Prediction of Relevant Biomedical Documents: a Human Microbiome Case Study

Background: Retrieving relevant biomedical literature has become increasingly difficult due to the large volume and rapid growth of biomedical publication. A query to a biomedical retrieval system often retrieves hundreds of results. Since the searcher will not likely consider all of these documents, ranking the documents is important. Ranking by recency, as PubMed does, takes into account only one factor indicating potential relevance. This study explores the use of the searcher’s relevance feedback judgments to support relevance ranking based on features more general than recency. Results: It was found that the researcher’s relevance judgments could be used to accurately predict the relevance of additional documents: both using tenfold cross-validation and by training on publications from 2008–2010 and testing on documents from 2011. Conclusions: This case study has shown the promise for relevance feedback to improve biomedical document retrieval. A researcher’s judgments as to which initially retrieved documents are relevant, or not, can be leveraged to predict additional relevant documents

Dynamical and thermodynamical analysis of the South China Sea winter cold tongue

Spatial distribution of the South China Sea (SCS) surface temperature shows strong cold anomalies over the Sunda Shelf during the boreal winter season. The band of low sea surface temperature (SST) region located south/southeast of Vietnam is called as the winter cold tongue (CT) in the SCS. Using observational and re-analysis datasets a comprehensive investigation of the dynamical and thermodynamical processes associated with the evolution of SCS CT is performed in this study. The role and relative importance of wind-driven ocean transports, air–sea heat fluxes and oceanic processes are explored. The north-south Sverdrup transport demonstrates strong southward transport during the northeast monsoon period aiding the SST cooling by bringing relatively cold water from the north. The zonal and meridional Ekman transports exhibit relatively weak westward and northward transports to the CT region during this period. The study suggests that wind-driven ocean transports have a significant role in regulating the shape and spatial extent of the CT. The heat budget analysis revealed that net surface heat flux decrease during the northeast monsoon acts as the primary cooling mechanism responsible for the development of the SCS CT, while the horizontal advection of cold water by the western boundary current along the coast of Vietnam plays a secondary role. The wintertime SST anomalies over the CT region are significantly linked to the Nino3 index. Most of the warming/cooling events in the SST anomalies coincide with the El Nino/La Nina phenomena in the Pacific Ocean.Singapore-MIT Alliance for Research and Technology. Center for Environmental Sensing and Modelin

A conflict management tool for conservation agencies

1. Growing pressure on natural resources is leading to more conservation conflicts. Governments and their statutory agencies devote increasing financial and human resources to this subject, but tend to adopt reactive, ad hoc approaches to management. 2. We combined theory and empirical data about five conservation conflicts in a transdisciplinary collaboration to co-develop a novel decision-making tool. 3. This tool uses a systematic stepwise approach with six distinct decision stages: (i) establishing whether there is a conflict or an impact; (ii) understanding the context of the conflict, including the stakeholders affected; (iii) developing shared understanding of the conflict and goals; (iv) building a consensus on how to reach the goals; (v) implementing measures; and (vi) monitoring the outcomes. 4. Policy implications. We argue this new tool has wide applicability and democratic legitimacy and offers an exciting and practical approach to improve the management of conservation conflicts

