Modelling competing risks in nephrology research: an example in peritoneal dialysis

BACKGROUND: Modelling competing risks is an essential issue in Nephrology Research. In peritoneal dialysis studies, sometimes inappropriate methods (i.e. Kaplan-Meier method) have been used to estimate probabilities for an event of interest in the presence of competing risks. In this situation a competing risk analysis should be preferable. The objectives of this study are to describe the bias resulting from the application of standard survival analysis to estimate peritonitis-free patient survival and to provide alternative statistical approaches taking competing risks into account. METHODS: The sample comprises patients included in a university hospital peritoneal dialysis program between October 1985 and June 2011 (n = 449). Cumulative incidence function and competing risk regression models based on cause-specific and subdistribution hazards were discussed. RESULTS: The probability of occurrence of the first peritonitis is wrongly overestimated using Kaplan-Meier method. The cause-specific hazard model showed that factors associated with shorter time to first peritonitis were age (>=55 years) and previous treatment (haemodialysis). Taking competing risks into account in the subdistribution hazard model, age remained significant while gender (female) but not previous treatment was identified as a factor associated with a higher probability of first peritonitis event. CONCLUSIONS: In the presence of competing risks outcomes, Kaplan-Meier estimates are biased as they overestimated the probability of the occurrence of an event of interest. Methods which take competing risks into account provide unbiased estimates of cumulative incidence for each specific outcome experienced by patients. Multivariable regression models such as those based on cause-specific hazard and on subdistribution hazard should be used in this competing risk setting

A comparison between pure active pharmaceutical ingredients and therapeutic deep eutectic solvents: solubility and permeability studies

THEDES, so called therapeutic deep eutectic solvents are here defined as a mixture of two components, which at a particular molar composition become liquid at room temperature and in which one of them is an active pharmaceutical ingredient (API). In this work, THEDES based on menthol complexed with three different APIs, ibuprofen (ibu), BA (BA) and phenylacetic acid (PA), were prepared. The interactions between the components that constitute the THEDES were studied by NMR, confirming that the eutectic system is formed by H-bonds between menthol and the API. The mobility of the THEDES components was studied by PFGSE NMR spectroscopy. It was determined that the self-diffusion of the species followed the same behavior as observed previously for ionic liquids, in which the components migrate via jumping between voids in the suprastructure created by punctual thermal fluctuations. The solubility and permeability of the systems in an isotonic solution was evaluated and a comparison with the pure APIs was established through diffusion and permeability studies carried out in a Franz cell. The solubility of the APIs when in the THEDES system can be improved up to 12 fold, namely for the system containing ibu. Furthermore, for this system the permeability was calculated to be 14 105 cm/s representing a 3 fold increase in comparison with the pure API. With the exception of the systems containing PA an increase in the solubility, coupled with an increase in permeability was observed. In this work, we hence demonstrate the efficiency of THEDES as a new formulation for the enhancement of the bioavailability of APIs by changing the physical state of the molecules from a solid dosage to a liquid system.he European Union’s Seventh Framework Programme (FP7/2007- 2013) under grant agreement nREGPOT-CT2012-316331- POLARIS and from Project ‘‘Novel smart and biomimetic materials for innovative regenerative medicine approaches (Ref.: RL1 - ABMR - NORTE-01-0124-FEDER-000016)” co-financed by North Portugal Regional Operational Programme (ON.2 – O Novo Norte), under the National Strategic Reference Framework (NSRF), through the European Regional Development Fund (ERDF). Funding was also provided by Fundação para a Ciência e a Tecnologia, through contracts LAQV-REQUIMTE: UID/QUI/50006/2013 and UCIBIOREQUIMTE: UID/Multi/04378/2013. This work was co-financed by the ERDF under the PT2020 Partnership Agreement (POCI-01- 0145-FEDER-007728).info:eu-repo/semantics/publishedVersio

