Simulations of Dynamic Relativistic Magnetospheres

Neutron stars and black holes are generally surrounded by magnetospheres of highly conducting plasma in which the magnetic flux density is so high that hydrodynamic forces are irrelevant. In this vanishing-inertia---or ultra-relativistic---limit, magnetohydrodynamics becomes force-free electrodynamics, a system of equations comprising only the magnetic and electric fields, and in which the plasma response is effected by a nonlinear current density term. In this dissertation I describe a new pseudospectral simulation code, designed for studying the dynamic magnetospheres of compact objects. A detailed description of the code and several numerical test problems are given. I first apply the code to the aligned rotator problem, in which a star with a dipole magnetic field is set rotating about its magnetic axis. The solution evolves to a steady state, which is nearly ideal and dissipationless everywhere except in a current sheet, or magnetic field discontinuity, at the equator, into which electromagnetic energy flows and is dissipated. Magnetars are believed to have twisted magnetospheres, due to internal magnetic evolution which deforms the crust, dragging the footpoints of external magnetic field lines. This twisting may be able to explain both magnetars' persistent hard X-ray emission and their energetic bursts and flares. Using the new code, I simulate the evolution of relativistic magnetospheres subjected to slow twisting through large angles. The field lines expand outward, forming a strong current layer; eventually the configuration loses equilibrium and a dynamic rearrangement occurs, involving large-scale rapid magnetic reconnection and dissipation of the free energy of the twisted magnetic field. When the star is rotating, the magnetospheric twisting leads to a large increase in the stellar spin-down rate, which may take place on the long twisting timescale or in brief explosive events, depending on where the twisting is applied and the history of the system. One such explosive field-expansion and reconnection event may have been responsible for the 27 August 1998 giant flare from SGR 1900+14, and the coincident sudden increase in spin period, or "braking glitch." The inner magnetospheres of relativistic compact objects are in strongly curved spacetimes. I describe the extension of the code to general-relativistic simulations, including the hypersurface foliation method and the 3+1 equations of force-free electrodynamics in curved, evolving spacetimes. A simple test problem for dynamical behavior in the Schwarzschild metric is presented, and the evolutions of the magnetospheres surrounding neutron stars and black holes, in vacuum and in force-free plasma, are compared

Bacterial diversification through geological time

Numerous studies have estimated plant and animal diversification dynamics; however, no comparable rigorous estimates exist for bacteria—the most ancient and widespread form of life on Earth. Here, we analyse phylogenies comprising up to 448,112 bacterial lineages to reconstruct global bacterial diversification dynamics. To handle such large phylogenies, we developed methods based on the statistical properties of infinitely large trees. We further analysed sequencing data from 60 environmental studies to determine the fraction of extant bacterial diversity missing from the phylogenies—a crucial parameter for estimating speciation and extinction rates. We estimate that there are about 1.4–1.9 million extant bacterial lineages when lineages are defined by 99% similarity in the 16S ribosomal RNA gene, and that bacterial diversity has been continuously increasing over the past 1 billion years (Gyr). Recent bacterial extinction rates are estimated at 0.03–0.05 per lineage per million years (lineage^(–1) Myr^(–1)), and are only slightly below estimated recent bacterial speciation rates. Most bacterial lineages ever to have inhabited this planet are estimated to be extinct. Our findings disprove the notion that bacteria are unlikely to go extinct, and provide a valuable perspective on the evolutionary history of a domain of life with a sparse and cryptic fossil record

Development and preliminary testing of the psychosocial adjustment to hereditary diseases scale

Background: The presence of Lynch syndrome (LS) can bring a lifetime of uncertainty to an entire family as members adjust to living with a high lifetime cancer risk. The research base on how individuals and families adjust to genetic-linked diseases following predictive genetic testing has increased our understanding of short-term impacts but gaps continue to exist in knowledge of important factors that facilitate or impede long-term adjustment. The failure of existing scales to detect psychosocial adjustment challenges in this population has led researchers to question the adequate sensitivity of these instruments. Furthermore, we have limited insight into the role of the family in promoting adjustment. Methods: The purpose of this study was to develop and initially validate the Psychosocial Adjustment to Hereditary Diseases (PAHD) scale. This scale consists of two subscales, the Burden of Knowing (BK) and Family Connectedness (FC). Items for the two subscales were generated from a qualitative data base and tested in a sample of 243 participants from families with LS. Results: The Multitrait/Multi-Item Analysis Program-Revised (MAP-R) was used to evaluate the psychometric properties of the PAHD. The findings support the convergent and discriminant validity of the subscales. Construct validity was confirmed by factor analysis and Cronbach’s alpha supported a strong internal consistency for BK (0.83) and FC (0.84). Conclusion: Preliminary testing suggests that the PAHD is a psychometrically sound scale capable of assessing psychosocial adjustment. We conclude that the PAHD may be a valuable monitoring tool to identify individuals and families who may require therapeutic interventions

