Forbidden Time Travel: Characterization of Time-Consistent Tree Reconciliation Maps

Motivation: In the absence of horizontal gene transfer it is possible to reconstruct the history of gene families from empirically determined orthology relations, which are equivalent to event-labeled gene trees. Knowledge of the event labels considerably simplifies the problem of reconciling a gene tree T with a species trees S, relative to the reconciliation problem without prior knowledge of the event types. It is well-known that optimal reconciliations in the unlabeled case may violate time-consistency and thus are not biologically feasible. Here we investigate the mathematical structure of the event labeled reconciliation problem with horizontal transfer. Results: We investigate the issue of time-consistency for the event-labeled version of the reconciliation problem, provide a convenient axiomatic framework, and derive a complete characterization of time-consistent reconciliations. This characterization depends on certain weak conditions on the event-labeled gene trees that reflect conditions under which evolutionary events are observable at least in principle. We give an O(|V(T)|log(|V(S)|))-time algorithm to decide whether a time-consistent reconciliation map exists. It does not require the construction of explicit timing maps, but relies entirely on the comparably easy task of checking whether a small auxiliary graph is acyclic. The algorithms are implemented in C++ using the boost graph library and are freely available at https://github.com/Nojgaard/tc-recon. Significance: The combinatorial characterization of time consistency and thus biologically feasible reconciliation is an important step towards the inference of gene family histories with hor- izontal transfer from orthology data, i.e., without presupposed gene and species trees. The fast algorithm to decide time consistency is useful in a broader context because it constitutes an attractive component for all tools that address tree reconciliation problems

YKL-40, a Marker of Inflammation and Endothelial Dysfunction, Is Elevated in Patients With Type 1 Diabetes and Increases With Levels of Albuminuria

OBJECTIVE—The inflammation marker YKL-40 is elevated in patients with type 2 diabetes and is associated with atherosclerosis and increased cardiovascular mortality. In the present study, YKL-40 levels were examined in patients with type 1 diabetes with increasing levels of albuminuria, known to be associated with an increased risk of cardiovascular disease

YKL ‐40 genetic polymorphisms and the risk of liver disease progression in patients with advanced fibrosis due to chronic hepatitis C

Background/Aims The aim of this study was to explore the association of a functional YKL ‐40 promoter polymorphism (rs4950928) with baseline disease stage, response to antiviral therapy and risk of liver disease progression in a group of patients with chronic hepatitis C ( CHC ). Methods YKL ‐40 promoter polymorphisms were determined in 456 H epatitis C A ntiviral L ong‐term T reatment against C irrhosis ( HALT ‐C) T rial patients with bridging fibrosis or cirrhosis entering a prerandomization lead‐in peginterferon/ribavirin 24‐week treatment phase and in 462 patients followed for a mean of 3.8 years after randomization to maintenance peginterferon or observation. Results Mean patient age was 49.5 years, 70.4% were men and 71.2% were Caucasian. The 17% frequency of the YKL ‐40 minor allele (T) was similar to that reported in the general population. YKL ‐40 genotype was associated significantly with baseline serum YKL ‐40 levels but was not associated with the likelihood of a virological response following 24–48 weeks of peginterferon/ribavirin therapy. Serum YKL ‐40 levels remained significantly lower during follow‐up in the randomized TT homozygotes compared with CT heterozygotes and CC homozygotes ( P  < 0.001). Despite this association, YKL ‐40 genotype was not associated with the risk of clinical or histological liver disease progression. Conclusions A reduced frequency of the protective YKL ‐40 promoter polymorphism was not observed in the HALT ‐C T rial patient population. The absence of an association between YKL ‐40 promoter polymorphisms and baseline liver disease severity as well as with the risk of liver disease progression over time suggests that this polymorphism is not associated with disease progression in CHC patients with established fibrosis.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/90574/1/liv2686.pd

Relationship of serum fibrosis markers with liver fibrosis stage and collagen content in patients with advanced chronic hepatitis C

