Batch fermentation process: Modelling and direct sensitivity analysis

Based on a nonlinear model, this article realizes an investigation of dynamic behaviour of a batch fermentation process using direct sensitivity analysis (DSA). The used nonlinear mathematical model has a good qualitative and quantitative description of the alcoholic fermentation process. This model has been discussed and validated by authors in other studies. The DSA of dynamic model was used to calculate the matrix of the sensitivity functions in order to determine the influence of the small deviations of initial state, control inputs, and parameters from the ideal nominal values on the state trajectory and system output in time. Process optimization and advanced control strategies can be developed based on this work

Mass scaling and non-adiabatic effects in photoassociation spectroscopy of ultracold strontium atoms

We report photoassociation spectroscopy of ultracold $^{86}$Sr atoms near the intercombination line and provide theoretical models to describe the obtained bound state energies. We show that using only the molecular states correlating with the $^1S_0$$+$$^3P_1$ asymptote is insufficient to provide a mass scaled theoretical model that would reproduce the bound state energies for all isotopes investigated to date: $^{84}$Sr, $^{86}$Sr and $^{88}$Sr. We attribute that to the recently discovered avoided crossing between the $^1S_0$$+$$^3P_1$ $0_u^+$ ($^3\Pi_u$) and $^1S_0$$+$$^1D_2$ $0_u^+$ ($^1\Sigma^+_u$) potential curves at short range and we build a mass scaled interaction model that quantitatively reproduces the available $0_u^+$ and $1_u$ bound state energies for the three stable bosonic isotopes. We also provide isotope-specific two-channel models that incorporate the rotational (Coriolis) mixing between the $0_u^+$ and $1_u$ curves which, while not mass scaled, are capable of quantitatively describing the vibrational splittings observed in experiment. We find that the use of state-of-the-art ab initio potential curves significantly improves the quantitative description of the Coriolis mixing between the two -8 GHz bound states in $^{88}$Sr over the previously used model potentials. We show that one of the recently reported energy levels in $^{84}$Sr does not follow the long range bound state series and theorize on the possible causes. Finally, we give the Coriolis mixing angles and linear Zeeman coefficients for all of the photoassociation lines. The long range van der Waals coefficients $C_6(0_u^+)=3868(50)$~a.u. and $C_6(1_u)=4085(50)$~a.u. are reported.Comment: 14 pages, 7 tables, 5 figures. Submitted to Phys. Rev.

Identification of osteopontin-dependent signaling pathways in a mouse model of human breast cancer

<p>Abstract</p> <p>Background</p> <p>Osteopontin (OPN) is a secreted phosphoprotein which functions as a cell attachment protein and cytokine that signals through two cell adhesion molecules, α_vβ₃-integrin and CD44, to regulate cancer growth and metastasis. However, the signaling pathways associated with OPN have not been extensively characterized. In an in vivo xenograft model of MDA-MB-231 human breast cancer, we have previously demonstrated that ablation of circulating OPN with an RNA aptamer blocks interaction with its cell surface receptors to significantly inhibit adhesion, migration and invasion in vitro and local progression and distant metastases.</p> <p>Findings</p> <p>In this study, we performed microarray analysis to compare the transcriptomes of primary tumor in the presence and absence of aptamer ablation of OPN. The results were corroborated with RT-PCR and Western blot analysis. Our results demonstrate that ablation of OPN cell surface receptor binding is associated with significant alteration in gene and protein expression critical in apoptosis, vascular endothelial growth factor (VEGF), platelet derived growth factor (PDGF), interleukin-10 (IL-10), granulocyte-macrophage colony stimulating factor (GM-CSF) and proliferation signaling pathways. Many of these proteins have not been previously associated with OPN.</p> <p>Conclusion</p> <p>We conclude that secreted OPN regulates multiple signaling pathways critical for local tumor progression.</p

PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways

PANTHER is a freely available, comprehensive software system for relating protein sequence evolution to the evolution of specific protein functions and biological roles. Since 2005, there have been three main improvements to PANTHER. First, the sequences used to create evolutionary trees are carefully selected to provide coverage of phylogenetic as well as functional information. Second, PANTHER is now a member of the InterPro Consortium, and the PANTHER hidden markov Models (HMMs) are distributed as part of InterProScan. Third, we have dramatically expanded the number of pathways associated with subfamilies in PANTHER. Pathways provide a detailed, structured representation of protein function in the context of biological reaction networks. PANTHER pathways were generated using the emerging Systems Biology Markup Language (SBML) standard using pathway network editing software called CellDesigner. The pathway collection currently contains ∼1500 reactions in 130 pathways, curated by expert biologists with authorship attribution. The curation environment is designed to be easy to use, and the number of pathways is growing steadily. Because the reaction participants are linked to subfamilies and corresponding HMMs, reactions can be inferred across numerous different organisms. The HMMs can be downloaded by FTP, and tools for analyzing data in the context of pathways and function ontologies are available at