Current State of JUMMP

In computational biology there is a strong need to exchange quantitative models of biological processes in a standardized way. For storing and retrieving peer-reviewed models the BioModels Database has been available for several years. But at the moment there is no tool available to bring a model from development in the lab directly to the peer-reviewed online resource.

The JUMMP (JUst a Model Management Platform) project aims at providing a generic model management platform for any standardized model file. Through a well-elaborated security layer models can be developed and shared privately and later on be made available to the curation process and the broader community. Each change to a model is recorded in a version control system allowing to easily track changes during the development.

In this presentation the current state of development of the JUMMP project is discussed as well as the future steps which are needed to get JUMMP into a shape so that it can be used as the infrastructure for the BioModels Database

Mechanism for SO2 poisoning of Cu-CHA during low temperature NH3-SCR

Density Functional Theory (DFT) calculations are used to investigate low temperature SO2 deactivation of Cu-CHA during ammonia assisted selective catalytic reduction of NO (NH3-SCR). SO2 is found to adsorb on [Cu2IINH34O2]2+ forming a copper sulfate complex. NO and NH3 react over the sulfate complex forming N2, H2O and H2SO4. H2SO4 undergoes an acid-base reaction with NH3 yielding SO4(NH4)2 and HSO4(NH4), where HSO4(NH4) is thermodynamically preferred during typical reaction conditions. The SO2-derived species are bulky and have considerable barriers for inter-cage diffusion. Moreover, the presence of HSO4(NH4) species reduces the probability of having two [CuI(NH3)2]+ complexes in one cage, which is a requirement for O2 activation. The results suggest that the key mechanism for low temperature SO2 deactivation is of physical origin and that the catalyst can be regenerated by exposure to high temperatures where HSO4(NH4) decomposes. The suggested mechanism agrees with experimental observations and provides atomistic understanding of sulfur poisoning of Cu-CHA during NH3-SCR

Regulation of advance directives in Italy: a bad law in the making.

PURPOSE: The Advance Directives (ADs) have been adopted in many countries to defend patients' autonomy. In Italy, the role of ADs has recently been the subject of heated debate involving political parties and the Roman Catholic Church. In February 2009, the conservative government coalition presented a bill of law on this issue. It has been passed by the Low Chamber and is now being discussed in the Senate. The purpose of the article is to highlight any possible bill's contradiction with Italian Constitution, Italian Code of Medical Ethics (ICME), and Oviedo Convention contents, relevant for intensivists. METHODS: Analysis of bill's content in the light of Italian Constitution, ICME, Oviedo Convention articles and in comparison with French legislation regarding end of life (Leonetti law). RESULTS: In the Authors' point of view the bill's articles -limit the moral and judicial importance of four main issues as informed consent, permanent incapacity, artificial nutrition/hydration, and withdraw/withhold treatments. CONCLUSIONS: In the Authors' opinion the ADs must represent informed preferences made freely by patients within the relationship with their physicians, as part of an advance care planning. When this relationship develops in accordance with the ICME rules, it contains all of the ethical/professional dimensions to legitimate right choices in each case. The law should draw inspiration from ICME principles, assigning them a juridical power, acknowledging their validity in legitimating end-of-life decisions, and defining a framework of juridical legitimacy for these decisions without infringing on patients' right to autonomy with prescriptions on the care

Tobacco Xenobiotics Release Nitric Oxide

Many xenobiotic compounds exert their actions through the release of free radicals and related oxidants [1,2], bringing about unwanted biological effects [3]. Indeed, oxidative events may play a significant role in tobacco toxicity from cigarette smoke. Here, we demonstrate the direct in vitro release of the free radical nitric oxide (•NO) from extracts and components of smokeless tobacco, including nicotine, nitrosonornicotine (NNN) and 4-(methyl-N-nitrosamino)-1-(3-pyridyl)-1-butanone (NNK) in phosphate buffered saline and human saliva using electron spin resonance and chemiluminescence detection. Our findings suggest that tobacco xenobiotics represent as yet unrecognized sources of •NO in the body

Hawk Eyes I: Diurnal Raptors Differ in Visual Fields and Degree of Eye Movement

BACKGROUND: Different strategies to search and detect prey may place specific demands on sensory modalities. We studied visual field configuration, degree of eye movement, and orbit orientation in three diurnal raptors belonging to the Accipitridae and Falconidae families. METHODOLOGY/PRINCIPAL FINDINGS: We used an ophthalmoscopic reflex technique and an integrated 3D digitizer system. We found inter-specific variation in visual field configuration and degree of eye movement, but not in orbit orientation. Red-tailed Hawks have relatively small binocular areas (∼33°) and wide blind areas (∼82°), but intermediate degree of eye movement (∼5°), which underscores the importance of lateral vision rather than binocular vision to scan for distant prey in open areas. Cooper's Hawks' have relatively wide binocular fields (∼36°), small blind areas (∼60°), and high degree of eye movement (∼8°), which may increase visual coverage and enhance prey detection in closed habitats. Additionally, we found that Cooper's Hawks can visually inspect the items held in the tip of the bill, which may facilitate food handling. American Kestrels have intermediate-sized binocular and lateral areas that may be used in prey detection at different distances through stereopsis and motion parallax; whereas the low degree eye movement (∼1°) may help stabilize the image when hovering above prey before an attack. CONCLUSIONS: We conclude that: (a) there are between-species differences in visual field configuration in these diurnal raptors; (b) these differences are consistent with prey searching strategies and degree of visual obstruction in the environment (e.g., open and closed habitats); (c) variations in the degree of eye movement between species appear associated with foraging strategies; and (d) the size of the binocular and blind areas in hawks can vary substantially due to eye movements. Inter-specific variation in visual fields and eye movements can influence behavioral strategies to visually search for and track prey while perching

Vision and Foraging in Cormorants: More like Herons than Hawks?

