A Study of time and temperature variables affecting apolipoprotein B-100 on iodipamide ethyl ester particles

The hypothesis tested in the epitope stability study is that apo B bound to a synthetic core of iodipamide ethyl ester (IDE) particles retain stability, as detected by immunoreactivity of apo B epitopes with two monoclonal antibodies. The mAB 3.01 binds to the carboxy terminal end of apo B-1 00. The mAB T4 binds to the T4 peptide fragment at the amino terminal end of both apo B-1 00 and apo B-48. Stability of LDL-coated IDE was evaluated over 40 days when stored at -20C, 4C and 25C. Stability of reconstituted lyophilized IDE was evaluated over 42 days, starting with particles that had been lyophilized for 14 days. For the nonlyophilized LDL-coated IDE, lower temperatures (-20C and 4C) appear to be more effective in slowing down degradation of apo B, as the epitope immunoreactivity detected by the mABs was greater for these temperatures than for 25C. Reconstituted lyophilized LDL-coated IDE particles are effective in stabilizing apo B antigenic sites for at least 28 days. Interpretation of the results of the study must include a consideration of the length of time LDL was stored at 4C before being bound to IDE particles (13 days) and the length of time the LDL-coated IDE was stored at 4C before lyophilization (14 days, or a total age of 27 days for LDL in vitro). This suggests that a future study of apo B epitope stability utilizing LDL-coated IDE should use fresher LDL (apo B) for coating IDE, followed by immediate lyophilization

Determination of Rapid-Equilibrium Kinetic Parameters of Ordered and Random Enzyme-Catalyzed Reaction A + B = P + Q

This article deals with the rapid-equilibrium kinetics of the forward and reverse reactions together for the ordered and random enzyme-catalyzed A + B = P + Q and emphasizes the importance of reporting the values of the full set of equilibrium constants. Equilibrium constants that are not in the rate equation can be calculated for random mechanisms using thermodynamic cycles. This treatment is based on the use of a computer to derive rate equations for three mechanisms and to estimate the kinetic parameters with the minimum number of velocity measurements. The most general of these three programs is the one to use first when the mechanism for A + B = P + Q is studied for the first time. This article shows the effects of experimental errors in velocity measurements on the values of the kinetic parameters and on the apparent equilibrium constant calculated using the Haldane relation

Calculation of the interfacial free energy of a fluid at a static wall by Gibbs–Cahn integration

This is the publisher's version, also available electronically from http://scitation.aip.org/content/aip/journal/jcp/132/20/10.1063/1.3428383.The interface between a fluid and a static wall is a useful model for a chemically heterogeneous solid-liquid interface. In this work, we outline the calculation of the wall-fluid interfacial free energy(γwf) for such systems using molecular simulation combined with adsorptionequations based on Cahn’s extension of the surface thermodynamics of Gibbs. As an example, we integrate such an adsorptionequation to obtain γwf as a function of pressure for a hard-sphere fluid at a hard wall. The results so obtained are shown to be in excellent agreement in both magnitude and precision with previous calculations of this quantity, but are obtained with significantly lower computational effort

Determination of the solid-liquid interfacial free energy along a coexistence line by Gibbs–Cahn integration

This is the publisher's version, also available electronically from http://scitation.aip.org/content/aip/journal/jcp/131/11/10.1063/1.3231693.We calculate the solid-liquid interfacial free energyγsl for the Lennard-Jones (LJ) system at several points along the pressure-temperature coexistence curve using molecular-dynamics simulation and Gibbs–Cahn integration. This method uses the excess interfacial energy(e) and stress (τ) along the coexistence curve to determine a differential equation for γsl as a function of temperature. Given the values of γsl for the (100), (110), and (111) LJ interfaces at the triple-point temperature (T∗=kT/ϵ=0.618), previously obtained using the cleaving method by Davidchack and Laird [J. Chem. Phys. 118, 7657 (2003)], this differential equation can be integrated to obtain γsl for these interfaces at higher coexistence temperatures. Our values for γsl calculated in this way at T∗=1.0 and 1.5 are in good agreement with those determined previously by cleaving, but were obtained with significantly less computational effort than required by either the cleaving method or the capillary fluctuation method of Hoyt, Asta, and Karma [Phys. Rev. Lett. 86, 5530 (2001)]. In addition, the orientational anisotropy in the excess interfaceenergy, stress and entropy, calculated using the conventional Gibbs dividing surface, are seen to be significantly larger than the relatively small anisotropies in γsl itself

