Effects of memory on the shapes of simple outbreak trees

Genomic tools, including phylogenetic trees derived from sequence data, are increasingly used to understand outbreaks of infectious diseases. One challenge is to link phylogenetic trees to patterns of transmission. Particularly in bacteria that cause chronic infections, this inference is affected by variable infectious periods and infectivity over time. It is known that non-exponential infectious periods can have substantial effects on pathogens’ transmission dynamics. Here we ask how this non-Markovian nature of an outbreak process affects the branching trees describing that process, with particular focus on tree shapes. We simulate Crump-Mode-Jagers branching processes and compare different patterns of infectivity over time. We find that memory (non-Markovian-ness) in the process can have a pronounced effect on the shapes of the outbreak’s branching pattern. However, memory also has a pronounced effect on the sizes of the trees, even when the duration of the simulation is fixed. When the sizes of the trees are constrained to a constant value, memory in our processes has little direct effect on tree shapes, but can bias inference of the birth rate from trees. We compare simulated branching trees to phylogenetic trees from an outbreak of tuberculosis in Canada, and discuss the relevance of memory to this dataset

Future observational and modelling needs identified on the basis of the existing shelf data

NOWESP has compiled a vast quantity of existing data from the North-West European Shelf. Such a focused task is without precedence. It is now highly recommended that one, or a few national and international data centres or agencies should be chosen and properly supported by the EU, where all available observational data, including the NOWESP data, are collected, stored, regularly updated by the providers of the data, and made available to the researchers. International agreement must be reached on the quality control procedures and quality standards for data to be stored in these data bases. Proper arrangements should be made to preserve the economic value of the data for their "owners" without compromising use of the data by researchers or duplicating data collecting efforts. The continental shelf data needed are concentration fields of temperature, salinity, nutrients, suspended matter and chlorophyll, which can be called "climatological" fields. For this purpose at least one monthly survey on the whole European shelf is needed at least during five years, with a proper spatial resolution e.g. 1 degree by 1 degree, and at least in those areas where climatological data are now totally lacking. From the modelling point of view an alternative would be the availability of data from sufficiently representative fixed stations on the shelf, with weekly sampling for several years

Annual variability in the seasonal cycles of chlorophyll, nutrients and zooplankton on the North-West European continental shelf

Seasonal cycles of salinity, nutrients, chlorophyll and zooplankton at 8 locations on the West-European shelf were analysed with respect to their timing and magnitude in the period 1980-1984. A late spring bloom with low chlorophyll values (2-4 mg.m-³) is observed in the Irish Sea, off the Scottish east coast and the Channel entrance. An early spring bloom and relatively high chlorophyll values (7-12 mg.m-³) are found in the southern Bight and the Skagerrak, whereas a late spring bloom with high chlorophyll concentrations (24 mg.m-³) is found along the Dutch and Belgian coast. In contrast to the other regions, the peak of the phytoplankton cycle in the German Bight (Helgoland) occurs in the summer period instead of the spring period. The peak in the yearly abundance of copepods shifts from May-June in the south to July-August in the north of the shelf. In the Irish Sea and the Channel entrance two seasonal copepods peaks are observed. The January nitrate values in Irish Sea, the southern Bight and the Skagerrak are about 20 % higher than those in the Atlantic input signal in the Channel entrance and east off Scotland. The January DIP values in these regions are comparable to those of the input signal, but the Irish Sea forms an exception here the level is increased by 10-20%. If compared with the Atlantic input signal the January values for nitrate and DIP at the Dutch and Belgium coast are about 10 and 4, and in the German Bight (Helgoland) 4 and 3 times higher, respectively. At most sites changes in the seasonal cycles of chorophyll coincide with changes in nutrient concentrations, wheras the maximum level of the seasonal signal is related to the nutrient levels

Implications of Lorentz covariance for the guidance equation in two-slit quantum interference

It is known that Lorentz covariance fixes uniquely the current and the associated guidance law in the trajectory interpretation of quantum mechanics for spin particles. In the non-relativistic domain this implies a guidance law for the electron which differs by an additional spin-dependent term from that originally proposed by de Broglie and Bohm. In this paper we explore some of the implications of the modified guidance law. We bring out a property of mutual dependence in the particle coordinates that arises in product states, and show that the quantum potential has scalar and vector components which implies the particle is subject to a Lorentz-like force. The conditions for the classical limit and the limit of negligible spin are given, and the empirical sufficiency of the model is demonstrated. We then present a series of calculations of the trajectories based on two-dimensional Gaussian wave packets which illustrate how the additional spin-dependent term plays a significant role in structuring both the individual trajectories and the ensemble. The single packet corresponds to quantum inertial motion. The distinct features encountered when the wavefunction is a product or a superposition are explored, and the trajectories that model the two-slit experiment are given. The latter paths exhibit several new characteristics compared with the original de Broglie-Bohm ones, such as crossing of the axis of symmetry.Comment: 27 pages including 6 pages of figure