Background Great cormorants (Phalacrocorax carbo L.) show the highest known foraging yield for a marine predator and they are often perceived to be in conflict with human economic interests. They are generally regarded as visually-guided, pursuit-dive foragers, so it would be expected that cormorants have excellent vision much like aerial predators, such as hawks which detect and pursue prey from a distance. Indeed cormorant eyes appear to show some specific adaptations to the amphibious life style. They are reported to have a highly pliable lens and powerful intraocular muscles which are thought to accommodate for the loss of corneal refractive power that accompanies immersion and ensures a well focussed image on the retina. However, nothing is known of the visual performance of these birds and how this might influence their prey capture technique. Methodology/Principal Findings We measured the aquatic visual acuity of great cormorants under a range of viewing conditions (illuminance, target contrast, viewing distance) and found it to be unexpectedly poor. Cormorant visual acuity under a range of viewing conditions is in fact comparable to unaided humans under water, and very inferior to that of aerial predators. We present a prey detectability model based upon the known acuity of cormorants at different illuminances, target contrasts and viewing distances. This shows that cormorants are able to detect individual prey only at close range (less than 1 m). Conclusions/Significance We conclude that cormorants are not the aquatic equivalent of hawks. Their efficient hunting involves the use of specialised foraging techniques which employ brief short-distance pursuit and/or rapid neck extension to capture prey that is visually detected or flushed only at short range. This technique appears to be driven proximately by the cormorant's limited visual capacities, and is analogous to the foraging techniques employed by herons

Multiplex cytokine analysis of dermal interstitial blister fluid defines local disease mechanisms in systemic sclerosis.

Clinical diversity in systemic sclerosis (SSc) reflects multifaceted pathogenesis and the effect of key growth factors or cytokines operating within a disease-specific microenvironment. Dermal interstitial fluid sampling offers the potential to examine local mechanisms and identify proteins expressed within lesional tissue. We used multiplex cytokine analysis to profile the inflammatory and immune activity in the lesions of SSc patients

Kiwi Forego Vision in the Guidance of Their Nocturnal Activities

BACKGROUND: In vision, there is a trade-off between sensitivity and resolution, and any eye which maximises information gain at low light levels needs to be large. This imposes exacting constraints upon vision in nocturnal flying birds. Eyes are essentially heavy, fluid-filled chambers, and in flying birds their increased size is countered by selection for both reduced body mass and the distribution of mass towards the body core. Freed from these mass constraints, it would be predicted that in flightless birds nocturnality should favour the evolution of large eyes and reliance upon visual cues for the guidance of activity. METHODOLOGY/PRINCIPAL FINDINGS: We show that in Kiwi (Apterygidae), flightlessness and nocturnality have, in fact, resulted in the opposite outcome. Kiwi show minimal reliance upon vision indicated by eye structure, visual field topography, and brain structures, and increased reliance upon tactile and olfactory information. CONCLUSIONS/SIGNIFICANCE: This lack of reliance upon vision and increased reliance upon tactile and olfactory information in Kiwi is markedly similar to the situation in nocturnal mammals that exploit the forest floor. That Kiwi and mammals evolved to exploit these habitats quite independently provides evidence for convergent evolution in their sensory capacities that are tuned to a common set of perceptual challenges found in forest floor habitats at night and which cannot be met by the vertebrate visual system. We propose that the Kiwi visual system has undergone adaptive regressive evolution driven by the trade-off between the relatively low rate of gain of visual information that is possible at low light levels, and the metabolic costs of extracting that information

Fluorescent Molecular Photoswitches for the Generation of All-Optical Encryption Keys

Herein, we report a tri-component photochromic molecular cocktail that can be used to encrypt and decrypt information. The time-dependent fluorescent response of this cocktail is highly non-linear with respect to the set of inputs used (concentrations of the three photochromic components, excitation- and emission wavelengths), a property required for the generation of so-called encryption keys. The all-optical system can generate more than 80 million unique fluorescence responses by applying different input combinations and is operated using a conventional fluorimeter

Higgs Messengers

We explore the consequences of the Higgs fields acting as messengers of supersymmetry breaking. The hidden-sector paradigm in the gauge mediation framework is relaxed by allowing two types of gauge-invariant, renormalizable operators that are typically discarded: direct coupling between the Higgses and supersymmetry breaking singlets, and Higgs-messenger mixing terms. The most important phenomenological consequence is a flavor-dependent shift in sfermion masses. This is from a one-loop contribution, which we compute for a general set of weak doublet messengers. We also study a couple of explicit models in detail, finding that precision electroweak constraints can be satisfied with a spectrum significantly different from that of gauge mediation.Comment: 20 pages, 5 figure