Phytophthora ramorum

Phytophthora ramorum is a recently emerged plant pathogen and causal agent of one of the most destructive and devastating diseases currently affecting US horticulture and forests (Rizzo et al. 2002, 2005). This oomycete pathogen was discovered in Marin County, California, in the mid-1990s, causing sudden oak death on coast live oak (Quercus agrifolia) and tanoak (Notholithocarpus densiflorus) and simultaneously discovered in Europe causing foliar blight on Rhododendron and Viburnum (Rizzo et al. 2002; Werres et al. 2001). It is now known to affect more than 100 plant species, including economically important nursery and forest host species (Frankel 2008; Rizzo et al. 2005; Tooley et al. 2004; Tooley and Kyde 2007)

Constraining multiple systems with GAIA

GAIA will provide observations of some multiple asteroid and dwarf systems. These observations are a way to determine and improve the quantification of dynamical parameters, such as the masses and the gravity fields, in these multiple systems. Here we investigate this problem in the cases of Pluto's and Eugenia's system. We simulate observations reproducing an approximate planning of the GAIA observations for both systems, as well as the New Horizons observations of Pluto. We have developed a numerical model reproducing the specific behavior of multiple asteroid system around the Sun and fit it to the simulated observations using least-square method, giving the uncertainties on the fitted parameters. We found that GAIA will improve significantly the precision of Pluto's and Charon's mass, as well as Petit Prince's orbital elements and Eugenia's polar oblateness.Comment: 5 pages, accepted by Planetary and Space Science, Gaia GREAT-SSO-Pis

Characterization of Three-Dimensional Spatial Aggregation and Association Patterns of Brown Rot Symptoms within Intensively Mapped Sour Cherry Trees

Characterization of spatial patterns of plant disease can provide insights into important epidemiological processes such as sources of inoculum, mechanisms of dissemination, and reproductive strategies of the pathogen population. While two-dimensional patterns of disease (among plants within fields) have been studied extensively, there is limited information on three-dimensional patterns within individual plant canopies. Reported here are the detailed mapping of different symptom types of brown rot (caused by Monilinia laxa) in individual sour cherry tree (Prunus cerasus) canopies, and the application of spatial statistics to the resulting data points to de-termine patterns of symptom aggregation and association. Methods – A magnetic digitizer was uti-lized to create detailed three-dimensional maps of three symptom types (blossom blight, shoot blight, and twig canker) in eight sour cherry tree canopies during the green fruit stage of develop-ment. The resulting point patterns were analyzed for aggregation (within a given symptom type) and pairwise association (between symptom types) using a three-dimensional extension of nearest-neighbor analysis. Key Results – Symptoms of M. laxa infection were generally aggregated within the canopy volume, but there was no consistent pattern for one symptom type to be more or less aggre-gated than the other. Analysis of spatial association among symptom types indicated that previous year’s twig cankers may play an important role in influencing the spatial pattern of current year’s symptoms. This observation provides quantitative support for the epidemiological role of twig can-kers as sources of primary inoculum within the tree. Conclusions – Presented here is a new approach to quantify spatial patterns of plant disease in complex fruit tree canopies using point pattern anal-ysis. This work provides a framework for quantitative analysis of three-dimensional spatial patterns within the finite tree canopy, applicable to many fields of research

Modulation of LISA free-fall orbits due to the Earth-Moon system

We calculate the effect of the Earth-Moon (EM) system on the free-fall motion of LISA test masses. We show that the periodic gravitational pulling of the EM system induces a resonance with fundamental frequency 1 yr^-1 and a series of periodic perturbations with frequencies equal to integer harmonics of the synodic month (9.92 10^-7 Hz). We then evaluate the effects of these perturbations (up to the 6th harmonics) on the relative motions between each test masses couple, finding that they range between 3mm and 10pm for the 2nd and 6th harmonic, respectively. If we take the LISA sensitivity curve, as extrapolated down to 10^-6 Hz, we obtain that a few harmonics of the EM system can be detected in the Doppler data collected by the LISA space mission. This suggests that the EM system gravitational near field could provide an absolute calibration for the LISA sensitivity at very low frequencies.Comment: 15 pages, 5 figure

Mitotic Recombination and Rapid Genome Evolution in the Invasive Forest Pathogen Phytophthora ramorum

Invasive alien species often have reduced genetic diversity and must adapt to new environments. Given the success of many invasions, this is sometimes called the genetic paradox of invasion. Phytophthora ramorum is invasive, limited to asexual reproduction within four lineages, and presumed clonal. It is responsible for sudden oak death in the United States, sudden larch death in Europe, and ramorum blight in North America and Europe. We sequenced the genomes of 107 isolates to determine how this pathogen can overcome the invasion paradox. Mitotic recombination (MR) associated with transposons and low gene density has generated runs of homozygosity (ROH) affecting 2,698 genes, resulting in novel genotypic diversity within the lineages. One ROH enriched in effectors was fixed in the NA1 lineage. An independent ROH affected the same scaffold in the EU1 lineage, suggesting an MR hot spot and a selection target. Differences in host infection between EU1 isolates with and without the ROH suggest that they may differ in aggressiveness. Non-core regions (not shared by all lineages) had signatures of accelerated evolution and were enriched in putative pathogenicity genes and transposons. There was a striking pattern of gene loss, including all effectors, in the non-core EU2 genome. Positive selection was observed in 8.0% of RxLR and 18.8% of Crinkler effector genes compared with 0.9% of the core eukaryotic gene set. We conclude that the P. ramorum lineages are diverging via a rapidly evolving non-core genome and that the invasive asexual lineages are not clonal, but display genotypic diversity caused by MR

