Accounting for baseline differences and measurement error in the analysis of change over time

If change over time is compared in several groups, it is important to take into account baseline values so that the comparison is carried out under the same preconditions. As the observed baseline measurements are distorted by measurement error, it may not be sufficient to include them as covariate. By fitting a longitudinal mixed-effects model to all data including the baseline observations and subsequently calculating the expected change conditional on the underlying baseline value, a solution to this problem has been provided recently so that groups with the same baseline characteristics can be compared. In this article, we present an extended approach where a broader set of models can be used. Specifically, it is possible to include any desired set of interactions between the time variable and the other covariates, and also, time-dependent covariates can be included. Additionally, we extend the method to adjust for baseline measurement error of other time-varying covariates. We apply the methodology to data from the Swiss HIV Cohort Study to address the question if a joint infection with HIV-1 and hepatitis C virus leads to a slower increase of CD4 lymphocyte counts over time after the start of antiretroviral therapy.

Development and validation of GT3X accelerometer cut-off points in 5- to 9-year-old children based on indirect calorimetry measurements

The ActiGraph accelerometer is commonly used to measure physical activity in children. Count cut-off points are needed when using accelerometer data to determine the time a person spent in moderate or vigorous physical activity. For the GT3X accelerometer no cut-off points for young children have been published yet. The aim of the current study was thus to develop and validate count cut-off points for young children. Thirty-two children aged 5 to 9 years performed four locomotor and four play activities. Activity classification into the light-, moderate- or vigorous-intensity category was based on energy expenditure measurements with indirect calorimetry. Vertical axis as well as vector magnitude cut-off points were determined through receiver operating characteristic curve analyses with the data of two thirds of the study group and validated with the data of the remaining third. The vertical axis cut-off points were 133 counts per 5 sec for moderate to vigorous physical activity (MVPA), 193 counts for vigorous activity (VPA) corresponding to a metabolic threshold of 5 MET and 233 for VPA corresponding to 6 MET. The vector magnitude cut-off points were 246 counts per 5 sec for MVPA, 316 counts for VPA - 5 MET and 381 counts for VPA - 6 MET. When validated, the current cut-off points generally showed high recognition rates for each category, high sensitivity and specificity values and moderate agreement in terms of the Kappa statistic. These results were similar for vertical axis and vector magnitude cut-off points. The current cut-off points adequately reflect MVPA and VPA in young children. Cut-off points based on vector magnitude counts did not appear to reflect the intensity categories better than cut-off points based on vertical axis counts alone.

Differences in Time to Disease Progression Do Not Predict for Cancer-specific Survival in Patients Receiving Immediate or Deferred Androgen-deprivation Therapy for Prostate Cancer: Final Results of EORTC Randomized Trial 30891 with 12 Years of Follow-up

BACKGROUND Trials assessing the benefit of immediate androgen-deprivation therapy (ADT) for treating prostate cancer (PCa) have often done so based on differences in detectable prostate-specific antigen (PSA) relapse or metastatic disease rates at a specific time after randomization. OBJECTIVE Based on the long-term results of European Organization for Research and Treatment of Cancer (EORTC) trial 30891, we questioned if differences in time to progression predict for survival differences. DESIGN, SETTING, AND PARTICIPANTS EORTC trial 30891 compared immediate ADT (n=492) with orchiectomy or luteinizing hormone-releasing hormone analog with deferred ADT (n=493) initiated upon symptomatic disease progression or life-threatening complications in randomly assigned T0-4 N0-2 M0 PCa patients. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS Time to first objective progression (documented metastases, ureteric obstruction, not PSA rise) and time to objective castration-resistant progressive disease were compared as well as PCa mortality and overall survival. RESULTS AND LIMITATIONS After a median of 12.8 yr, 769 of the 985 patients had died (78%), 269 of PCa (27%). For patients receiving deferred ADT, the overall treatment time was 31% of that for patients on immediate ADT. Deferred ADT was significantly worse than immediate ADT for time to first objective disease progression (p<0.0001; 10-yr progression rates 42% vs 30%). However, time to objective castration-resistant disease after deferred ADT did not differ significantly (p=0.42) from that after immediate ADT. In addition, PCa mortality did not differ significantly, except in patients with aggressive PCa resulting in death within 3-5 yr after diagnosis. Deferred ADT was inferior to immediate ADT in terms of overall survival (hazard ratio: 1.21; 95% confidence interval, 1.05-1.39; p [noninferiority]=0.72, p [difference] = 0.0085). CONCLUSIONS This study shows that if hormonal manipulation is used at different times during the disease course, differences in time to first disease progression cannot predict differences in disease-specific survival. A deferred ADT policy may substantially reduce the time on treatment, but it is not suitable for patients with rapidly progressing disease.

