Emv2, the only endogenous ecotropic murine leukemia virus of C57BL/6J mice

With the proliferation of sequence data, great challenges are posed in the correct annotation of endogenous retroviruses, which together comprise up to ten per cent of the genomes of many organisms. It is therefore essential that all sources of information are carefully considered before drawing conclusions concerning the phylogeny, distribution and biological properties of endogenous retroviruses. We suggest that such due diligence has not been applied in the description of an endogenous ecotropic retrovirus that recently appeared in Retrovirology

Hidden Donors: The Censoring Problem in U.S. Federal Campaign Finance Data

Inferences about individual campaign contributors are limited by how the Federal Election Commission collects and reports data. Only transactions that exceed a cycle-to-date total of $200 are individually disclosed, so that contributions of many donors are unobserved. We contrast visible and "hidden" donors, i.e., small donors who are invisible due to censoring—and routinely ignored in existing research. We use the Sanders presidential campaign in 2016, whose unique campaign structure received money only through an intermediary/conduit committee. These are governed by stricter disclosure statutes, allowing us to study donors who are normally hidden. For Sanders, there were seven hidden donors for every visible donor, and altogether, hidden donors were responsible for 33.8% of Sanders' campaign funds. We show that hidden donors start giving relatively later, with contributions concentrated around early primaries. We suggest that as presidential campaign strategies change towards wooing smaller donors, more research on what motivates them is necessary

Finding qualitative research: an evaluation of search strategies

BACKGROUND: Qualitative research makes an important contribution to our understanding of health and healthcare. However, qualitative evidence can be difficult to search for and identify, and the effectiveness of different types of search strategies is unknown. METHODS: Three search strategies for qualitative research in the example area of support for breast-feeding were evaluated using six electronic bibliographic databases. The strategies were based on using thesaurus terms, free-text terms and broad-based terms. These strategies were combined with recognised search terms for support for breast-feeding previously used in a Cochrane review. For each strategy, we evaluated the recall (potentially relevant records found) and precision (actually relevant records found). RESULTS: A total yield of 7420 potentially relevant records was retrieved by the three strategies combined. Of these, 262 were judged relevant. Using one strategy alone would miss relevant records. The broad-based strategy had the highest recall and the thesaurus strategy the highest precision. Precision was generally poor: 96% of records initially identified as potentially relevant were deemed irrelevant. Searching for qualitative research involves trade-offs between recall and precision. CONCLUSIONS: These findings confirm that strategies that attempt to maximise the number of potentially relevant records found are likely to result in a large number of false positives. The findings also suggest that a range of search terms is required to optimise searching for qualitative evidence. This underlines the problems of current methods for indexing qualitative research in bibliographic databases and indicates where improvements need to be made

Anharmonicity-induced isostructural phase transition of Zirconium under pressure

We have performed a detailed x-ray diffraction structural study of Zr under pressure and unambiguously identify the existence of a first-order isostructural bcc-to-bcc phase transition near 58 GPa. First-principles quantum molecular dynamics lattice dynamics calculations support the existence of this phase transition, in excellent agreement with experimental results, triggered by anharmonic effects. Our results highlight the potential ubiquity of anharmonically driven isostructural transitions within the periodic table under pressure and calls for follow-up experimental and theoretical studies

Climate Change and Biosphere Response: Unlocking the Collections Vault

Natural history collections (NHCs) are an important source of the long-term data needed to understand how biota respond to ongoing anthropogenic climate change. These include taxon occurrence data for ecological modeling, as well as information that can be used to reconstruct mechanisms through which biota respond to changing climates. The full potential of NHCs for climate change research cannot be fully realized until high-quality data sets are conveniently accessible for research, but this requires that higher priority be placed on digitizing the holdings most useful for climate change research (e.g., whole-biota studies, time series, records of intensively sampled common taxa). Natural history collections must not neglect the proliferation of new information from efforts to understand how present-day ecosystems are responding to environmental change. These new directions require a strategic realignment for many NHC holders to complement their existing focus on taxonomy and systematics. To set these new priorities, we need strong partnerships between NHC holders and global change biologists

