Quantum thermodynamics at critical points during melting and solidification processes

We systematically explore and show the existence of finite-temperature continuous quantum phase transition (CTQPT) at a critical point, namely, during solidification or melting such that the first-order thermal phase transition is a special case within CTQPT. Infact, CTQPT is related to chemical reaction where quantum fluctuation (due to wavefunction transformation) is caused by thermal energy and it can occur maximally for temperatures much higher than zero Kelvin. To extract the quantity related to CTQPT, we use the ionization energy theory and the energy-level spacing renormalization group method to derive the energy-level spacing entropy, renormalized Bose-Einstein distribution and the time-dependent specific heat capacity. This work unambiguously shows that the quantum phase transition applies for any finite temperatures.Comment: To be published in Indian Journal of Physics (Kolkata

Symmetry structure in discrete models of biochemical systems : natural subsystems and the weak control hierarchy in a new model of computation driven by interactions

© 2015 The Authors. Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited.Interaction Computing (IC) is inspired by the observation that cell metabolic/regulatory systems construct order dynamically, through constrained interactions between their components and based on a wide range of possible inputs and environmental conditions. The goals of this work are (1) to identify and understand mathematically the natural subsystems and hierarchical relations in natural systems enabling this, and (2) to use the resulting insights to define a new model of computation based on interactions that is useful for both biology and computation. The dynamical characteristics of the cellular pathways studied in Systems Biology relate, mathematically, to the computational characteristics of automata derived from them, and their internal symmetry structures to computational power. Finite discrete automata models of biological systems such as the lac operon, Krebs cycle, and p53-mdm2 genetic regulation constructed from Systems Biology models have canonically associated algebraic structures { transformation semigroups. These contain permutation groups (local substructures exhibiting symmetry) that correspond to "pools of reversibility". These natural subsystems are related to one another in a hierarchical manner by the notion of "weak control ". We present natural subsystems arising from several biological examples and their weak control hierarchies in detail. Finite simple non-abelian groups (SNAGs) are found in biological examples and can be harnessed to realize nitary universal computation. This allows ensembles of cells to achieve any desired finitary computational transformation, depending on external inputs, via suitably constrained interactions. Based on this, interaction machines that grow and change their structure recursively are introduced and applied, providing a natural model of computation driven by interactions.Peer reviewe

Energy Generation from Palm Oil Mill Effluent (POME): The Environmental Impact Perspective

Palm oil is the most commonly used vegetable oil and is found in consumer products ranging from soap and chocolate to cooking oil. Approximately 90 % of global palm oil is supplied by Malaysia and Indonesia. In 2018, Malaysia and Indonesia set a target to increase their palm oil production to approximately 37.8 Mt and 20.5 Mt. It is anticipated that the palm oil residues generated from the production process will also increase. Palm oil mill residues such as oil palm fronds, oil palm trunks, palm oil mill effluent (POME), mesocarp fibres, palm kernel shells and empty fruit bunches have emerging potential to be converted into value-added products. This study focuses on POME because it has the potential to be used for the generation of renewable energy and Malaysia aims to utilise a greater amount of affordable, clean energy in line with the United Nations’ Sustainable Development Goals. To this end, this study analyses and compares the CO₂ equivalent (CO₂-eq) of two palm oil mills (POMs 1 and 2) that use different POME treatment technologies, namely the covered lagoon bio-digester (CLB; POM 1) and the continuous stirred tank reactor (CSTR; POM 2) systems. The results of the analysis show that POM 1 produces 1,077.67 kg CO₂-eq, which is lower than that produced by POM 2 which emits 1,429.28 kg CO₂-eq

Research on Teaching and Learning Mathematics at the Tertiary Level:State-of-the-art and Looking Ahead

This topical survey focuses on research in tertiary mathematics education, a field that has experienced considerable growth over the last 10 years. Drawing on the most recent journal publication as well as the latest advances from recent high quality conference proceedings, our review culls out the following five emergent areas of interest: mathematics teaching at the tertiary level; the role of mathematics in other disciplines; textbooks, assessment and students’ studying practices; transition to the tertiary level; and theoretical-methodological advances. We conclude the survey with a discussion of some potential ways forward for future research in this new and rapidly developing domain of inquiry

Stoichiometric representation of geneproteinreaction associations leverages constraint-based analysis from reaction to gene-level phenotype prediction

