A multi-state model incorporating estimation of excess hazards and multiple time scales

As cancer patient survival improves, late effects from treatment are becoming the next clinical challenge. Chemotherapy and radiotherapy, for example, potentially increase the risk of both morbidity and mortality from second malignancies and cardiovascular disease. To provide clinically relevant population-level measures of late effects, it is of importance to (1) simultaneously estimate the risks of both morbidity and mortality, (2) partition these risks into the component expected in the absence of cancer and the component due to the cancer and its treatment, and (3) incorporate the multiple time scales of attained age, calendar time, and time since diagnosis. Multi-state models provide a framework for simultaneously studying morbidity and mortality, but do not solve the problem of partitioning the risks. However, this partitioning can be achieved by applying a relative survival framework, by allowing is to directly quantify the excess risk. This paper proposes a combination of these two frameworks, providing one approach to address (1)-(3). Using recently developed methods in multi-state modeling, we incorporate estimation of excess hazards into a multi-state model. Both intermediate and absorbing state risks can be partitioned and different transitions are allowed to have different and/or multiple time scales. We illustrate our approach using data on Hodgkin lymphoma patients and excess risk of diseases of the circulatory system, and provide user-friendly Stata software with accompanying example code

Patterns of survival among patients with myeloproliferative neoplasms diagnosed in Sweden from 1973 to 2008: a population-based study.

To access publisher full text version of this article. Please click on the hyperlink in Additional Links field.Reported survival in patients with myeloproliferative neoplasms (MPNs) shows great variation. Patients with primary myelofibrosis (PMF) have substantially reduced life expectancy, whereas patients with polycythemia vera (PV) and essential thrombocythemia (ET) have moderately reduced survival in most, but not all, studies. We conducted a large population-based study to establish patterns of survival in more than 9,000 patients with MPNs. We identified 9,384 patients with MPNs (from the Swedish Cancer Register) diagnosed from 1973 to 2008 (divided into four calendar periods) with follow-up to 2009. Relative survival ratios (RSRs) and excess mortality rate ratios were computed as measures of survival. Patient survival was considerably lower in all MPN subtypes compared with expected survival in the general population, reflected in 10-year RSRs of 0.64 (95% CI, 0.62 to 0.67) in patients with PV, 0.68 (95% CI, 0.64 to 0.71) in those with ET, and 0.21 (95% CI, 0.18 to 0.25) in those with PMF. Excess mortality was observed in patients with any MPN subtype during all four calendar periods (P < .001). Survival improved significantly over time (P < .001); however, the improvement was less pronounced after the year 2000 and was confined to patients with PV and ET. We found patients with any MPN subtype to have significantly reduced life expectancy compared with the general population. The improvement over time is most likely explained by better overall clinical management of patients with MPN. The decreased life expectancy even in the most recent calendar period emphasizes the need for new treatment options for these patients.Swedish Cancer Society CAN 2009/1203 Stockholm County Council SLL 20090201 Karolinska Institutet SLL 20090201 Karolinska Institutet Foundations 2009Fobi0072 Shire Pharmaceuticals Adolf H. Lundin Charitable Foundatio

Cyclone-induced surface ozone and HDO depletion in the Arctic

Ground-based, satellite, and reanalysis datasets were used to identify two similar cyclone-induced surface ozone depletion events at Eureka, Canada (80.1° N, 86.4° W), in March 2007 and April 2011. These two events were coincident with observations of hydrogen deuterium oxide (HDO) depletion, indicating that condensation and sublimation occurred during the transport of the ozone-depleted air masses. Ice clouds (vapour and crystals) and aerosols were detected by lidar and radar when the ozone- and HDO-depleted air masses arrived over Eureka. For the 2007 event, an ice cloud layer was coincident with an aloft ozone depletion layer at 870 m altitude on 2–3 March, indicating this ice cloud layer contained bromine-enriched blowing-snow particles. Over the following 3 days, a shallow surface ozone depletion event (ODE) was observed at Eureka after the precipitation of bromine-enriched particles onto the local snowpack. A chemistry–climate model (UKCA) and a chemical transport model (pTOMCAT) were used to simulate the surface ozone depletion events. Incorporating the latest surface snow salinity data obtained for the Weddell Sea into the models resulted in improved agreement between the modelled and measured BrO concentrations above Eureka. MERRA-2 global reanalysis data and the FLEXPART particle dispersion model were used to study the link between the ozone and HDO depletion. In general, the modelled ozone and BrO showed good agreement with the ground-based observations; however, the modelled BrO and ozone in the near-surface layer are quite sensitive to the snow salinity. HDO depletion observed during these two blowing-snow ODEs was found to be weaker than pure Rayleigh fractionation. This work provides evidence of a blowing-snow sublimation process, which is a key step in producing bromine-enriched sea-salt aerosol

Genetic predisposition to adiposity is associated with increased objectively assessed sedentary time in young children.