Negative Selection by an Endogenous Retrovirus Promotes a Higher-Avidity CD4+ T Cell Response to Retroviral Infection

Effective T cell responses can decisively influence the outcome of retroviral infection. However, what constitutes protective T cell responses or determines the ability of the host to mount such responses is incompletely understood. Here we studied the requirements for development and induction of CD4+ T cells that were essential for immunity to Friend virus (FV) infection of mice, according to their TCR avidity for an FV-derived epitope. We showed that a self peptide, encoded by an endogenous retrovirus, negatively selected a significant fraction of polyclonal FV-specific CD4+ T cells and diminished the response to FV infection. Surprisingly, however, CD4+ T cell-mediated antiviral activity was fully preserved. Detailed repertoire analysis revealed that clones with low avidity for FV-derived peptides were more cross-reactive with self peptides and were consequently preferentially deleted. Negative selection of low-avidity FV-reactive CD4+ T cells was responsible for the dominance of high-avidity clones in the response to FV infection, suggesting that protection against the primary infecting virus was mediated exclusively by high-avidity CD4+ T cells. Thus, although negative selection reduced the size and cross-reactivity of the available FV-reactive naïve CD4+ T cell repertoire, it increased the overall avidity of the repertoire that responded to infection. These findings demonstrate that self proteins expressed by replication-defective endogenous retroviruses can heavily influence the formation of the TCR repertoire reactive with exogenous retroviruses and determine the avidity of the response to retroviral infection. Given the overabundance of endogenous retroviruses in the human genome, these findings also suggest that endogenous retroviral proteins, presented by products of highly polymorphic HLA alleles, may shape the human TCR repertoire that reacts with exogenous retroviruses or other infecting pathogens, leading to interindividual heterogeneity

Transient Cavity Dynamics and Divergence from the Stokes-Einstein Equation in Organic Aerosol

The diffusion of small molecules through viscous matrices formed by large organic molecules is important across a range of domains, including pharmaceutical science, materials chemistry, and atmospheric science, impacting on, for example, the formation of amorphous and crystalline phases. Here we report significant breakdowns in the Stokes–Einstein (SE) equation from measurements of the diffusion of water (spanning 5 decades) and viscosity (spanning 12 decades) in saccharide aerosol droplets. Molecular dynamics simulations show water diffusion is not continuous, but proceeds by discrete hops between transient cavities that arise and dissipate as a result of dynamical fluctuations within the saccharide lattice. The ratio of transient cavity volume to solvent volume increases with size of molecules making up the lattice, increasing divergence from SE predictions. This improved mechanistic understanding of diffusion in viscous matrices explains, for example, why organic compounds equilibrate according to SE predictions and water equilibrates more rapidly in aerosols

Transient two-dimensional electronic spectroscopy: coherent dynamics at arbitrary times along the reaction coordinate

Recent advances in two-dimensional electronic spectroscopy (2DES) have enabled identification of fragile quantum coherences in condensed-phase systems near the equilibrium molecular geometry. In general, traditional 2DES cannot measure such coherences associated with photophysical processes that occur at times significantly after the initially prepared state has dephased, such as the evolution of the initial excited state into a charge transfer state. We demonstrate the use of transient two-dimensional electronic spectroscopy (t-2DES) to probe coherences in an electron donor–acceptor dyad consisting of a perylenediimide (PDI) acceptor and a perylene (Per) donor. An actinic pump pulse prepares the lowest excited singlet state of PDI followed by formation of the PDI•––Per•+ ion pair, which is probed at different times following the actinic pulse using 2DES. Analysis of the observed coherences provides information about electronic, vibronic, and vibrational interactions at any time along the reaction coordinate for ion pair formation