Bioinformatics advances in saliva diagnostics

There is a need recognized by the National Institute of Dental & Craniofacial Research and the National Cancer Institute to advance basic, translational and clinical saliva research. The goal of the Salivaomics Knowledge Base (SKB) is to create a data management system and web resource constructed to support human salivaomics research. To maximize the utility of the SKB for retrieval, integration and analysis of data, we have developed the Saliva Ontology and SDxMart. This article reviews the informatics advances in saliva diagnostics made possible by the Saliva Ontology and SDxMart

Disparities in access to and use of HIV-related health services in the Netherlands by migrant status and sexual orientation: a cross-sectional study among people recently diagnosed with HIV infection

Background Migrants often face barriers to accessing healthcare. We examined disparities in access to and use of HIV-related health services between migrant and non-migrant people recently diagnosed with HIV living in the Netherlands, taken into account sexual orientation. Also, we examined differences in experiences in living with HIV between these groups. Methods We used a questionnaire and clinical data collected between July 2013 and June 2015 among migrant and non-migrant participants of the European cross-sectional aMASE (Advancing Migrant Access to health Services in Europe) study in the Netherlands. Using univariable logistic regression analyses, we compared outcomes on between migrants and non-migrants, stratified by sexual orientation (with non-migrant men having sex with men [MSM] as the reference group). Results We included 77 migrant MSM, 115 non-migrant MSM, 21 migrant heterosexual men, 14 non-migrant heterosexual men and 20 migrant women. In univariable analyses, all heterosexual groups were less likely to ever have had an HIV-negative test before their diagnosis and were more likely to be diagnosed late than non-migrant MSM. All migrant groups were more likely to have experienced difficulties accessing general healthcare in the Netherlands and were less likely to have heard of post-exposure prophylaxis than non-migrant MSM. Migrants frequently reported uncertainty about their rights to healthcare and language barriers. Most (93%) participants visited a healthcare facility in the 2 years before HIV diagnosis but only in 41% an HIV test was discussed during that visit (no statistical difference between groups). Migrant heterosexuals were more likely to have missed appointments at their HIV clinic due to the travel costs than non-migrant MSM. Migrant MSM and women were more likely to have experienced HIV discrimination in the Netherlands than non-migrant MSM. Conclusion Disparities in access to and use of HIV-related health services and experiences exist by migrant status but also by sexual orientation. Our data suggests heterosexual men and women may particularly benefit from improved access to HIV testing (e.g., through provider-initiated testing), while migrant MSM may benefit from improved access to HIV prevention interventions (e.g., pre-exposure prophylaxis)

Direct observation of incommensurate magnetism in Hubbard chains

The interplay between magnetism and doping is at the origin of exotic strongly correlated electronic phases and can lead to novel forms of magnetic ordering. One example is the emergence of incommensurate spin-density waves with a wave vector that does not match the reciprocal lattice. In one dimension this effect is a hallmark of Luttinger liquid theory, which also describes the low energy physics of the Hubbard model. Here we use a quantum simulator based on ultracold fermions in an optical lattice to directly observe such incommensurate spin correlations in doped and spin-imbalanced Hubbard chains using fully spin and density resolved quantum gas microscopy. Doping is found to induce a linear change of the spin-density wave vector in excellent agreement with Luttinger theory predictions. For non-zero polarization we observe a decrease of the wave vector with magnetization as expected from the Heisenberg model in a magnetic field. We trace the microscopic origin of these incommensurate correlations to holes, doublons and excess spins which act as delocalized domain walls for the antiferromagnetic order. Finally, when inducing interchain coupling we observe fundamentally different spin correlations around doublons indicating the formation of a magnetic polaron

A computational framework to emulate the human perspective in flow cytometric data analysis

