Loss of B1 and marginal zone B cells during ovarian cancer

Recent advances in immunotherapy have not addressed the challenge presented by ovarian cancer. Although the peritoneum is an "accessible" locus for this disease there has been limited characterization of the immunobiology therein. We investigated the ID8-C57BL/6J ovarian cancer model and found marked depletion of B1 cells from the ascites of the peritoneal cavity. There was also selective loss of the B1 and marginal zone B cell subsets from the spleen. Immunity to antigens that activate these subsets validated their loss rather than relocation. A marked influx of myeloid-derived suppressor cells correlated with B cell subset depletion. These observations are discussed in the context of the housekeeping burden placed on innate B cells during ovarian cancer and to foster consideration of B cell biology in therapeutic strategies to address this challenge.

Intrinsically disordered domain of transcription factor TCF-1 is required for T cell developmental fidelity

In development, pioneer transcription factors access silent chromatin to reveal lineage-specific gene programs. The structured DNA-binding domains of pioneer factors have been well characterized, but whether and how intrinsically disordered regions affect chromatin and control cell fate is unclear. Here, we report that deletion of an intrinsically disordered region of the pioneer factor TCF-1 (termed L1) leads to an early developmental block in T cells. The few T cells that develop from progenitors expressing TCF-1 lacking L1 exhibit lineage infidelity distinct from the lineage diversion of TCF-1-deficient cells. Mechanistically, L1 is required for activation of T cell genes and repression of GATA2-driven genes, normally reserved to the mast cell and dendritic cell lineages. Underlying this lineage diversion, L1 mediates binding of TCF-1 to its earliest target genes, which are subject to repression as T cells develop. These data suggest that the intrinsically disordered N terminus of TCF-1 maintains T cell lineage fidelity.

Quantitative control of Ets1 dosage by a multi-enhancer hub promotes Th1 cell differentiation and protects from allergic inflammation

Multi-enhancer hubs are spatial clusters of enhancers present across numerous developmental programs. Here, we studied the functional relevance of these three-dimensional structures in T cell biology. Mathematical modeling identified a highly connected multi-enhancer hub at the Ets1 locus, comprising a noncoding regulatory element that was a hotspot for sequence variation associated with allergic disease in humans. Deletion of this regulatory element in mice revealed that the multi-enhancer connectivity was dispensable for T cell development but required for CD4+ T helper 1 (Th1) differentiation. These mice were protected from Th1-mediated colitis but exhibited overt allergic responses. Mechanistically, the multi-enhancer hub controlled the dosage of Ets1 that was required for CTCF recruitment and assembly of Th1-specific genome topology. Our findings establish a paradigm wherein multi-enhancer hubs control cellular competence to respond to an inductive cue through quantitative control of gene dosage and provide insight into how sequence variation within noncoding elements at the Ets1 locus predisposes individuals to allergic responses.

TCF-1 promotes chromatin interactions across topologically associating domains in T cell progenitors

The high mobility group (HMG) transcription factor TCF-1 is essential for early T cell development. Although in vitro biochemical assays suggest that HMG proteins can serve as architectural elements in the assembly of higher-order nuclear organization, the contribution of TCF-1 on the control of three-dimensional (3D) genome structures during T cell development remains unknown. Here, we investigated the role of TCF-1 in 3D genome reconfiguration. Using gain- and loss-of-function experiments, we discovered that the co-occupancy of TCF-1 and the architectural protein CTCF altered the structure of topologically associating domains in T cell progenitors, leading to interactions between previously insulated regulatory elements and target genes at late stages of T cell development. The TCF-1-dependent gain in long-range interactions was linked to deposition of active enhancer mark H3K27ac and recruitment of the cohesin-loading factor NIPBL at active enhancers. These data indicate that TCF-1 has a role in controlling global genome organization during T cell development.