Genome-scale metabolic reconstructions are currently available for hundreds of organisms. Constraint-based modeling enables the analysis of the phenotypic landscape of these organisms, predicting the response to genetic and environmental perturbations. However, since constraint-based models can only describe the metabolic phenotype at the reaction level, understanding the mechanistic link between genotype and phenotype is still hampered by the complexity of gene-protein-reaction associations. We implement a model transformation that enables constraint-based methods to be applied at the gene level by explicitly accounting for the individual fluxes of enzymes (and subunits) encoded by each gene. We show how this can be applied to different kinds of constraint-based analysis: flux distribution prediction, gene essentiality analysis, random flux sampling, elementary mode analysis, transcriptomics data integration, and rational strain design. In each case we demonstrate how this approach can lead to improved phenotype predictions and a deeper understanding of the genotype-to-phenotype link. In particular, we show that a large fraction of reaction-based designs obtained by current strain design methods are not actually feasible, and show how our approach allows using the same methods to obtain feasible gene-based designs. We also show, by extensive comparison with experimental 13C-flux data, how simple reformulations of different simulation methods with gene-wise objective functions result in improved prediction accuracy. The model transformation proposed in this work enables existing constraint-based methods to be used at the gene level without modification. This automatically leverages phenotype analysis from reaction to gene level, improving the biological insight that can be obtained from genome-scale models.DM was supported by the Portuguese Foundationfor Science and Technologythrough a post-doc fellowship (ref: SFRH/BPD/111519/ 2015). This study was supported by the PortugueseFoundationfor Science and Technology (FCT) under the scope of the strategic fundingof UID/BIO/04469/2013 unitand COMPETE2020 (POCI-01-0145-FEDER-006684) and BioTecNorte operation (NORTE-01-0145FEDER-000004) fundedby EuropeanRegional Development Fund under the scope of Norte2020Programa Operacional Regional do Norte. This project has received fundingfrom the European Union’s Horizon 2020 research and innovation programme under grant agreementNo 686070. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

LIM and SH3 Protein -1 Modulates CXCR2-Mediated Cell Migration

BACKGROUND: The chemokine receptor CXCR2 plays a pivotal role in migration of neutrophils, macrophages and endothelial cells, modulating several biological responses such as angiogenesis, wound healing and acute inflammation. CXCR2 is also involved in pathogenesis of chronic inflammation, sepsis and atherosclerosis. The ability of CXCR2 to associate with a variety of proteins dynamically is responsible for its effects on directed cell migration or chemotaxis. The dynamic network of such CXCR2 binding proteins is termed as "CXCR2 chemosynapse". Proteomic analysis of proteins that co-immunoprecipitated with CXCR2 in neutrophil-like dHL-60 cells revealed a novel protein, LIM and SH3 protein 1 (LASP-1), binds CXCR2 under both basal and ligand activated conditions. LASP-1 is an actin binding cytoskeletal protein, involved in the cell migration. METHODOLOGY/PRINCIPAL FINDINGS: We demonstrate that CXCR2 and LASP-1 co-immunoprecipitate and co-localize at the leading edge of migrating cells. The LIM domain of LASP-1 directly binds to the carboxy-terminal domain (CTD) of CXCR2. Moreover, LASP-1 also directly binds the CTD of CXCR1, CXCR3 and CXCR4. Using a site-directed and deletion mutagenesis approach, Iso323-Leu324 of the conserved LKIL motif on CXCR2-CTD was identified as the binding site for LASP-1. Interruption of the interaction between CXCR2-CTD and LIM domain of LASP-1 by dominant negative and knock down approaches inhibited CXCR2-mediated chemotaxis. Analysis for the mechanism for inhibition of CXCR2-mediated chemotaxis indicated that LASP-1/CXCR2 interaction is essential for cell motility and focal adhesion turnover involving activation of Src, paxillin, PAK1, p130CAS and ERK1/2. CONCLUSIONS/SIGNIFICANCE: We demonstrate here for the first time that LASP-1 is a key component of the "CXCR2 chemosynapse" and LASP-1 interaction with CXCR2 is critical for CXCR2-mediated chemotaxis. Furthermore, LASP-1 also directly binds the CTD of CXCR1, CXCR3 and CXCR4, suggesting that LASP-1 is a general mediator of CXC chemokine mediated chemotaxis. Thus, LASP-1 may serve as a new link coordinating the flow of information between chemokine receptors and nascent focal adhesions, especially at the leading edge. Thus the association between the chemokine receptors and LASP-1 suggests to the presence of a CXC chemokine receptor-LASP-1 pro-migratory module in cells governing the cell migration

