Data access and integration in the ISPIDER proteomics grid

Grid computing has great potential for supporting the integration of complex, fast changing biological data repositories to enable distributed data analysis. One scenario where Grid computing has such potential is provided by proteomics resources which are rapidly being developed with the emergence of affordable, reliable methods to study the proteome. The protein identifications arising from these methods derive from multiple repositories which need to be integrated to enable uniform access to them. A number of technologies exist which enable these resources to be accessed in a Grid environment, but the independent development of these resources means that significant data integration challenges, such as heterogeneity and schema evolution, have to be met. This paper presents an architecture which supports the combined use of Grid data access (OGSA-DAI), Grid distributed querying (OGSA-DQP) and data integration (AutoMed) software tools to support distributed data analysis. We discuss the application of this architecture for the integration of several autonomous proteomics data resources

The Pontine Marshes:An integrated study of the origin, history, and future of a famous coastal wetland in Central Italy

The Pontine Marshes (Central Italy) are known for their long drainage history starting early in Roman times and culminating in their reclamation (bonificaintegrale) by the Fascist’s regime under Mussolini, mostly in the 1930s of past century. The geology of this coastal wetland and causes for its drainageproblems received limited attention till recently. We reviewed results from recent studies, identified still existing knowledge gaps and performedadditional research to fill these, to produce a full description of the Holocene history and drainage of these marshes. Massive coring data that servedto map the soils and surficial geology, observations in archaeological excavations, analytical data on soil and sediment characteristics, and radiocarbondatings allowed us to distinguish several phases in this history, with a main break in the early Roman Republican period with the first systematic drainageworks. Earlier, natural processes brought about by sea level rise largely controlled its drainage. Once artificial drainage started, soil subsidence became animportant process, aggravating the drainage problems. The bonifica introduced mechanical drainage, temporarily masking the impacts of subsidence. Wequantified the historical subsidence using DTMs and developed scenarios for the impacts of sea level rise and subsidence in 2100 and 2200, assuming thatthis rise will be mitigated by a coastal defence system and enhanced capacity of the mechanical drainage. Our results demonstrate the important role ofsoil subsidence throughout the history of this wetland and need to include subsidence in scenarios for the impacts of sea level rise

Excitation Spectra and Thermodynamic Response of Segmented Heisenberg Spin Chains

The spectral and thermodynamic response of segmented quantum spin chains is analyzed using a combination of numerical techniques and finite-size scaling arguments. Various distributions of segment lengths are considered, including the two extreme cases of quenched and annealed averages. As the impurity concentration is increased, it is found that (i) the integrated spectral weight is rapidly reduced, (ii) a pseudo-gap feature opens up at small frequencies, and (iii) at larger frequencies a discrete peak structure emerges, dominated by the contributions of the smallest cluster segments. The corresponding low-temperature thermodynamic response has a divergent contribution due to the odd-site clusters and a sub-dominant exponentially activated component due to the even-site segments whose finite-size gap is responsible for the spectral weight suppression at small frequencies. Based on simple scaling arguments, approximate low-temperature expressions are derived for the uniform susceptibility and the heat capacity. These are shown to be in good agreement with numerical solutions of the Bethe ansatz equations for ensembles of open-end chains.Comment: RevTex, 9 pages with 6 figure

Asymptomatic Pulmonary Hypertension in Systemic Lupus Erythematosus

Introduction Pulmonary arterial hypertension (PAH) is a serious and often fatal complication of systemic lupus erythematosus (SLE). Because the diagnosis of PAH often is made years after symptom onset, early diagnostic strategies are essential. Doppler echocardiography currently is considered the noninvasive screening test of choice for evaluating pulmonary hypertension. Aim Screening for asymptomatic pulmonary hypertension in systemic lupus erythematosus patients using Doppler echocardiography, and correlating it with inflammatory parameters of the disease. Patients and Methods Doppler echocardiography was performed in 74 patients with systemic lupus erythematosus over one year (66 adult and 8 juvenile), adult SLE included 57 patients with adult-onset and 9 patients with childhood-onset. Pulmonary hypertension was diagnosed if the peak systolic pressure gradient at the tricuspid valve was more than 30 mmHg. All patients were subjected to full history taking, rheumatological examination, laboratory studies and chest x-ray. Results In seventy four SLE patients, the pulmonary hypertension was detected in 8 patients (10.8%), 7 adult-onset SLE patients (aged from 19 to 30 years) and 1 juvenile SLE (aged 12 years). The range of pulmonary artery systolic pressure was 34–61.2 mmHg (43.19 ± 9.28). No significant differences between patients with and those without pulmonary hypertension as regard clinical features. Significantly higher frequencies of rheumatoid factor and anti-cardiolipin antibodies were found in patients with pulmonary hypertension versus those without ( P = 0.02, P = 0.008 respectively). Positive rheumatoid factor and ACL were significantly associated with occurrence of PAH in SLE ( P = 0.007, P = 0.006 respectively). No significant correlations were found between pulmonary artery pressure, disease duration, SLE Disease Activity Index (SLEDAI), ESR, and anti-ds DNA. Conclusion Patients with SLE have an increased risk of pulmonary arterial hypertension. Echocardiography should be used as a screening tool in patients at high risk for development of pulmonary hypertension. Positive anti-cardiolipin antibodies and rheumatoid factor were significant predictors of pulmonary hypertension in our study

