The structure of causal sets

More often than not, recently popular structuralist interpretations of physical theories leave the central concept of a structure insufficiently precisified. The incipient causal sets approach to quantum gravity offers a paradigmatic case of a physical theory predestined to be interpreted in structuralist terms. It is shown how employing structuralism lends itself to a natural interpretation of the physical meaning of causal sets theory. Conversely, the conceptually exceptionally clear case of causal sets is used as a foil to illustrate how a mathematically informed rigorous conceptualization of structure serves to identify structures in physical theories. Furthermore, a number of technical issues infesting structuralist interpretations of physical theories such as difficulties with grounding the identity of the places of highly symmetrical physical structures in their relational profile and what may resolve these difficulties can be vividly illustrated with causal sets.Comment: 19 pages, 4 figure

Antarctic and Arctic populations of the ciliate Euplotes nobilii show common pheromone-mediated cell-cell signaling and cross-mating.

Wild-type strains of the protozoan ciliate Euplotes collected from different locations on the coasts of Antarctica, Tierra del Fuego and the Arctic were taxonomically identified as the morpho-species Euplotes nobilii, based on morphometric and phylogenetic analyses. Subsequent studies of their sexual interactions revealed that mating combinations of Antarctic and Arctic strains form stable pairs of conjugant cells. These conjugant pairs were isolated and shown to complete mutual gene exchange and cross-fertilization. The biological significance of this finding was further substantiated by demonstrating that close homology exists among the threedimensional structures determined by NMR of the water-borne signaling pheromones that are constitutively secreted into the extracellular space by these interbreeding strains, in which these molecules trigger the switch between the growth stage and the sexual stage of the life cycle. The fact that Antarctic and Arctic E. nobilii populations share the same gene pool and belong to the same biological species provides new support to the biogeographic model of global distribution of eukaryotic microorganisms, which had so far been based exclusively on studies of morphological and phylogenetic taxonomy

Whole-genome sequence-informed MALDI-TOF MS diagnostics reveal importance of Klebsiella oxytoca group in invasive infections: a retrospective clinical study

Background: Klebsiella spp. are opportunistic pathogens which can cause severe infections, are often multi-drug resistant and are a common cause of hospital-acquired infections. Multiple new Klebsiella species have recently been described, yet their clinical impact and antibiotic resistance profiles are largely unknown. We aimed to explore Klebsiella group- and species-specific clinical impact, antimicrobial resistance (AMR) and virulence. Methods: We analysed whole-genome sequence data of a diverse selection of Klebsiella spp. isolates and identified resistance and virulence factors. Using the genomes of 3594 Klebsiella isolates, we predicted the masses of 56 ribosomal subunit proteins and identified species-specific marker masses. We then re-analysed over 22,000 Matrix- Assisted Laser Desorption Ionization - Time Of Flight (MALDI-TOF) mass spectra routinely acquired at eight healthcare institutions in four countries looking for these species-specific markers. Analyses of clinical and microbiological endpoints from a subset of 957 patients with infections from Klebsiella species were performed using generalized linear mixed-effects models. Results: Our comparative genomic analysis shows group- and species-specific trends in accessory genome composition. With the identified species-specific marker masses, eight Klebsiella species can be distinguished using MALDI-TOF MS. We identified K. pneumoniae (71.2%; n = 12,523), K. quasipneumoniae (3.3%; n = 575), K. variicola (9.8%; n = 1717), “K. quasivariicola” (0.3%; n = 52), K. oxytoca (8.2%; n = 1445), K. michiganensis (4.8%; n = 836), K. grimontii (2.4%; n = 425) and K. huaxensis (0.1%; n = 12). Isolates belonging to the K. oxytoca group, which includes the species K. oxytoca, K. michiganensis and K. grimontii, were less often resistant to 4th-generation cephalosporins than isolates of the K. pneumoniae group, which includes the species K. pneumoniae, K. quasipneumoniae, K. variicola and “K. quasivariicola” (odds ratio = 0.17, p \u3c 0.001, 95% confidence interval [0.09,0.28]). Within the K. pneumoniae group, isolates identified as K. pneumoniae were more often resistant to 4th-generation cephalosporins than K. variicola isolates (odds ratio = 2.61, p = 0.003, 95% confidence interval [1.38,5.06]). K. oxytoca group isolates were found to be more likely associated with invasive infection to primary sterile sites than K. pneumoniae group isolates (odds ratio = 2.39, p = 0.0044, 95% confidence interval [1.05,5.53]). Conclusions: Currently misdiagnosed Klebsiella spp. can be distinguished using a ribosomal marker-based approach for MALDI-TOF MS. Klebsiella groups and species differed in AMR profiles, and in their association with invasive infection, highlighting the importance for species identification to enable effective treatment options