Repeated measurements of cerebral blood flow in the left superior temporal gyrus reveal tonic hyperactivity in patients with auditory verbal hallucinations: a possible trait marker

Background: The left superior temporal gyrus (STG) has been suggested to play a key role in auditory verbal hallucinations (AVH) in patients with schizophrenia. Methods: Eleven medicated subjects with schizophrenia and medication-resistant AVH and 19 healthy controls underwent perfusion magnetic resonance (MR) imaging with arterial spin labeling (ASL). Three additional repeated measurements were conducted in the patients. Patients underwent a treatment with transcranial magnetic stimulation (TMS) between the first 2 measurements. The main outcome measure was the pooled cerebral blood flow (CBF), which consisted of the regional CBF measurement in the left STG and the global CBF measurement in the whole brain. Results: Regional CBF in the left STG in patients was significantly higher compared to controls (p < 0.0001) and to the global CBF in patients (p < 0.004) at baseline. Regional CBF in the left STG remained significantly increased compared to the global CBF in patients across time (p < 0.0007), and it remained increased in patients after TMS compared to the baseline CBF in controls (p < 0.0001). After TMS, PANSS (p = 0.003) and PSYRATS (p = 0.01) scores decreased significantly in patients. Conclusions: This study demonstrated tonically increased regional CBF in the left STG in patients with schizophrenia and auditory hallucinations despite a decrease in symptoms after TMS. These findings were consistent with what has previously been termed a trait marker of AVH in schizophrenia.

Highly accurate isotope composition measurements by a miniature laser ablation mass spectrometer designed for in situ investigations on planetary surface

An experimental procedure for precise and accurate measurements of isotope abundances by a miniature laser ablation mass spectrometer for space research is described. The measurements were conducted on different untreated NIST standards and galena samples by applying pulsed UV laser radiation (266 nm, 3 ns and 20 Hz) for ablation, atomisation, and ionisation of the sample material. Mass spectra of released ions are measured by a reflectron-type time-of-flight mass analyser. A computer controlled performance optimiser was used to operate the system at maximum ion transmission and mass resolution. At optimal experimental conditions, the best relative accuracy and precision achieved for Pb isotope compositions are at the per mill level and were obtained in a range of applied laser irradiances and a defined number of accumulated spectra. A similar relative accuracy and precision was achieved in the study of Pb isotope compositions in terrestrial galena samples. The results for the galena samples are similar to those obtained with a thermal ionisation mass spectrometer (TIMS). The studies of the isotope composition of other elements yielded relative accuracy and precision at the per mill level too, with characteristic instrument parameters for each element. The relative accuracy and precision of the measurements is degrading with lower element/isotope concentration in a sample. For the elements with abundances below 100 ppm these values drop to the percent level. Depending on the isotopic abundances of Pb in minerals, 207Pb/206Pb ages with accuracy in the range of tens of millions of years can be achieved.

Absolute quantitative real-time polymerase chain reaction for the measurement of human papillomavirus E7 mRNA in cervical cytobrush specimens.

