Energy distribution and equation of state of the early Universe: matching the end of inflation and the onset of radiation domination

We study the energy distribution and equation of state of the universe between the end of inflation and the onset of radiation domination (RD), considering observationally consistent single-field inflationary scenarios, with a potential 'flattening' at large field values, and a monomial shape $V(\phi) \propto |\phi|^p$ around the origin. As a proxy for (p)reheating, we include a quadratic interaction $g^2\phi^2X^2$ between the inflaton $\phi$ and a light scalar 'daughter' field $X$, with $g^2>0$. We capture the non-perturbative and non-linear nature of the system dynamics with lattice simulations, obtaining that: $i)$ the final energy transferred to $X$ depends only on $p$, not on $g^2$, ; $ii)$ the final transfer of energy is always negligible for $2 \leq p < 4$, and of order $\sim 50\%$ for $p \geq 4$; $iii)$ the system goes at late times to matter-domination for $p = 2$, and always to RD for $p > 2$. In the latter case we calculate the number of e-folds until RD, significantly reducing the uncertainty in the inflationary observables $n_s$ and $r$.Comment: 7 pages + references, 5 figures. It matches published versio

Characterizing the post-inflationary reheating history, Part II: Multiple interacting daughter fields

We characterize the post-inflationary dynamics of an inflaton $\phi$ coupled to multiple interacting daughter fields $X_n$ ($n=1,\dots N_d$) through quadratic-quadratic interactions $g_n^ 2\phi^2 X_n^2$. We assume a monomial inflaton potential $V(\phi) \propto |\phi|^p$ ($p \geq 2$) around the minimum. By simulating the system in 2+1-dimensional lattices, we study the post-inflationary evolution of the energy distribution and equation of state, from the end of inflation until a stationary regime is achieved. We show that in this scenario, the energy transferred to the daughter field sector can be larger than $50\%$, surpassing this way the upper bound found previously for single daughter field models. In particular, for $p \geq 4$ the energy at very late times is equally distributed between all fields, and only $100/(N_d + 1) \%$ of the energy remains in the inflaton. We also consider scenarios in which the daughter fields have scale-free interactions $\lambda_{nm} X_n^2 X_m^2$, including the case of quartic daughter field self-interactions (for $n=m$). We show that these interactions trigger a resonance process during the non-linear regime, which in the single daughter field case already allows to deplete more than $50\%$ of the energy from the inflaton for $p\geq 4$.Comment: 23 pages + appendix, 15 figure

CLEVER: Clique-Enumerating Variant Finder

Next-generation sequencing techniques have facilitated a large scale analysis of human genetic variation. Despite the advances in sequencing speeds, the computational discovery of structural variants is not yet standard. It is likely that many variants have remained undiscovered in most sequenced individuals. Here we present a novel internal segment size based approach, which organizes all, including also concordant reads into a read alignment graph where max-cliques represent maximal contradiction-free groups of alignments. A specifically engineered algorithm then enumerates all max-cliques and statistically evaluates them for their potential to reflect insertions or deletions (indels). For the first time in the literature, we compare a large range of state-of-the-art approaches using simulated Illumina reads from a fully annotated genome and present various relevant performance statistics. We achieve superior performance rates in particular on indels of sizes 20--100, which have been exposed as a current major challenge in the SV discovery literature and where prior insert size based approaches have limitations. In that size range, we outperform even split read aligners. We achieve good results also on real data where we make a substantial amount of correct predictions as the only tool, which complement the predictions of split-read aligners. CLEVER is open source (GPL) and available from http://clever-sv.googlecode.com.Comment: 30 pages, 8 figure

Surveillance quality correlates with surgical site infection rates in knee and hip arthroplasty and colorectal surgeries: A call to action to adjust reporting of SSI rates.

OBJECTIVE The incidence of surgical site infections may be underreported if the data are not routinely validated for accuracy. Our goal was to investigate the communicated SSI rate from a large network of Swiss hospitals compared with the results from on-site surveillance quality audits. DESIGN Retrospective cohort study. PATIENTS In total, 81,957 knee and hip prosthetic arthroplasties from 125 hospitals and 33,315 colorectal surgeries from 110 hospitals were included in the study. METHODS Hospitals had at least 2 external audits to assess the surveillance quality. The 50-point standardized score per audit summarizes quantitative and qualitative information from both structured interviews and a random selection of patient records. We calculated the mean National Healthcare Safety Network (NHSN) risk index adjusted infection rates in both surgery groups. RESULTS The median NHSN adjusted infection rate per hospital was 1.0% (interquartile range [IQR], 0.6%-1.5%) with median audit score of 37 (IQR, 33-42) for knee and hip arthroplasty, and 12.7% (IQR, 9.0%-16.6%), with median audit score 38 (IQR, 35-42) for colorectal surgeries. We observed a wide range of SSI rates and surveillance quality, with discernible clustering for public and private hospitals, and both lower infection rates and audit scores for private hospitals. Infection rates increased with audit scores for knee and hip arthroplasty (P value for the slope = .002), and this was also the case for planned (P = .002), and unplanned (P = .02) colorectal surgeries. CONCLUSIONS Surveillance systems without routine evaluation of validity may underestimate the true incidence of SSIs. Audit quality should be taken into account when interpreting SSI rates, perhaps by adjusting infection rates for those hospitals with lower audit scores