Proliferation and survival molecules implicated in the inhibition of BRAF pathway in thyroid cancer cells harbouring different genetic mutations

<p>Abstract</p> <p>Background</p> <p>Thyroid carcinomas show a high prevalence of mutations in the oncogene BRAF which are inversely associated with RAS or RET/PTC oncogenic activation. The possibility of using inhibitors on the BRAF pathway as became an interesting therapeutic approach. In thyroid cancer cells the target molecules, implicated on the cellular effects, mediated by inhibition of BRAF are not well established. In order to fill this lack of knowledge we studied the proliferation and survival pathways and associated molecules induced by BRAF inhibition in thyroid carcinoma cell lines harbouring distinct genetic backgrounds.</p> <p>Methods</p> <p>Suppression of BRAF pathway in thyroid cancer cell lines (8505C, TPC1 and C643) was achieved using RNA interference (RNAi) for BRAF and the kinase inhibitor, sorafenib. Proliferation analysis was performed by BrdU incorporation and apoptosis was accessed by TUNEL assay. Levels of protein expression were analysed by western-blot.</p> <p>Results</p> <p>Both BRAF RNAi and sorafenib inhibited proliferation in all the cell lines independently of the genetic background, mostly in cells with BRAF^V600Emutation. In BRAF^V600Emutated cells inhibition of BRAF pathway lead to a decrease in ERK1/2 phosphorylation and cyclin D1 levels and an increase in p27^Kip1. Specific inhibition of BRAF by RNAi in cells with BRAF^V600Emutation had no effect on apoptosis. In the case of sorafenib treatment, cells harbouring BRAF^V600Emutation showed increase levels of apoptosis due to a balance of the anti-apoptotic proteins Mcl-1 and Bcl-2.</p> <p>Conclusion</p> <p>Our results in thyroid cancer cells, namely those harbouring BRAF^V600Emutation showed that BRAF signalling pathway provides important proliferation signals. We have shown that in thyroid cancer cells sorafenib induces apoptosis by affecting Mcl-1 and Bcl-2 in BRAF^V600Emutated cells which was independent of BRAF. These results suggest that sorafenib may prove useful in the treatment of thyroid carcinomas, particularly those refractory to conventional treatment and harbouring BRAF mutations.</p

Range and Heterogeneity of Outcomes in Randomized Trials of Pediatric Chronic Kidney Disease

OBJECTIVE: To determine the range and heterogeneity of outcomes reported in randomized controlled trials of interventions for children with chronic kidney disease (CKD). STUDY DESIGN: The Cochrane Kidney and Transplant Specialized Register was searched to March 2016. Randomized trials involving children across all stages of CKD were selected. All outcome domains and measurements were extracted from included trials. The frequency and characteristics of the outcome domains and measures were evaluated. RESULTS: From 205 trials included, 6158 different measurements of 100 different outcome domains were reported, with a median of 22 domains per trial (IQR 13-41). Overall, 52 domains (52%) were surrogate, 38 (38%) were clinical, and 10 (10%) were patient-reported. The 5 most commonly reported domains were blood pressure (76 [37%] trials), relapse/remission (70 [34%]), kidney function (66 [32%]), infection (61 [30%]), and height/pubertal development (51 [25%]). Mortality (14%), cardiovascular disease (4%), and quality of life (1%) were reported infrequently. The 2 most frequently reported outcomes, blood pressure and relapse/remission, had 56 and 81 different outcome measures, respectively. CONCLUSIONS: The outcomes reported in clinical trials involving children with CKD are extremely heterogeneous and are most often surrogate outcomes, rather than clinical and patient-centered outcomes such as cardiovascular disease and quality of life. Efforts to ensure consistent reporting of outcomes that are important to patients and clinicians will improve the value of trials to guide clinical decision-making. In our study, non-English articles were excluded

Protein 3D Structure Computed from Evolutionary Sequence Variation

The evolutionary trajectory of a protein through sequence space is constrained by its function. Collections of sequence homologs record the outcomes of millions of evolutionary experiments in which the protein evolves according to these constraints. Deciphering the evolutionary record held in these sequences and exploiting it for predictive and engineering purposes presents a formidable challenge. The potential benefit of solving this challenge is amplified by the advent of inexpensive high-throughput genomic sequencing