Selection criteria of Zebrafish male donors for sperm cryopreservation

Selection criteria for sperm cryopreservation are highly relevant in zebrafish since sperm quality is particularly variable in this species. Successful cryopreservation depends on high-quality sperm, which can only be ensured by the selection of breeders. Consequently, male selection and management are a priority to improve cryopreservation, and therefore, this study aimed to characterize optimal age and sperm collection frequency in zebrafish. For this purpose, males from wild type (AB) and from a transgenic line [Tg(runx2:eGFP)] were sampled at 6, 8, 12, and 14 months. For each age, sperm were collected at time 0 followed by samplings at 2, 7, and 14 days of rest. Sperm quality was assessed according to motility and membrane viability parameters. Quality assessment showed that Tg(runx2:eGFP) displayed significantly higher motility than AB and younger males showed higher motility in both lines. Sperm collection frequency affected membrane viability. While AB fish recovered sperm viability after 14 days of rest, Tg(runx2:eGFP) could not recover. Consequently, it may be important to study the sperm quality of each zebrafish line before sperm cryopreservation. Taking into consideration the results achieved in both lines, sperm collection should be performed between 6 and 8 months of age with a minimum collection interval of 14 days.N730984, EBB-EAPA_501/2016, PEst-C/MAR/LA0015/2011info:eu-repo/semantics/publishedVersio

Better outcomes of peritoneal dialysis in diabetic patients in spite of risk of loss of autonomy for home dialysis

Introduction: Diabetes mellitus is a leading cause of chronic renal failure, challenging therapy strategies. Patients with diabetes may benefit from peritoneal dialysis (PD) but higher technique failure is feared. Our purpose was to critically evaluate clinical outcomes of this modality in diabetics, in order to find quality improvement strategies in these risk patients. Methods: A registry-based study of 432 incident patients, 23% with diabetes, from a university hospital PD program was performed. Traditional methods (Kaplan-Meier, Cox models) and innovative survival analysis, taking competing risks into account, were performed, as well as exploring the trends in cohorts according to the decade of PD start. Results: In spite of the detrimental effect of diabetes in patient survival compared to non-diabetics (77%, 52% vs 86%, 71%, at 2 and 4 years, respectively; p < 0.0001) the hazard ratio (HR) for death decreased in the more contemporary cohort (0.303, 95% confidence interval (CI) 0.150 - 0.614, p < 0.001). It is noteworthy that diabetes was not associated with lower technique survival: 74%, 51% vs 79%, 57%, at 2 and 4 years, respectively (p = not significant (NS)). On multivariate analysis, diabetes was an independent predictor for mortality, but not for technique failure. The hazard ratio (HR) for technique failure also decreased in the more recent cohort (0.566, 95% CI 0.348 - 0.919, p = 0.021). Among reasons for transfer to hemodialysis, proportion of ultrafiltration failure was similar between groups (26% vs 22%, p = NS), but drop-out due to loss of autonomy occurred more in the group with diabetes (23% vs 5%, p = 0.004), mainly due to ischemic stroke. The hospitalization rate was also higher in diabetic patients (1.39 vs 0.84 episodes per patient-year (E/PY), p = 0.004) but the peritonitis rate was not increased (0.53 vs 0.61 E/PY, p = NS). Conclusion: PD was an effective long-term renal replacement therapy in diabetics, without higher rates of technique failure, ultrafiltration failure or peritonitis. Better outcomes were achieved in the contemporary cohort. The menace of autonomy loss due to stroke and higher hospitalization rates enhance the need for assisted PD strategies and better control of comorbidities

Sprouty2 mediated tuning of signalling is essential for somite myogenesis

Background: Negative regulators of signal transduction cascades play critical roles in controlling different aspects of normal embryonic development. Sprouty2 (Spry2) negatively regulates receptor tyrosine kinases (RTK) and FGF signalling and is important in differentiation, cell migration and proliferation. In vertebrate embryos, Spry2 is expressed in paraxial mesoderm and in forming somites. Expression is maintained in the myotome until late stages of somite differentiation. However, its role and mode of action during somite myogenesis is still unclear. Results: Here, we analysed chick Spry2 expression and showed that it overlaps with that of myogenic regulatory factors MyoD and Mgn. Targeted mis-expression of Spry2 led to inhibition of myogenesis, whilst its C-terminal domain led to an increased number of myogenic cells by stimulating cell proliferation. Conclusions: Spry2 is expressed in somite myotomes and its expression overlaps with myogenic regulatory factors. Overexpression and dominant-negative interference showed that Spry2 plays a crucial role in regulating chick myogenesis by fine tuning of FGF signaling through a negative feedback loop. We also propose that mir-23, mir-27 and mir-128 could be part of the negative feedback loop mechanism. Our analysis is the first to shed some light on in vivo Spry2 function during chick somite myogenesis

