Capturing optically important constituents and properties in a marine biogeochemical and ecosystem model

We present a numerical model of the ocean that couples a three-stream radiative transfer component with a marine biogeochemical–ecosystem component in a dynamic three-dimensional physical framework. The radiative transfer component resolves the penetration of spectral irradiance as it is absorbed and scattered within the water column. We explicitly include the effect of several optically important water constituents (different phytoplankton functional types; detrital particles; and coloured dissolved organic matter, CDOM). The model is evaluated against in situ-observed and satellite-derived products. In particular we compare to concurrently measured biogeochemical, ecosystem, and optical data along a meridional transect of the Atlantic Ocean. The simulation captures the patterns and magnitudes of these data, and estimates surface upwelling irradiance analogous to that observed by ocean colour satellite instruments. We find that incorporating the different optically important constituents explicitly and including spectral irradiance was crucial to capture the variability in the depth of the subsurface chlorophyll a (Chl a) maximum. We conduct a series of sensitivity experiments to demonstrate, globally, the relative importance of each of the water constituents, as well as the crucial feedbacks between the light field, the relative fitness of phytoplankton types, and the biogeochemistry of the ocean. CDOM has proportionally more importance at attenuating light at short wavelengths and in more productive waters, phytoplankton absorption is relatively more important at the subsurface Chl a maximum, and water molecules have the greatest contribution when concentrations of other constituents are low, such as in the oligotrophic gyres. Scattering had less effect on attenuation, but since it is important for the amount and type of upwelling irradiance, it is crucial for setting sea surface reflectance. Strikingly, sensitivity experiments in which absorption by any of the optical constituents was increased led to a decrease in the size of the oligotrophic regions of the subtropical gyres: lateral nutrient supplies were enhanced as a result of decreasing high-latitude productivity. This new model that captures bio-optical feedbacks will be important for improving our understanding of the role of light and optical constituents on ocean biogeochemistry, especially in a changing environment. Further, resolving surface upwelling irradiance will make it easier to connect to satellite-derived products in the future

Time and Time Functions in Parametrized Non-Relativistic Quantum Mechanics

The ``evolving constants'' method of defining the quantum dynamics of time-reparametrization-invariant theories is investigated for a particular implementation of parametrized non-relativistic quantum mechanics (PNRQM). The wide range of time functions that are available to define evolving constants raises issues of interpretation, consistency, and the degree to which the resulting quantum theory coincides with, or generalizes, the usual non-relativistic theory. The allowed time functions must be restricted for the predictions of PNRQM to coincide with those of usual quantum theory. They must be restricted to have a notion of quantum evolution in a time-parameter connected to spacetime geometry. They must be restricted to prevent the theory from making inconsistent predictions for the probabilities of histories. Suitable restrictions can be introduced in PNRQM but these seem unlikely to apply to a reparametrization invariant theory like general relativity.Comment: 18pages, 1postscript figure in separate file, uses REVTEX 3.

Contrasting Controls on Microzooplankton Grazing and Viral Infection of Microbial Prey

The encounter and capture of bacteria and phytoplankton by microbial predators and parasites is fundamental to marine ecosystem organization and activity. Here, we combined classic biophysical models with published laboratory measurements to infer functional traits, including encounter kernel and capture efficiency, for a wide range of marine viruses and microzooplankton grazers. Despite virus particles being orders of magnitude smaller than microzooplankton grazers, virus encounter kernels and adsorption rates were in many cases comparable in magnitude to grazer encounter kernel and clearance, pointing to Brownian motion as a highly effective method of transport for viruses. Inferred virus adsorption efficiency covered many orders of magnitude, but the median virus adsorption efficiency was between 5 and 25% depending on the assumed host swimming speed. Uncertainty on predator detection area and swimming speed prevented robust inference of grazer capture efficiency, but sensitivity analysis was used to identify bounds on unconstrained processes. These results provide a common functional trait framework for understanding marine host-virus and predator-prey interactions, and highlight the value of theory for interpreting measured life-history traits

Mapping and Functional Characterisation of a CTCF-Dependent Insulator Element at the 3′ Border of the Murine Scl Transcriptional Domain

The Scl gene encodes a transcription factor essential for haematopoietic development. Scl transcription is regulated by a panel of cis-elements spread over 55 kb with the most distal 3′ element being located downstream of the neighbouring gene Map17, which is co-regulated with Scl in haematopoietic cells. The Scl/Map17 domain is flanked upstream by the ubiquitously expressed Sil gene and downstream by a cluster of Cyp genes active in liver, but the mechanisms responsible for delineating the domain boundaries remain unclear. Here we report identification of a DNaseI hypersensitive site at the 3′ end of the Scl/Map17 domain and 45 kb downstream of the Scl transcription start site. This element is located at the boundary of active and inactive chromatin, does not function as a classical tissue-specific enhancer, binds CTCF and is both necessary and sufficient for insulator function in haematopoietic cells in vitro. Moreover, in a transgenic reporter assay, tissue-specific expression of the Scl promoter in brain was increased by incorporation of 350 bp flanking fragments from the +45 element. Our data suggests that the +45 region functions as a boundary element that separates the Scl/Map17 and Cyp transcriptional domains, and raise the possibility that this element may be useful for improving tissue-specific expression of transgenic constructs