The impact of uncertainty on cooperation intent in a conservation conflict

1. Stakeholder cooperation can be vital in managing conservation conflicts. Laboratory experiments show cooperation is less likely in the presence of uncertainty. Much less is known about how stakeholders in real‐life conservation conflicts respond to different types of uncertainty. 2. We tested the effects of different sources of uncertainty on cooperative behaviour using a framed field experiment and interviews. The experiment compared a baseline scenario of perfect certainty with scenarios including either: (a) scientific uncertainty about the effectiveness of a conflict‐reduction intervention; (b) administrative uncertainty about intervention funding; or (c) political uncertainty about the extent of community support. We applied these scenarios to a conservation conflict in the Outer Hebrides, Scotland, involving the management of geese to simultaneously meet both conservation and farming objectives. We asked 149 crofters (small‐scale farmers) if they would commit to cooperate with others by helping fund a goose management plan given the three sources of uncertainty. 3. On average, intention to cooperate was highest (99%) in scenarios without uncertainty, and lowest under administrative uncertainty (77%). Scientific uncertainty and political uncertainty both had less of an effect, with over 95% of crofters predicted to be willing to cooperate in these scenarios. Crofters who indicated concern for other crofters suffering the impact of geese were more likely to cooperate. The longer an individual had been a crofter, the less likely they were to cooperate. 4. Synthesis and applications. Crofters’ intention to cooperate is high but lessened by uncertainty, especially over the commitment from other stakeholders such as government, to cooperate on goose management. Existing cooperation on goose management may be at risk if uncertainty is not reduced outright or commitments between parties are not strengthened. This has wide applicability, supporting the need for researchers and government advisers to: (a) determine how uncertainty will impact intention of stakeholders to cooperate; and (b) take steps (such as uncertainty reduction, communication or acceptance) to reduce the negative impact of uncertainty on cooperation

Improving the science-policy dialogue to meet the challenges of biodiversity conservation: having conversations rather than talking at one-another

A better, more effective dialogue is needed between biodiversity science and policy to underpin the sustainable use and conservation of biodiversity. Many initiatives exist to improve communication, but these largely conform to a ‘linear’ or technocratic model of communication in which scientific “facts” are transmitted directly to policy advisers to “solve problems”. While this model can help start a dialogue, it is, on its own, insufficient, as decision taking is complex, iterative and often selective in the information used. Here, we draw on the literature, interviews and a workshop with individuals working at the interface between biodiversity science and government policy development to present practical recommendations aimed at individuals, teams, organisations and funders. Building on these recommendations, we stress the need to: (a) frame research and policy jointly; (b) promote inter- and trans-disciplinary research and “multi-domain” working groups that include both scientists and policy makers from various fields and sectors; (c) put in place structures and incentive schemes that support interactive dialogue in the long-term. These are changes that are needed in light of continuing loss of biodiversity and its consequences for societal dependence on and benefits from nature

Mortality and drug therapy in patients with chronic obstructive pulmonary disease: a network meta-analysis

Background: Increasing evidence suggests pharmacological treatments may impact on overall survival in Chronic Obstructive Pulmonary Disease (COPD) patients. Individual clinical trials are rarely powered to detect mortality differences between treatments and may not include all treatment options relevant to healthcare decision makers. Methods: A systematic review was conducted to identify RCTs of COPD treatments reporting mortality; evidence was synthesised using network meta-analysis (NMA). The analysis included 40 RCTs; a quantitative indirect comparison between 14 treatments using data from 55,220 patients was conducted. Results: The analysis reported two treatments reducing all-cause mortality; salmeterol/fluticasone propionate combination (SFC) was associated with a reduction in mortality versus placebo in the fixed effects (HR 0.79; 95 % Crl 0.67, 0.94) but not the random effects model (0.79; 0.56, 1.09). Indacaterol was associated with a reduction in mortality versus placebo in fixed (0.28; 0.08 to 0.85) and random effects (0.29; 0.08, 0.89) models. Mean estimates and credible intervals for hazard ratios for indacaterol versus placebo are based on a small number of events; estimates may change when the results of future studies are included. These results were maintained across a variety of assumptions and provide evidence that SFC and indacaterol may lead to improved survival in COPD patients. Conclusion: Results of an NMA of COPD treatments suggest that SFC and indacaterol may reduce mortality. Further research is warranted to strengthen this conclusion. Electronic supplementary material The online version of this article (doi:10.1186/s12890-015-0138-4) contains supplementary material, which is available to authorized users

Mortality and drug therapy in patients with chronic obstructive pulmonary disease: a network meta-analysis