Random Exchange Disorder in the Spin-1/2 XXZ Chain

The one-dimensional XXZ model is studied in the presence of disorder in the Heisenberg Exchange Integral. Recent predictions obtained from renormalization group calculations are investigated numerically using a Lanczos algorithm on chains of up to 18 sites. It is found that in the presence of strong X-Y-symmetric random exchange couplings, a ``random singlet'' phase with quasi-long-range order in the spin-spin correlations persists. As the planar anisotropy is varied, the full zero-temperature phase diagram is obtained and compared with predictions of Doty and Fisher [Phys. Rev. B {\bf 45 }, 2167 (1992)].Comment: 9 pages + 8 plots appended, RevTex, FSU-SCRI-93-98 and ORNL/CCIP/93/1

Predicting the population viability of an endangered amphibian under environmental and demographic uncertainty

Population viability analyses (PVAs) represent a key component of many recovery plans for threatened and endangered species. Demography links the processes that affect individuals to population-level patterns, and hence projections constructed from demographic data are the most common tools for PVAs. We constructed a size-structured integral projection model (IPM) for the United States federally endangered Reticulated Flatwoods Salamander, Ambystoma bishopi, to evaluate demographic influences on population growth and predict the efficacy of future management actions. Flatwoods salamanders breed in ephemeral wetlands in the Southeastern United States. The ephemeral nature of breeding sites can result in complete recruitment failure in drought years when wetlands fail to fill, or dry before metamorphosis occurs. As a result, this species exhibits marked temporal variability in vital rates that must be accounted for in projection models. We constructed a stochastic IPM using 13 years of mark-recapture data (2010–2023) from two breeding wetlands. Variable survival rates exhibited by flatwoods salamanders, coupled with a high probability of recruitment failure, result in a low predicted probability of population persistence. Sensitivity analyses revealed age at maturity and the frequency of recruitment exerted the greatest influence on population growth, and thus managers should prioritize conservation efforts that target these demographic processes. Additional management should consider strategies to dampen temporal variability in larval survival, something that could be achieved through emergency salvage operations, captive rearing efforts, and manipulation of wetland hydroperiods

Local genomic adaptation of coral reef-associated microbiomes to gradients of natural variability and anthropogenic stressors

Holobionts are species-specific associations between macro- and microorganisms. On coral reefs, the benthic coverage of coral and algal holobionts varies due to natural and anthropogenic forcings. Different benthic macroorganisms are predicted to have specific microbiomes. In contrast, local environmental factors are predicted to select for specific metabolic pathways in microbes. To reconcile these two predictions, we hypothesized that adaptation of microbiomes to local conditions is facilitated by the horizontal transfer of genes responsible for specific metabolic capabilities. To test this hypothesis, microbial metagenomes were sequenced from 22 coral reefs at 11 Line Islands in the central Pacific that together span a wide range of biogeochemical and anthropogenic influences. Consistent with our hypothesis, the percent cover of major benthic functional groups significantly correlated with particular microbial taxa. Reefs with higher coral cover had a coral microbiome with higher abundances of Alphaproteobacteria (such as Rhodobacterales and Sphingomonadales), whereas microbiomes of algae-dominated reefs had higher abundances of Gammaproteobacteria (such as Alteromonadales, Pseudomonadales, and Vibrionales), Betaproteobacteria, and Bacteriodetes. In contrast to taxa, geography was the strongest predictor of microbial community metabolism. Microbial communities on reefs with higher nutrient availability (e.g., equatorial upwelling zones) were enriched in genes involved in nutrient-related metabolisms (e.g., nitrate and nitrite ammonification, Ton/Tol transport, etc.). On reefs further from the equator, microbes had more genes encoding chlorophyll biosynthesis and photosystems I/II. These results support the hypothesis that core microbiomes are determined by holobiont macroorganisms, and that those core taxa adapt to local conditions by selecting for advantageous metabolic genes

Random Exchange Quantum Heisenberg Chains

The one-dimensional quantum Heisenberg model with random $\pm J$ bonds is studied for $S=\frac{1}{2}$ and $S=1$. The specific heat and the zero-field susceptibility are calculated by using high-temperature series expansions and quantum transfer matrix method. The susceptibility shows a Curie-like temperature dependence at low temperatures as well as at high temperatures. The numerical results for the specific heat suggest that there are anomalously many low-lying excitations. The qualitative nature of these excitations is discussed based on the exact diagonalization of finite size systems.Comment: 13 pages, RevTex, 12 figures available on request ([email protected]

Fusion of 28Si + 28Si: oscillations above the barrier and the behavior down to 1μb

Fusion excitation functions of light heavy-ion systems show oscillatory structures above the Coulomb barrier, caused by resonances or due to the penetration of successive centrifugal barriers well separated in energy. In heavier systems, the amplitude of oscillations decreases and the peaks get nearer to each other. This makes the measurements very challenging. We have performed a first experiment for 28Si + 28Si, by measuring fusion cross sections (σ) in an energy range of ≃15 MeV above the barrier, with a small ΔElab = 0.5 MeV step. Three regular oscillations are clearly observed, which are best revealed by plotting the energy-weighted derivative of the excitation function. The excitation function has been recently measured down to cross sections ≤1μb with larger energy steps. Coupled-channel (CC) calculations based on a shallow potential in the entrance channel are able to reproduce the oscillations. A further analysis will provide a stringent test for the calculations, in particular for the choice of the ion-ion potential, because the subbarrier excitation function has to be reproduced as well. Coupled-channel (CC) calculations based on a shallow potential in the entrance channel are able to reproduce the oscillations. A further analysis will provide a stringent test for the calculations, in particular for the choice of the ion-ion potential, because the subbarrier excitation function has to be reproduced as well