RF Score of the Supertree of Life

Constructing the Supertree of Life can provide crucially valuable knowledge to address many critical contemporary challenges such as fighting diseases, improving global agriculture, and protecting ecosystems to name a few. However, building such a tree is among the most complicated and challenging scientific problems. In the case of biological data, the true species tree is not available. Hence, the accuracy of the supertree is usually evaluated based on its similarity to the given source input trees. In this work, we aim at improving the accuracy of the supertree in terms of its cumulative Robinson Foulds (RF) distance to the source trees. This problem is NP-hard. Therefore, we have to resort to heuristic algorithms. We have two main contributions in this work. First, we propose a new technique, Edge Ratchet, which is used in a hill-climbing based algorithm to deal with local optimum problem. Second, we develop a Simulated Annealing algorithm to minimize total RF distance of the supertree to the source trees. Our results demonstrate that these two algorithms are able to improve the accuracy of the best existing supertree algorithms with regard to RF distance

POST-TRANSLATIONAL REGULATION OF ZEB1 CONTRIBUTES TO TGFβ-MEDIATED EMT

Non-small cell lung cancer (NSCLC) is the leading cause of cancer-related death in the United States due in part to the affinity of tumors to metastasize. Understanding the process which contributes to metastasis provides promise for the discovery of novel therapeutic targets. Epithelial-to-mesenchymal transition (EMT) is a proposed model for the initiation of metastasis. During EMT epithelial cells lose their cell adhesion properties and acquire a mesenchymal-like phenotype, allowing tumor cells to migrate from their epithelial cell community and invade remote locations. EMT is mediated by several signaling pathways, with transforming growth factor-beta (TGF-β) receiving attention for its up-regulation in the metastatic tumor microenvironment. TGF-β facilitates EMT through a variety of mechanisms but a prominent feature of TGF-β induced EMT is the activation of the transcription factor zinc finger E-box-binding homeobox 1 (Zeb1). Although Zeb1 has an established role in EMT the mechanism by which Zeb1 is regulated has not been fully elucidated. Here we demonstrate that Zeb1 undergoes post-translational modification and that this modification contributes to protein stability. We also expose novel Zeb1 interactions using the BioID method for proximity-dependent labeling of proteins. These results lead us to hypothesize that by targeting factors which mediate Zeb1 post-translational modification we may provide a therapeutic approach for metastasis suppression in NSCLC

Axion-Like Dark Matter Detection Using Stern-Gerlach Interferometer

Quantum sensors based on the superposition of neutral atoms are promising for sensing the nature of dark matter (DM). This work uses the Stern-Gerlach (SG) interferometer configuration to seek a novel method to detect axion-like particles (ALPs). Using an SG interferometer, we create a spatial quantum superposition of neutral atoms such as $^{3}$He and $^{87}$Rb. It is shown that the interaction of ALPs with this superposition induces a relative phase between superposed quantum components. We use the quantum Boltzmann equation (QBE) to introduce a first principal analysis that describes the temporal evolution of the sensing system. QBE approach uses quantum field theory (QFT) to highlight the role of the quantum nature of the interactions with the quantum systems. The resulting exclusion area shows that our scheme allows for the exclusion of a range of ALPs mass between $m_{a}=10^{-10}-10^{2}\,\mathrm{eV}$ and ALPs-atom coupling constant between $g=10^{-13}-10^{0}\,\mathrm{eV}$.Comment: 14 pages, 3 figures, submitted to EPJ

K811 acetylation regulates ZEB1 dimerization, protein stability, and NuRD complex interactions to promote lung adenocarcinoma progression and metastasis

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Isotherm and Kinetic Studies on Adsorption of Pb, Zn and Cu by Kaolinite

The feasibility of kaolinite used as a low-cost adsorbent for the removal of Pb(II), Zn(II) and Cu(II) from aqueous solutions was investigated. During the removal process, batch technique was used, and the effects of heavy metal concentration and contact time on adsorption efficiency at pH of 4.5, under a constant temperature of 20±1 °C were studied. The experimental results were analyzed using four adsorption isotherm models; Freundlich, Langmuir, Temkin and Redlich-Peterson. Evaluating the correlation coefficients showed that the Redlich-Peterson isotherm described the data appropriable than others. The adsorption capacities (qm) from the Langmuir isotherm for Pb(II), Zn(II) and Cu(II) are found as 7.75 mg/g, 4.95 mg/g and 4.42 mg/g respectively. The effectiveness of kaolinite in the sorption of the three metals from aqueous system was Pb(II) > Zn(II) > Cu(II). Kinetic studies showed that a pseudosecond order model was more suitable than the pseudo first order model. It is concluded that kaolinite can be used as an effective adsorbent for removing Pb(II), Zn(II) and Cu(II) from aqueous solutions

Seroprevalence of Hepatitis a in Hemodialysis Patient Candidate for Kidney Transplant Younger Than Forty Years

Background: Hepatitis A is a common infection during childhood, especially in developing countries. It can cause severe complications in immunocompromised patients. Due to the increasing number of kidney transplants in the country and epidemiologic shift of HAV which was observed in previous studies, we're going to evaluate the seroprevalence of hepatitis A in hemodialysis patients less than forty years serving kidney transplant candidates to follow vaccination policy for them.Materials and Methods: In a cross sectional study during 2014-2015 hepatitis A antibody levels in hemodialysis patients less than forty years in kidney transplant candidates examined in 12 hospitals in Tehran, Iran. Their serums were tested for anti HAV IgM and IgG by ELISA kits.Results: Hepatitis A virus antibody was positive in 66 (72.5%) of 91 patients. The prevalence of HAV was 0% at the range of younger than 20 and 45% in under 25 years age group. This significantly increased prevalence by increasing the age, and there was according to epidemiological shifts which were shown in other studies.Conclusion: Due to the availability of vaccine and hepatitis severe complications in immunocompromised individuals, as well as a low prevalence of positive serology in individuals under 25 years, it seems the check of antibodies in patients undergoing kidney transplantation and vaccination in seronegative persons is a logical