Constraints on Automorphic Forms of Higher Derivative Terms from Compactification

By dimensionally reducing the higher derivative corrections of ten-dimensional IIB theory on a torus we deduce constraints on the E_{n+1} automorphic forms that occur in d=10-n dimensions. In particular we argue that these automorphic forms involve the representation of E_{n+1} with fundamental weight \lambda^{n+1}, which is also the representation to which the string charges in d dimensions belong. We also consider a similar calculation for the reduction of higher derivative terms in eleven-dimensional M-theory.Comment: Minor corrections, to appear in JHE

Orientifolds and the Refined Topological String

We study refined topological string theory in the presence of orientifolds by counting second-quantized BPS states in M-theory. This leads us to propose a new integrality condition for both refined and unrefined topological strings when orientifolds are present. We define the SO(2N) refined Chern-Simons theory which computes refined open string amplitudes for branes wrapping Seifert three-manifolds. We use the SO(2N) refined Chern-Simons theory to compute new invariants of torus knots that generalize the Kauffman polynomials. At large N, the SO(2N) refined Chern-Simons theory on the three-sphere is dual to refined topological strings on an orientifold of the resolved conifold, generalizing the Gopakumar-Sinha-Vafa duality. Finally, we use the (2,0) theory to define and solve refined Chern-Simons theory for all ADE gauge groups

Higher derivative type II string effective actions, automorphic forms and E11

By dimensionally reducing the ten-dimensional higher derivative type IIA string theory effective action we place constraints on the automorphic forms that appear in the effective action in lower dimensions. We propose a number of properties of such automorphic forms and consider the prospects that E11 can play a role in the formulation of the higher derivative string theory effective action.Comment: 34 page

String theory of the Omega deformation

In this article, we construct a supersymmetric real mass deformation for the adjoint chiral multiplets in the gauge theory describing the dynamics of a stack of D2-branes in type II string theory. We do so by placing the D2-branes into the T-dual of a supersymmetric NS fluxbrane background. We furthermore note that this background is the string theoretic realization of an Omega-deformation of flat space in the directions transverse to the branes where the deformation parameters satisfy \epsilon_1 = - \epsilon_2. This \Omega-deformation therefore serves to give supersymmetric real masses to the chiral multiplets of the 3D gauge theory. To illustrate the physical effect of the real mass term, we derive BPS-saturated classical solutions for the branes rotating in this background. Finally, we reproduce all the same structure in the presence of NS fivebranes and comment on the relationship to the gauge theory/spin-chain correspondence of Nekrasov and Shatashvili.Comment: 36 pages. References added, brane construction clarified, edited for styl

HCoV- and SARS-CoV-2 Cross-Reactive T Cells in CVID Patients

The inability of patients with CVID to mount specific antibody responses to pathogens has raised concerns on the risk and severity of SARS-CoV-2 infection, but there might be a role for protective T cells in these patients. SARS-CoV-2 reactive T cells have been reported for SARS-CoV-2 unexposed healthy individuals. Until now, there is no data on T cell immunity to SARS-CoV-2 infection in CVID. This study aimed to evaluate reactive T cells to human endemic corona viruses (HCoV) and to study pre-existing SARS-CoV-2 reactive T cells in unexposed CVID patients. We evaluated SARS-CoV-2- and HCoV-229E and -OC43 reactive T cells in response to seven peptide pools, including spike and nucleocapsid (NCAP) proteins, in 11 unexposed CVID, 12 unexposed and 11 post COVID-19 healthy controls (HC). We further characterized reactive T cells by IFNγ, TNFα and IL-2 profiles. SARS-CoV-2 spike-reactive CD4+ T cells were detected in 7 of 11 unexposed CVID patients, albeit with fewer multifunctional (IFNγ/TNFα/IL-2) cells than unexposed HC. CVID patients had no SARS-CoV-2 NCAP reactive CD4+ T cells and less reactive CD8+ cells compared to unexposed HC. We observed a correlation between T cell reactivity against spike of SARS-CoV-2 and HCoVs in unexposed, but not post COVID-19 HC, suggesting cross-reactivity. T cell responses in post COVID-19 HC could be distinguished from unexposed HC by higher frequencies of triple-positive NCAP reactive CD4+ T cells. Taken together, SARS-CoV-2 reactive T cells are detectable in unexposed CVID patients albeit with lower recognition frequencies and polyfunctional potential. Frequencies of triple-functional reactive CD4+ cells might provide a marker to distinguish HCoV cross-reactive from SARS-CoV-2 specific T cell responses. Our data provides evidence, that anti-viral T cell immunity is not relevantly impaired in most CVID patients

Long-term observation of the frequency of secondary colorectal cancer and other malignancies in tyrosine kinase inhibitor treated chronic myeloid leukemia patients and controls

In this analysis, we examined the risk of secondary malignancies for tyrosine kinase inhibitor (TKI) therapy in chronic myeloid leukemia (CML) patients. We also collected data on specific risk factors for colorectal cancer. Ninety-one patients with CML and 76 controls were included and in total 4 (4.4%) secondary malignancies were found in patients and 8 (10.5%) in controls. The risk for secondary malignancies was not significantly elevated for CML patients (p = 0.141). Two (2.2%) CML patients developed colorectal cancer compared to 4 (5.3%) in the reference group. A higher risk for CML patients for colorectal cancer could not be found (p = 0.414)