IgD ligation allows peritoneal cavity B cell proliferation

Atypical cytokine production and immune cell subset ratios, particularly those that include high proportions of macrophages, characterize tumor microenvironments (TMEs). TMEs can be modeled by culturing peritoneal cavity (PerC) cells which have a high macrophage to lymphocyte ratio. With TCR or BCR ligation, PerC lymphocyte proliferation is tempered by macrophages. However, PHA (T cells) and anti-CD40 (B cells) are activators that induce proliferation. Herein, we report that ligating IgD, in contrast to IgM, triggers PerC B cell proliferation. IL-4 addition enhanced the IgD response for BALB/c PerC B cells but suppressed that of C57BL/6 mice. Intriguingly, concurrent ligation of IgD and CD3_ε rescued a PerC T cell proliferative response. These results serve to expand the list of targets for promoting cellular and humoral immunity in conditions that model macrophage-rich TMEs.

Single-cell multi-omics analysis of human pancreatic islets reveals novel cellular states in type 1 diabetes

Type 1 diabetes (T1D) is an autoimmune disease in which immune cells destroy insulin-producing beta cells. The aetiology of this complex disease is dependent on the interplay of multiple heterogeneous cell types in the pancreatic environment. Here, we provide a single-cell atlas of pancreatic islets of 24 T1D, autoantibody-positive and nondiabetic organ donors across multiple quantitative modalities including ~80,000 cells using single-cell transcriptomics, ~7,000,000 cells using cytometry by time of flight and ~1,000,000 cells using in situ imaging mass cytometry. We develop an advanced integrative analytical strategy to assess pancreatic islets and identify canonical cell types. We show that a subset of exocrine ductal cells acquires a signature of tolerogenic dendritic cells in an apparent attempt at immune suppression in T1D donors. Our multimodal analyses delineate cell types and processes that may contribute to T1D immunopathogenesis and provide an integrative procedure for exploration and discovery of human pancreatic function.

Development and internal validation of a diagnostic prediction model for COVID-19 at time of admission to hospital

BACKGROUND

Early coronavirus disease 2019 (COVID-19) diagnosis prior to laboratory testing results is crucial for infection control in hospitals. Models exist predicting COVID-19 diagnosis, but significant concerns exist regarding methodology and generalizability.

AIM

To generate the first COVID-19 diagnosis risk score for use at the time of hospital admission using the TRIPOD (transparent reporting of a multivariable prediction model for individual prognosis or diagnosis) checklist.

DESIGN

A multivariable diagnostic prediction model for COVID-19 using the TRIPOD checklist applied to a large single-centre retrospective observational study of patients with suspected COVID-19.

METHODS

581 individuals were admitted with suspected COVID-19; the majority had laboratory-confirmed COVID-19 (420/581, 72.2%). Retrospective collection was performed of electronic clinical records and pathology data.

RESULTS

The final multivariable model demonstrated AUC 0.8535 (95% confidence interval 0.8121-0.8950). The final model used six clinical variables that are routinely available in most low and high-resource settings. Using a cut-off of 2, the derived risk score has a sensitivity of 78.1% and specificity of 86.8%. At COVID-19 prevalence of 10% the model has a negative predictive value (NPV) of 96.5%.

CONCLUSIONS

Our risk score is intended for diagnosis of COVID-19 in individuals admitted to hospital with suspected COVID-19. The score is the first developed for COVID-19 diagnosis using the TRIPOD checklist. It may be effective as a tool to rule out COVID-19 and function at different pandemic phases of variable COVID-19 prevalence. The simple score could be used by any healthcare worker to support hospital infection control prior to laboratory testing results.

Transcription factors combine to paint the methylation landscape

There is paucity of information about DNA methylation dynamics in immune cells. Roy et al. mapped the DNA methylation status of several thousand differentially methylated CpGs in human immune cells. They reported that the extent of cell type-specific hypermethylation is intriguingly most prevalent in adaptive immune cells rather than innate cells.