Free Will in a Quantum World?

In this paper, I argue that Conway and Kochen’s Free Will Theorem (1,2) to the conclusion that quantum mechanics and relativity entail freedom for the particles, does not change the situation in favor of a libertarian position as they would like. In fact, the theorem more or less implicitly assumes that people are free, and thus it begs the question. Moreover, it does not prove neither that if people are free, so are particles, nor that the property people possess when they are said to be free is the same as the one particles possess when they are claimed to be free. I then analyze the Free State Theorem (2), which generalizes the Free Will Theorem without the assumption that people are free, and I show that it does not prove anything about free will, since the notion of freedom for particles is either inconsistent, or it does not concern our common understanding of freedom. In both cases, the Free Will Theorem and the Free State Theorem do not provide any enlightenment on the constraints physics can pose on free will

Approaching the Problem of Time with a Combined Semiclassical-Records-Histories Scheme

I approach the Problem of Time and other foundations of Quantum Cosmology using a combined histories, timeless and semiclassical approach. This approach is along the lines pursued by Halliwell. It involves the timeless probabilities for dynamical trajectories entering regions of configuration space, which are computed within the semiclassical regime. Moreover, the objects that Halliwell uses in this approach commute with the Hamiltonian constraint, H. This approach has not hitherto been considered for models that also possess nontrivial linear constraints, Lin. This paper carries this out for some concrete relational particle models (RPM's). If there is also commutation with Lin - the Kuchar observables condition - the constructed objects are Dirac observables. Moreover, this paper shows that the problem of Kuchar observables is explicitly resolved for 1- and 2-d RPM's. Then as a first route to Halliwell's approach for nontrivial linear constraints that is also a construction of Dirac observables, I consider theories for which Kuchar observables are formally known, giving the relational triangle as an example. As a second route, I apply an indirect method that generalizes both group-averaging and Barbour's best matching. For conceptual clarity, my study involves the simpler case of Halliwell 2003 sharp-edged window function. I leave the elsewise-improved softened case of Halliwell 2009 for a subsequent Paper II. Finally, I provide comments on Halliwell's approach and how well it fares as regards the various facets of the Problem of Time and as an implementation of QM propositions.Comment: An improved version of the text, and with various further references. 25 pages, 4 figure

Reduction in benefits of total flux expansion on divertor detachment due to parallel flows

The Super-X divertor (SXD) is an alternative divertor configuration leveraging total flux expansion at the outer strike point (OSP). Key features for the attractiveness of the SXD are facilitated detachment access and control, as predicted by the extended 2-point model (2PM). However, parallel flows are not consistently included in the 2PM. In this work, the 2PM is refined to overcome this limitation: the role of total flux expansion on the pressure balance is made explicit, by including the effect of parallel flows. In consequence, the effect of total flux expansion on detachment access and control is weakened, compared to predictions of the 2PM. This new model partially explains discrepancies between the 2PM and experiments performed on TCV, in ohmic L-mode scenarios, where in core density ramps in lower single-null (SN) configuration, the impact of the OSP major radius Rt on the CIII emission front movement in the divertor outer leg - used as a proxy for the plasma temperature - is substantially weaker than 2PM predictions; and in OSP sweeps in lower and upper SN configurations, with a constant core density, the peak parallel particle flux density at the OSP is almost independent of Rt, while the 2PM predicts a linear dependence. Finally, analytical and numerical modelling of parallel flows in the divertor is presented, to support the argument. It is shown that an increase in total flux expansion can favour supersonic flows at the OSP. Parallel flows are also shown to be relevant by analysing SOLPS-ITER simulations of TCV