Simulations of events for the LUX-ZEPLIN (LZ) dark matter experiment

The LUX-ZEPLIN dark matter search aims to achieve a sensitivity to the WIMP-nucleon spin-independent cross-section down to (1–2)×10−12 pb at a WIMP mass of 40 GeV/c2. This paper describes the simulations framework that, along with radioactivity measurements, was used to support this projection, and also to provide mock data for validating reconstruction and analysis software. Of particular note are the event generators, which allow us to model the background radiation, and the detector response physics used in the production of raw signals, which can be converted into digitized waveforms similar to data from the operational detector. Inclusion of the detector response allows us to process simulated data using the same analysis routines as developed to process the experimental data

Quantification of cell cycle kinetics by EdU (5-ethynyl-2′-deoxyuridine)-coupled-fluorescence-intensity analysis

Copyright: Pereira et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License 3.0 (CC BY3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.We propose a novel single-deoxynucleoside-based assay that is easy to perform and provides accurate values for the absolute length (in units of time) of each of the cell cycle stages (G1, S and G2/M). This flow-cytometric assay takes advantage of the excellent stoichiometric properties of azide-fluorochrome detection of DNA substituted with 5-ethynyl-2'-deoxyuridine (EdU). We show that by pulsing cells with EdU for incremental periods of time maximal EdU-coupled fluorescence is reached when pulsing times match the length of S phase. These pulsing times, allowing labelling for a full S phase of a fraction of cells in asynchronous populations, provide accurate values for the absolute length of S phase. We characterized additional, lower intensity signals that allowed quantification of the absolute durations of G1 and G2 phases.Importantly, using this novel assay data on the lengths of G1, S and G2/M phases are obtained in parallel. Therefore, these parameters can be estimated within a time frame that is shorter than a full cell cycle. This method, which we designate as EdU-Coupled Fluorescence Intensity (E-CFI) analysis, was successfully applied to cell types with distinctive cell cycle features and shows excellent agreement with established methodologies for analysis of cell cycle kinetics.João A. Ferreira received support from a Calouste Gulbenkian Foundation grant (96526) and Pedro Pereira is an FCT fellow (SFRH/BD/45502/2008). Evguenia Bekman is the recipient of an IMM-Lisbon fellowship (iMM/BPD/60-2016; project PTDC/BEXBCM/5899/2014).info:eu-repo/semantics/publishedVersio

Projected sensitivity of the LUX-ZEPLIN experiment to the 0νββ decay of Xe 136

The LUX-ZEPLIN (LZ) experiment will enable a neutrinoless double β decay search in parallel to the main science goal of discovering dark matter particle interactions. We report the expected LZ sensitivity to Xe136 neutrinoless double β decay, taking advantage of the significant (&gt;600 kg) Xe136 mass contained within the active volume of LZ without isotopic enrichment. After 1000 live-days, the median exclusion sensitivity to the half-life of Xe136 is projected to be 1.06×1026 years (90% confidence level), similar to existing constraints. We also report the expected sensitivity of a possible subsequent dedicated exposure using 90% enrichment with Xe136 at 1.06×1027 years

Increasing the sensitivity of NMR diffusion measurements by paramagnetic longitudinal relaxation enhancement, with application to ribosome–nascent chain complexes

The translational diffusion of macromolecules can be examined non-invasively by stimulated echo (STE) NMR experiments to accurately determine their molecular sizes. These measurements can be important probes of intermolecular interactions and protein folding and unfolding, and are crucial in monitoring the integrity of large macromolecular assemblies such as ribosome–nascent chain complexes (RNCs). However, NMR studies of these complexes can be severely constrained by their slow tumbling, low solubility (with maximum concentrations of up to 10 μM), and short lifetimes resulting in weak signal, and therefore continuing improvements in experimental sensitivity are essential. Here we explore the use of the paramagnetic longitudinal relaxation enhancement (PLRE) agent NiDO2A on the sensitivity of 15N XSTE and SORDID heteronuclear STE experiments, which can be used to monitor the integrity of these unstable complexes. We exploit the dependence of the PLRE effect on the gyromagnetic ratio and electronic relaxation time to accelerate recovery of 1H magnetization without adversely affecting storage on N z during diffusion delays or introducing significant transverse relaxation line broadening. By applying the longitudinal relaxation-optimized SORDID pulse sequence together with NiDO2A to 70S Escherichia coli ribosomes and RNCs, NMR diffusion sensitivity enhancements of up to 4.5-fold relative to XSTE are achieved, alongside ~1.9-fold improvements in two-dimensional NMR sensitivity, without compromising the sample integrity. We anticipate these results will significantly advance the use of NMR to probe dynamic regions of ribosomes and other large, unstable macromolecular assemblies