Radius measurements of cataclysmic variable accretion disks

Abstract. Cataclysmic variables (CVs) are interacting binary systems with a white dwarf primary and a low-mass main sequence star secondary. The secondary star fills its Roche lobe and transfers mass onto the white dwarf. Often the gas flow forms an accretion disk around the primary. CVs are characterised by outbursts caused by changes in the mass transfer. In outbursts they can brighten from a couple of magnitudes to tens of magnitudes. Between the outbursts CVs are said to be in quiescence. Accretion disks in cataclysmic variables are the main source of emission in visual wavelengths. Thus, with their assistance, much has been revealed about the stars forming CVs and the ongoing mass transfer process between them. The outburst cycle has been thought to affect the size of the accretion disk: its radius has been thought to shrink in quiescence and expand in outburst. This idea has been recently questioned, and the seemingly varying radius might be caused by radii measurement methods tracking the location of the gas stream hitting the accretion disk instead the actual edge of the disk. In this thesis the standard model for CVs is reviewed and the formation of characteristically double-peaked emission lines from accretion disks is explained. The knowledge is then applied to measuring the radius of the accretion disk of OY Carinae in quiescence. It is found to be close to its theoretical maximum value, not significantly smaller as it should be if the disk size varied during the outburst cycle. This result backs up the idea of a consistently large accretion disk

Kinematics of the outer accretion disk in cataclysmic variables

Abstract. This Masters thesis focuses on studying the kinematics of the outer accretion disk in cataclysmic variables. Cataclysmic variables are a type of interacting binary stars featuring a white dwarf and a main sequence star. Accretion disks in cataclysmic variables are born, when a secondary star still in main sequence overfills its Roche lobe and starts leaking gas towards the primary star (the white dwarf). The extent of the accretion disk has been a cause for discussion; methods measuring it from the hot spot, the place where accretion stream hits the disk, characteristically lead to smaller radii than measuring the radius from outer disk velocities. However, disk size estimates from the outer disk velocities heavily depend on the velocity field. The aim here is to check how close the outer accretion disk is to Keplerian velocities and simple three-body orbits. To do this, they are compared to simulated accretion disks using Smoothed Particle Hydrodynamics. Same comparisons are then done against observational data using Doppler tomography. Our study finds that the Keplerian velocity at the tidal truncation limit can safely be used as a lower limit for orbit-averaged disk. Furthermore, last non-intersecting three-body orbit seems to trace the disk edge quite well, and it can be used as an estimate for accretion disk size

Estimating Use-Values and Relative Importance of Amazonian Flood Plain Trees and Forests to Local Inhabitants

Use-values have been advocated as a tool to compare the value of not just individual species, but also of plant families and forest types to local people, in order, for example, to identify species or habitats in need of special management or conservation. We estimated use-values in three forest types (upper restinga, lower restinga, tahuampa) on the Amazon flood plain south of Iquitos (Peru), compared two methodologies, identified the most valuable species and contrasted these valuations with the actual use of forest resources in local villages. A new method for estimating use-values was contrasted with the method of Phillips and Gentry (1993a). Despite philosophical and procedural differences, estimates were highly correlated (R2=0.86). We discuss limitations of both methods and suggest some possible enhancements. The need to discriminate between past, present and potential uses is emphasised

The role of the P2X7 receptor on bone loss in a mouse model of inflammation-mediated osteoporosis

In inflammatory autoimmune diseases, bone loss is frequent. In most cases, secondary osteoporosis is caused by treatment with systemic glucocorticoid. However, the pathogenesis behind the bone loss is presumed multifactorial. We aimed to elucidate the role of the P2X7 receptor on bone mineral density (BMD), microarchitecture, and bone strength in a standardized mouse model of inflammation-mediated osteoporosis (IMO). In total 146 mice completed our protocol, 70 wild type (WT) mice and 76 P2X7−/− (knockout, KO). BMD at the femur and spine decreased significantly from baseline to day 20 in the WT IMO mice (p < 0.01). In the WT vehicle, KO vehicle and KO IMO, no significant BMD changes were found. Bone strength showed a lower mid-shaft max strength (p = 0.038) and also a non-significant trend towards lower strength at the femoral neck of the WT IMO group. Trabecular bone volume fraction (BV/TV) and connectivity density (CD) after 20 days were significantly decreased in the WT IMO group (p = 0.001). In contrast, the WT vehicle and KO vehicle, BV/TV and CD did no change at 20 days. Cortical bone revealed no significant microarchitectural changes after 20 days in the WT IMO group, whereas the total cortical area increased significantly in WT vehicle and KO IMO after 20 days (5.2% and 8.8%, respectively). In conclusion, the P2X7 receptor KO mice did not respond to inflammation with loss of BMD whereas the WT mice had a significant loss of BMD, bone strength and trabecular microarchitecture, demonstrating a role for the P2X7 receptor in inflammatory bone loss

Murine nephrotoxic nephritis as a model of chronic kidney disease

Using the nonaccelerated murine nephrotoxic nephritis (NTN) as a model of chronic kidney disease (CKD) could provide an easily inducible model that enables a rapid test of treatments. Originally, the NTN model was developed as an acute model of glomerulonephritis, but in this study we evaluate the model as a CKD model and compare CD1 and C57BL/6 female and male mice. CD1 mice have previously showed an increased susceptibility to CKD in other CKD models. NTN was induced by injecting nephrotoxic serum (NTS) and evaluated by CKD parameters including albuminuria, glomerular filtration rate (GFR), mesangial expansion, and renal fibrosis. Both strains showed significant albuminuria on days 2-3 which remained significant until the last time point on days 36-37 supporting dysfunctional filtration also observed by a significantly declined GFR on days 5-6, 15–17, and 34–37. Both strains showed early progressive mesangial expansion and significant renal fibrosis within three weeks suggesting CKD development. CD1 and C57BL/6 females showed a similar disease progression, but female mice seemed more susceptible to NTS compared to male mice. The presence of albuminuria, GFR decline, mesangial expansion, and fibrosis showed that the NTN model is a relevant CKD model both in C57BL/6 and in CD1 mice