Background: In recent years, intense research efforts have focused on developing methods for automated flow cytometric data analysis. However, while designing such applications, little or no attention has been paid to the human perspective that is absolutely central to the manual gating process of identifying and characterizing cell populations. In particular, the assumption of many common techniques that cell populations could be modeled reliably with pre-specified distributions may not hold true in real-life samples, which can have populations of arbitrary shapes and considerable inter-sample variation. <p/>Results: To address this, we developed a new framework flowScape for emulating certain key aspects of the human perspective in analyzing flow data, which we implemented in multiple steps. First, flowScape begins with creating a mathematically rigorous map of the high-dimensional flow data landscape based on dense and sparse regions defined by relative concentrations of events around modes. In the second step, these modal clusters are connected with a global hierarchical structure. This representation allows flowScape to perform ridgeline analysis for both traversing the landscape and isolating cell populations at different levels of resolution. Finally, we extended manual gating with a new capacity for constructing templates that can identify target populations in terms of their relative parameters, as opposed to the more commonly used absolute or physical parameters. This allows flowScape to apply such templates in batch mode for detecting the corresponding populations in a flexible, sample-specific manner. We also demonstrated different applications of our framework to flow data analysis and show its superiority over other analytical methods. <p/>Conclusions: The human perspective, built on top of intuition and experience, is a very important component of flow cytometric data analysis. By emulating some of its approaches and extending these with automation and rigor, flowScape provides a flexible and robust framework for computational cytomics

Dietary intake of micronutrients and the risk of developing bladder cancer: results from the Belgian case–control study on bladder cancer risk

OBJECTIVE: We aimed to investigate the effect of dietary intake of micronutrients that are metabolized and excreted via the urinary tract on bladder cancer risk. METHODS: A semi-quantitative 322 item food frequency questionnaire (FFQ) was used to collect dietary data from 200 bladder cancer cases and 386 control subjects participating in the Belgian case-control study on bladder cancer risk. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated using unconditional logistic regression adjusting for age, sex, smoking characteristics, occupational exposures, and energy intake. RESULTS: We observed a positive association between calcium intake and bladder cancer (OR: 1.77; 95% CI: 1.00-3.15; p-trend = 0.049) and increased odds, although not statistically significant, for highest tertile of phosphorus intake (OR: 1.82; 95% CI: 0.95-3.49; p-trend = 0.06). We identified possible modification of the effects of both calcium and phosphorus by level of magnesium intake. Increased odds of bladder cancer were also observed for participants with highest intake of phosphorus and lowest intake of vitamin D (OR: 4.25; 95% CI: 1.44-12.55) and among older participants with the highest intakes of calcium (OR: 1.90; 95% CI: 1.08-3.36) and phosphorus (OR: 2.02; 95% CI: 1.05-3.92). CONCLUSION: The positive associations we observed between bladder cancer and intake of calcium and phosphorus require confirmation by other studies. The balances between inter-related micronutrients also warrant further examination

The consequences of a new software package for the quantification of gated-SPECT myocardial perfusion studies

Semiquantitative analysis of myocardial perfusion scintigraphy (MPS) has reduced inter- and intraobserver variability, and enables researchers to compare parameters in the same patient over time, or between groups of patients. There are several software packages available that are designed to process MPS data and quantify parameters. In this study the performances of two systems, quantitative gated SPECT (QGS) and 4D-MSPECT, in the processing of clinical patient data and phantom data were compared. The clinical MPS data of 148 consecutive patients were analysed using QGS and 4D-MSPECT to determine the end-diastolic volume, end-systolic volume and left ventricular ejection fraction. Patients were divided into groups based on gender, body mass index, heart size, stressor type and defect type. The AGATE dynamic heart phantom was used to provide reference values for the left ventricular ejection fraction. Although the correlations were excellent (correlation coefficients 0.886 to 0.980) for all parameters, significant differences (p < 0.001) were found between the systems. Bland-Altman plots indicated that 4D-MSPECT provided overall higher values of all parameters than QGS. These differences between the systems were not significant in patients with a small heart (end-diastolic volume < 70 ml). Other clinical factors had no direct influence on the relationship. Additionally, the phantom data indicated good linear responses of both systems. The discrepancies between these software packages were clinically relevant, and influenced by heart size. The possibility of such discrepancies should be taken into account when a new quantitative software system is introduced, or when multiple software systems are used in the same institution.Vascular Biology and Interventio