Ecosystem biogeochemistry considered as a distributed metabolic network ordered by maximum entropy production

Author Posting. © The Author(s), 2009. This is the author's version of the work. It is posted here by permission of The Royal Society for personal use, not for redistribution. The definitive version was published in Philosophical Transactions of the Royal Society B 365 (2010): 1417-1427, doi:10.1098/rstb.2009.0272.We examine the application of the maximum entropy production principle for describing ecosystem biogeochemistry. Since ecosystems can be functionally stable despite changes in species composition, we utilize a distributed metabolic network for describing biogeochemistry, which synthesizes generic biological structures that catalyze reaction pathways, but is otherwise organism independent. Allocation of biological structure and regulation of biogeochemical reactions is determined via solution of an optimal control problem in which entropy production is maximized. However, because synthesis of biological structures cannot occur if entropy production is maximized instantaneously, we propose that information stored within the metagenome allows biological systems to maximize entropy production when averaged over time. This differs from abiotic systems that maximize entropy production at a point in space-time, which we refer to as the steepest descent pathway. It is the spatiotemporal averaging that allows biological systems to outperform abiotic processes in entropy production, at least in many situations. A simulation of a methanotrophic system is used to demonstrate the approach. We conclude with a brief discussion on the implications of viewing ecosystems as self organizing molecular machines that function to maximize entropy production at the ecosystem level of organization.The work presented here was funded by the PIE-LTER program (NSF OCE-0423565), as well as from NSF CBET-0756562, NSF EF-0928742 and NASA Exobiology and Evolutionary Biology (NNG05GN61G)

Multiplicity Distributions and Rapidity Gaps

I examine the phenomenology of particle multiplicity distributions, with special emphasis on the low multiplicities that are a background in the study of rapidity gaps. In particular, I analyze the multiplicity distribution in a rapidity interval between two jets, using the HERWIG QCD simulation with some necessary modifications. The distribution is not of the negative binomial form, and displays an anomalous enhancement at zero multiplicity. Some useful mathematical tools for working with multiplicity distributions are presented. It is demonstrated that ignoring particles with pt<0.2 has theoretical advantages, in addition to being convenient experimentally.Comment: 24 pages, LaTeX, MSUHEP/94071

anNET: a tool for network-embedded thermodynamic analysis of quantitative metabolome data

Background: Compared to other omics techniques, quantitative metabolomics is still at its infancy. Complex sample preparation and analytical procedures render exact quantification extremely difficult. Furthermore, not only the actual measurement but also the subsequent interpretation of quantitative metabolome data to obtain mechanistic insights is still lacking behind the current expectations. Recently, the method of network-embedded thermodynamic (NET) analysis was introduced to address some of these open issues. Building upon principles of thermodynamics, this method allows for a quality check of measured metabolite concentrations and enables to spot metabolic reactions where active regulation potentially controls metabolic flux. So far, however, widespread application of NET analysis in metabolomics labs was hindered by the absence of suitable software. Results: We have developed in Matlab a generalized software called 'anNET' that affords a user-friendly implementation of the NET analysis algorithm. anNET supports the analysis of any metabolic network for which a stoichiometric model can be compiled. The model size can span from a single reaction to a complete genome-wide network reconstruction including compartments. anNET can (i) test quantitative data sets for thermodynamic consistency, (ii) predict metabolite concentrations beyond the actually measured data, (iii) identify putative sites of active regulation in the metabolic reaction network, and (iv) help in localizing errors in data sets that were found to be thermodynamically infeasible. We demonstrate the application of anNET with three published Escherichia coli metabolome data sets. Conclusion: Our user-friendly and generalized implementation of the NET analysis method in the software anNET allows users to rapidly integrate quantitative metabolome data obtained from virtually any organism. We envision that use of anNET in labs working on quantitative metabolomics will provide the systems biology and metabolic engineering communities with a mean to proof the quality of metabolome data sets and with all further benefits of the NET analysis approach.