Holographic non-perturbative corrections to gauge couplings

We give a direct microscopic derivation of the F-theory background that corresponds to four D7 branes of type I' theory by taking into account the D-instanton contributions to the emission of the axio-dilaton field in the directions transverse to the D7's. The couplings of the axio-dilaton to the D-instanton moduli modify its classical source terms which are shown to be proportional to the elements of the D7 brane chiral ring. Solving the bulk field equations with the non-perturbatively corrected sources yields the full F-theory background. This solution represents the gravitational dual of the four-dimensional theory living on a probe D3 brane of type I', namely of the N=2, Sp(1) SYM theory with Nf=4. Our results provide an explicit microscopic derivation of the non-perturbative gravitational dual of this theory. They also explain the recent observation that the exact coupling for this theory can be entirely reconstructed from its perturbative part plus the knowledge of the chiral ring on the D7 branes supporting its flavor degrees of freedom.Comment: Latex, 39 pages, 6 figure

Microevolution of Helicobacter pylori during prolonged infection of single hosts and within families

Our understanding of basic evolutionary processes in bacteria is still very limited. For example, multiple recent dating estimates are based on a universal inter-species molecular clock rate, but that rate was calibrated using estimates of geological dates that are no longer accepted. We therefore estimated the short-term rates of mutation and recombination in Helicobacter pylori by sequencing an average of 39,300 bp in 78 gene fragments from 97 isolates. These isolates included 34 pairs of sequential samples, which were sampled at intervals of 0.25 to 10.2 years. They also included single isolates from 29 individuals (average age: 45 years) from 10 families. The accumulation of sequence diversity increased with time of separation in a clock-like manner in the sequential isolates. We used Approximate Bayesian Computation to estimate the rates of mutation, recombination, mean length of recombination tracts, and average diversity in those tracts. The estimates indicate that the short-term mutation rate is 1.4×10−6 (serial isolates) to 4.5×10−6 (family isolates) per nucleotide per year and that three times as many substitutions are introduced by recombination as by mutation. The long-term mutation rate over millennia is 5–17-fold lower, partly due to the removal of non-synonymous mutations due to purifying selection. Comparisons with the recent literature show that short-term mutation rates vary dramatically in different bacterial species and can span a range of several orders of magnitude

PCA-based population structure inference with generic clustering algorithms

<p>Abstract</p> <p>Background</p> <p>Handling genotype data typed at hundreds of thousands of loci is very time-consuming and it is no exception for population structure inference. Therefore, we propose to apply PCA to the genotype data of a population, select the significant principal components using the Tracy-Widom distribution, and assign the individuals to one or more subpopulations using generic clustering algorithms.</p> <p>Results</p> <p>We investigated K-means, soft K-means and spectral clustering and made comparison to STRUCTURE, a model-based algorithm specifically designed for population structure inference. Moreover, we investigated methods for predicting the number of subpopulations in a population. The results on four simulated datasets and two real datasets indicate that our approach performs comparably well to STRUCTURE. For the simulated datasets, STRUCTURE and soft K-means with BIC produced identical predictions on the number of subpopulations. We also showed that, for real dataset, BIC is a better index than likelihood in predicting the number of subpopulations.</p> <p>Conclusion</p> <p>Our approach has the advantage of being fast and scalable, while STRUCTURE is very time-consuming because of the nature of MCMC in parameter estimation. Therefore, we suggest choosing the proper algorithm based on the application of population structure inference.</p

Recent acquisition of Helicobacter pylori by Baka Pygmies

Both anatomically modern humans and the gastric pathogen Helicobacter pylori originated in Africa, and both species have been associated for at least 100,000 years. Seven geographically distinct H. pylori populations exist, three of which are indigenous to Africa: hpAfrica1, hpAfrica2, and hpNEAfrica. The oldest and most divergent population, hpAfrica2, evolved within San hunter-gatherers, who represent one of the deepest branches of the human population tree. Anticipating the presence of ancient H. pylori lineages within all hunter-gatherer populations, we investigated the prevalence and population structure of H. pylori within Baka Pygmies in Cameroon. Gastric biopsies were obtained by esophagogastroduodenoscopy from 77 Baka from two geographically separated populations, and from 101 non-Baka individuals from neighboring agriculturalist populations, and subsequently cultured for H. pylori. Unexpectedly, Baka Pygmies showed a significantly lower H. pylori infection rate (20.8%) than non-Baka (80.2%). We generated multilocus haplotypes for each H. pylori isolate by DNA sequencing, but were not able to identify Baka-specific lineages, and most isolates in our sample were assigned to hpNEAfrica or hpAfrica1. The population hpNEAfrica, a marker for the expansion of the Nilo-Saharan language family, was divided into East African and Central West African subpopulations. Similarly, a new hpAfrica1 subpopulation, identified mainly among Cameroonians, supports eastern and western expansions of Bantu languages. An age-structured transmission model shows that the low H. pylori prevalence among Baka Pygmies is achievable within the timeframe of a few hundred years and suggests that demographic factors such as small population size and unusually low life expectancy can lead to the eradication of H. pylori from individual human populations. The Baka were thus either H. pylori-free or lost their ancient lineages during past demographic fluctuations. Using coalescent simulations and phylogenetic inference, we show that Baka almost certainly acquired their extant H. pylori through secondary contact with their agriculturalist neighbors