JSBML: a flexible Java library for working with SBML

The specifications of the Systems Biology Markup Language (SBML) define standards for storing and exchanging computer models of biological processes in text files. In order to perform model simulations, graphical visualizations and other software manipulations, an in-memory representation of SBML is required. We developed JSBML for this purpose. In contrast to prior implementations of SBML APIs, JSBML has been designed from the ground up for the Java™ programming language, and can therefore be used on all platforms supported by a Java Runtime Environment. This offers important benefits for Java users, including the ability to distribute software as Java Web Start applications. JSBML supports all SBML Levels and Versions through Level 3 Version 1, and we have strived to maintain the highest possible degree of compatibility with the popular library libSBML. JSBML also supports modules that can facilitate the development of plugins for end user applications, as well as ease migration from a libSBML-based backend

Screening masses in quenched (2+1)d Yang-Mills theory: universality from dynamics?

We compute the spectrum of gluonic screening-masses in the $0^{++}$ channel of quenched 3d Yang-Mills theory near the phase-transition. Our finite-temperature lattice simulations are performed at scaling region, using state-of-art techniques for thermalization and spectroscopy, which allows for thorough data extrapolations to thermodynamic limit. Ratios among mass-excitations with the same quantum numbers on the gauge theory, 2d Ising and $\lambda\phi^{4}$ models are compared, resulting in a nice agreement with predictions from universality. In addition, a gauge-to-scalar mapping, previously employed to fit QCD Green's functions at deep IR, is verified to dynamically describe these universal spectroscopic patternsComment: 15 pages, 4 eps figures. Revised version, to appear in Nucl. Phys.

NsrR from Streptomyces coelicolor is a nitric oxide-sensing [4Fe-4S] cluster protein with a specialized regulatory function

The Rrf2 family transcription factor NsrR controls expression of genes in a wide range of bacteria in response to nitric oxide (NO). The precise form of the NO-sensing module of NsrR is the subject of controversy because NsrR proteins containing either [2Fe-2S] or [4Fe-4S] clusters have been observed previously. Optical, Mössbauer, resonance Raman spectroscopies and native mass spectrometry demonstrate that Streptomyces coelicolor NsrR (ScNsrR), previously reported to contain a [2Fe-2S] cluster, can be isolated containing a [4Fe-4S] cluster. ChIP-seq experiments indicated that the ScNsrR regulon is small, consisting of only hmpA1, hmpA2, and nsrR itself. The hmpA genes encode NO-detoxifying flavohemoglobins, indicating that ScNsrR has a specialized regulatory function focused on NO detoxification and is not a global regulator like some NsrR orthologues. EMSAs and DNase I footprinting showed that the [4Fe-4S] form of ScNsrR binds specifically and tightly to an 11-bp inverted repeat sequence in the promoter regions of the identified target genes and that DNA binding is abolished following reaction with NO. Resonance Raman data were consistent with cluster coordination by three Cys residues and one oxygen-containing residue, and analysis of ScNsrR variants suggested that highly conserved Glu-85 may be the fourth ligand. Finally, we demonstrate that some low molecular weight thiols, but importantly not physiologically relevant thiols, such as cysteine and an analogue of mycothiol, bind weakly to the [4Fe-4S] cluster, and exposure of this bound form to O2 results in cluster conversion to the [2Fe-2S] form, which does not bind to DNA. These data help to account for the observation of [2Fe-2S] forms of NsrR

Assembling life history narratives from quantitative longitudinal panel data: what’s the story for families using social work?

Embedded within quantitative longitudinal panel or cohort studies is narrative potential that is arguably untapped but might enrich our understanding of individual and social lives across time. This paper discusses a methodology to assemble the life history narratives of families using social work by drawing on quantitative data from the British Household Panel Survey. It explores whether this person-centred approach helps us to understand the counterintuitive results of a parallel multivariate analyses, which suggest that families using social work fare worse than similar others over time. Our findings are tentative, due to the experimental use of this narrative method and the limits of social work information in the dataset. Nonetheless, the life histories presented bring to light complexities, diversity and the non-linear pathways between families’ needs, support and outcomes that the aggregates obscure. We conclude that reconstructing families’ lives in this way, especially in the absence of complementary longitudinal qualitative data, affords the wider opportunity to interrogate and better understand the findings of quantitative longitudinal studies

A Qualitative Exploration of the Role of Vape Shop Environments in Supporting Smoking Abstinence