Constitutive Model of Radiation Aging Effects in Filled Silicone Elastomers under Strain

Filled silicone elastomers, an essential component in many technological applications, are often subjected to controlled or unintended radiation for a variety of reasons. Radiation exposure can lead to permanent mechanical and structural changes in the material, which is manifested as altered mechanical response, and in some cases, a permanent set. For unfilled elastomers, network theories developed and refined over decades can explain these effects in terms of chain-scission and cross-link formation and a hypothesis involving independent networks formed at different strain levels of the material. Here, we expose a filled silicone rubber to gamma radiation while being under finite elongational strain and show that the observed mechanical and structural changes can be quantitatively modeled within the same theoretical framework developed for unfilled elastomers as long as nuances associated with the Mullins effect are accounted for in a consistent manner. In this work, we employ Ogden's incompressible hyperelastic model within the framework of Tobolsky's two-network scheme to describe the observed permanent set and mechanical modulus changes as a function of radiation dosage. In the process, we conclude that gamma radiation induces both direct cross-linking at chain crossings (H-links) and main-chain-scission followed by cross-linking (Y-links). We provide an estimate of the ratio of chain-scission to cross-linking rates, which is in reasonable agreement with previous experimental estimate from Charlesby-Pinner analysis. We use density functional theory (DFT)-based quantum mechanical calculations to explore the stability of -Si and -SiO radicals that form upon a radiation-induced chain-scission event, which sheds light on the relative rates of Y-linking and H-linking processes.

Non-Abelian Bloch oscillations in higher-order topological insulators

Bloch oscillations (BOs) are a fundamental phenomenon by which a wave packet undergoes a periodic motion in a lattice when subjected to a force. Observed in a wide range of synthetic systems, BOs are intrinsically related to geometric and topological properties of the underlying band structure. This has established BOs as a prominent tool for the detection of Berry-phase effects, including those described by non-Abelian gauge fields. In this work, we unveil a unique topological effect that manifests in the BOs of higher-order topological insulators through the interplay of non-Abelian Berry curvature and quantized Wilson loops. It is characterized by an oscillating Hall drift synchronized with a topologically-protected inter-band beating and a multiplied Bloch period. We elucidate that the origin of this synchronization mechanism relies on the periodic quantum dynamics of Wannier centers. Our work paves the way to the experimental detection of non-Abelian topological properties through the measurement of Berry phases and center-of-mass displacements.

Foxp3 Re-distributes Its Heavy Lifting

Understanding the mechanisms that establish regulatory T (Treg) cell identity is central to understanding Treg cell function. van der Veeken et al. now show that the lineage-determining transcription factor Foxp3 establishes Treg-cell-specific chromatin architecture indirectly, mostly by decreasing the expression of other transcriptional regulators, including TCF1.

Joint profiling of chromatin accessibility and CAR-T integration site analysis at population and single-cell levels

Chimeric antigen receptor (CAR)-T immunotherapy has yielded impressive results in several B cell malignancies, establishing itself as a powerful means to redirect the natural properties of T lymphocytes. In this strategy, the T cell genome is modified by the integration of lentiviral vectors encoding CAR that direct tumor cell killing. However, this therapeutic approach is often limited by the extent of CAR-T cell expansion in vivo. A major outstanding question is whether or not CAR-T integration itself enhances the proliferative competence of individual T cells by rewiring their regulatory landscape. To address this question, it is critical to define the identity of an individual CAR-T cell and simultaneously chart where the CAR-T vector integrates into the genome. Here, we report the development of a method called EpiVIA (https://github.com/VahediLab/epiVIA) for the joint profiling of the chromatin accessibility and lentiviral integration site analysis at the population and single-cell levels. We validate our technique in clonal cells with previously defined integration sites and further demonstrate the ability to measure lentiviral integration sites and chromatin accessibility of host and viral genomes at the single-cell resolution in CAR-T cells. We anticipate that EpiVIA will enable the single-cell deconstruction of gene regulation during CAR-T therapy, leading to the discovery of cellular factors associated with durable treatment.

B Cell Subset Changes During Ovarian Cancer

Early biomarkers of ovarian cancer (OvCa) are needed for timely disease detection. Monitoring alterations in the immune system might be informative in this regard. To study humoral immunity during OvCa, we transplant murine epithelial carcinoma cells (ID8) into the peritoneal cavity (PerC). As the PerC is enriched for B1 cells, we assessed B cell subset composition via flow cytometry. As OvCa developed PerC B1 cells were lost while B2 cells persisted in the PerC and spleen (SP). This difference might reflect that self-reactive B1 cells have a role in housekeeping and lack progenitors in adult mice. We tested the latter hypothesis by monitoring transitional (T) B cells, and found the T1, T2, and T3 subsets were markedly reduced in late stage disease, suggesting depletion of B1 B cells, as opposed to expansion of B2 B cells. Intriguingly, marginal zone B cells (MZB) expanded early then contracted as OvCa progressed. We speculate that housekeeping burden grows with OvCa progression and the cells most associated with this vital homeostatic process, notably B1 and MZB cells, are most at risk. These findings highlight the disruption of B cell biology in mice challenged with OvCa, and may help to inform strategies to develop biomarkers for the disease.