Development of human antibody fragments using antibody phage display for the detection and diagnosis of Venezuelan equine encephalitis virus (VEEV)

<p>Abstract</p> <p>Background</p> <p>Venezuelan equine encephalitis virus (VEEV) belongs to the Alphavirus group. Several species of this family are also pathogenic to humans and are recognized as potential agents of biological warfare and terrorism. The objective of this work was the generation of recombinant antibodies for the detection of VEEV after a potential bioterrorism assault or an natural outbreak of VEEV.</p> <p>Results</p> <p>In this work, human anti-VEEV single chain Fragments variable (scFv) were isolated for the first time from a human naïve antibody gene library using optimized selection processes. In total eleven different scFvs were identified and their immunological specificity was assessed. The specific detection of the VEEV strains TC83, H12/93 and 230 by the selected antibody fragments was proved. Active as well as formalin inactivated virus particles were recognized by the selected antibody fragments which could be also used for Western blot analysis of VEEV proteins and immunohistochemistry of VEEV infected cells. The anti-VEEV scFv phage clones did not show any cross-reactivity with Alphavirus species of the Western equine encephalitis virus (WEEV) and Eastern equine encephalitis virus (EEEV) antigenic complex, nor did they react with Chikungunya virus (CHIKV), if they were used as detection reagent.</p> <p>Conclusion</p> <p>For the first time, this study describes the selection of antibodies against a human pathogenic virus from a human naïve scFv antibody gene library using complete, active virus particles as antigen. The broad and sensitive applicability of scFv-presenting phage for the immunological detection and diagnosis of Alphavirus species was demonstrated. The selected antibody fragments will improve the fast identification of VEEV in case of a biological warfare or terroristic attack or a natural outbreak.</p

Assessment of Subsampling Schemes for Compressive Nano-FTIR Imaging

Nano-Fourier transform infrared (FTIR) imaging is a powerful scanning-based technique at nanometer spatial resolution that combines FTIR spectroscopy and scattering-type scanning near-field optical microscopy (s-SNOM). Recording large spatial areas using nano-FTIR is, however, limited, because its sequential data acquisition entails long measurement times. Compressed sensing and low-rank matrix reconstruction are mathematical techniques that can reduce the number of these measurements significantly by requiring only a small fraction of randomly chosen measurements. However, choosing this small set of measurements in a random fashion poses practical challenges for scanning procedures and does not save as much time as desired. We, therefore, consider different subsampling schemes of practical relevance that ensure rapid data acquisition, much faster than random subsampling, in combination with a low-rank matrix reconstruction procedure. It is demonstrated that the quality of the results for almost all subsampling schemes considered, namely, original Lissajous, triangle Lissajous, and random reflection subsampling, is similar to that achieved for random subsampling. This implies that nano-FTIR imaging can be significantly extended to also cover samples extended over large areas while maintaining its high spatial resolution

Genome sequence analysis with MonetDB - A case study on Ebola virus diversity

Next-generation sequencing (NGS) technology has led the life sciences into the big data era. Today, sequencing genomes takes little time and cost, but yields terabytes of data to be stored and analyzed. Biologists are often exposed to excessively time consuming and error-prone data management and analysis hurdles. In this paper, we propose a database management system (DBMS) based approach to accelerate and substantially simplify genome sequence analysis. We have extended MonetDB, an open-source column-based DBMS, with a BAM module, which enables \textit{easy}, \textit{flexible}, and \textit{rapid} management and analysis of sequence alignment data stored as Sequence Alignment/Map \\(SAM/BAM) files. We describe the main features of MonetDB/BAM using a case study on Ebola virus \\genomes

Genome sequence analysis with MonetDB: a case study on Ebola virus diversity

Next-generation sequencing (NGS) technology has led the life sciences into the big data era. Today, sequencing genomes takes little time and cost, but results in terabytes of data to be stored and analysed. Biologists are often exposed to excessively time consuming and error-prone data management and analysis hurdles. In this paper, we propose a database management system (DBMS) based approach to accelerate and substantially simplify genome sequence analysis. We have extended MonetDB, an open-source column-based DBMS, with a BAM module, which enables easy, flexible, and rapid management and analysis of sequence alignment data stored as Sequence Alignment/Map (SAM/BAM) files. We describe the main features of MonetDB/BAM using a case study on Ebola virus genomes

Earthquakes in Switzerland and surrounding regions during 2005

Abstract.: This report of the Swiss Seismological Service summarizes the seismic activity in Switzerland and surrounding regions during 2005. During this period, 611 earthquakes, 96 quarry blasts and two landslides were detected and located in the region under consideration. With 19 events with ML ≥ 2.5, the seismic activity in the year 2005 was below the average over the last 30 years. However, with the earthquake of Vallorcine (ML 4.9) located just across the border to France, between Martigny and Chamonix, and the two earthquakes of Rumisberg and Brugg (ML 4.1), located in the lower crust beneath the Jura Mountains of northern Switzerland, the year 2005 saw three events that produced shaking of intensity IV and V (EMS98). Of the 611 recorded earthquakes more than 110 events are aftershocks of the Vallorcine quake. Moreover, 51 events occurred within two days at the end of August during a period of very intense rainfalls. The epicenters of these events were concentrated in several clusters distributed over a wide area of central Switzerland, and their focal depths were shallow, so that they most likely constitute a case of precipitationinduced seismicit