This study determined the utility of a panel of serum fibrosis markers along with routine laboratory tests in estimating the likelihood of histological cirrhosis in a cohort of prior nonresponders with chronic hepatitis C. The relationship between serum markers and quantitative hepatic collagen content was also determined. Liver biopsy samples from 513 subjects enrolled in the HALT-C trial were assigned Ishak fibrosis scores. The collagen content of 386 sirius-red stained, nonfragmented biopsy samples was quantified using computerized morphometry. Serum tissue inhibitor of matrix metalloproteinase-1 (TIMP-1), amino-terminal peptide of type III procollagen (PIIINP), hyaluronic acid (HA), and YKL-40 levels were determined using commercially available assays.Sixty-two percent of patients had noncirrhotic fibrosis (Ishak stage 2-4) whereas 38% had cirrhosis (Ishak stage 5,6). Multivariate analysis identified a 3-variable model (HA, TIMP-1, and platelet count) that had an area under the receiver operating curve (AUROC) of 0.81 for estimating the presence of cirrhosis. This model was significantly better than that derived from the cirrhosis discriminant score (AUROC 0.70), the AST-to-platelet ratio (AUROC 0.73), and a prior model developed in HALT-C patients (AUROC 0.79). Multivariate analysis demonstrated that the serum fibrosis markers correlated substantially better with Ishak fibrosis scores than with the log hepatic collagen content (AUROC 0.84 versus 0.72). Conclusion: A 3-variable model consisting of serum HA, TIMP-1, and platelet count was better than other published models in identifying cirrhosis in HALT-C Trial subjects. The stronger correlation of the serum markers with Ishak scores suggests that serum fibrosis markers reflect the pattern of fibrosis more closely than the quantity of hepatic collagen. (H EPATOLOGY 2008.)Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/58027/1/22099_ftp.pd

A full year of aerosol size distribution data from the central Arctic under an extreme positive Arctic Oscillation : insights from the Multidisciplinarydrifting Observatory for the Study of Arctic Climate (MOSAiC) expedition

The Arctic environment is rapidly changing due to accelerated warming in the region. The warming trend is driving a decline in sea ice extent, which thereby enhances feedback loops in the surface energy budget in the Arctic. Arctic aerosols play an important role in the radiative balance and hence the climate response in the region, yet direct observations of aerosols over the Arctic Ocean are limited. In this study, we investigate the annual cycle in the aerosol particle number size distribution (PNSD), particle number concentration (PNC), and black carbon (BC) mass concentration in the central Arctic during the Multidisciplinary drifting Observatory for the Study of Arctic Climate (MOSAiC) expedition. This is the first continuous, year-long data set of aerosol PNSD ever collected over the sea ice in the central Arctic Ocean. We use a k-means cluster analysis, FLEXPART simulations, and inverse modeling to evaluate seasonal patterns and the influence of different source regions on the Arctic aerosol population. Furthermore, we compare the aerosol observations to land-based sites across the Arctic, using both long-term measurements and observations during the year of the MOSAiC expedition (2019-2020), to investigate interannual variability and to give context to the aerosol characteristics from within the central Arctic. Our analysis identifies that, overall, the central Arctic exhibits typical seasonal patterns of aerosols, including anthropogenic influence from Arctic haze in winter and secondary aerosol processes in summer. The seasonal pattern corresponds to the global radiation, surface air temperature, and timing of sea ice melting/freezing, which drive changes in transport patterns and secondary aerosol processes. In winter, the Norilsk region in Russia/Siberia was the dominant source of Arctic haze signals in the PNSD and BC observations, which contributed to higher accumulation-mode PNC and BC mass concentrations in the central Arctic than at land-based observatories. We also show that the wintertime Arctic Oscillation (AO) phenomenon, which was reported to achieve a record-breaking positive phase during January-March 2020, explains the unusual timing and magnitude of Arctic haze across the Arctic region compared to longer-term observations. In summer, the aerosol PNCs of the nucleation and Aitken modes are enhanced; however, concentrations were notably lower in the central Arctic over the ice pack than at land-based sites further south. The analysis presented herein provides a current snapshot of Arctic aerosol processes in an environment that is characterized by rapid changes, which will be crucial for improving climate model predictions, understanding linkages between different environmental processes, and investigating the impacts of climate change in future Arctic aerosol studies.Peer reviewe

Variation in CHI3LI in Relation to Type 2 Diabetes and Related Quantitative Traits

