Errors-in-Variables Modeling of Personalized Treatment-Response Trajectories

Estimating the impact of a treatment on a given response is needed in many biomedical applications. However, methodology is lacking for the case when the response is a continuous temporal curve, treatment covariates suffer extensively from measurement error, and even the exact timing of the treatments is unknown. We introduce a novel method for this challenging scenario. We model personalized treatment-response curves as a combination of parametric response functions, hierarchically sharing information across individuals, and a sparse Gaussian process for the baseline trend. Importantly, our model accounts for errors not only in treatment covariates, but also in treatment timings, a problem arising in practice for example when data on treatments are based on user self-reporting. We validate our model with simulated and real patient data, and show that in a challenging application of estimating the impact of diet on continuous blood glucose measurements, accounting for measurement error significantly improves estimation and prediction accuracy.Peer reviewe

Effects of oligomerization and decomposition on the nanoparticle growth : a model study

The rate at which freshly formed secondary aerosol particles grow is an important factor in determining their climate impacts. The growth rate of atmospheric nanoparticles may be affected by particle-phase oligomerization and decomposition of condensing organic molecules. We used the Model for Oligomerization and Decomposition in Nanoparticle Growth (MODNAG) to investigate the potential atmospheric significance of these effects. This was done by conducting multiple simulations with varying reaction-related parameters (volatilities of the involved compounds and reaction rates) using both artificial and ambient measured gas-phase concentrations of organic vapors to define the condensing vapors. While our study does not aim at providing information on any specific reaction, our results indicate that particle-phase reactions have significant potential to affect the nanoparticle growth. In simulations in which one-third of a volatility basis set bin was allowed to go through particle-phase reactions, the maximum increase in growth rates was 71% and the decrease 26% compared to the base case in which no particle-phase reactions were assumed to take place. These results highlight the importance of investigating and increasing our understanding of particle-phase reactions.Peer reviewe

Design and development of poly-L/D-lactide copolymer and barium titanate nanoparticle 3D composite scaffolds using breath figure method for tissue engineering applications

In tissue engineering, the scaffold topography influences the adhesion, proliferation, and function of cells. Specifically, the interconnected porosity is crucial for cell migration and nutrient delivery in 3D scaffolds. The objective of this study was to develop a 3D porous composite scaffold for musculoskeletal tissue engineering applications by incorporating barium titanate nanoparticles (BTNPs) into a poly-L/D-lactide copolymer (PLDLA) scaffold using the breath figure method. The porous scaffold fabrication utilised 96/04 PLDLA, dioleoyl phosphatidylethanolamine (DOPE), and different types of BTNPs, including uncoated BTNPs, Al2O3-coated BTNPs, and SiO2-coated BTNPs. The BTNPs were incorporated into the polymer scaffold, which was subsequently analysed using field emission scanning electron microscopy (FE-SEM). The biocompatibility of each scaffold was tested using ovine bone marrow stromal stem cells. The cell morphology, viability, and proliferation were evaluated using FE-SEM, LIVE/DEAD staining, and Prestoblue assay. Porous 3D composite scaffolds were successfully produced, and it was observed that the incorporation of uncoated BTNPs increased the average pore size from 1.6 mu m (PLDLA) to 16.2 mu m (PLDLA/BTNP). The increased pore size in the PLDLA/BTNP scaffolds provided a suitable porosity for the cells to migrate inside the scaffold, while in the pure PLDLA scaffolds with their much smaller pore size, cells elongated on the surface. To conclude, the breath figure method was successfully used to develop a PLDLA/BTNP scaffold. The use of uncoated BTNPs resulted in a composite scaffold with an optimal pore size while maintaining the honeycomb-like structure. The composite scaffolds were biocompatible and yielded promising structures for future tissue engineering applications.Peer reviewe

Toll-like receptor 2 and Toll-like receptor 4 predict favorable prognosis in local pancreatic cancer