Detecting Fractional Chern Insulators through Circular Dichroism

Great efforts are currently devoted to the engineering of topological Bloch bands in ultracold atomic gases. Recent achievements in this direction, together with the possibility of tuning interparticle interactions, suggest that strongly correlated states reminiscent of fractional quantum Hall (FQH) liquids could soon be generated in these systems. In this experimental framework, where transport measurements are limited, identifying unambiguous signatures of FQH-type states constitutes a challenge on its own. Here, we demonstrate that the fractional nature of the quantized Hall conductance, a fundamental characteristic of FQH states, could be detected in ultracold gases through a circular-dichroic measurement, namely, by monitoring the energy absorbed by the atomic cloud upon a circular drive. We validate this approach by comparing the circular-dichroic signal to the many-body Chern number and discuss how such measurements could be performed to distinguish FQH-type states from competing states. Our scheme offers a practical tool for the detection of topologically ordered states in quantum-engineered systems, with potential applications in solid state.

Oncogenic Notch Promotes Long-Range Regulatory Interactions within Hyperconnected 3D Cliques

Chromatin loops enable transcription-factor-bound distal enhancers to interact with their target promoters to regulate transcriptional programs. Although developmental transcription factors such as active forms of Notch can directly stimulate transcription by activating enhancers, the effect of their oncogenic subversion on the 3D organization of cancer genomes is largely undetermined. By mapping chromatin looping genome-wide in Notch-dependent triple-negative breast cancer and B cell lymphoma, we show that beyond the well-characterized role of Notch as an activator of distal enhancers, Notch regulates its direct target genes by instructing enhancer repositioning. Moreover, a large fraction of Notch-instructed regulatory loops form highly interacting enhancer and promoter spatial clusters termed "3D cliques." Loss- and gain-of-function experiments show that Notch preferentially targets hyperconnected 3D cliques that regulate the expression of crucial proto-oncogenes. Our observations suggest that oncogenic hijacking of developmental transcription factors can dysregulate transcription through widespread effects on the spatial organization of cancer genomes.

Parametric heating in a 2D periodically-driven bosonic system: Beyond the weakly-interacting regime

We experimentally investigate the effects of parametric instabilities on the short-time heating process of periodically-driven bosons in 2D optical lattices with a continuous transverse (tube) degree of freedom. We analyze three types of periodic drives: (i) linear along the x-lattice direction only, (ii) linear along the lattice diagonal, and (iii) circular in the lattice plane. In all cases, we demonstrate that the BEC decay is dominated by the emergence of unstable Bogoliubov modes, rather than scattering in higher Floquet bands, in agreement with recent theoretical predictions. The observed BEC depletion rates are much higher when shaking both along x and y directions, as opposed to only x or only y. We also report an explosion of the decay rates at large drive amplitudes, and suggest a phenomenological description beyond Bogoliubov theory. In this strongly-coupled regime, circular drives heat faster than diagonal drives, which illustrates the non-trivial dependence of the heating on the choice of drive.

IgD Ligation Promotes B Cell Proliferation in a Model of the Tumor Microenvironment

Potent immune suppression within tumor microenvironments (TMEs) is a hallmark of cancer. We model the TME by culture of C57BL/6J peritoneal cavity (PerC) cells. PerC cells include a significant fraction of immune-suppressive macrophages that, depending on the form of activation, temper T and B cell proliferation. PerC B cell responses to both BCR (F[ab′]2 anti-IgM) and TLR4 (LPS) ligation are suppressed. Here, we show that IgD receptor ligation (anti-IgD) induces modest B cell proliferation in this suppressive environment. Unlike other forms of B cell stimulation, the anti-IgD response is optimal at high PerC cell concentrations. Both polyclonal anti-IgD and monoclonal anti-IgDa(AMS 9.1) reagents trigger B cell proliferation. Strain comparisons revealed better responses with PerC cells from BALB/c (“Th2-like”) mice. Interestingly, while IL-4 enhanced spleen B cell proliferation, this cytokine suppressed the PerC cell response to IgD ligation. We are testing other cytokines to optimize this response and are assessing the impact of IgD ligation on T cell survival in the PerC cell/TME model. These studies may inform strategies to enhance lymphocyte activation within TMEs.