Comment on "On the subtleties of searching for dark matter with liquid xenon detectors"

In a recent manuscript (arXiv:1208.5046) Peter Sorensen claims that XENON100's upper limits on spin-independent WIMP-nucleon cross sections for WIMP masses below 10 GeV "may be understated by one order of magnitude or more". Having performed a similar, though more detailed analysis prior to the submission of our new result (arXiv:1207.5988), we do not confirm these findings. We point out the rationale for not considering the described effect in our final analysis and list several potential problems with his study.Comment: 3 pages, no figure

Removing krypton from xenon by cryogenic distillation to the ppq level

The XENON1T experiment aims for the direct detection of dark matter in a cryostat filled with 3.3 tons of liquid xenon. In order to achieve the desired sensitivity, the background induced by radioactive decays inside the detector has to be sufficiently low. One major contributor is the $\beta$-emitter $^{85}$Kr which is an intrinsic contamination of the xenon. For the XENON1T experiment a concentration of natural krypton in xenon $\rm{^{nat}}$Kr/Xe < 200 ppq (parts per quadrillion, 1 ppq = 10$^{-15}$ mol/mol) is required. In this work, the design of a novel cryogenic distillation column using the common McCabe-Thiele approach is described. The system demonstrated a krypton reduction factor of 6.4$\cdot$10$^5$ with thermodynamic stability at process speeds above 3 kg/h. The resulting concentration of $\rm{^{nat}}$Kr/Xe < 26 ppq is the lowest ever achieved, almost one order of magnitude below the requirements for XENON1T and even sufficient for future dark matter experiments using liquid xenon, such as XENONnT and DARWIN

Intratympanic gentamicin treatment for Ménière's disease: A randomized, double-blind, placebo-controlled trial on dose efficacy - results of a prematurely ended study

Background: Gentamicin is used as a therapeutic agent for Ménière's disease because of its vestibulotoxicity causing chemo-ablation of the vestibular sensory epithelia. Its use has increased in recent years. However, there is still no consensus about the dose regimen of gentamicin in the treatment of Ménière's disease. In this study two different dose regimen treatment protocols are compared in a placebo controlled study design. The primary objective is to quantify the treatment effect on dizziness, the secondary objective is hearing evaluation.Methods: We performed a randomized, double-blind, placebo-controlled study in adults with unilateral Ménière's disease according to the AAO-HNS guidelines resistant to conservative medication. Three groups received four injections, administered weekly (four intratympanic injections with 40 mg/mL gentamicin solution, two injections gentamicin solution and two injections of placebo in random order, or four injections with placebo). Outcome measures were the score on the Dizziness Handicap Inventory and pure tone audiometry (PTA). Intended follow-up was 2 years.Results: During follow-up one patient exceeded the accepted amount of hearing loss. Further, enrollment was very slow (until 12 months between two patients) and new insights showed an apparent benefit of intratympanic gentamicin treatment (ITG). Therefore we performed an unscheduled interim analysis which showed that PTA threshold shifts reached the stopping criteria in two more patients. Because of this, this study was ended. Of the three patients with the significant PTA threshold shift two were enrolled in the gentamicin group.Conclusion: No conclusions can be drawn concerning doses regimens. Now that new publications have shown that ITG treatment can be an effective and safe treatment, a placebo-controlled randomized controlled trial may not pass the ethical committee because of these recent reports in literature. Still, a dose regimen study (without placebo) on ITG treatment needs to be performed.Trial registration: This trial was registered in The University Medical Center Utrecht/ Gelre hospital Apeldoorn. Protocol ID: 07/343, EudraCT number 2006-005913-37

Search for Extra Dimensions in Boson and Fermion Pair Production in e+e- Interactions at LEP

Extra spatial dimensions are proposed by recent theories that postulate the scale of gravity to be of the same order as the electroweak scale. A sizeable interaction between gravitons and Standard Model particles is then predicted. Effects of these new interactions in boson and fermion pair production are searched for in the data sample collected at centre-of-mass energies above the Z pole by the L3 detector at LEP. In addition, the direct production of a graviton associated with a Z boson is investigated. No statistically significant hints for the existence of these effects are found and lower limits in excess of 1 TeV are derived on the scale of this new theory of gravity