Impact of host DNA and sequencing depth on the taxonomic resolution of whole metagenome sequencing for microbiome analysis

The amount of host DNA poses a major challenge to metagenome analysis. However, there is no guidance on the levels of host DNA, nor on the depth of sequencing needed to acquire meaningful information from whole metagenome sequencing (WMS). Here, we evaluated the impact of a wide range of amounts of host DNA and sequencing depths on microbiome taxonomic profiling using WMS. Synthetic samples with increasing levels of host DNA were created by spiking DNA of a mock bacterial community, with DNA from a mouse-derived cell line. Taxonomic analysis revealed that increasing proportions of host DNA led to decreased sensitivity in detecting very low and low abundant species. Reduction of sequencing depth had major impact on the sensitivity of WMS for profiling samples with 90% host DNA, increasing the number of undetected species. Finally, analysis of simulated datasets with fixed depth of 10 million reads confirmed that microbiome profiling becomes more inaccurate as the level of host DNA increases in a sample. In conclusion, samples with high amounts of host DNA coupled with reduced sequencing depths, decrease WMS coverage for characterization of the microbiome. This study highlights the importance of carefully considering these aspects in the design of WMS experiments to maximize microbiome analyses.This work was supported by European Regional Development Funds (ERDF) funds through the COMPETE 2020 – Operacional Programme for Competitiveness and Internationalization (POCI), Portugal 2020, and by FCT – Fundação para a Ciência e a Tecnologia (POCI-01-0145-FEDER-032532). JP-M and IP-R have fellowships from FCT (PD/BD/114014/2015 and SFRH/BD/110803/2015, respectively) through Programa Operacional Capital Humano (POCH) and the European Social Fund. JP-M’s have fellowship from the framework of FCT’s Ph.D. Program Biotech Health (Ref. PD/0016/2012)

Tax evasion and exchange equity: a reference-dependent approach

The standard portfolio model of tax evasion with a public good produces the perverse conclusion that when taxpayers perceive the public good to be under-/overprovided, an increase in the tax rate increases/decreases evasion. The author treats taxpayers as thinking in terms of gains and losses relative to an endogenous reference level, which reflects perceived exchange equity between the value of taxes paid and the value of public goods supplied. With these alternative behavioral assumptions, the author overturns the aforementioned result in a direction consistent with the empirical evidence. The author also finds a role for relative income in determining individual responses to a change in the marginal rate of tax

Non-Fermi liquid normal state of the Heavy Fermion superconductor UBe13

Non-Fermi liquid (NFL) behavior in the normal state of the heavy-fermion superconductor UBe13 is studied by means of low-temperature measurements of the specific heat, C, and electrical resistivity, \rho, on a high-quality single crystal in magnetic fields up to 15.5 T. At B=0, unconventional superconductivity forms at Tc=0.9 K out of an incoherent state, characterized by a large and strongly temperature dependent \rho(T). In the magnetic field interval 4 T \leq B \leq 10 T, \rho(T) follows a T^3/2 behavior for Tc(B)\leq T \leq 1 K, while \rho is proportional to T at higher temperatures. Corresponding Non-Fermi liquid behavior is observed in C/T as well and hints at a nearby antiferromagnetic (AF) quantum critical point (QCP) covered by the superconducting state. We speculate that the suppression of short-range AF correlations observed by thermal expansion and specific heat measurements below T_L \simeq 0.7 K (B=0) yields a field-induced QCP, T_L \to 0, at B=4.5 T.Comment: Presented at the M2S-2003 conference in Rio / Brazi

An outbreak of Clostridium difficile infections due to new PCR ribotype 826

__Objectives:__ To investigate an unusual outbreak of five patients with a total of eight episodes of a Clostridium difficile infection on a gastrointestinal surgical ward of a Dutch tertiary-care, university-affiliated hospital. __Methods:__ Clinical case investigations and laboratory analyses were performed. Laboratory analyses included PCR ribotyping, multiple-locus variable-number tandem repeat analysis typing, toxin typing, antimicrobial susceptibility testing and whole genome sequencing. __Results:__ The outbreak was associated with recurrent and severe disease in two of five patients. All episodes were due to a unique ribotype that was not recognized in the collection of an international network of reference laboratories and was assigned PCR ribotype 826. PCR ribotype 826 is a toxin A-, toxin B- and binary toxin-positive ribotype which according to molecular typing belongs to clade 5 and resembles the so-called hypervirulent ribotype 078. The presence of a clonal outbreak was confirmed by whole genome sequencing, yet the source of this newly identified ribotype remained unclear. __Conclusions:__ This newly identified C. difficile PCR ribotype 826 is part of clade 5 and might also have increased virulence. The recognition of this outbreak highlights the need for ongoing C. difficile infection surveillance to monitor new circulating ribotypes with assumed increased virulence

Plasma lensing of a laser wakefield accelerated electron bunch

We report on the first all-optical demonstration of plasma lensing using laser wakefield accelerated elec-trons in a two-stage setup. The LWFA electron bunch was focused by a second plasma stage without any ex-ternal fields applied..