Phytohemagglutinin activates CD8 T cells in a model of the tumor microenvironment

Tumors often include a high proportion of immune modulatory cells and molecules that restrain the anti-cancer response. Activation of T cells to eliminate cancer cells within the immune suppressive tumor microenvironment (TME) remains a challenge. We have shown that C57BL/6J peritoneal cavity (PerC) cell culture models features of macrophage (Mθ)-rich TMEs as TCR ligation fails to activate T cells unless IFNγ is neutralized or iNOS is inhibited. We tested other forms of T cell activation and found phytohemagglutinin (PHA) distinctive in the ability to markedly expand CD8 T cells in the TME model. Neither IFNγ neutralization or iNOS inhibition were required for this response. IFNγR−/− PerC cells revealed that the PHA response is IFNg-dependent, yet this mitogen triggered less IFNγ production than TCR ligation. PHA-FITC staining revealed strong binding to Mfs and PerC cell addition to normally quiescent spleen (SP) cell cultures led to a marked increase in T cell expansion. The stimulatory capacity of PHA might reflect an ability to bind Mθs with CD8 T cells. Intriguingly, PerC Mf expression of the T cell inhibitory PD-L1 molecule was lower after PHA stimulation than that seen following TCR ligation. If PHA can increase CD8 T cell activation within the TME without increasing PD-L1 expression it might serve as an antitumor immune stimulant.

High macrophage PD-L1 expression not responsible for T cell suppression

Tumors are often comprised of microenvironments (TMEs) with a high proportion of cells and molecules that regulate immunity. Peritoneal cavity (PerC) cell culture reproduces key features of TMEs as lymphocyte proliferation is suppressed by PerC macrophages (Mϕs). We monitored the expression of T cell stimulatory (Class II MHC, B7) and inhibitory (PD-L1) molecules by PerC APCs before and after culture and report here that IFNγ-driven PD-L1 expression increased markedly on PerC Mϕs after TCR ligation, even more so than seen with direct APC activation by LPS. Considering the high APC composition of and pronounced PD-L1 expression by PerC cells, it was surprising that blocking PD-1/PD-L1 interaction by mAb neutralization or genetic ablation did not relieve suppression. This result parallels TME challenges observed in the clinic and validates the need for further study of this culture model to inform strategies to promote anti-tumor immunity.

Macrophage regulation of B cell proliferation

Unlike organized lymphoid tissue, the tumor microenvironment (TME) often includes a high proportion of immunosuppressive macrophages. We model the TME by culturing peritoneal cavity (PerC) cells that naturally have a high macrophage to lymphocyte ratio. Prior studies revealed that, following TCR ligation, PerC T cell proliferation is suppressed due to IFNγ-triggered inducible nitric oxide synthase expression. In this study we assessed the ability of PerC B cells to respond to surrogate activating signals in the presence of high numbers of macrophages. Surface IgM (BCR) ligation led to cyclooxygenase-mediated, and TLR-4 ligation to IL10-mediated, suppression of PerC B cell proliferation. In contrast, PerC B cells had a robust response to CD40 ligation, which could overcome the suppression generated by the BCR or TLR-4 response. However, the CD40 response was suppressed by concurrent TCR ligation. These results reveal the challenges of promoting B and T cell responses in macrophage-rich conditions that model the TME.