BACKGROUND: Few reports of the utilization of an accurate, cost-effective means for measuring HPV oncogene transcripts have been published. Several papers have reported the use of relative quantitation or more expensive Taqman methods. Here, we report a method of absolute quantitative real-time PCR utilizing SYBR-green fluorescence for the measurement of HPV E7 expression in cervical cytobrush specimens. RESULTS: The construction of a standard curve based on the serial dilution of an E7-containing plasmid was the key for being able to accurately compare measurements between cervical samples. The assay was highly reproducible with an overall coefficient of variation of 10.4%. CONCLUSION: The use of highly reproducible and accurate SYBR-based real-time polymerase chain reaction (PCR) assays instead of performing Taqman-type assays allows low-cost, high-throughput analysis of viral mRNA expression. The development of such assays will help in refining the current screening programs for HPV-related carcinomas.

Measurements of a water potential and water content in unsaturated crystalline rock

A water desaturation zone develops around a tunnel in water-saturated rock when the evaporative water loss at the rock surface is larger than the water flow from the surrounding saturated region of restricted permeability. We describe the methods with which such water desaturation processes in rock materials can be quantified. The water retention characteristic theta(psi) of crystalline rock samples was determined with a pressure membrane apparatus. The negative water potential, identical to the capillary pressure, psi, below the tensiometric range (psi < -0.1 MPa) can be measured with thermocouple psychrometers (TP), and the volumetric water contents, theta, by means of time domain reflectometry (TDR). These standard methods were adapted for measuring the water status in a macroscopically unfissured granodiorite with a total porosity of approximately 0.01. The measured water retention curve of granodiorite samples from the Grimsel test site (central Switzerland) exhibits a shape which is typical for bimodal pore size distributions. The measured bimodality is probably an artifact of a large surface ratio of solid/voids. The thermocouples were installed without a metallic screen using the cavity drilled into the granodiorite as a measuring chamber. The water potentials observed in a cylindrical granodiorite monolith ranged between -0.1 and -3.0 MPa; those near the wall in a ventilated tunnel between -0.1 and -2.2 MPa. Two types of three-rod TDR Probes were used, one as a depth probe inserted into the rock, the other as a surface probe using three copper stripes attached to the surface for detecting water content changes in the rock-to-air boundary. The TDR signal was smoothed with a low-pass filter, and the signal length determined based on the first derivative of the trace. Despite the low porosity of crystalline rock these standard methods are applicable to describe the unsaturated zone in solid rock and may also be used in other consolidated materials such as concrete.

Coupling of LMS with a fs-laser ablation ion source: elemental and isotope composition measurements

Mass spectrometric analysis of elemental and isotopic compositions of several NIST standards is performed by a miniature laser ablation/ionisation reflectron-type time-of-flight mass spectrometer (LMS) using a fs-laser ablation ion source (775 nm, 190 fs, 1 kHz). The results of the mass spectrometric studies indicate that in a defined range of laser irradiance (fluence) and for a certain number of accumulations of single laser shot spectra, the measurements of isotope abundances can be conducted with a measurement accuracy at the per mill level and at the per cent level for isotope concentrations higher and lower than 100 ppm, respectively. Also the elemental analysis can be performed with a good accuracy. The LMS instrument combined with a fs-laser ablation ion source exhibits similar detection efficiency for both metallic and non-metallic elements. Relative sensitivity coefficients were determined and found to be close to one, which is of considerable importance for the development of standard-less instruments. Negligible thermal effects, sample damage and excellent characteristics of the fs-laser beam are thought to be the main reason for substantial improvement of the instrumental performance compared to other laser ablation mass spectrometers.