Oncocytic carcinoma of parotid gland: a case report with clinical, immunohistochemical and ultrastructural features

BACKGROUND: Oncocytic carcinoma is an extremely rare neoplasm of the salivary glands. We report a case of oncocytic carcinoma arising in a parotid gland in a 66-year-old female. METHOD: An excisional biopsy of the parotid tumor was performed. The specimen was submitted for histology and after fixation in formalin solution and inclusion in paraffin, 3–5 μm sections were stained with hematoxylin and eosin for conventional evaluation and Periodic acid Schiff stain. Immunohistochemical studies were performed using antibodies against mitochondrial antigen, keratin, S-100, alpha-actin, vimentin, alpha-1-antichymotrypsin as well as an ultrastructural analysis was performed. RESULTS: Frozen sections revealed an infiltrative growth pattern and the diagnosis of a malignant epithelial lesion was made. Permanent sections stained with haematoxylin and eosin revealed a neoplasm that had replaced a wide area of the parotid gland and had invaded subcutaneous adipose tissue. Perineural invasion was evident, but vascular invasion was not found. Neoplastic elements were large, round or polyhedral cells and were arranged in solid sheets, islands and cords. The cytoplasm was abundant, eosinophilic and finely granular. The nuclei were large and located centrally or peripherally. The nucleoli were distinct and large. Periodic acid Schiff stain demonstrated a granular cytoplasm. Immunohistochemistry demonstrated mithochondrial antigen, keratin, and chymotrypsin immunoreactivity in the neoplastic cells. Ultrastructural analysis revealed numerous mitochondria packed into the cytoplasm of the neoplastic cells. Thus, the final diagnosis was that of oncocytic carcinoma of parotid gland. CONCLUSION: This neoplasm shows clinical, microscopical, histological and ultrastructural features of oncocytic carcinoma and this must be considered in the differential diagnosis of other proliferations in the parotid gland with abundant granular cytoplasm and metastatic oncocytic carcinomas

Personality preference influences medical student use of specific computer-aided instruction (CAI)

BACKGROUND: The objective of this study was to test the hypothesis that personality preference, which can be related to learning style, influences individual utilization of CAI applications developed specifically for the undergraduate medical curriculum. METHODS: Personality preferences of students were obtained using the Myers-Briggs Type Indicator (MBTI) test. CAI utilization for individual students was collected from entry logs for two different web-based applications (a discussion forum and a tutorial) used in the basic science course on human anatomy. Individual login data were sorted by personality preference and the data statistically analyzed by 2-way mixed ANOVA and correlation. RESULTS: There was a wide discrepancy in the level and pattern of student use of both CAI. Although individual use of both CAI was positively correlated irrespective of MBTI preference, students with a "Sensing" preference tended to use both CAI applications more than the "iNtuitives". Differences in the level of use of these CAI applications (i.e., higher use of discussion forum vs. a tutorial) were also found for the "Perceiving/Judging" dimension. CONCLUSION: We conclude that personality/learning preferences of individual students influence their use of CAI in the medical curriculum

Monophasic synovial sarcoma of the pharynx: a case report

Synovial sarcomas are a rare form of soft tissue sarcomas. We present a case of a 62 year-old male presenting with a left thyroid lump initially though to be a thyroid adenoma but subsequently diagnosed as a monophasic synovial sarcoma of the pharynx. We discuss the diagnosis and treatment of this case