ParMap, an algorithm for the identification of small genomic insertions and deletions in nextgen sequencing data

<p>Abstract</p> <p>Background</p> <p>Next-generation sequencing produces high-throughput data, albeit with greater error and shorter reads than traditional Sanger sequencing methods. This complicates the detection of genomic variations, especially, small insertions and deletions.</p> <p>Findings</p> <p>Here we describe ParMap, a statistical algorithm for the identification of complex genetic variants, such as small insertion and deletions, using partially mapped reads in nextgen sequencing data.</p> <p>Conclusions</p> <p>We report ParMap's successful application to the mutation analysis of chromosome X exome-captured leukemia DNA samples.</p

Atmospheric Evolution

Earth's atmosphere has evolved as volatile species cycle between the atmosphere, ocean, biomass and the solid Earth. The geochemical, biological and astrophysical processes that control atmospheric evolution are reviewed from an "Earth Systems" perspective, with a view not only to understanding the history of Earth, but also to generalizing to other solar system planets and exoplanets.Comment: 34 pages, 3 figures, 2 tables. Accepted as a chapter in "Encyclopaedia of Geochemistry", Editor Bill White, Springer-Nature, 201

Towards quantum computing with single atoms and optical cavities on atom chips

We report on recent developments in the integration of optical microresonators into atom chips and describe some fabrication and implementation challenges. We also review theoretical proposals for quantum computing with single atoms based on the observation of photons leaking through the cavity mirrors. The use of measurements to generate entanglement can result in simpler, more robust and scalable quantum computing architectures. Indeed, we show that quantum computing with atom-cavity systems is feasible even in the presence of relatively large spontaneous decay rates and finite photon detector efficiencies.Comment: 14 pages, 6 figure

Do Political Attitudes Matter for Epistemic Decisions of Scientists?

The epistemic attitudes of scientists, such as epistemic tolerance and authoritarianism, play important roles in the discourse about rivaling theories. Epistemic tolerance stands for the mental attitude of an epistemic agent, e.g., a scientist, who is open to opposing views, while epistemic authoritarianism represents the tendency to uncritically accept views of authorities. Another relevant epistemic factor when it comes to the epistemic decisions of scientists is the skepticism towards the scientific method. However, the question is whether these epistemic attitudes are influenced by their sociopolitical counterparts, such as the researcher's degree of conservatism. To empirically investigate the interplay between epistemic and sociopolitical attitudes of scientists, we conducted a survey with researchers (N = 655) across different disciplines. We propose scales for measuring epistemic tolerance and epistemic authoritarianism, as well as a scale for detecting the participants' readiness to question the scientific method. Furthermore, we investigate the relationship between epistemic tolerance and epistemic authoritarianism on the one hand, and career stage and sociopolitical views on the other hand. Interestingly, our study found only small correlations between the participants' degree of conservatism and their epistemic attitudes. This suggests that political views, against common argumentation, actually do not play an important role in one's scientific decisions. Moreover, social scientists scored higher on the epistemic tolerance and lower on the epistemic authoritarianism scale than natural scientists. Finally, the results indicate that natural scientists question the scientific method less than social scientists

Social sciences research in neglected tropical diseases 2: A bibliographic analysis

The official published version of the article can be found at the link below.Background There are strong arguments for social science and interdisciplinary research in the neglected tropical diseases. These diseases represent a rich and dynamic interplay between vector, host, and pathogen which occurs within social, physical and biological contexts. The overwhelming sense, however, is that neglected tropical diseases research is a biomedical endeavour largely excluding the social sciences. The purpose of this review is to provide a baseline for discussing the quantum and nature of the science that is being conducted, and the extent to which the social sciences are a part of that. Methods A bibliographic analysis was conducted of neglected tropical diseases related research papers published over the past 10 years in biomedical and social sciences. The analysis had textual and bibliometric facets, and focussed on chikungunya, dengue, visceral leishmaniasis, and onchocerciasis. Results There is substantial variation in the number of publications associated with each disease. The proportion of the research that is social science based appears remarkably consistent (<4%). A textual analysis, however, reveals a degree of misclassification by the abstracting service where a surprising proportion of the "social sciences" research was pure clinical research. Much of the social sciences research also tends to be "hand maiden" research focused on the implementation of biomedical solutions. Conclusion There is little evidence that scientists pay any attention to the complex social, cultural, biological, and environmental dynamic involved in human pathogenesis. There is little investigator driven social science and a poor presence of interdisciplinary science. The research needs more sophisticated funders and priority setters who are not beguiled by uncritical biomedical promises

Altered intercellular communication in lung fibroblast cultures from patients with idiopathic pulmonary fibrosis

