Project description:As a follow-up to a previous article, this review provides several in-depth concepts regarding a survival analysis. Also, several codes for specific survival analysis are listed to enhance the understanding of such an analysis and to provide an applicable survival analysis method. A proportional hazard assumption is an important concept in survival analysis. Validation of this assumption is crucial for survival analysis. For this purpose, a graphical analysis method and a goodnessof- fit test are introduced along with detailed codes and examples. In the case of a violated proportional hazard assumption, the extended models of a Cox regression are required. Simplified concepts of a stratified Cox proportional hazard model and time-dependent Cox regression are also described. The source code for an actual analysis using an available statistical package with a detailed interpretation of the results can enable the realization of survival analysis with personal data. To enhance the statistical power of survival analysis, an evaluation of the basic assumptions and the interaction between variables and time is important. In doing so, survival analysis can provide reliable scientific results with a high level of confidence.
Project description:BackgroundAlterations in striatal dopamine neurotransmission are central to the emergence of psychotic symptoms and to the mechanism of action of antipsychotics. Although the functional integrity of the presynaptic system can be assessed by measuring striatal dopamine synthesis capacity (DSC), no quantitative meta-analysis is available.MethodsEleven striatal (caudate and putamen) [(11)C/(18)F]-DOPA positron emission tomography studies comparing 113 patients with schizophrenia and 131 healthy controls were included in a quantitative meta-analysis of DSC. Demographic, clinical, and methodological variables were extracted from each study or obtained from the authors and tested as covariates. Hedges' g was used as a measure of effect size in Comprehensive Meta-Analysis. Publication bias was assessed with funnel plots and Egger's intercept. Heterogeneity was addressed with the Q statistic and I(2) index.ResultsPatients and controls were well matched in sociodemographic variables (P > .05). Quantitative evaluation of publication bias was nonsignificant (P = .276). Heterogeneity across study was modest in magnitude and statistically nonsignificant (Q = 19.19; P = .078; I (2) = 39.17). Patients with schizophrenia showed increased striatal DSC as compared with controls (Hedges' g = 0.867, CI 95% from 0.594 to 1.140, Z = 6.222, P < .001). The DSC schizophrenia/control ratio showed a relatively homogenous elevation of around 14% in schizophrenic patients as compared with controls. DSC elevation was regionally confirmed in both caudate and putamen. Controlling for potential confounders such as age, illness duration, gender, psychotic symptoms, and exposure to antipsychotics had no impact on the results. Sensitivity analysis confirmed robustness of meta-analytic findings.ConclusionsThe present meta-analysis showed consistently increased striatal DSC in schizophrenia, with a 14% elevation in patients as compared with healthy controls.
Project description:In this follow-up study the collaboration between two research groups from the USA and the Netherlands was continued to expand the framework of chemical attribution for the homemade explosive erythritol tetranitrate (ETN). Isotope ratio mass spectrometry (IRMS) analysis was performed to predict possible links between ETN samples and its precursors. Carbon, nitrogen, hydrogen and oxygen isotope ratios were determined for a wide variety of precursor sources and for ETN samples that were prepared with selected precursors. The stability of isotope ratios of ETN has been demonstrated for melt-cast samples and two-year old samples, which enables sample comparison of ETN in forensic casework independent of age and appearance. Erythritol and nitric acid (or nitrate salt) are the exclusive donor of carbon and nitrogen atoms in ETN, respectively, and robust linear relationships between precursor and the end-product were observed for these isotopes. This allowed for defining isotopic enrichment ranges for carbon and nitrogen that support the hypothesis that a given erythritol or nitrate precursor was used to synthesize a specific ETN batch. The hydrogen and oxygen atoms in ETN do not originate from one exclusive donor material, making linkage prediction more difficult. However, the large negative enrichments observed for both isotopes do provide powerful information to exclude suspected precursor materials as donor of ETN. Additionally, combing the isotopic data of all elements results in a higher discrimination power for ETN samples and its precursor materials. Combining the findings of our previously reported LC-MS analysis of ETN with this IRMS study is expected to increase the robustness of the forensic comparison even further. The partially nitrated impurities can provide insight on the synthesis conditions while the isotope data contain information on the raw materials used for the production of ETN.
Project description:The magnitude of contaminant mass-flux reduction associated with a specific amount of contaminant mass removed is a key consideration for evaluating the effectiveness of a source-zone remediation effort. Thus, there is great interest in characterizing, estimating, and predicting relationships between mass-flux reduction and mass removal. Published data collected for several field studies were examined to evaluate relationships between mass-flux reduction and source-zone mass removal. The studies analyzed herein represent a variety of source-zone architectures, immiscible-liquid compositions, and implemented remediation technologies. There are two general approaches to characterizing the mass-flux-reduction/mass-removal relationship, end-point analysis and time-continuous analysis. End-point analysis, based on comparing masses and mass fluxes measured before and after a source-zone remediation effort, was conducted for 21 remediation projects. Mass removals were greater than 60% for all but three of the studies. Mass-flux reductions ranging from slightly less than to slightly greater than one-to-one were observed for the majority of the sites. However, these single-snapshot characterizations are limited in that the antecedent behavior is indeterminate. Time-continuous analysis, based on continuous monitoring of mass removal and mass flux, was performed for two sites, both for which data were obtained under water-flushing conditions. The reductions in mass flux were significantly different for the two sites (90% vs. approximately 8%) for similar mass removals ( approximately 40%). These results illustrate the dependence of the mass-flux-reduction/mass-removal relationship on source-zone architecture and associated mass-transfer processes. Minimal mass-flux reduction was observed for a system wherein mass removal was relatively efficient (ideal mass-transfer and displacement). Conversely, a significant degree of mass-flux reduction was observed for a site wherein mass removal was inefficient (non-ideal mass-transfer and displacement). The mass-flux-reduction/mass-removal relationship for the latter site exhibited a multi-step behavior, which cannot be predicted using some of the available simple estimation functions.