CHI3LI encoding the inflammatory glycoprotein YKL-40 is located on chromosome 1q32.1. YKL-40 is involved in inflammatory processes and patients with Type 2 Diabetes (T2D) have elevated circulating YKL-40 levels which correlate with their level of insulin resistance. Interestingly, it has been reported that rs10399931 (-329 G/A) of CHI3LI contributes to the inter-individual plasma YKL-40 levels in patients with sarcoidosis, and that rs4950928 (-131 C/G) is a susceptibility polymorphism for asthma and a decline in lung function. We hypothesized that single nucleotide polymorphisms (SNPs) or haplotypes thereof the CHI3LI locus might influence risk of T2D. The aim of the present study was to investigate the putative association between SNPs and haplotype blocks of CHI3LI and T2D and T2D related quantitative traits.Eleven SNPs of CHI3LI were genotyped in 6514 individuals from the Inter99 cohort and 2924 individuals from the outpatient clinic at Steno Diabetes Center. In cas-control studies a total of 2345 T2D patients and 5302 individuals with a normal glucose tolerance test were examined. We found no association between rs10399931 (OR, 0.98 (CI, 0.88-1.10), p = 0.76), rs4950928 (0.98 (0.87-1.10), p = 0.68) or any of the other SNPs with T2D. Similarly, we found no significant association between any of the 11 tgSNPs and T2D related quantitative traits, all p>0.14. None of the identified haplotype blocks of CHI3LI showed any association with T2D, all p>0.16.None of the examined SNPs or haplotype blocks of CHI3LI showed any association with T2D or T2D related quantitative traits. Estimates of insulin resistance and dysregulated glucose homeostasis in T2D do not seem to be accounted for by the examined variations of CHI3LI

NT-proBNP and Circulating Inflammation Markers in Prediction of a Normal Myocardial Scintigraphy in Patients with Symptoms of Coronary Artery Disease

Myocardial perfusion imaging (MPI) can detect myocardial perfusion abnormalities but many examinations are without pathological findings. This study examines whether circulating biomarkers can be used as screening modality prior to MPI.243 patients with an intermediate risk of CAD or with known CAD with renewed suspicion of ischemia were referred to MPI. Blood samples were analyzed for N-terminal fragment of the prohormone brain natriuretic peptide (NT-proBNP), YKL-40, IL-6, matrix metalloproteinase 9 (MMP-9) and high sensitive C-reactive protein (hsCRP). Patients with myocardial perfusion defects had elevated levels of NT-proBNP (p<0.0001), YKL-40 (p = 0.03) and IL-6 (p = 0.03) but not of hsCRP (p = 0.58) nor of MMP-9 (p = 0.14). The NT-proBNP increase was observed in both genders (p<0.0001), whereas YKL-40 (p = 0.005) and IL-6 (p = 0.02) were elevated only in men. A NT-proBNP cut off-concentration at 25 ng/l predicted a normal MPI with a negative predictive value >95% regardless of existing CAD.20-25% of patients suspected of CAD could have been spared a MPI by using a NT-proBNP cut-off concentration at 25 ng/l with a negative predictive value >95%. NT-proBNP has the potential use of being a screening marker of CAD before referral of the patient to MPI

Differing mechanisms of new particle formation at two Arctic sites.

New particle formation in the Arctic atmosphere is an important source of aerosol particles. Understanding the processes of Arctic secondary aerosol formation is crucial due to their significant impact on cloud properties and therefore Arctic amplification. We observed the molecular formation of new particles from low-volatility vapors at two Arctic sites with differing surroundings. In Svalbard, sulfuric acid (SA) and methane sulfonic acid (MSA) contribute to the formation of secondary aerosol and to some extent to cloud condensation nuclei (CCN). This occurs via ion-induced nucleation of SA and NH3 and subsequent growth by mainly SA and MSA condensation during springtime and highly oxygenated organic molecules during summertime. By contrast, in an ice-covered region around Villum, we observed new particle formation driven by iodic acid but its concentration was insufficient to grow nucleated particles to CCN sizes. Our results provide new insight about sources and precursors of Arctic secondary aerosol particles.Peer reviewe