An analysis of the Sargasso Sea resource and the consequences for database composition

Background: The environmental sequencing of the Sargasso Sea has introduced a huge new resource of genomic information. Unlike the protein sequences held in the current searchable databases, the Sargasso Sea sequences originate from a single marine environment and have been sequenced from species that are not easily obtainable by laboratory cultivation. The resource also contains very many fragments of whole protein sequences, a side effect of the shotgun sequencing method.These sequences form a significant addendum to the current searchable databases but also present us with some intrinsic difficulties. While it is important to know whether it is possible to assign function to these sequences with the current methods and whether they will increase our capacity to explore sequence space, it is also interesting to know how current bioinformatics techniques will deal with the new sequences in the resource.Results: The Sargasso Sea sequences seem to introduce a bias that decreases the potential of current methods to propose structure and function for new proteins. In particular the high proportion of sequence fragments in the resource seems to result in poor quality multiple alignments.Conclusion: These observations suggest that the new sequences should be used with care, especially if the information is to be used in large scale analyses. On a positive note, the results may just spark improvements in computational and experimental methods to take into account the fragments generated by environmental sequencing techniques

Beyond Biomass: Valuing Genetic Diversity in Natural Resource Management

Strategies for increasing production of goods from working and natural systems have raised concerns that the diversity of species on which these services depend may be eroding. This loss of natural capital threatens to homogenize global food supplies and compromise the stability of human welfare. We assess the trade off between artificial augmentation of biomass and degradation of biodiversity underlying a populations' ability to adapt to shocks. Our application involves the augmentation of wild stocks of salmon. Practices in this system have generated warnings that genetic erosion may lead to a loss of the “portfolio effect” and the value of this loss is not accounted for in decision making. We construct an integrated bioeconomic model of salmon biomass and genetic diversity. Our results show how practices that homogenize natural systems can still generate positive returns. However, the substitution of more physical capital and labor for natural capital must be maintained for gains to persist, weakens the capacity for adaptation should this investment cease, and can cause substantial loss of population wildness. We apply an emerging optimization method—approximate dynamic programming—to solve the model without simplifying restrictions imposed previously

Risk factors for central venous catheter-related infections in surgical and intensive care units. The Central Venous Catheter-Related Infections Study Group.

To identify avoidable risk factors for central venous catheter (CVC) infections in patients undergoing short-term catheterization

High frequency of inadequate test requests for antiphospholipid antibodies in daily clinical practice

Abstract Background: We have empirically noted that many physicians routinely request anti-phospholipid antibodies (aPL) without a correct clinical indication. The aim of this study was to evaluate retrospectively whether aPL testing at our Thrombosis Centre was justified. Methods: Medical records from 520 subjects for aPL screening tests for various clinical conditions were reviewed. The aPL screening tests were: lupus anticoagulant (LA), anti-cardiolipin antibodies (aCL) and anti-β(2) glycoptotein I (aβ(2) GPI). Requests for aPL screening were divided into justified, potentially justified or not adequately justified. Results: aPL testing requests were considered justified in 358 (69%) patients, potentially justified in 66 (12.6%) and not adequately justified in 96 (18.4%). LA was positive in 65 (18%) of justified requests and in only one (1%) of the 96 potentially justified requests. None of the 66 not adequately justified for aPL testing was positive for LA. aβ(2) ..

A clinician’s guide to management of intra-abdominal hypertension and abdominal compartment syndrome in critically ill patients

This article is one of ten reviews selected from the Annual Update in Intensive Care and Emergency Medicine 2020. Other selected articles can be found online at . Further information about the Annual Update in Intensive Care and Emergency Medicine is available from http://www.springer.com/series/8901

Extending Hybrid CSP with Probability and Stochasticity

Probabilistic and stochastic behavior are omnipresent in computer controlled systems, in particular, so-called safety-critical hybrid systems, because of fundamental properties of nature, uncertain environments, or simplifications to overcome complexity. Tightly intertwining discrete, continuous and stochastic dynamics complicates modelling, analysis and verification of stochastic hybrid systems (SHSs). In the literature, this issue has been extensively investigated, but unfortunately it still remains challenging as no promising general solutions are available yet. In this paper, we give our effort by proposing a general compositional approach for modelling and verification of SHSs. First, we extend Hybrid CSP (HCSP), a very expressive and process algebra-like formal modeling language for hybrid systems, by introducing probability and stochasticity to model SHSs, which is called stochastic HCSP (SHCSP). To this end, ordinary differential equations (ODEs) are generalized by stochastic differential equations (SDEs) and non-deterministic choice is replaced by probabilistic choice. Then, we extend Hybrid Hoare Logic (HHL) to specify and reason about SHCSP processes. We demonstrate our approach by an example from real-world.Comment: The conference version of this paper is accepted by SETTA 201

Spectral Indices of Stars at Super-solar Regime

We derived Lick narrow-band indices for 139 candidate super metal-rich stars of different luminosity class previously studied in Malagnini et al. (2000). Indices include Iron Fe50, Fe52, Fe53, and Magnesium Mgb and Mg2 features. By comparing observations with Kurucz' synthetic model atmospheres, no evidence is found for non-standard Mg vs. Fe relative abundance (i.e. [Mg/Fe]~ 0, on the average, for our sample). A comparison with the Worthey et al.(1994) and Buzzoni et al.(1992, 1994) fitting function predictions for [Fe/H] > 0 is performed and briefly discussed.Comment: 4 pages, 3 figures; proceedings of "New Quests in Stellar Astrophysics: The link between Stars and Cosmology", 26-30 March, 2001, Puerto Vallarta, Mexico, eds. M. Chavez, A. Bressan, A. Buzzoni & D. Mayya, to be published by the Kluwer Academic Publisher

Attention bias dynamics and symptom severity during and following CBT for social anxiety disorder

Objective: Threat-related attention bias figures prominently in contemporary accounts of the maintenance of anxiety disorders, yet longitudinal intervention research relating attention bias to anxiety symptom severity is limited. Capitalizing on recent advances in the conceptualization and measurement of attention bias, we aimed to examine the relation between attention bias, indexed using trial-level bias scores (TLBSs) to quantify temporal dynamics reflecting dysregulation of attentional processing of threat (as opposed to aggregated mean bias scores) and social anxiety symptom severity over the course of cognitive-behavioral therapy (CBT) and 1-month follow-up. Method: Adults with social anxiety disorder (N = 39) assigned to either yohimbine-or placebo-augmented CBT completed measures of attention bias and social anxiety symptom severity weekly throughout CBT (5 sessions) and at 1-week and 1-month posttreatment. Results: TLBSs of attention bias temporal dynamics showed stronger psychometric properties than mean aggregated scores and were highly interrelated, in line with within-subject temporal variability fluctuating in time between attentional overengagement and strategic avoidance from threat. Attention bias toward threat and temporal variability in attention bias (i.e., attentional dysregulation), but not attention bias away from threat, significantly reduced over the course of CBT. Cross-lag analyses revealed no evidence of a causal relation between reductions in attentional dysregulation leading to symptom severity reduction, or vice versa. Observed relations did not vary as a function of time. Conclusions: We found no evidence for attentional dysregulation as a causal mechanism for symptom reduction in CBT for social anxiety disorders. Implications for future research are discussed