Project description:The Modern-Era Retrospective Analysis for Research and Applications, version 2 (MERRA-2), is NASA's latest reanalysis for the satellite era (1980 onward) using the Goddard Earth Observing System, version 5 (GEOS-5), Earth system model. MERRA-2 provides several improvements over its predecessor (MERRA-1), including aerosol assimilation for the entire period. MERRA-2 assimilates bias-corrected aerosol optical depth (AOD) from the Moderate Resolution Imaging Spectroradiometer and the Advanced Very High Resolution Radiometer instruments. Additionally, MERRA-2 assimilates (non bias corrected) AOD from the Multiangle Imaging SpectroRadiometer over bright surfaces and AOD from Aerosol Robotic Network sunphotometer stations. This paper, the second of a pair, summarizes the efforts to assess the quality of the MERRA-2 aerosol products. First, MERRA-2 aerosols are evaluated using independent observations. It is shown that the MERRA-2 absorption aerosol optical depth (AAOD) and ultraviolet aerosol index (AI) compare well with Ozone Monitoring Instrument observations. Next, aerosol vertical structure and surface fine particulate matter (PM2.5) are evaluated using available satellite, aircraft, and ground-based observations. While MERRA-2 generally compares well to these observations, the assimilation cannot correct for all deficiencies in the model (e.g., missing emissions). Such deficiencies can explain many of the biases with observations. Finally, a focus is placed on several major aerosol events to illustrate successes and weaknesses of the AOD assimilation: the Mount Pinatubo eruption, a Saharan dust transport episode, the California Rim Fire, and an extreme pollution event over China. The article concludes with a summary that points to best practices for using the MERRA-2 aerosol reanalysis in future studies.
Project description:With increasing reports of resistance to artemisinins and artemisinin-combination therapies, targeting the Plasmodium proteasome is a promising strategy for antimalarial development. We recently reported a highly selective Plasmodium falciparum proteasome inhibitor with anti-malarial activity in the humanized mouse model. To balance the permeability of the series of macrocycles with other drug-like properties, we conducted further structure-activity relationship studies on a biphenyl ether-tethered macrocyclic scaffold. Extensive SAR studies around the P1, P3, and P5 groups and peptide backbone identified compound TDI-8414. TDI-8414 showed nanomolar antiparasitic activity, no toxicity to HepG2 cells, high selectivity against the Plasmodium proteasome over the human constitutive proteasome and immunoproteasome, improved solubility and PAMPA permeability, and enhanced metabolic stability in microsomes and plasma of both humans and mice.
Project description:A regulated genome-scale model for Clostridium acetobutylicum ATCC 824 was developed based on its metabolic network reconstruction. To aid model convergence and limit the number of flux-vector possible solutions (the size of the phenotypic solution space), modeling strategies were developed to impose a new type of constraint at the endo-exo-metabolome interface. This constraint is termed the specific proton flux state, and its use enabled accurate prediction of the extracellular medium pH during vegetative growth of batch cultures. The specific proton flux refers to the influx or efflux of free protons (per unit biomass) across the cell membrane. A specific proton flux state encompasses a defined range of specific proton fluxes and includes all metabolic flux distributions resulting in a specific proton flux within this range. Effective simulation of time-course batch fermentation required the use of independent flux balance solutions from an optimum set of specific proton flux states. Using a real-coded genetic algorithm to optimize temporal bounds of specific proton flux states, we show that six separate specific proton flux states are required to model vegetative-growth metabolism and accurately predict the extracellular medium pH. Further, we define the apparent proton flux stoichiometry per weak acids efflux and show that this value decreases from approximately 3.5 mol of protons secreted per mole of weak acids at the start of the culture to approximately 0 at the end of vegetative growth. Calculations revealed that when specific weak acids production is maximized in vegetative growth, the net proton exchange between the cell and environment occurs primarily through weak acids efflux (apparent proton flux stoichiometry is 1). However, proton efflux through cation channels during the early stages of acidogenesis was found to be significant. We have also developed the concept of numerically determined sub-systems of genome-scale metabolic networks here as a sub-network with a one-dimensional null space basis set. A numerically determined sub-system was constructed in the genome-scale metabolic network to study the flux magnitudes and directions of acetylornithine transaminase, alanine racemase, and D-alanine transaminase. These results were then used to establish additional constraints for the genome-scale model.