Sequential NMR assignments of labile protons in DNA using two-dimensional nuclear-Overhauser-enhancement spectroscopy with three jump-and-return pulse sequences

Two-dimensional nuclear Overhauser enhancement (NOESY) spectra of labile protons were recorded in H2O solutions of a protein and of a DNA duplex, using a modification of the standard NOESY experiment with all three 90 degree pulses replaced by jump-and-return sequences. For the protein as well as the DNA fragment the strategically important spectral regions could be recorded with good sensitivity and free of artifacts. Using this procedure, sequence-specific assignments were obtained for the imino protons, C2H of adenine, and C4NH2 of cytosine in a 23-base-pair DNA duplex which includes the 17-base-pair OR3 repressor binding site of bacteriophage lambda. Based on comparison with previously published results on the isolated OR3 binding site, these data were used for a study of chain termination effects on the chemical shifts of imino proton resonances of DNA duplexes

Nitrogen-seeded divertor detachment in TCV L-mode plasmas

Most of the detachment experiments done to date on the tokamak à configuration variable (TCV), both in standard and alternative divertor geometries, focused on L-mode integrated core density ramps. In view of extending these studies to high-power, high-confinement regimes, where impurity seeding will be necessary for detachment, the properties of nitrogen seeded L-mode detachment in TCV are assessed here with the extensive set of edge and divertor diagnostics and similarities and differences with integrated core density ramp detachment experiments are elucidated. It is found that in high current, reversed field plasmas, detachment at the outer target is achieved with N2-seeding and density ramps, with target heat flux reductions of up to 90%, while the inner target only detaches with seeding. The Scrape-Off Layer radiation fraction reaches values of 60%-80% and in all situations, a stable radiator can form around the X-point. The most striking difference between seeding and density ramp is the behavior of the upstream quantities. During the ramp, a broadening of the upstream density profile (density 'shoulder') occurs, concurrent with the outer target ion flux roll-over, while no such behavior occurs during nitrogen seeded detachment. Separatrix density, electron temperature and pressure also evolve strongly with increasing density, and are largely unaffected by the injection of nitrogen. Comparison of upstream and target pressures reveals that, in all cases, the outer target ion flux reduction coincides with the development of a parallel gradient of the total pressure. Common to all cases is also a reduction of energy confinement time with detachment, although this effect is weak for seeding at relatively high density. Studying the impact of the ∇B-drift direction in both nitrogen seeding and core density ramps reveals that drifts mainly affect the behavior at the inner strike point, highlighting the need to include them in edge transport simulations

The p12 Domain Is Unstructured in a Murine Leukemia Virus p12-CAN Gag Construct

The Gag polyproteins of gammaretroviruses contain a conserved p12 domain between MA and CA that plays critical roles in virus assembly, reverse transcription and nuclear integration. Here we show using nuclear magnetic resonance, that p12 is unstructured in a Moloney murine leukemia virus (MMLV) Gag fragment that includes the N-terminal domain of CA (p12-CAN). Furthermore, no long range interactions were observed between the domains, as has been previously predicted. Flexibility appears to be a common feature of Gag “late” domains required for virus release during budding. Residues near the N-terminus of CAN that form a β-hairpin in the mature CA protein are unfolded in p12-CAN, consistent with proposals that hairpin formation helps trigger capsid assembly