Background: Increasing evidence suggests pharmacological treatments may impact on overall survival in Chronic Obstructive Pulmonary Disease (COPD) patients. Individual clinical trials are rarely powered to detect mortality differences between treatments and may not include all treatment options relevant to healthcare decision makers. Methods: A systematic review was conducted to identify RCTs of COPD treatments reporting mortality; evidence was synthesised using network meta-analysis (NMA). The analysis included 40 RCTs; a quantitative indirect comparison between 14 treatments using data from 55,220 patients was conducted. Results: The analysis reported two treatments reducing all-cause mortality; salmeterol/fluticasone propionate combination (SFC) was associated with a reduction in mortality versus placebo in the fixed effects (HR 0.79; 95 % Crl 0.67, 0.94) but not the random effects model (0.79; 0.56, 1.09). Indacaterol was associated with a reduction in mortality versus placebo in fixed (0.28; 0.08 to 0.85) and random effects (0.29; 0.08, 0.89) models. Mean estimates and credible intervals for hazard ratios for indacaterol versus placebo are based on a small number of events; estimates may change when the results of future studies are included. These results were maintained across a variety of assumptions and provide evidence that SFC and indacaterol may lead to improved survival in COPD patients. Conclusion: Results of an NMA of COPD treatments suggest that SFC and indacaterol may reduce mortality. Further research is warranted to strengthen this conclusion. Electronic supplementary material The online version of this article (doi:10.1186/s12890-015-0138-4) contains supplementary material, which is available to authorized users

4D Super-Resolution Microscopy with Conventional Fluorophores and Single Wavelength Excitation in Optically Thick Cells and Tissues

Optical super-resolution imaging of fluorescently stained biological samples is rapidly becoming an important tool to investigate protein distribution at the molecular scale. It is therefore important to develop practical super-resolution methods that allow capturing the full three-dimensional nature of biological systems and also can visualize multiple protein species in the same sample

A comprehensive characterization of the caspase gene family in insects from the order Lepidoptera

<p>Abstract</p> <p>Background</p> <p>The cell suicide pathway of apoptosis is a necessary event in the life of multicellular organisms. It is involved in many biological processes ranging from development to the immune response. Evolutionarily conserved proteases, called caspases, play a central role in regulating apoptosis. Reception of death stimuli triggers the activation of initiator caspases, which in turn activate the effector caspases. In Lepidoptera, apoptosis is crucial in processes such as metamorphosis or defending against baculovirus infection. The discovery of p35, a baculovirus protein inhibiting caspase activity, has led to the characterization of the first lepidopteran caspase, Sf-Caspase-1. Studies on Sf-Caspase-1 mode of activation suggested that apoptosis in Lepidoptera requires a cascade of caspase activation, as demonstrated in many other species.</p> <p>Results</p> <p>In order to get insights into this gene family in Lepidoptera, we performed an extensive survey of lepidopteran-derived EST datasets. We identified 66 sequences distributed among 27 species encoding putative caspases. Phylogenetic analyses showed that Lepidoptera possess at least 5 caspases, for which we propose a unified nomenclature. According to homology to their <it>Drosophila </it>counterparts and their primary structure, we determined that Lep-Caspase-1, -2 and -3 are putative effector caspases, whereas Lep-Caspase-5 and -6 are putative initiators. The likely function of Lep-Caspase-4 remains unclear. Lep-Caspase-2 is absent from the silkworm genome and appears to be noctuid-specific, and to have arisen from a tandem duplication of the Caspase-1 gene. In the tobacco hawkmoth, 3 distinct transcripts encoding putative Caspase-4 were identified, suggesting at least 2 duplication events in this species.</p> <p>Conclusions</p> <p>The basic repertoire of five major types of caspases shared among Lepidoptera seems to be smaller than for most other groups studied to date, but gene duplication still plays a role in lineage-specific increases in diversity, just as in Diptera and mammals.</p