Erythropoietin increases macrophage-mediated T cell suppression

Erythropoietin (EPO), used to treat anemia in cancer patients, has been reported to accelerate tumor progression and increase mortality. Research of the mechanism for this effect has focused upon EPOR expression by tumor cells. We model the high macrophage to lymphocyte ratio found in tumor microenvironments (TMEs) by culturing peritoneal cavity (PerC) cells that naturally have a high macrophage to T cell ratio. Following TCR ligation, C57BL/6J PerC T cell proliferation is suppressed due to IFNγ-triggered inducible nitric oxide synthase (iNOS) expression. EPO was tested in the PerC culture model and found to increase T cell suppression. This effect could be abrogated by inhibiting iNOS by enzyme inhibition, genetic ablation, or blocking IFNγ signaling. Flow cytometry revealed the EPOR on CD11b(+)F4/80(+) macrophages. These results suggest that EPO could increase T cell suppression in the TME by acting directly on macrophages.

B cell subset biology in a tumor microenvironment model

The high myeloid to lymphoid ratio of cultured peritoneal cavity (PerC) leukocytes can serve as an in vitro model to study the tumor microenvironment (TME). C57BL/6J PerC T cell responses to TCR ligation (anti-CD3) and mitogen (ConA) are suppressed in these cultures. Likewise, the PerC B cell response to BCR (F[ab’2] anti-IgM) and TLR4 (TLR4L/LPS) ligation are suppressed. T cell suppression can be liberated by neutralizing IFNγ or by blocking iNOS with 1-methyl arginine. The BCR response is recovered by blocking prostaglandin production with indomethacin; the LPS response by neutralizing IL10. To dissect putative receptor-ligand signals in this model, we investigated expression of the inhibitory cell surface marker PDL1/B7H1/CD274 on PerC cells. TCR ligation increased PDL1 expression on macrophages (Mfs), B1, and B2 cells and was reduced by blocking IFNγ. TLR4 ligation increased PDL1 expression on Mfs and both B cell subsets and was reduced by blocking IFNAR1. Interestingly, BCR ligation increased B7H1 and Class II expression on Mfs and B2 cells, but not B-1 cells. Increased B7H1 expression could be reduced by neutralizing IL6, IFNβ, IFNγ, or IFNAR1. TCR ligation led to B1, but not B2, cell division and proliferating B cells increased IL10 production. These findings illustrate that TCR, and surprisingly BCR, ligation can foster immune suppression in macrophage-dense cultures and suggest that regulatory B cells must be considered when designing immunomodulatory cancer therapies.

Loss of humoral immunity in a mouse model of ovarian cancer

Although a low incidence cancer, ovarian carcinoma (OvCa) has a high mortality rate due to late detection. To study the humoral immune response to OvCa we transplant ID8 cells (mouse epithelial carcinoma) into the murine peritoneal cavity (PerC). We found that as the OvCa developed PerC B cells, particularly B-1 B cells, were depleted. To assess the systemic impact of this depletion we assessed humoral immunity. We found a reduction in “natural” IgM and IgG3 production and increased IgA and IgG1. Following immunization, there was loss of the TI-2 response (FITC-dextran, FITC-Ficoll); the TI-1 (FITC-LPS) response was intact until very late stage disease. Since B-1 cells also serve a housekeeping role in apoptotic corpse clearance, we used a FACS assay and a cell-based ELISA to monitor antibodies directed at apoptotic ID8 cells. Mice with OvCa had lower titers of sera that bound apoptotic ID8 cells. Collectively these data validate the systemic loss of B-1 B cells in mice with OvCa. These results could serve to inform strategies designed for early detection of OvCa.

Four-Dimensional Quantum Hall Effect with Ultracold Atoms

We propose a realistic scheme to detect the 4D quantum Hall effect using ultracold atoms. Based on contemporary technology, motion along a synthetic fourth dimension can be accomplished through controlled transitions between internal states of atoms arranged in a 3D optical lattice. From a semiclassical analysis, we identify the linear and nonlinear quantized current responses of our 4D model, relating these to the topology of the Bloch bands. We then propose experimental protocols, based on current or center-of-mass-drift measurements, to extract the topological second Chern number. Our proposal sets the stage for the exploration of novel topological phases in higher dimensions.

