Theory of Bose-Einstein condensation in trapped gases

The phenomenon of Bose-Einstein condensation of dilute gases in traps is reviewed from a theoretical perspective. Mean-field theory provides a framework to understand the main features of the condensation and the role of interactions between particles. Various properties of these systems are discussed, including the density profiles and the energy of the ground state configurations, the collective oscillations and the dynamics of the expansion, the condensate fraction and the thermodynamic functions. The thermodynamic limit exhibits a scaling behavior in the relevant length and energy scales. Despite the dilute nature of the gases, interactions profoundly modify the static as well as the dynamic properties of the system; the predictions of mean-field theory are in excellent agreement with available experimental results. Effects of superfluidity including the existence of quantized vortices and the reduction of the moment of inertia are discussed, as well as the consequences of coherence such as the Josephson effect and interference phenomena. The review also assesses the accuracy and limitations of the mean-field approach.Comment: revtex, 69 pages, 38 eps figures, new version with more references, new figures, various changes and corrections, for publ. in Rev. Mod. Phys., available also at http://www-phys.science.unitn.it/bec/BEC.htm

NucTools: analysis of chromatin feature occupancy profiles from high-throughput sequencing data

Background: Biomedical applications of high-throughput sequencing methods generate a vast amount of data in which numerous chromatin features are mapped along the genome. The results are frequently analysed by creating binary data sets that link the presence/absence of a given feature to specific genomic loci. However, the nucleosome occupancy or chromatin accessibility landscape is essentially continuous. It is currently a challenge in the field to cope with continuous distributions of deep sequencing chromatin readouts and to integrate the different types of discrete chromatin features to reveal linkages between them. Results: Here we introduce the NucTools suite of Perl scripts as well as MATLAB- and R-based visualization programs for a nucleosome-centred downstream analysis of deep sequencing data. NucTools accounts for the continuous distribution of nucleosome occupancy. It allows calculations of nucleosome occupancy profiles averaged over several replicates, comparisons of nucleosome occupancy landscapes between different experimental conditions, and the estimation of the changes of integral chromatin properties such as the nucleosome repeat length. Furthermore, NucTools facilitates the annotation of nucleosome occupancy with other chromatin features like binding of transcription factors or architectural proteins, and epigenetic marks like histone modifications or DNA methylation. The applications of NucTools are demonstrated for the comparison of several datasets for nucleosome occupancy in mouse embryonic stem cells (ESCs) and mouse embryonic fibroblasts (MEFs). Conclusions: The typical workflows of data processing and integrative analysis with NucTools reveal information on the interplay of nucleosome positioning with other features such as for example binding of a transcription factor CTCF, regions with stable and unstable nucleosomes, and domains of large organized chromatin K9me2 modifications (LOCKs). As potential limitations and problems we discuss how inter-replicate variability of MNase-seq experiments can be addressed

Importance sampling method of correction for multiple testing in affected sib-pair linkage analysis

Using the Genetic Analysis Workshop 13 simulated data set, we compared the technique of importance sampling to several other methods designed to adjust p-values for multiple testing: the Bonferroni correction, the method proposed by Feingold et al., and naïve Monte Carlo simulation. We performed affected sib-pair linkage analysis for each of the 100 replicates for each of five binary traits and adjusted the derived p-values using each of the correction methods. The type I error rates for each correction method and the ability of each of the methods to detect loci known to influence trait values were compared. All of the methods considered were conservative with respect to type I error, especially the Bonferroni method. The ability of these methods to detect trait loci was also low. However, this may be partially due to a limitation inherent in our binary trait definitions

Endotoxin Is Not Essential for the Development of Cockroach Induced Allergic Airway Inflammation