Toll-like receptors play an essential role in our innate immune system and are a focus of interest in contemporary cancer research. Thus far, Toll-like receptors have shown promising prognostic value in carcinomas of the oral cavity, colon, and ovaries, but the prognostic role of Toll-like receptors in pancreatic ductal adenocarcinoma has not been established. We set out to investigate whether Toll-like receptor expression could serve in prognostic evaluation in pancreatic ductal adenocarcinoma, as well. Our study comprised 154 consecutive stage I?III pancreatic ductal adenocarcinoma patients surgically treated at Helsinki University Hospital between 2002 and 2011. Patients who received neoadjuvant therapy were excluded. Tissue microarrays and immunohistochemistry allowed assessment of the expression of Toll-like receptor 2 and Toll-like receptor 4 in pancreatic ductal adenocarcinoma tissue, and we matched staining results against clinicopathological parameters using Fisher?s test. For survival analysis, we used the Kaplan?Meier method and the log-rank test, and the Cox regression proportional hazard model for univariate and multivariate analyses. The hazard ratios were calculated for disease-specific overall survival. Strong Toll-like receptor 2 expression was observable in 51 (34%) patients and strong Toll-like receptor 4 in 50 (33%) patients. Overall, neither marker showed any direct coeffect on survival. However, strong Toll-like receptor 2 expression predicted better survival when tumor size was less than 30?mm (hazard ratio?=?0.30; 95% confidence interval?=?0.13?0.69; p?=?0.005), and strong Toll-like receptor 4 expression predicted better survival in patients with lymph-node-negative disease (hazard ratio?=?0.21; 95% confidence interval?=?0.07?0.65; p?=?0.006). In conclusion, we found strong Toll-like receptor 2 and Toll-like receptor 4 expressions to be independent factors of better prognosis in pancreatic ductal adenocarcinoma patients with stage I?II disease.Peer reviewe

THE RESULTS OF PANCREATIC RESECTIONS AND LONG- TERM SURVIVAL FOR PANCREATIC DUCTAL ADENOCARCINOMA : A SINGLE-INSTITUTION EXPERIENCE

Objectives: Since the early 1990s, low long-term survival rates following pancreatic surgery for pancreatic ductal adenocarcinoma have challenged us to improve treatment. In this series, we aim to show improved survival from pancreatic ductal adenocarcinoma during the era of centralized pancreatic surgery. Methods: Analysis of all pancreatic resections performed at Helsinki University Hospital and survival of pancreatic ductal adenocarcinoma patients during 2000-2013 were included. Post-operative complications such as fistulas, reoperations, and mortality rates were recorded. Patient and tumor characteristics were compared with survival data. Results: Of the 853 patients undergoing pancreatic surgery, 581 (68%) were pancreaticoduodenectomies, 195 (21%) distal resections, 28 (3%) total pancreatectomies, and 49 (6%) other procedures. Mortality after pancreaticoduodenectomy was 2.1%. The clinically relevant B/C fistula rate was 7% after pancreaticoduodenectomy and 13% after distal resection, and the re-operation rate was 5%. The 5- and 10-year survival rates for pancreatic ductal adenocarcinoma were 22% and 14%; for T1-2, N0 and R0 tumors, the corresponding survival rates were 49% and 31%. Carbohydrate antigen 19-9 >75 kU/L, carcinoembryonic antigen >5 mu g/L, N1, lymph-node ratio >20%, R1, and lack of adjuvant therapy were independent risk factors for decreased survival. Conclusion: After centralization of pancreatic surgery in southern Finland, we have managed to enable pancreatic ductal adenocarcinoma patients to survive markedly longer than in the early 1990s. Based on a 1.7-million population in our clinic, mortality rates are equal to those of other high-volume centers and long-term survival rates for pancreatic ductal adenocarcinoma have now risen to some of the highest reported.Peer reviewe

Characteristics of new particle formation events and cluster ions at K-puszta, Hungary

Atmospheric new particle formation events were analyzed based on particle size distributions measured with a Differential Mobility Particle Sizer (DMPS) and an Air Ion Spectrometer (AIS) during the BIOSOL (Formation mechanisms, marker compounds, and source apportionment for biogenic atmospheric aerosols) campaign on 22 May-29 June 2006 at the K-puszta measurement site in Hungary. The particle size distribution data were classified into different new particle event classes and growth and formation rates of the particles were calculated. New particle formation was observed on almost all days and the median diameter growth rates of nucleation mode particles increased with increasing particle size. The observed formation rate of 10 nm particles was typically somewhat larger than 1 cm(-3) s(-3) (median 1.2), and the growth rate for sub 3 nm particles was 1.7 nm h(-1) and for nucleation mode 6 nm h(-1). The ambient concentrations of gases or meteorological data were not able to explain the differences in the growth and formation rates or in the particle formation between the days. However, 0.3-1.8 nm cluster ion concentrations correlated negatively with wind speed