Analysis of mesoscale effects in high-shear granulation through a computational fluid dynamics-population balance coupled compartment model

There is a need for mesoscale resolution and coupling between flow-field information and the evolution of particle properties in high-shear granulation. We have developed a modelling framework that compartmentalizes the high-shear granulation process based on relevant process parameters in time and space. The model comprises a coupled-flow-field and population-balance solver and is used to resolve and analyze the effects of mesoscales on the evolution of particle properties. A Diosna high-shear mixer was modelled with microcrystalline cellulose powder as the granulation material. An analysis of the flow-field solution and compartmentalization allows for a resolution of the stress and collision peak at the impeller blades. Different compartmentalizations showed the importance of resolving the impeller region, for aggregating systems and systems with breakage. An independent study investigated the time evolution of the flow field by changing the particle properties in three discrete steps that represent powder mixing, the initial granulation stage mixing and the late stage granular mixing. The results of the temporal resolution study show clear changes in collision behavior, especially from powder to granular mixing, which indicates the importance of resolving mesoscale phenomena in time and space

Sex‐ and age group‐specific fracture incidence rates trends for type 1 and 2 diabetes mellitus

The incidence of major osteoporotic fractures has declined in men and women in Western countries over the last two decades. Although fracture risk is higher in persons with diabetes mellitus, trends of fractures remain unknown in men and women with diabetes. We investigated the trends in fracture incidence rates (IRs) in men and women with type 1 diabetes mellitus (T1D) and type 2 diabetes mellitus (T2D) in Denmark between 1997 and 2017. We identified men and women aged 18+ years who sustained a fracture (excluding skull and facial fractures) between 1997 and 2017 using the Danish National Patient Registry. We calculated sex-specific IRs of fractures per 10,000 person-years separately in persons with T1D, T2D, or without diabetes. Furthermore, we compared median IRs of the first 5 years (1997–2002) to the median IRs of the last 5 years (2012–2017). We identified 1,235,628 persons with fractures including 4863 (43.6% women) with T1D, 65,366 (57.5% women) with T2D, and 1,165,399 (54.1% women) without diabetes. The median IRs of fractures declined 20.2%, 19.9%, and 7.8% in men with T1D, T2D, and without diabetes, respectively (p-trend <0.05). The median IRs decreased 6.4% in women with T1D (p-trend = 0.35) and 25.6% in women with T2D (p-trend <0.05) but increased 2.3% in women without diabetes (p-trend = 0.08). Fracture IRs decreased in men with both diabetes types and only in women with T2D, highlighting the need for further attention behind the stable trend observed in women with T1D. © 2023 The Authors. JBMR Plus published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research

Optimizing protocols for extraction of bacteriophages prior to metagenomic analyses of phage communities in the human gut

BACKGROUND: The human gut is densely populated with archaea, eukaryotes, bacteria, and their viruses, such as bacteriophages. Advances in high-throughput sequencing (HTS) as well as bioinformatics have opened new opportunities for characterizing the viral communities harbored in our gut. However, limited attention has been given to the efficiency of protocols dealing with extraction of phages from fecal communities prior to HTS and their impact on the metagenomic dataset. RESULTS: We describe two optimized methods for extraction of phages from fecal samples based on tangential-flow filtration (TFF) and polyethylene glycol precipitation (PEG) approaches using an adapted method from a published protocol as control (literature-adapted protocol (LIT)). To quantify phage recovery, samples were spiked with low numbers of c2, ϕ29, and T4 phages (representatives of the Siphoviridae, Podoviridae, and Myoviridae families, respectively) and their concentration (plaque-forming units) followed at every step during the extraction procedure. Compared with LIT, TFF and PEG had higher recovery of all spiked phages, yielding up to 16 times more phage particles (PPs) and up to 68 times more phage DNA per volume, increasing thus the chances of extracting low abundant phages. TFF- and PEG-derived metaviromes showed 10 % increase in relative abundance of Caudovirales and unclassified phages infecting gut-associated bacteria (>92 % for TFF and PEG, 82.4 % for LIT). Our methods obtained lower relative abundance of the Myoviridae family (<16 %) as compared to the reference protocol (22 %). This decline, however, was not considered a true loss of Myoviridae phages but rather a greater level of extraction of Siphoviridae phages (TFF and PEG >32.5 %, LIT 22.6 %), which was achieved with the enhanced conditions of our procedures (e.g., reduced filter clogging). A high degree of phage diversity in samples extracted using TFF and PEG was documented by transmission electron microscopy. CONCLUSIONS: Two procedures (TFF and PEG) for extraction of bacteriophages from fecal samples were optimized using a set of spiked bacteriophages as process control. These protocols are highly efficient tools for extraction and purification of PPs prior to HTS in phage-metavirome studies. Our methods can be easily modified, being thus applicable and adjustable for in principle any solid environmental material in dissolution. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s40168-015-0131-4) contains supplementary material, which is available to authorized users