Contrast nephropathy in patients with impaired renal function: High versus low osmolar media

Contrast nephropathy in patients with impaired renal function: High versus low osmolar media. Prescription of low osmolar contrast to prevent nephrotoxicity in subjects with pre-existing renal impairment is costly and has not been clearly shown to be effective. We entered 249 subjects with a pre-contrast serum creatinine greater than 120 /xmol/liter (1.35 mg/dl) having cardiac catheterization or intravenous contrast into a randomized controlled trial comparing high and low osmolar contrast. The outcome assessed was a rise in serum creatinine repeated 48 to 72 hours after contrast. A further 117 patients entered the non-randomized prospective arm of the study. In the randomized study the serum creatinine rose by at least 25% after contrast in 8 of 117 (6.8%) given high and in 5 of 132 (3.8%) given low osmolar contrast (P > 0.05, one-tailed 95% confidence interval for the difference 3 to 7.8%). More severe renal failure (greater than 50% increase in serum creatinine) after contrast was uncommon (3.4% with high and 1.5% with low osmolar contrast). A rise in serum creatinine after contrast was significantly associated with the severity of the pre-contrast renal impairment and the presence of diabetes mellitus, but not with type of contrast. Diabetics with a serum creatinine greater than 200 µl/liter (2.25 mg/dl) pre-contrast had a highest risk of deterioration in renal function after contrast. We conclude that in patients with pre-existing renal impairment the incidence of contrast nephropathy was not significantly different comparing high osmolar and nonionic contrast. The potential benefit of nonionic contrast in moderate renal impairment is likely to be small, but trials in diabetics with severe renal impairment should be undertaken urgently

C-Reactive protein and risk of ESRD: results from the Trial to Reduce Cardiovascular Events With Aranesp Therapy (TREAT)

Background: To better understand a potential association of elevated C-reactive protein (CRP) level with progression of chronic kidney disease (CKD), we examined the relationship of CRP level with the development of end-stage renal disease (ESRD) in the Trial to Reduce Cardiovascular Events With Aranesp Therapy (TREAT). Study Design Post hoc analysis of a randomized controlled trial. Setting & Participants: 4,038 patients with type 2 diabetes, CKD, and anemia in TREAT. Predictor: Baseline serum CRP concentrations. Outcomes: The primary outcome was development of ESRD; secondary outcomes included doubling of serum creatinine level, a composite of ESRD/serum creatinine doubling, and a composite of death or ESRD. Measurements: We fit unadjusted and adjusted Cox regression models to test the association of baseline CRP level with time to the development of the outcomes of interest. Results: Mean age of participants was 67 years, 43% were men, and 64% were white. Approximately half (48%) the patients had CRP levels > 3.0 mg/L; 668 patients developed ESRD, and 1,270 developed the composite outcome of death or ESRD. Compared with patients with baseline CRP levels ≤ 3.0 mg/L, those with moderately/markedly elevated CRP levels (≥6.9 mg/L; 24% of patients) had a higher adjusted risk for ESRD (HR, 1.32; 95% CI, 1.07-1.63) and the composite outcome of death or ESRD (HR, 1.41; 95% CI, 1.21-1.64). Although nonsignificant, similar trends were noted in competing-risk models. Limitations: Results may not be generalizable to nondiabetic CKD or diabetic CKD in the absence of anemia. Conclusions: Elevated baseline CRP levels are common in type 2 diabetic patients with anemia and CKD and are associated with the future development of ESRD and the composite of death or ESRD

