Recycling bins, garbage cans or think tanks? Three myths regarding policy analysis institutes

The phrase 'think tank' has become ubiquitous – overworked and underspecified – in the political lexicon. It is entrenched in scholarly discussions of public policy as well as in the 'policy wonk' of journalists, lobbyists and spin-doctors. This does not mean that there is an agreed definition of think tank or consensual understanding of their roles and functions. Nevertheless, the majority of organizations with this label undertake policy research of some kind. The idea of think tanks as a research communication 'bridge' presupposes that there are discernible boundaries between (social) science and policy. This paper will investigate some of these boundaries. The frontiers are not only organizational and legal; they also exist in how the 'public interest' is conceived by these bodies and their financiers. Moreover, the social interactions and exchanges involved in 'bridging', themselves muddy the conception of 'boundary', allowing for analysis to go beyond the dualism imposed in seeing science on one side of the bridge, and the state on the other, to address the complex relations between experts and public policy

Drawing a line in the sand: affect and testimony in autism assessment teams in the UK.

Diagnosis of autism in the UK is generally made within a multidisciplinary team setting and is primarily based on observation and clinical interview. We examined how clinicians diagnose autism in practice by observing post-assessment meetings in specialist autism teams. Eighteen meetings across four teams based in the south of England and covering 88 cases were audio-recorded, transcribed and analysed using thematic analysis. We drew out two themes, related to the way in which clinicians expressed their specialist disciplinary knowledge to come to diagnostic consensus: Feeling Autism in the Encounter; and Evaluating Testimonies of Non-present Actors. We show how clinicians produce objective accounts through their situated practices and perform diagnosis as an act of interpretation, affect and evaluation to meet the institutional demands of the diagnostic setting. Our study contributes to our understanding of how diagnosis is accomplished in practice.Wellcome Trust Investigator Awar

Fitness Landscape Transformation through a Single Amino Acid Change in the Rho Terminator

Regulatory networks allow organisms to match adaptive behavior to the complex and dynamic contingencies of their native habitats. Upon a sudden transition to a novel environment, the mismatch between the native behavior and the new niche provides selective pressure for adaptive evolution through mutations in elements that control gene expression. In the case of core components of cellular regulation and metabolism, with broad control over diverse biological processes, such mutations may have substantial pleiotropic consequences. Through extensive phenotypic analyses, we have characterized the systems-level consequences of one such mutation (rho*) in the global transcriptional terminator Rho of Escherichia coli. We find that a single amino acid change in Rho results in a massive change in the fitness landscape of the cell, with widely discrepant fitness consequences of identical single locus perturbations in rho* versus rhoWT backgrounds. Our observations reveal the extent to which a single regulatory mutation can transform the entire fitness landscape of the cell, causing a massive change in the interpretation of individual mutations and altering the evolutionary trajectories which may be accessible to a bacterial population

Roadmap on STIRAP applications

STIRAP (stimulated Raman adiabatic passage) is a powerful laser-based method, usually involving two photons, for efficient and selective transfer of populations between quantum states. A particularly interesting feature is the fact that the coupling between the initial and the final quantum states is via an intermediate state, even though the lifetime of the latter can be much shorter than the interaction time with the laser radiation. Nevertheless, spontaneous emission from the intermediate state is prevented by quantum interference. Maintaining the coherence between the initial and final state throughout the transfer process is crucial. STIRAP was initially developed with applications in chemical dynamics in mind. That is why the original paper of 1990 was published in The Journal of Chemical Physics. However, from about the year 2000, the unique capabilities of STIRAP and its robustness with respect to small variations in some experimental parameters stimulated many researchers to apply the scheme to a variety of other fields of physics. The successes of these efforts are documented in this collection of articles. In Part A the experimental success of STIRAP in manipulating or controlling molecules, photons, ions or even quantum systems in a solid-state environment is documented. After a brief introduction to the basic physics of STIRAP, the central role of the method in the formation of ultracold molecules is discussed, followed by a presentation of how precision experiments (measurement of the upper limit of the electric dipole moment of the electron or detecting the consequences of parity violation in chiral molecules) or chemical dynamics studies at ultralow temperatures benefit from STIRAP. Next comes the STIRAP-based control of photons in cavities followed by a group of three contributions which highlight the potential of the STIRAP concept in classical physics by presenting data on the transfer of waves (photonic, magnonic and phononic) between respective waveguides. The works on ions or ion strings discuss options for applications, e.g. in quantum information. Finally, the success of STIRAP in the controlled manipulation of quantum states in solid-state systems, which are usually hostile towards coherent processes, is presented, dealing with data storage in rare-earth ion doped crystals and in nitrogen vacancy (NV) centers or even in superconducting quantum circuits. The works on ions and those involving solid-state systems emphasize the relevance of the results for quantum information protocols. Part B deals with theoretical work, including further concepts relevant to quantum information or invoking STIRAP for the manipulation of matter waves. The subsequent articles discuss the experiments underway to demonstrate the potential of STIRAP for populating otherwise inaccessible high-lying Rydberg states of molecules, or controlling and cooling the translational motion of particles in a molecular beam or the polarization of angular-momentum states. The series of articles concludes with a more speculative application of STIRAP in nuclear physics, which, if suitable radiation fields become available, could lead to spectacular results

Hypergraph models of biological networks to identify genes critical to pathogenic viral response

Background: Representing biological networks as graphs is a powerful approach to reveal underlying patterns, signatures, and critical components from high-throughput biomolecular data. However, graphs do not natively capture the multi-way relationships present among genes and proteins in biological systems. Hypergraphs are generalizations of graphs that naturally model multi-way relationships and have shown promise in modeling systems such as protein complexes and metabolic reactions. In this paper we seek to understand how hypergraphs can more faithfully identify, and potentially predict, important genes based on complex relationships inferred from genomic expression data sets. Results: We compiled a novel data set of transcriptional host response to pathogenic viral infections and formulated relationships between genes as a hypergraph where hyperedges represent significantly perturbed genes, and vertices represent individual biological samples with specific experimental conditions. We find that hypergraph betweenness centrality is a superior method for identification of genes important to viral response when compared with graph centrality. Conclusions: Our results demonstrate the utility of using hypergraphs to represent complex biological systems and highlight central important responses in common to a variety of highly pathogenic viruses

Novel modulators of p53-signaling encoded by unknown genes of emerging viruses

The p53 transcription factor plays a key role both in cancer and in the cell-intrinsic response to infections. The ORFEOME project hypothesized that novel p53-virus interactions reside in hitherto uncharacterized, unknown, or hypothetical open reading frames (orfs) of human viruses. Hence, 172 orfs of unknown function from the emerging viruses SARS-Coronavirus, MERS-Coronavirus, influenza, Ebola, Zika (ZIKV), Chikungunya and Kaposi Sarcomaassociated herpesvirus (KSHV) were de novo synthesized, validated and tested in a functional screen of p53 signaling. This screen revealed novel mechanisms of p53 virus interactions and two viral proteins KSHV orf10 and ZIKV NS2A binding to p53. Originally identified as the target of small DNA tumor viruses, these experiments reinforce the notion that all viruses, including RNA viruses, interfere with p53 functions. These results validate this resource for analogous systems biology approaches to identify functional properties of uncharacterized viral proteins, long non-coding RNAs and micro RNAs

MPLEx: a method for simultaneous pathogen inactivation and extraction of samples for multi-omics profiling

The continued emergence and spread of infectious agents is of great concern, and systems biology approaches to infectious disease research can advance our understanding of host–pathogen relationships and facilitate the development of new therapies and vaccines