Second Generation of 'Miranda Procedure' for CP Violation in Dalitz Studies of B (\& D \& \tau) Decays

The `Miranda Procedure' proposed for analyzing Dalitz plots for CP asymmetries in charged B and D decays in a model-independent manner is extended and refined. The complexity of CKM CP phenomenology through order $\lambda^6$ is needed in searches for New Dynamics (ND). Detailed analyses of three-body final states other great advantages: (i) They give us more powerful tools for deciding whether an observed CP asymmetry rep- resents the manifestation of ND and its features. (ii) Many advantages can already be obtained by the `Miranda Procedure' without construction of a detailed Dalitz plot de- scription. (iii) One studies CP asymmetries independent of production asymmetries. We illustrate the power of a second generation Miranda Procedure with examples with time integrated rates for $B_d/\bar B_d$ decays to final states $K_S\pi+\pi-$ as trial runs with comments on $B^{\pm} \to K^{\pm}\pi^+\pi^-/K^{\pm}K^+K^-$.Comment: 29 pages, 7 figure

Nanotribology of biopolymer brushes in aqueous solution using dissipative particle dynamics simulations: an application to PEG covered liposomes in theta solvent

We undertake the investigation of sheared polymer chains grafted on flat surfaces to model liposomes covered with polyethylene glycol brushes as a case study for the mechanisms of efficient drug delivery in biologically relevant situations, for example, as carriers for topical treatments of illnesses in the human vasculature. For these applications, specific rheological properties are required, such as low viscosity at high shear rate to improve the transport of the liposomes. Therefore non - equilibrium, DPD simulations of polymer brushes of various length and shear rates are performed to obtain the average viscosity and friction coefficient of the system as functions of the shear rate and polymerization degree under theta solvent conditions, and find that the brushes experience shear thinning at large shear rates.The viscosity and the friction coefficient are shown to obey scaling laws at high shear rate in theta solvent, irrespective of the brushes degree of polymerization. These results confirm recent scaling predictions and reproduce very well trends in measurements of the viscosity at high shear of red blood cells in a liposome containing medium.Comment: 32 pages, 8 figure

Phospho‐RNA‐seq: a modified small RNA‐seq method that reveals circulating mRNA and lncRNA fragments as potential biomarkers in human plasma

Extracellular RNAs (exRNAs) in biofluids have attracted great interest as potential biomarkers. Although extracellular microRNAs in blood plasma are extensively characterized, extracellular messenger RNA (mRNA) and long non‐coding RNA (lncRNA) studies are limited. We report that plasma contains fragmented mRNAs and lncRNAs that are missed by standard small RNA‐seq protocols due to lack of 5′ phosphate or presence of 3′ phosphate. These fragments were revealed using a modified protocol (“phospho‐RNA‐seq”) incorporating RNA treatment with T4‐polynucleotide kinase, which we compared with standard small RNA‐seq for sequencing synthetic RNAs with varied 5′ and 3′ ends, as well as human plasma exRNA. Analyzing phospho‐RNA‐seq data using a custom, high‐stringency bioinformatic pipeline, we identified mRNA/lncRNA transcriptome fingerprints in plasma, including tissue‐specific gene sets. In a longitudinal study of hematopoietic stem cell transplant patients, bone marrow‐ and liver‐enriched exRNA genes were tracked with bone marrow recovery and liver injury, respectively, providing proof‐of‐concept validation as a biomarker approach. By enabling access to an unexplored realm of mRNA and lncRNA fragments, phospho‐RNA‐seq opens up new possibilities for plasma transcriptomic biomarker development.SynopsisA modified RNA‐seq method (Phospho‐RNA‐seq) revealed a new population of mRNA/lncRNA fragments in plasma, including ones that track with disease. This opens up new possibilities for disease detection via RNA profiling of plasma and other biofluids.Phospho‐RNA‐seq reveals a large population of mRNA and long non‐coding RNA fragments in human plasma, which are missed by standard small RNA‐seq protocols that depend on target RNAs having a 5′ P and 3′ OH.Accurate detection of plasma mRNA and lncRNA fragments requires a stringent bioinformatic analysis pipeline to avoid false positive alignments to mRNA and lncRNA genes.Phospho‐RNA‐seq identified ensembles of tissue‐specific transcripts in plasma of hematopoietic stem cell transplant patients, which show co‐expression patterns that vary dynamically and track with pathophysiological processes.By enabling access to an unexplored space of extracellular mRNA and lncRNA fragments, phospho‐RNA‐seq opens up new possibilities for monitoring health and disease via transcriptome fragment profiling of plasma and potentially other biofluids.A modified RNA‐seq method reveals a large population of mRNA/lncRNA fragments in plasma that are missed by standard small RNA‐seq protocols including ones that are associated with disease.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/149518/1/embj2019101695_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/149518/2/embj2019101695-sup-0002-EVFigs.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/149518/3/embj2019101695.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/149518/4/embj2019101695-sup-0001-Appendix.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/149518/5/embj2019101695.reviewer_comments.pd