A missense mutation in PKD1 attenuates the severity of renal disease

Mutations of PKD1 and PKD2 account for most cases of autosomal dominant polycystic kidney disease (ADPKD). Compared with PKD2, patients with PKD1 typically have more severe renal disease. Here, we report a follow-up study of a unique multigeneration family with bilineal ADPKD (NFL10) in which a PKD1 disease haplotype and a PKD2 (L736X) mutation co-segregated with 18 and 14 affected individuals, respectively. In our updated genotype–phenotype analysis of the family, we found that PKD1-affected individuals had uniformly mild renal disease similar to the PKD2-affected individuals. By sequencing all the exons and splice junctions of PKD1, we identified two missense mutations (Y528C and R1942H) from a PKD1-affected individual. Although both variants were predicted to be damaging to the mutant protein, only Y528C co-segregated with all of the PKD1-affected individuals in NFL10. Studies in MDCK cells stably expressing wild-type and mutant forms of PKD found that cell lines expressing the Y528C variant formed cysts in culture and displayed increased rates of growth and apoptosis. Thus, Y528C functions as a hypomorphic PKD1 allele. These findings have important implications for pathogenic mechanisms and molecular diagnostics of ADPKD

Variable neurologic phenotype in a GEFS+ family with a novel mutation in SCN1A

AbstractPurposeTo describe the spectrum of clinical disease in a mutliplex family with an autosomal dominant form of generalized epilepsy with febrile seizures plus (GEFS+) and determine its genetic etiology.MethodsMedical and family history was obtained on 11 clinically affected individuals and their relatives across three generations through medical chart review and home visits. A candidate gene approach including haplotype analysis and direct sequencing was used.ResultsAn epilepsy-associated haplotype was identified on 2q24. Direct sequencing of the entire SCN1A gene identified seven sequence variants. However, only one of these, c.1162 T>C, was not found in population controls. This transition in exon 8 of SCN1A predicts a substitution (Y388H) of a highly conserved tyrosine residue in the loop between transmembrane segments S5 and S6 of the sodium channel protein (Nav1.1). Clinical features in mutation carriers of this novel missense mutation were highly variable, ranging from febrile seizures to severe refractory epilepsy.ConclusionA novel missense mutation in the pore-forming region of the sodium channel gene SCN1A causes GEFS+ with a variable phenotype that includes mood and anxiety disorders, as well as ataxia, expanding the GEFS+ spectrum to include neuropsychiatric disease

Two functional indel polymorphisms in the promoter region of the Brahma gene (BRM) and disease risk and progression-free survival in colorectal cancer

Background and objective The Brahma gene (BRM) encodes a catalytic ATPase subunit of the Switch/Sucrose non-fermentable (SWI/SNF) complex, which modulates gene expression and many important cellular processes. Two indel polymorphisms in the promoter region of BRM (BRM-741 and BRM-1321) are associated with its reduced expression and the risk of susceptibility or survival outcomes in multiple solid cancers. In this study, we have examined these variants in relation to susceptibility and survival outcomes in colorectal cancer. Methods Genotypes were obtained using TaqMan assays in 427 cases and 408 controls. Multivariate logistic and Cox regression models were fitted to examine the associations of the BRM-741 and BRM-1321 genotypes adjusting for relevant covariates. Sub-group analyses based on tumor location and patient sex were also performed. In all analyses, indels were examined individually as well as in combination. Results Our results showed that there was no association between the BRM polymorphisms and the risk of colorectal cancer. However, genotype combinations of the BRM-741 and BRM-1321 variants were associated with the risk of colon cancer. Particularly, patients having at least one variant allele had increased risk of colon cancer when compared to patients with the double wild-type genotype. In the survival analyses, BRM-741 heterozygosity was associated with longer progression-free survival time in the colorectal cancer patients. A stronger association was detected in the male patients under the recessive genetic model where the homozygosity for the variant allele of BRM-741 was associated with shorter progression-free survival time. Conclusions Our analyses suggest that BRM-741 and BRM-1321 indels are associated with the risk of developing colon cancer and the BRM-741 indel is associated with the disease progression in colorectal cancer patients, especially in the male patients. Although our results show a different relationship between these indels and colorectal cancer compared to other cancer sites, they also suggest that BRM and its promoter variants may have biological roles in susceptibility and survival outcomes in colorectal cancers. Performing further analyses in additional and larger cohorts are needed to confirm our conclusions