EPOR expression by peritoneal macrophages and B1b cells (TUM6P.1010)

Erythropoietin (EPO) is used in the treatment of chemotherapy-related anemia. A higher mortality rate among cancer patients treated with EPO has been documented. Research in this area has focused upon EPOR expression by cancer cells, either cell lines or ex vivo tumor tissue. We find that addition of exogenous EPO suppresses the activation of peritoneal cavity (PerC) T cells. Via FACs analysis of cultured C57BL/6J (wildtype,WT) PerC cells, we detected the EPO receptor (EPOR) on F4/80+, CD11b+ macrophages (Mfs). The specificity of the anti-EPOR pAb was validated by inhibition of staining with soluble EPOR. The percentage of Mfs expressing the EPOR increased with culture duration. EPOR+ Mfs also increased expression of the immunoinhibitory molecule PDL1/B7H1. Interestingly, EPOR expression also appeared on cultured B1b (IgMhi, CD11blo) cells. Although less evident in WT mice assessed ex vivo, EPOR+ PerC Mfs were found in IL10KO mice. Considerably more EPOR+ B1b cells were observed in the inflammatory ascites of mice with the ovarian cancer that develops following injection of the ID8 mouse epithelial carcinoma cell line. We are currently investigating how EPO contributes to T cell suppression in vitro and impacts Mf and B1b cell function and phenotype. Our data support a link between inflammation and EPOR expression by PerC Mfs and B1b cells.

Light-induced gauge fields for ultracold atoms

Gauge fields are central in our modern understanding of physics at all scales. At the highest energy scales known, the microscopic universe is governed by particles interacting with each other through the exchange of gauge bosons. At the largest length scales, our Universe is ruled by gravity, whose gauge structure suggests the existence of a particle-the graviton-that mediates the gravitational force. At the mesoscopic scale, solid-state systems are subjected to gauge fields of different nature: materials can be immersed in external electromagnetic fields, but they can also feature emerging gauge fields in their low-energy description. In this review, we focus on another kind of gauge field: those engineered in systems of ultracold neutral atoms. In these setups, atoms are suitably coupled to laser fields that generate effective gauge potentials in their description. Neutral atoms 'feeling' laser-induced gauge potentials can potentially mimic the behavior of an electron gas subjected to a magnetic field, but also, the interaction of elementary particles with non-Abelian gauge fields. Here, we review different realized and proposed techniques for creating gauge potentials-both Abelian and non-Abelian-in atomic systems and discuss their implication in the context of quantum simulation. While most of these setups concern the realization of background and classical gauge potentials, we conclude with more exotic proposals where these synthetic fields might be made dynamical, in view of simulating interacting gauge theories with cold atoms.

Synthetic gauge fields in synthetic dimensions

We describe a simple technique for generating a cold-atom lattice pierced by a uniform magnetic field. Our method is to extend a one-dimensional optical lattice into the "dimension" provided by the internal atomic degrees of freedom, yielding a synthetic two-dimensional lattice. Suitable laser coupling between these internal states leads to a uniform magnetic flux within the two-dimensional lattice. We show that this setup reproduces the main features of magnetic lattice systems, such as the fractal Hofstadter-butterfly spectrum and the chiral edge states of the associated Chern insulating phases.

Realistic time-reversal invariant topological insulators with neutral atoms

We lay out an experiment to realize time-reversal invariant topological insulators in alkali atomic gases. We introduce an original method to synthesize a gauge field in the near field of an atom chip, which effectively mimics the effects of spin-orbit coupling and produces quantum spin-Hall states. We also propose a feasible scheme to engineer sharp boundaries where the hallmark edge states are localized. Our multiband system has a large parameter space exhibiting a variety of quantum phase transitions between topological and normal insulating phases. Because of their remarkable versatility, cold-atom systems are ideally suited to realize topological states of matter and drive the development of topological quantum computing.

Wilson fermions and axion electrodynamics in optical lattices

We show that ultracold Fermi gases in optical superlattices can be used as quantum simulators of relativistic lattice fermions in 3+1 dimensions. By exploiting laser-assisted tunneling, we find an analogue of the so-called naive Dirac fermions, and thus provide a realization of the fermion doubling problem. Moreover, we show how to implement Wilson fermions, and discuss how their mass can be inverted by tuning the laser intensities. In this regime, our atomic gas corresponds to a phase of matter where Maxwell electrodynamics is replaced by axion electrodynamics: a 3D topological insulator.

