A stew of mixed ingredients: Observational omics in the post-GWAS era

The past 20 years have seen extensive profiling of the DNA. Collectively, scientists all across the world have identified many places in the DNA, known as loci, that impact human traits such as disease state or immune function. However, interpreting the results from these studies, known as genome wide association studies (GWAS), has been challenging. This thesis studies several approaches for interpreting GWAS results, with a specific focus on our immune system given its important role in preventing and causing disease. This is done through the use of so called ‘omics’ technologies, that can study the role of thousands of genes, proteins and genetic variants at the same time. By doing this, maps can be constructed of which genes and proteins interact to impact human traits. The ultimate goal of this research is to provide a better understanding of the cascade between the DNA and human traits. The hope is that building a specific understanding of how the variation in the DNA leads to the development of human traits, such as disease, will ultimately aid the development of drugs for these diseases

Seismic Fault Preserving Diffusion

This paper focuses on the denoising and enhancing of 3-D reflection seismic data. We propose a pre-processing step based on a non linear diffusion filtering leading to a better detection of seismic faults. The non linear diffusion approaches are based on the definition of a partial differential equation that allows us to simplify the images without blurring relevant details or discontinuities. Computing the structure tensor which provides information on the local orientation of the geological layers, we propose to drive the diffusion along these layers using a new approach called SFPD (Seismic Fault Preserving Diffusion). In SFPD, the eigenvalues of the tensor are fixed according to a confidence measure that takes into account the regularity of the local seismic structure. Results on both synthesized and real 3-D blocks show the efficiency of the proposed approach.Comment: 10 page

Letter to the Editor regarding Falstie-Jensen et al:"Labeled white blood cell/bone marrow single-photon emission computed tomography with computed tomography fails in diagnosing chronic periprosthetic shoulder joint infection''

No abstract availabl

INSIG1 influences obesity-related hypertriglyceridemia in humans

In our analysis of a quantitative trait locus (QTL) for plasma triglyceride (TG) levels [logarithm of odds (LOD) = 3.7] on human chromosome 7q36, we examined 29 single nucleotide polymorphisms (SNPs) across INSIG1, a biological candidate gene in the region. Insulin-induced genes (INSIGs) are feedback mediators of cholesterol and fatty acid synthesis in animals, but their role in human lipid regulation is unclear. In our cohort, the INSIG1 promoter SNP rs2721 was associated with TG levels (P = 2 × 10−3 in 1,560 individuals of the original linkage cohort, P = 8 × 10−4 in 920 unrelated individuals of the replication cohort, combined P = 9.9 × 10−6). Individuals homozygous for the T allele had 9% higher TG levels and 2-fold lower expression of INSIG1 in surgical liver biopsy samples when compared with individuals homozygous for the G allele. Also, the T allele showed additional binding of nuclear proteins from HepG2 liver cells in gel shift assays. Finally, the variant rs7566605 in INSIG2, the only homolog of INSIG1, enhances the effect of rs2721 (P = 0.00117). The variant rs2721 alone explains 5.4% of the observed linkage in our cohort, suggesting that additional, yet-undiscovered genes and sequence variants in the QTL interval also contribute to alterations in TG levels in humans

Optical spectrum of the post-AGB star HD56126 in the region 4010-8790 AA

We studied in detail the optical spectrum of the post-AGB star HD56126 (IRAS07134+1005). We use high resolution spectra (R=25000 and 60000) obtained with the echelle spectrographs of the 6-m telescope. About one and a half thousand absorptions of neutral atoms and ions, absorption bands of C_2, CN, and CH molecules, and interstellar bands (DIBs) are identified in the 4010 to 8790 AA wavelength region, and the depths and radial velocities of these spectral features are measured. Differences are revealed between the variations of the radial velocities measured from spectral features of different excitation. In addition to the well-known variability of the Halpha profile, we found variations in the profiles of a number of FeII, YII, and BaII lines. We also produce an atlas of the spectrum of HD56126 and its comparison staralpha Per. The full version of the atlas is available in electronic form from Web-address: http://www.sao.ru/hq/ssl/Atlas/Atlas.htmlComment: 42 pages, 6 figure

Monitoring pulmonary pressures during long-term continuous-flow left ventricular assist device and fixed pulmonary hypertension: redefining alleged pathophysiological mechanisms?