DETECTING ANTARCTIC SEALS AND FLYING SEABIRDS BY UAV

In recent years Unmanned Aerial Vehicles (UAVs) became a fast-developing technology with manifold fields of application. In the field of wildlife biology, it offers the opportunity to quantify populations, to map the spatial distribution of species and to observe the behavior of animals with no or low disturbance. Moreover, UAV based mapping allows to obtain data from sites which are hardly or not accessible and to cover much larger areas than by traditional ground based methods. The advantages of UAV based mapping are of particular relevance under the harsh conditions of Antarctic fieldwork. Whether certain species qualify for UAV based monitoring depends on their detectability from the distance and the distinctiveness of their characteristics in comparison to other species, which has not been studied for Antarctic species in detail so far. This study aims to evaluate how and under which conditions, particularly flight height, Antarctic flying seabird and seal species are detectable in aerial imagery. A trial was conducted comparing the detection rate of different observers for several Antarctic species in aerial images of different ground sample distances. Descriptions of individual appearance as well as body size dimensions are delivered for all species. For most of the investigated species, monitoring proves to be possible from practical flight heights, while others are still very hard to detect even in low altitudes. A concluding table is given aiming to provide a guide for future surveys on which flight altitudes to chose and how to identify focal study objects

The FLASHForward Facility at DESY

The FLASHForward project at DESY is a pioneering plasma-wakefield acceleration experiment that aims to produce, in a few centimetres of ionised hydrogen, beams with energy of order GeV that are of quality sufficient to be used in a free-electron laser. The plasma wave will be driven by high-current density electron beams from the FLASH linear accelerator and will explore both external and internal witness-beam injection techniques. The plasma is created by ionising a gas in a gas cell with a multi-TW laser system, which can also be used to provide optical diagnostics of the plasma and electron beams due to the <30 fs synchronisation between the laser and the driving electron beam. The operation parameters of the experiment are discussed, as well as the scientific program.Comment: 19 pages, 9 figure

29-Si NMR and Hidden Order in URu2Si2

We present new 29-Si NMR spectra in URu2Si2 for varying temperature T, and external field H. On lowering T, the systematics of the low-field lineshape and width reveal an extra component (lambda) to the linewidth below T_N ~ 17 K not observed previously. We find that lambda is magnetic-field independent and dominates the low-field lineshape for all orientations of H with respect to the tetragonal c axis. The behavior of lambda indicates a direct relationship between the 29-Si spin and the transition at T_N, but it is inconsistent with a coupling of the nuclei to static antiferromagnetic order/disorder of the U-spin magnetization. This leads us to conjecture that lambda is due to a coupling of 29-Si to the system's hidden-order parameter. A possible coupling mechanism involving charge degrees of freedom and indirect nuclear spin/spin interactions is proposed. We also propose further experiments to test for the existence of this coupling mechanism.Comment: 4 pages, 4 figures, submitted to PR

Demonstration of passive plasma lensing of a laser wakefield accelerated electron bunch

We report on the first demonstration of passive all-optical plasma lensing using a two-stage setup. An intense femtosecond laser accelerates electrons in a laser wakefield accelerator (LWFA) to 100 MeV over millimeter length scales. By adding a second gas target behind the initial LWFA stage we introduce a robust and independently tunable plasma lens. We observe a density dependent reduction of the LWFA electron beam divergence from an initial value of 2.3 mrad, down to 1.4 mrad (rms), when the plasma lens is in operation. Such a plasma lens provides a simple and compact approach for divergence reduction well matched to the mm-scale length of the LWFA accelerator. The focusing forces are provided solely by the plasma and driven by the bunch itself only, making this a highly useful and conceptually new approach to electron beam focusing. Possible applications of this lens are not limited to laser plasma accelerators. Since no active driver is needed the passive plasma lens is also suited for high repetition rate focusing of electron bunches. Its understanding is also required for modeling the evolution of the driving particle bunch in particle driven wake field acceleration