PURPOSE: Cockroach (CR) is an important inhalant allergen and can induce allergic asthma. However, the mechanism by which CR induces airway allergic inflammation and the role of endotoxin in CR extract are not clearly understood in regards to the development of airway inflammation. In this study, we evaluated whether endotoxin is essential to the development of CR induced airway allergic inflammation in mice. MATERIALS AND METHODS: Airway allergic inflammation was induced by intranasal administration of either CR extract, CR with additional endotoxin, or endotoxin depleted CR extract, respectively, in BALB/c wild type mice. CR induced inflammation was also evaluated with toll like receptor-4 (TLR-4) mutant (C3H/HeJ) and wild type (C3H/HeN) mice. RESULTS: Intranasal administration of CR extracts significantly induced airway hyperresponsiveness (AHR), eosinophilic and neutrophilic airway inflammation, as well as goblet cell hyperplasia in a dose-dependent manner. The addition of endotoxin along with CR allergen attenuated eosinophilic inflammation, interleukin (IL)-13 level, and goblet cell hyperplasia of respiratory epithelium; however, it did not affect the development of AHR. Endotoxin depletion in CR extract did not attenuate eosinophilic inflammation and lymphocytosis in BAL fluid, AHR and IL-13 expression in the lungs compared to CR alone. The attenuation of AHR, eosinophilic inflammation, and goblet cell hyperplasia induced by CR extract alone was not different between TLR-4 mutant and the wild type mice. In addition, heat inactivated CR extract administration induced attenuated AHR and eosinophilic inflammation. CONCLUSION: Endotoxin in CR extracts may not be essential to the development of airway inflammation

Inflammatory Gene Regulatory Networks in Amnion Cells Following Cytokine Stimulation: Translational Systems Approach to Modeling Human Parturition

A majority of the studies examining the molecular regulation of human labor have been conducted using single gene approaches. While the technology to produce multi-dimensional datasets is readily available, the means for facile analysis of such data are limited. The objective of this study was to develop a systems approach to infer regulatory mechanisms governing global gene expression in cytokine-challenged cells in vitro, and to apply these methods to predict gene regulatory networks (GRNs) in intrauterine tissues during term parturition. To this end, microarray analysis was applied to human amnion mesenchymal cells (AMCs) stimulated with interleukin-1β, and differentially expressed transcripts were subjected to hierarchical clustering, temporal expression profiling, and motif enrichment analysis, from which a GRN was constructed. These methods were then applied to fetal membrane specimens collected in the absence or presence of spontaneous term labor. Analysis of cytokine-responsive genes in AMCs revealed a sterile immune response signature, with promoters enriched in response elements for several inflammation-associated transcription factors. In comparison to the fetal membrane dataset, there were 34 genes commonly upregulated, many of which were part of an acute inflammation gene expression signature. Binding motifs for nuclear factor-κB were prominent in the gene interaction and regulatory networks for both datasets; however, we found little evidence to support the utilization of pathogen-associated molecular pattern (PAMP) signaling. The tissue specimens were also enriched for transcripts governed by hypoxia-inducible factor. The approach presented here provides an uncomplicated means to infer global relationships among gene clusters involved in cellular responses to labor-associated signals

Quantitative Assessment of Hard Surface Disinfectant Activity Against the Foodborne Pathogen Listeria monocytogenes

Abstract Listeria monocytogenes is an important foodborne pathogen that must be controlled to ensure food safety. For the years 2003 and 2004, L. monocytogenes caused 20 deaths per 100 listeriosis cases and was responsible for most food recalls for pathogen contamination. The objective of this work was to develop a quantitative method to assess disinfectant activity against L. monocytogenes. Standard procedures for testing disinfectants against 3 bacteria are described in the AOAC Official Methods of Analysis as use-dilution methods. No standard methods are provided for L. monocytogenes. In this study, preliminary efficacy of a quaternary ammonium compound with hydroperoxide ion was determined for 25 bacterial strains. The zones of inhibition ranged from 7.0 to 12.5 mm, and the minimum inhibitory concentration ranged from 5 to 250 ppm. For final efficacy, stainless steel carriers were contaminated with L. monocytogenes and tested separately for 5, 10, and 15 min in disinfectant or phenol. After exposure, the carriers were placed into 2 series of D/E neutralization broth. For 3 replications with duplicate samples, the phenol coefficient was 3.3. This research presents a technique-sensitive method that provides quantitative data for comparison and analysis of disinfectant activity against L. monocytogenes.</jats:p