Pulmonary hypertension (PH) type II (classified by the World Health Organization) is a common complication in chronic left-sided heart failure. In advanced heart failure therapy, fixed PH is an absolute contraindication for heart transplantation after which a left ventricular assist device (LVAD) is the only remaining option. With remote monitoring, we can now continuously evaluate the pulmonary artery pressures during long-term LV unloading by the LVAD. In this case, we demonstrate that fixed PH can be reversed with LVAD implantation, whereby previous thoughts of this concept should be redefined in the era of assist devices

Pretransplant characteristics of kidney transplant recipients that predict posttransplant outcome

Better characterization of the potential kidney transplant recipient using novel biomarkers, for example, pretransplant plasma endotrophin, will lead to improved outcome after transplantation. This mini-review will focus on current knowledge about pretransplant recipients’ characteristics, biomarkers, and immunology. Clinical characteristics of recipients including age, obesity, blood pressure, comorbidities, and estimated survival scores have been introduced for prediction of recipient and allograft survival. The pretransplant immunologic risk assessment include histocompatibility leukocyte antigens (HLAs), anti-HLA donor-specific antibodies, HLA-DQ mismatch, and non-HLA antibodies. Recently, there has been the hope that pretransplant determination of markers can further improve the prediction of posttransplant complications, both short-term and long-term outcomes including rejections, allograft loss, and mortality. Higher pretransplant plasma endotrophin levels were independently associated with posttransplant acute allograft injury in three prospective European cohorts. Elevated numbers of non-synonymous single-nucleotide polymorphism mismatch have been associated with increased allograft loss in a multivariable analysis. It is concluded that there is a need for integration of clinical characteristics and novel molecular and immunological markers to improve future transplant medicine to reach better diagnostic decisions tailored to the individual patient

Female sexual behavior in mice is controlled by kisspeptin neurons.

Sexual behavior is essential for the survival of many species. In female rodents, mate preference and copulatory behavior depend on pheromones and are synchronized with ovulation to ensure reproductive success. The neural circuits driving this orchestration in the brain have, however, remained elusive. Here, we demonstrate that neurons controlling ovulation in the mammalian brain are at the core of a branching neural circuit governing both mate preference and copulatory behavior. We show that male odors detected in the vomeronasal organ activate kisspeptin neurons in female mice. Classical kisspeptin/Kiss1R signaling subsequently triggers olfactory-driven mate preference. In contrast, copulatory behavior is elicited by kisspeptin neurons in a parallel circuit independent of Kiss1R involving nitric oxide signaling. Consistent with this, we find that kisspeptin neurons impinge onto nitric oxide-synthesizing neurons in the ventromedial hypothalamus. Our data establish kisspeptin neurons as a central regulatory hub orchestrating sexual behavior in the female mouse brain

Integrating GWAS with bulk and single-cell RNA-sequencing reveals a role for LY86 in the anti-Candida host response

Contains fulltext : 220669.pdf (publisher's version ) (Open Access)Candida bloodstream infection, i.e. candidemia, is the most frequently encountered life-threatening fungal infection worldwide, with mortality rates up to almost 50%. In the majority of candidemia cases, Candida albicans is responsible. Worryingly, a global increase in the number of patients who are susceptible to infection (e.g. immunocompromised patients), has led to a rise in the incidence of candidemia in the last few decades. Therefore, a better understanding of the anti-Candida host response is essential to overcome this poor prognosis and to lower disease incidence. Here, we integrated genome-wide association studies with bulk and single-cell transcriptomic analyses of immune cells stimulated with Candida albicans to further our understanding of the anti-Candida host response. We show that differential expression analysis upon Candida stimulation in single-cell expression data can reveal the important cell types involved in the host response against Candida. This confirmed the known major role of monocytes, but more interestingly, also uncovered an important role for NK cells. Moreover, combining the power of bulk RNA-seq with the high resolution of single-cell RNA-seq data led to the identification of 27 Candida-response QTLs and revealed the cell types potentially involved herein. Integration of these response QTLs with a GWAS on candidemia susceptibility uncovered a potential new role for LY86 in candidemia susceptibility. Finally, experimental follow-up confirmed that LY86 knockdown results in reduced monocyte migration towards the chemokine MCP-1, thereby implying that this reduced migration may underlie the increased susceptibility to candidemia. Altogether, our integrative systems genetics approach identifies previously unknown mechanisms underlying the immune response to Candida infection

Mycobacterium chelonae, an ‘atypical’ cause of an LVAD driveline infection

We describe the first patient with a left ventricular assist device (LVAD) driveline infection caused by Mycobacterium chelonae presenting with persistent infection despite conventional antibiotics. Treatment was successful with surgical debridement, driveline exit relocation, and a 4-month period of antibiotics. In the case of a culture-negative LVAD driveline infection, non-tuberculous mycobacteria should be considered. This case illustrates tha