RATIONALE: Gap junctions are membrane channels formed by an array of connexins which links adjacent cells realizing an electro- metabolic synapse. Connexin-mediated communication is crucial in the regulation of cell growth, differentiation, and development. The activation and proliferation of phenotypically altered fibroblasts are central events in the pathogenesis of idiopathic pulmonary fibrosis. We sought to evaluate the role of connexin-43, the most abundant gap-junction subunit in the human lung, in the pathogenesis of this condition. METHODS: We investigated the transcription and protein expression of connexin-43 and the gap-junctional intercellular communication (GJIC) in 5 primary lung fibroblast lines derived from normal subjects (NF) and from 3 histologically proven IPF patients (FF). RESULTS: Here we show that connexin-43 mRNA was significantly reduced in FF as demonstrated by standard and quantitative RT-PCR. GJIC was functionally evaluated by means of flow-cytometry. In order to demonstrate that dye spreading was taking place through gap junctions, we used carbenoxolone as a pharmacological gap-junction blocker. Carbenoxolone specifically blocked GJIC in our system in a concentration dependent manner. FF showed a significantly reduced homologous GJIC compared to NF. Similarly, GJIC was significantly impaired in FF when a heterologous NF line was used as dye donor, suggesting a complete defect in GJIC of FF. CONCLUSION: These results suggest a novel alteration in primary lung fibroblasts from IPF patients. The reduced Cx43 expression and the associated alteration in cell-to-cell communication may justify some of the known pathological characteristic of this devastating disease that still represents a challenge to the medical practice

Cooperation, Norms, and Revolutions: A Unified Game-Theoretical Approach

Cooperation is of utmost importance to society as a whole, but is often challenged by individual self-interests. While game theory has studied this problem extensively, there is little work on interactions within and across groups with different preferences or beliefs. Yet, people from different social or cultural backgrounds often meet and interact. This can yield conflict, since behavior that is considered cooperative by one population might be perceived as non-cooperative from the viewpoint of another. To understand the dynamics and outcome of the competitive interactions within and between groups, we study game-dynamical replicator equations for multiple populations with incompatible interests and different power (be this due to different population sizes, material resources, social capital, or other factors). These equations allow us to address various important questions: For example, can cooperation in the prisoner's dilemma be promoted, when two interacting groups have different preferences? Under what conditions can costly punishment, or other mechanisms, foster the evolution of norms? When does cooperation fail, leading to antagonistic behavior, conflict, or even revolutions? And what incentives are needed to reach peaceful agreements between groups with conflicting interests? Our detailed quantitative analysis reveals a large variety of interesting results, which are relevant for society, law and economics, and have implications for the evolution of language and culture as well

Evaluating treatments in health care: The instability of a one-legged stool

<p>Abstract</p> <p>Background</p> <p>Both scientists and the public routinely refer to randomized controlled trials (RCTs) as being the 'gold standard' of scientific evidence. Although there is no question that placebo-controlled RCTs play a significant role in the evaluation of new pharmaceutical treatments, especially when it is important to rule out placebo effects, they have many inherent limitations which constrain their ability to inform medical decision making. The purpose of this paper is to raise questions about <it>over-reliance </it>on RCTs and to point out an additional perspective for evaluating healthcare evidence, as embodied in the Hill criteria. The arguments presented here are generally relevant to all areas of health care, though mental health applications provide the primary context for this essay.</p> <p>Discussion</p> <p>This article first traces the history of RCTs, and then evaluates five of their major limitations: they often lack external validity, they have the potential for increasing health risk in the general population, they are no less likely to overestimate treatment effects than many other methods, they make a relatively weak contribution to clinical practice, and they are excessively expensive (leading to several additional vulnerabilities in the quality of evidence produced). Next, the nine Hill criteria are presented and discussed as a richer approach to the evaluation of health care treatments. Reliance on these multi-faceted criteria requires more analytical thinking than simply examining RCT data, but will also enhance confidence in the evaluation of novel treatments.</p> <p>Summary</p> <p>Excessive reliance on RCTs tends to stifle funding of other types of research, and publication of other forms of evidence. We call upon our research and clinical colleagues to consider additional methods of evaluating data, such as the Hill criteria. Over-reliance on RCTs is similar to resting all of health care evidence on a one-legged stool.</p

Host Gene Expression Profiling of Dengue Virus Infection in Cell Lines and Patients

Dengue is the most prevalent mosquito-born viral disease affecting humans, yet there is, at present, no drug treatment for the disease nor are there any validated host targets for therapeutic intervention. Using microarray technology to monitor the response of virtually every human gene, we aimed to identify the ways in which humans interact with dengue virus during infection in order to discover new therapeutic targets that could be exploited to control viral replication. From the activated genes, we identified three pathways common to in vitro and in vivo infection; the NF-κB initiated immune pathway, the type I interferon pathway, and the ubiquitin proteasome pathway. We next found that inhibiting the ubiquitin proteasome pathway, or activating the type I interferon pathway, resulted in significant inhibition of viral replication. However, inhibiting the NF-κB initiated immune pathway had no effect on viral replication. We suggest that drugs that target the ubiquitin proteasome pathway may prove effective at killing the dengue virus, and, if used therapeutically, improve clinical outcome in dengue disease