Does social status predict adult smoking and obesity? Results from the 2000 Mexican National Health Survey

Socioeconomic status is generally associated with better health, but recent evidence suggests that this 'social gradient' in health is far from universal. This study examines whether social gradients in smoking and obesity in Mexico - a country in the midst of rapid socioeconomic change - conform to or diverge from results for richer countries. Using a nationally representative sample of 39,129 Mexican adults, we calculate the odds of smoking and of being obese by educational attainment and by household wealth. We conclude that socioeconomic determinants of smoking and obesity in Mexico are complex, with some flat gradients and some strong positive or negative gradients. Higher social status (education and assets) is associated with more smoking and less obesity for urban women. Higher status rural women also smoke more, but obesity for these women has a non-linear relationship to education. For urban men, higher asset levels (but not education) are associated with obesity, whereas education is protective of smoking. Higher status rural men with more assets are more likely to smoke and be obese. As household wealth, education and urbanisation continue to increase in Mexico, these patterns suggest potential targets for public health intervention now and in the future.

Non-Abelian optical lattices: anomalous quantum Hall effect and Dirac fermions

We study the properties of an ultracold Fermi gas loaded in an optical square lattice and subjected to an external and classical non-Abelian gauge field. We show that this system can be exploited as an optical analogue of relativistic quantum electrodynamics, offering a remarkable route to access the exotic properties of massless Dirac fermions with cold atoms experiments. In particular, we show that the underlying Minkowski space-time can also be modified, reaching anisotropic regimes where a remarkable anomalous quantum Hall effect and a squeezed Landau vacuum could be observed.

Statistics of the log-det estimator

The log-det estimator is a measure of divergence (evolutionary distance) between sequences of biological characters, DNA or amino acids, for example, and has been shown to be robust to biases in composition that can cause problems for other estimators. We provide a statistical framework to construct high-accuracy confidence intervals for log-det estimates and compare the efficiency of the estimator to that of maximum likelihood using time-reversible Markov models. The log-det estimator is found to have good statistical properties under such general models.

Social inequalities in health disentangling the underlying mechanisms

Differentials in health and longevity by socioeconomic status and by the nature of social relationships have been found in innumerable studies in the social and medical sciences. Three categories of explanations for the observed patterns have been proposed: causal mechanisms through which the social environment affects health status or the risk of dying; selection or reverse causal pathways whereby a person's health status affects their social position; and artifactual mechanisms, such as measurement error. The general consensus among researchers is that the observed disparities in health are driven largely by a complex set of causal processes rather than by selection or by artifactual mechanisms. This paper explores the set of arguments and strategies that researchers have used to arrive at this conclusion. As part of this undertaking, we assess whether inferences regarding the minor contribution of selection to the overall association between social factors and health are justifiable. In addition, we identify current avenues of research that are providing new insights into the causal pathways linking social factors and health.

Complete characterization of the (D2O)2 ground state: high Ka rotation-tunneling levels

We report the observation of extensive a- and c-type rotation-tunneling (RT) spectra of (D2O)2 for Ka = 0-4. These data allow quantification of molecular constants and tunneling splittings for a number of previously unobserved RT states of (D2O)2. The vibrational ground state has thus been characterized to energies as high as those of some of the intermolecular vibrations, and we present the first test of the VRT(ASP-W) potential at these high Ka states.

Molecular phylogenetics: state-of-the-art methods for looking into the past

As the amount of molecular sequence data in the public domain grows, so does the range of biological topics that it influences through evolutionary considerations. In recent years, a number of developments have enabled molecular phylogenetic methodology to keep pace. Likelihood-based inferential techniques, although controversial in the past, lie at the heart of these new methods and are producing the promised advances in the understanding of sequence evolution. They allow both a wide variety of phylogenetic inferences from sequence data and robust statistical assessment of all results. It cannot remain acceptable to use outdated data analysis techniques when superior alternatives exist. Here, we discuss the most important and exciting methods currently available to the molecular phylogeneticist.