Increased sedentariness has been linked to the growing prevalence of obesity in children, but some longitudinal studies suggest that sedentariness may be a consequence rather than a cause of increased adiposity. We used Mendelian randomization to examine the causal relations between body mass index (BMI) and objectively assessed sedentary time and physical activity in 3-8 year-old children from one Finnish and two Danish cohorts [NTOTAL=679]. A genetic risk score (GRS) comprised of 15 independent genetic variants associated with childhood BMI was used as the instrumental variable to test causal effects of BMI on sedentary time, total physical activity, and moderate-to-vigorous physical activity (MVPA). In fixed effects meta-analyses, the GRS was associated with 0.05 SD/allele increase in sedentary time (P=0.019), but there was no significant association with total physical activity (beta=0.011 SD/allele, P=0.58) or MVPA (beta=0.001 SD/allele, P=0.96), adjusting for age, sex, monitor wear-time and first three genome-wide principal components. In two-stage least squares regression analyses, each genetically instrumented one unit increase in BMI z-score increased sedentary time by 0.47 SD (P=0.072). Childhood BMI may have a causal influence on sedentary time but not on total physical activity or MVPA in young children. Our results provide important insights into the regulation of movement behaviour in childhood

A rare regulatory variant in the MEF2D gene affects gene regulation and splicing and is associated with a SLE sub-phenotype in Swedish cohorts

© 2018, The Author(s). Systemic lupus erythematosus (SLE) is an autoimmune disorder with heterogeneous clinical presentation and complex etiology involving the interplay between genetic, epigenetic, environmental and hormonal factors. Many common SNPs identified by genome wide-association studies (GWAS) explain only a small part of the disease heritability suggesting the contribution from rare genetic variants, undetectable in GWAS, and complex epistatic interactions. Using targeted re-sequencing of coding and conserved regulatory regions within and around 215 candidate genes selected on the basis of their known role in autoimmunity and genes associated with canine immune-mediated diseases, we identified a rare regulatory variant rs200395694:G > T located in intron 4 of the MEF2D gene encoding the myocyte-specific enhancer factor 2D transcription factor and associated with SLE in Swedish cohorts (504 SLE patients and 839 healthy controls, p = 0.014, CI = 1.1–10). Fisher’s exact test revealed an association between the genetic variant and a triad of disease manifestations including Raynaud, anti-U1-ribonucleoprotein (anti-RNP), and anti-Smith (anti-Sm) antibodies (p = 0.00037) among the patients. The DNA-binding activity of the allele was further studied by EMSA, reporter assays, and minigenes. The region has properties of an active cell-specific enhancer, differentially affected by the alleles of rs200395694:G > T. In addition, the risk allele exerts an inhibitory effect on the splicing of the alternative tissue-specific isoform, and thus may modify the target gene set regulated by this isoform. These findings emphasize the potential of dissecting traits of complex diseases and correlating them with rare risk alleles with strong biological effects

A risk haplotype of STAT4 for systemic lupus erythematosus is over-expressed, correlates with anti-dsDNA and shows additive effects with two risk alleles of IRF5

Systemic lupus erythematosus (SLE) is the prototype autoimmune disease where genes regulated by type I interferon (IFN) are over-expressed and contribute to the disease pathogenesis. Because signal transducer and activator of transcription 4 (STAT4) plays a key role in the type I IFN receptor signaling, we performed a candidate gene study of a comprehensive set of single nucleotide polymorphism (SNPs) in STAT4 in Swedish patients with SLE. We found that 10 out of 53 analyzed SNPs in STAT4 were associated with SLE, with the strongest signal of association (P = 7.1 × 10−8) for two perfectly linked SNPs rs10181656 and rs7582694. The risk alleles of these 10 SNPs form a common risk haplotype for SLE (P = 1.7 × 10−5). According to conditional logistic regression analysis the SNP rs10181656 or rs7582694 accounts for all of the observed association signal. By quantitative analysis of the allelic expression of STAT4 we found that the risk allele of STAT4 was over-expressed in primary human cells of mesenchymal origin, but not in B-cells, and that the risk allele of STAT4 was over-expressed (P = 8.4 × 10−5) in cells carrying the risk haplotype for SLE compared with cells with a non-risk haplotype. The risk allele of the SNP rs7582694 in STAT4 correlated to production of anti-dsDNA (double-stranded DNA) antibodies and displayed a multiplicatively increased, 1.82-fold risk of SLE with two independent risk alleles of the IRF5 (interferon regulatory factor 5) gene

The silence of the archives:business history, Postcolonialism and archival ethnography

History as a discipline has been accused of being a-theoretical. Business historians working at business schools, however, need to better explicate their historical methodology, not theory, in order to communicate the value of archival research to social scientists, and to train future doctoral students outside history departments. This paper seeks to outline an important aspect of historical methodology, which is data collection from archives. In this area, postcolonialism and archival ethnography have made significant methodological contributions not just for non-Western history, as it has emphasized the importance of considering how archives were created, and how one can legitimately use them despite their limitations. I argue that these approaches offer new insights into the particularities of researching business archives

Ultrafast resonant interatomic coulombic decay induced by quantum fluid dynamics

Interatomic processes play a crucial role in weakly bound complexes exposed to ionizing radiation; therefore, gaining a thorough understanding of their efficiency is of fundamental importance. Here, we directly measure the timescale of interatomic Coulombic decay (ICD) in resonantly excited helium nanodroplets using a high-resolution, tunable, extreme ultraviolet free-electron laser. Over an extensive range of droplet sizes and laser intensities, we discover the decay to be surprisingly fast, with decay times as short as 400 fs, nearly independent of the density of the excited states. Using a combination of time- dependent density functional theory and ab initio quantum chemistry calculations, we elucidate the mechanisms of this ultrafast decay process, where pairs of excited helium atoms in one droplet strongly attract each other and form merging void bubbles, which drastically accelerates ICD