A transient liquid-like phase in the displacement cascades of zircon, hafnon and thorite

The study of radiation effects in solids is important for the development of 'radiation-resistant' materials for fission-reactor applications'. The effects of heavy-ion irradiation in the isostructural orthosilicates zircon (ZrSiO4), hafnon (HfSiO4) and thorite (ThSiO4) are particularly important because these minerals are under active investigation for use as a waste form for plutonium-239 resulting from the dismantling of nuclear weapons(2-4). During ion irradiation, localized 'cascades' of displaced atoms can form as a result of ballistic collisions in the target material, and the temperature inside these regions may for a short time exceed the bulk melting temperature. Whether these cascades do indeed generate a localized liquid state(5-8) has, however, remained unclear. Here we investigate the irradiation-induced decomposition of zircon and hafnon, and find evidence for formation of a liquidlike state in the displacement cascades. Our results explain the frequent occurrence of ZrO2 in natural amorphous zircong(9-12) Moreover, we conclude that zircon-based nuclear waste forms should be maintained within strict temperature Limits, to avoid potentially detrimental irradiation-induced amorphization or phase decomposition of the zircon.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/62853/1/395056a0.pd

The pattern of influenza virus attachment varies among wild bird species

The ability to attach to host cells is one of the main determinants of the host range of influenza A viruses. By using virus histochemistry, we investigate the pattern of virus attachment of both a human and an avian influenza virus in colon and trachea sections from 12 wild bird species. We show that significant variations exist, even between closely related avian species, which suggests that the ability of wild birds to serve as hosts for influenza viruses strongly varies among species. These results will prove valuable to assess the possibilities of interspecies transmission of influenza viruses in natural environments and better understand the ecology of influenza

X-Ray Spectroscopy of Stars

(abridged) Non-degenerate stars of essentially all spectral classes are soft X-ray sources. Low-mass stars on the cooler part of the main sequence and their pre-main sequence predecessors define the dominant stellar population in the galaxy by number. Their X-ray spectra are reminiscent, in the broadest sense, of X-ray spectra from the solar corona. X-ray emission from cool stars is indeed ascribed to magnetically trapped hot gas analogous to the solar coronal plasma. Coronal structure, its thermal stratification and geometric extent can be interpreted based on various spectral diagnostics. New features have been identified in pre-main sequence stars; some of these may be related to accretion shocks on the stellar surface, fluorescence on circumstellar disks due to X-ray irradiation, or shock heating in stellar outflows. Massive, hot stars clearly dominate the interaction with the galactic interstellar medium: they are the main sources of ionizing radiation, mechanical energy and chemical enrichment in galaxies. High-energy emission permits to probe some of the most important processes at work in these stars, and put constraints on their most peculiar feature: the stellar wind. Here, we review recent advances in our understanding of cool and hot stars through the study of X-ray spectra, in particular high-resolution spectra now available from XMM-Newton and Chandra. We address issues related to coronal structure, flares, the composition of coronal plasma, X-ray production in accretion streams and outflows, X-rays from single OB-type stars, massive binaries, magnetic hot objects and evolved WR stars.Comment: accepted for Astron. Astrophys. Rev., 98 journal pages, 30 figures (partly multiple); some corrections made after proof stag

Dynamical Mean-Field Theory

The dynamical mean-field theory (DMFT) is a widely applicable approximation scheme for the investigation of correlated quantum many-particle systems on a lattice, e.g., electrons in solids and cold atoms in optical lattices. In particular, the combination of the DMFT with conventional methods for the calculation of electronic band structures has led to a powerful numerical approach which allows one to explore the properties of correlated materials. In this introductory article we discuss the foundations of the DMFT, derive the underlying self-consistency equations, and present several applications which have provided important insights into the properties of correlated matter.Comment: Chapter in "Theoretical Methods for Strongly Correlated Systems", edited by A. Avella and F. Mancini, Springer (2011), 31 pages, 5 figure