Recipient Morbidity After Living and Deceased Donor Liver Transplantation: Findings from the A2ALL Retrospective Cohort Study †

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/72284/1/j.1600-6143.2008.02440.x.pd

Liver transplantation for alcoholic cirrhosis: Long term follow-up and impact of disease recurrence

Background. Alcoholic liver disease has emerged as a leading indication for hepatic transplantation, although it is a controversial use of resources. We aimed to examine all aspects of liver transplantation associated with alcohol abuse. Methods. Retrospective cohort analysis of 123 alcoholic patients with a median of 7 years follow-up at one center. Results. In addition to alcohol, 43 (35%) patients had another possible factor contributing to cirrhosis. Actuarial patient and graft survival rates were, respectively, 84% and 81% (1 year); 72% and 66% (5 years); and 63% and 59% (7 years). After transplantation, 18 patients (15%) manifested 21 noncutaneous de novo malignancies, which is significantly more than controls (P=0.0001); upper aerodigestive squamous carcinomas were over-represented (P=0.03). Thirteen patients had definitely relapsed and three others were suspected to have relapsed. Relapse was predicted by daily ethanol consumption (P=0.0314), but not by duration of pretransplant sobriety or explant histology. No patient had alcoholic hepatitis after transplantation and neither late onset acute nor chronic rejection was significantly increased. Multiple regression analyses for predictors of graft failure identified major biliary/vascular complications (P=0.01), chronic bile duct injury on biopsy (P=0.002), and pericellular fibrosis on biopsy (P=0.05); graft viral hepatitis was marginally significant (P=0.07) on univariate analysis. Conclusions. Alcoholic liver disease is an excellent indication for liver transplantation in those without coexistent conditions. Recurrent alcoholic liver disease alone is not an important cause of graft pathology or failure. Potential recipients should be heavily screened before transplantation for coexistent conditions (e.g., hepatitis C, metabolic diseases) and other target-organ damage, especially aerodigestive malignancy, which are greater causes of morbidity and mortality than is recurrent alcohol liver disease

Modern Electronic Techniques Applied to Physics and Engineering

Contains reports on seven research projects.Office of Scientific Research and Development (OSRD) OEMsr-26

Diabetes status and post-load plasma glucose concentration in relation to site-specific cancer mortality: findings from the original Whitehall study

ObjectiveWhile several studies have reported on the relation of diabetes status with pancreatic cancer risk, the predictive value of this disorder for other malignancies is unclear. Methods: The Whitehall study, a 25year follow-up for mortality experience of 18,006 men with data on post-challenge blood glucose and self-reported diabetes, allowed us to address these issues. Results: There were 2158 cancer deaths at follow-up. Of the 15 cancer outcomes, diabetes status was positively associated with mortality from carcinoma of the pancreas and liver, while the relationship with lung cancer was inverse, after controlling for a range of potential covariates and mediators which included obesity and socioeconomic position. After excluding deaths occurring in the first 10years of follow-up to examine the effect of reverse causality, the magnitude of the relationships for carcinoma of the pancreas and lung was little altered, while for liver cancer it was markedly attenuated. Conclusions: In the present study, diabetes status was related to pancreatic, liver, and lung cancer risk. Cohorts with serially collected data on blood glucose and covariates are required to further examine this area

Prognostic value of Ishak fibrosis stage: Findings from the hepatitis C antiviral long-term treatment against cirrhosis trial

Studies of the prognostic value of Ishak fibrosis stage are lacking. We used multi-year follow-up of the Hepatitis C Antiviral Long-Term Treatment Against Cirrhosis (HALT-C) Trial to determine whether individual Ishak fibrosis stages predicted clinical outcomes in patients with chronic hepatitis C. Baseline liver biopsy specimens from 1050 patients with compensated chronic hepatitis C who had failed combination peginterferon and ribavirin were reviewed by a panel of expert hepatopathologists. Fibrosis was staged with the Ishak scale (ranging from 0 = no fibrosis to 6 = cirrhosis). Biopsy fragmentation and length as well as number of portal tracts were recorded. We compared rates of prespecified clinical outcomes of hepatic decompensation and hepatocellular carcinoma across individual Ishak fibrosis stages. Of 1050 biopsy specimens, 25% were fragmented, 63% longer than 1.5 cm, 69% larger than 10 mm 2 , and 75% had 10 or more portal tracts. Baseline laboratory markers of liver disease severity were worse and the frequency of esophageal varices higher with increasing Ishak stage ( P < 0.0001). The 6-year cumulative incidence of first clinical outcome was 5.6% for stage 2, 16.1% for stage 3, 19.3% for stage 4, 37.8% for stage 5, and 49.3% for stage 6. Among nonfragmented biopsy specimens, the predictive ability of Ishak staging was enhanced; however, no association was observed between Ishak stage and outcomes for fragmented biopsy specimens because of high rates of outcomes for patients with noncirrhotic stages. Similar results were observed with liver transplantation or liver-related death as the outcome. Conclusion : Ishak fibrosis stage predicts clinical outcomes, need for liver transplantation, and liver-related death in patients with chronic hepatitis C. Patients with fragmented biopsy specimens with low Ishak stage may be understaged histologically. (H EPATOLOGY 2010;51:585–594.)Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/64929/1/23315_ftp.pd