Intercomparison of air ion spectrometers: An evaluation of results in varying conditions

We evaluated 11 air ion spectrometers from Airel Ltd. after they had spent one year in field measurements as a part of the EUCAARI project: 5 Air Ion Spectrometers (AIS), 5 Neutral cluster and Air Ion Spectrometers (NAIS) and one Airborne NAIS (ANAIS). This is the first time that an ANAIS is evaluated and compared so extensively. The ion spectrometers' mobility and concentration accuracy was evaluated. Their measurements of ambient air were compared between themselves and to reference instruments: a Differential Mobility Particle Sizer (DMPS), a Balanced Scanning Mobility Analyzer (BSMA), and an Ion-DMPS. We report on the simultaneous measurement of a new particle formation (NPF) event by all 11 instruments and the 3 reference instruments. To our knowledge, it is the first time that the size distribution of ions and particles is measured by so many ion spectrometers during a NPF event. The new particle formation rates (~0.2 cm−3 s−1 for ions and ~2 cm−3 s−1 for particles) and growth rates (~25 nm h−1 in the 3–7 nm size range) were calculated for all the instruments. The NAISs and the ANAIS gave higher concentrations and formation rates than the AISs. For example, the AISs agreed with the BSMA within 11 % and 28 % for negative and positive ion concentration respectively, whereas the NAISs agreed within 23 % and 29 %. Finally, based on the results presented here, we give guidelines for data evaluation, when data from different individual ion spectrometers are compared

Growth rates of nucleation mode particles in Hyytiälä during 2003−2009: variation with particle size, season, data analysis method and ambient conditions

The condensational growth rate of aerosol particles formed in atmospheric new particle formation events is one of the most important factors influencing the lifetime of these particles and their ability to become climatically relevant. Diameter growth rates (GR) of nucleation mode particles were studied based on almost 7 yr of data measured during the years 2003–2009 at a boreal forest measurement station SMEAR II in Hyytiälä, Finland. The particle growth rates were estimated using particle size distributions measured with a Differential Mobility Particle Sizer (DMPS), a Balanced Scanning Mobility Analyzer (BSMA) and an Air Ion Spectrometer (AIS). Two GR analysis methods were tested. The particle growth rates were also compared to an extensive set of ambient meteorological parameters and trace gas concentrations to investigate the processes/constituents limiting the aerosol growth. The median growth rates of particles in the nucleation mode size ranges with diameters of 1.5–3 nm, 3–7 nm and 7–20 nm were 1.9 nm h⁻¹, 3.8 nm h⁻¹, and 4.3 nm h⁻¹, respectively. The median relative uncertainties in the growth rates due to the size distribution instrumentation in these size ranges were 25%, 19%, and 8%, respectively. For the smallest particles (1.5–3 nm) the AIS data yielded on average higher growth rate values than the BSMA data, and higher growth rates were obtained from positively charged size distributions as compared with negatively charged particles. For particles larger than 3 nm in diameter no such systematic differences were found. For these particles the uncertainty in the growth rate related to the analysis method, with relative uncertainty of 16%, was similar to that related to the instruments. The growth rates of 7–20 nm particles showed positive correlation with monoterpene concentrations and their oxidation rate by ozone. The oxidation rate by OH did not show a connection with GR. Our results indicate that the growth of nucleation mode particles in Hyytiälä is mainly limited by the concentrations of organic precursors

Molecular identification of organic vapors driving atmospheric nanoparticle growth

Particles formed in the atmosphere via nucleation provide about half the number of atmospheric cloud condensation nuclei, but in many locations, this process is limited by the growth of the newly formed particles. That growth is often via condensation of organic vapors. Identification of these vapors and their sources is thus fundamental for simulating changes to aerosol-cloud interactions, which are one of the most uncertain aspects of anthropogenic climate forcing. Here we present direct molecular-level observations of a distribution of organic vapors in a forested environment that can explain simultaneously observed atmospheric nanoparticle growth from 3 to 50 nm. Furthermore, the volatility distribution of these vapors is sufficient to explain nanoparticle growth without invoking particle-phase processes. The agreement between observed mass growth, and the growth predicted from the observed mass of condensing vapors in a forested environment thus represents an important step forward in the characterization of atmospheric particle growth.Peer reviewe