E-cigarettes are the most popular method of quitting smoking in England and most are purchased in specialist vape shops. This qualitative study explores how the vape shop environment is experienced by quitters to support smoking abstinence. Semi-structured qualitative interviews were conducted to elicit experiences of e-cigarette use, including experiences of vape shops, in 40 people who had used e-cigarettes in a quit attempt. Observations of six shops in a range of locations were also undertaken. Interview and observation data were analysed using inductive thematic analysis and triangulated. At an individual level, smoking abstinence was supported through shop assistants’ attempts to understand customers’ smoking preferences in order to: (i) tailor advice about the most appropriate product; and (ii) offer an ongoing point of contact for practical help. At an interpersonal level, shops offered opportunity to socialise and reinforce a vaping identity, although the environment was perceived as intimidating for some (e.g., new and female users). At a structural level, shops ensured easy access to products perceived to be good value by customers and had adapted to legislative changes. Vape shops can provide effective behavioural support to quitters to maintain smoking abstinence. Health professionals could capitalise on this through partnership working with shops, to ensure best outcomes for clients wanting to use e-cigarettes to quit smoking

Dynamic structure and protein expression of the live embryonic heart captured by 2-photon light sheet microscopy and retrospective registration

We present an imaging and image reconstruction pipeline that captures the dynamic three-dimensional beating motion of the live embryonic zebrafish heart at subcellular resolution. Live, intact zebrafish embryos were imaged using 2-photon light sheet microscopy, which offers deep and fast imaging at 70 frames per second, and the individual optical sections were assembled into a full 4D reconstruction of the beating heart using an optimized retrospective image registration algorithm. This imaging and reconstruction platform permitted us to visualize protein expression patterns at endogenous concentrations in zebrafish gene trap lines

Global geometry optimization of clusters using a growth strategy optimized by a genetic algorithm

A new strategy for global geometry optimization of clusters is presented. Important features are a restriction of search space to favorable nearest-neighbor distance ranges, a suitable cluster growth representation with diminished correlations, and easy transferability of the results to larger clusters. The strengths and possible limitations of the method are demonstrated for Si10 using an empirical potential.Comment: accepted by Chem.Phys.Letters; 10 pages text, plus 3 pages for Title, abstract, and figure caption; figures 1a and 1

A mesocosm experiment investigating the effects of substratum quality and wave exposure on the survival of fish eggs

In a mesocosm experiment, the attachment of bream (Abramis brama) eggs to spawning substrata with and without periphytic biofilm coverage and their subsequent survival with and without low-intensity wave exposure were investigated. Egg attachment was reduced by 73% on spawning substrata with a natural periphytic biofilm, compared to clean substrata. Overall, this initial difference in egg numbers persisted until hatching. The difference in egg numbers was even increased in the wave treatment, while it was reduced in the no-wave control treatment. Exposure to a low-intensity wave regime affected egg development between the two biofilm treatments differently. Waves enhanced egg survival on substrata without a biofilm but reduced the survival of eggs on substrata with biofilm coverage. In the treatment combining biofilm-covered substrata and waves, no attached eggs survived until hatching. In all treatments, more than 75% of the eggs became detached from the spawning substrata during the egg incubation period, an

Probing the cosmic star formation using long Gamma-Ray Bursts: New constraints from the Spitzer Space Telescope

We report on IRAC-4.5mic, IRAC-8.0mic and MIPS-24mic deep observations of 16 Gamma-Ray Burst (GRBs) host galaxies performed with the Spitzer Space Telescope, and we investigate in the thermal infrared the presence of evolved stellar populations and dust-enshrouded star-forming activity associated with these objects. Our sample is derived from GRBs that were identified with sub-arcsec localization between 1997 and 2001, and only a very small fraction (~20%) of the targeted sources is detected down to f_4.5mic ~3.5microJy and f_24mic ~85microJy (3sigma). This likely argues against a population dominated by massive and strongly-starbursting (i.e., SFR > ~100 Msol/yr) galaxies as it has been recently suggested from submillimeter/radio and optical studies of similarly-selected GRB hosts. Furthermore we find evidence that some GRBs do not occur in the most infrared-luminous regions -- hence the most actively star-forming environments -- of their host galaxies. Should the GRB hosts be representative of all star-forming galaxies at high redshift, models of infrared galaxy evolution indicate that > ~50% of GRB hosts should have f_24mic > ~100microJy. Unless the identification of GRBs prior to 2001 was prone to strong selection effects biasing our sample against dusty galaxies, we infer in this context that the GRBs identified with the current techniques can not be directly used as unbiased probes of the global and integrated star formation history of the Universe.Comment: ApJ in press, 23 pages, 8 figures (scheduled for the ApJ 10 May 2006, v642 2 issue). Full resolution available at http://perceval.as.arizona.edu/~elefloch/Publis/ms_grb_spitzer.pd

Trade-Space Analysis Tool for Designing Constellations (TAT-C)

While there is growing interest in implementing future NASA Earth Science missions as Distributed Spacecraft Missions (DSMs), there are currently no tool to help in the design of DSMs. The objective of our project is to provide a framework that facilitates DSM Pre-Phase A investigations and optimizes DSM designs with respect to a-priori Science goals. Our Trade-space Analysis Tool for Constellations (TAT-C) allows to investigate questions such as: "Which type of constellations should be chosen? How many spacecraft should be included in the constellation? Which design has the best cost/risk value?" This paper provides a description of the TAT-C tool and its components