Contrasting Controls on Microzooplankton Grazing and Viral Infection of Microbial Prey

The encounter and capture of bacteria and phytoplankton by microbial predators and parasites is fundamental to marine ecosystem organization and activity. Here, we combined classic biophysical models with published laboratory measurements to infer functional traits, including encounter kernel and capture efficiency, for a wide range of marine viruses and microzooplankton grazers. Despite virus particles being orders of magnitude smaller than microzooplankton grazers, virus encounter kernels and adsorption rates were in many cases comparable in magnitude to grazer encounter kernel and clearance, pointing to Brownian motion as a highly effective method of transport for viruses. Inferred virus adsorption efficiency covered many orders of magnitude, but the median virus adsorption efficiency was between 5 and 25% depending on the assumed host swimming speed. Uncertainty on predator detection area and swimming speed prevented robust inference of grazer capture efficiency, but sensitivity analysis was used to identify bounds on unconstrained processes. These results provide a common functional trait framework for understanding marine host-virus and predator-prey interactions, and highlight the value of theory for interpreting measured life-history traits

Quark mixing from softly broken symmetries

Quark flavor mixing may originate in the soft breaking of horizontal symmetries. Those symmetries, which in the simplest case are three family U(1) groups, are obeyed only by the dimension-4 Yukawa couplings and lead, when unbroken, to the absence of mixing. Their breaking may arise from the dimension-3 mass terms of SU(2)-singlet vector-like quarks. Those gauge-singlet mass terms break the horizontal symmetries at a scale much higher than the Fermi scale, yet softly, leading to quark mixing while the quark masses remain unsuppressed.Comment: 9 pages, plain Latex, no figure

T-cell subpopulations αβ and γδ in cord blood of very preterm infants : The influence of intrauterine infection

Open Access: This article is distributed under the terms of the Creative Commons Attribution License which permits any use, distribution, and reproduction in any medium, provided the original author(s) and the source are creditedPreterm infants are very susceptible to infections. Immune response mechanisms in this group of patients and factors that influence cord blood mononuclear cell populations remain poorly understood and are considered insufficient. However, competent immune functions of the cord blood mononuclear cells are also described. The aim of this work was to evaluate the T-cell population (CD3+) with its subpopulations bearing T-cell receptor (TCR) αβ or TCR γδ in the cord blood of preterm infants born before 32 weeks of gestation by mothers with or without an intrauterine infection. Being a pilot study, it also aimed at feasibility check and assessment of an expected effect size. The cord blood samples of 46 infants age were subjected to direct immunofluorescent staining with monoclonal antibodies and then analyzed by flow cytometry. The percentage of CD3+ cells in neonates born by mothers with diagnosis of intrauterine infection was significantly lower than in neonates born by mothers without infection (p = 0.005; Mann-Whitney U test). The number of cells did not differ between groups. Infection present in the mother did not have an influence on the TCR αβ or TCR γδ subpopulations. Our study contributes to a better understanding of preterm infants' immune mechanisms, and sets the stage for further investigations.Peer reviewedFinal Published versio

Germ line mutations in shelterin complex genes are associated with familial chronic lymphocytic leukemia.

Chronic lymphocytic leukemia (CLL) can be familial; however, thus far no rare germ line disruptive alleles for CLL have been identified. We performed whole-exome sequencing of 66 CLL families, identifying 4 families where loss-of-function mutations in protection of telomeres 1 (POT1) co-segregated with CLL. The p.Tyr36Cys mutation is predicted to disrupt the interaction between POT1 and the telomeric overhang. The c.1164-1G>A splice-site, p.Gln358SerfsTer13 frameshift, and p.Gln376Arg missense mutations are likely to impact the interaction between POT1 and adrenocortical dysplasia homolog (ACD), which is a part of the telomere-capping shelterin complex. We also identified mutations in ACD (c.752-2A>C) and another shelterin component, telomeric repeat binding factor 2, interacting protein (p.Ala104Pro and p.Arg133Gln), in 3 CLL families. In a complementary analysis of 1083 cases and 5854 controls, the POT1 p.Gln376Arg variant, which has a global minor allele frequency of 0.0005, conferred a 3.61-fold increased risk of CLL (P = .009). This study further highlights telomere dysregulation as a key process in CLL development

Cinema-going trajectories in the digital age

The activity of cinema-going constantly evolves and gradually integrates the use of digital data and platforms to become more engaging for the audiences. Combining methods from the fields of Human Computer Interaction and Film Studies, we conducted two workshops seeking to understand cinema audiences’ digital practices and explore how the contemporary cinema-going experience is shaped in the digital age. Our findings suggest that going to the movies constitutes a trajectory during which cinemagoers interact with multiple digital platforms. At the same time, depending on their choices, they construct unique digital identities that represent a set of online behaviours and rituals that cinemagoers adopt before, while and after cinema-going. To inform the design of new, engaging cinemagoing experiences, this research establishes a preliminary map of contemporary cinema-going including digital data and platforms. We then discuss how audiences perceive the potential improvement of the experience and how that would lead to the construction of digital identities