Spread of the fascioliasis endemic area assessed by seasonal follow-up of rDNA ITS-2 sequenced lymnaeid populations in Cajamarca, Peru

Fascioliasis is a worldwide emerging snail-borne zoonotic trematodiasis with a great spreading capacity linked to animal and human movements, climate change, and anthropogenic modifications of freshwater environments. South America is the continent with more human endemic areas caused by Fasciola hepatica, mainly in high altitude areas of Andean regions. The Peruvian Cajamarca area presents the highest human prevalences reported, only lower than those in the Bolivian Altiplano. Sequencing of the complete rDNA ITS-2 allowed for the specific and haplotype classification of lymnaeid snails collected in seasonal field surveys along a transect including 2007–3473 m altitudes. The species Galba truncatula (one haplotype preferentially in higher altitudes) and Pseudosuccinea columella (one haplotype in an isolated population), and the non-transmitting species Lymnaea schirazensis (two haplotypes mainly in lower altitudes) were found. Climatic seasonality proved to influence G. truncatula populations in temporarily dried habitats, whereas L. schirazensis appeared to be more climatologically independent due to its extreme amphibious ecology. Along the southeastern transect from Cajamarca city, G. truncatula and L. schirazensis shared the same site in 7 localities (46.7% of the water collections studied). The detection of G. truncatula in 11 new foci (73.3%), predominantly in northern localities closer to the city, demonstrate that the Cajamarca transmission risk area is markedly wider than previously considered. Lymnaea schirazensis progressively increases its presence when moving away from the city. Results highlight the usefulness of lymnaeid surveys to assess borders of the endemic area and inner distribution of transmission foci. Similar lymnaeid surveys are still in need to be performed in the wide northern and western zones of the Cajamarca city. The coexistence of more than one lymnaeid transmitting species, together with a morphologically indistinguishable non-transmitting species and livestock movements inside the area, conform a complex scenario which poses difficulties for the needed One Health control intervention.Ministerio de Economía y CompetitividadRevisión por pare

Laura ++ : a Dalitz plot fitter

The Dalitz plot analysis technique has become an increasingly important method in heavy flavour physics. The Laura fitter has been developed as a flexible tool that can be used for Dalitz plot analyses in different experimental environments. Explicitly designed for three-body decays of heavy-flavoured mesons to spinless final state particles, it is optimised in order to describe all possible resonant or nonresonant contributions, and to accommodate possible violation effects

Search for CP violation in D+→K−K+π+D^{+} \to K^{-}K^{+}\pi^{+} decays

A model-independent search for direct CP violation in the Cabibbo suppressed decay $D^+ \to K^- K^+\pi^+$ in a sample of approximately 370,000 decays is carried out. The data were collected by the LHCb experiment in 2010 and correspond to an integrated luminosity of 35 pb$^{-1}$. The normalized Dalitz plot distributions for $D^+$ and $D^-$ are compared using four different binning schemes that are sensitive to different manifestations of CP violation. No evidence for CP asymmetry is found.Comment: 13 pages, 8 figures, submitted to Phys. Rev.