Performance evaluation of a miniature laser ablation time-of-flight mass spectrometer designed for in situ investigations in planetary space research

Key performance features of a miniature laser ablation time-of-flight mass spectrometer designed for in situ investigations of the chemical composition of planetary surfaces are presented. This mass spectrometer is well suited for elemental and isotopic analysis of raw solid materials with high sensitivity and high spatial resolution. In this study, ultraviolet laser radiation with irradiances suitable for ablation (< 1 GW/cm2) is used to achieve stable ion formation and low sample consumption. In comparison to our previous laser ablation studies at infrared wavelengths, several improvements to the experimental setup have been made, which allow accurate control over the experimental conditions and good reproducibility of measurements. Current performance evaluations indicate significant improvements to several instrumental figures of merit. Calibration of the mass scale is performed within a mass accuracy (Δm/m) in the range of 100 ppm, and a typical mass resolution (m/Δm) ~600 is achieved at the lead mass peaks. At lower laser irradiances, the mass resolution is better, about (m/Δm) ~900 for lead, and limited by the laser pulse duration of 3 ns. The effective dynamic range of the instrument was enhanced from about 6 decades determined in previous study up to more than 8 decades at present. Current studies show high sensitivity in detection of both metallic and non-metallic elements. Their abundance down to tens of ppb can be measured together with their isotopic patterns. Due to strict control of the experimental parameters, e.g. laser characteristics, ion-optical parameters and sample position, by computer control, measurements can be performed with high reproducibility. Copyright © 2012 John Wiley & Sons, Ltd.

First measurements with ARGONTUBE, a 5m long drift Liquid Argon TPC

The Liquid Argon Time Projection Chamber (LAr TPC) technique is a promising technology for future neutrino detectors. At LHEP of the University of Bern (Switzerland), an R&D program towards large detectors are on-going. The main goal is to show the feasibility of long drift paths over many meters. Therefore, a liquid Argon TPC with 5m of drift distance was constructed. Many other aspects of the liquid Argon TPC technology are also investigated, such as a new device to generate high voltage in liquid Argon (Greinacher circuit), a recirculation filtering system and the multi-photon ionization of liquid Argon with a UV laser. Two detectors are built: a medium size prototype for specific detector technology studies, and ARGONTUBE, a 5m long device.

Time of emergence of trends in ocean biogeochemistry

For the detection of climate change, not only the magnitude of a trend signal is of significance. An essential issue is the time period required by the trend to be detectable in the first place. An illustrative measure for this is time of emergence (ToE), that is, the point in time when a signal finally emerges from the background noise of natural variability. We investigate the ToE of trend signals in different biogeochemical and physical surface variables utilizing a multi-model ensemble comprising simulations of 17 Earth system models (ESMs). We find that signals in ocean biogeochemical variables emerge on much shorter timescales than the physical variable sea surface temperature (SST). The ToE patterns of pCO2 and pH are spatially very similar to DIC (dissolved inorganic carbon), yet the trends emerge much faster – after roughly 12 yr for the majority of the global ocean area, compared to between 10 and 30 yr for DIC. ToE of 45–90 yr are even larger for SST. In general, the background noise is of higher importance in determining ToE than the strength of the trend signal. In areas with high natural variability, even strong trends both in the physical climate and carbon cycle system are masked by variability over decadal timescales. In contrast to the trend, natural variability is affected by the seasonal cycle. This has important implications for observations, since it implies that intra-annual variability could question the representativeness of irregularly sampled seasonal measurements for the entire year and, thus, the interpretation of observed trends.

Real-time simulation of large open quantum spin systems driven by dissipation

We consider a large quantum system with spins 12 whose dynamics is driven entirely by measurements of the total spin of spin pairs. This gives rise to a dissipative coupling to the environment. When one averages over the measurement results, the corresponding real-time path integral does not suffer from a sign problem. Using an efficient cluster algorithm, we study the real-time evolution from an initial antiferromagnetic state of the two-dimensional Heisenberg model, which is driven to a disordered phase, not by a Hamiltonian, but by sporadic measurements or by continuous Lindblad evolution.

Preliminary study on carprofen concentration measurements after transcutaneous treatment with Vetdrop® in a microfracture joint defect model in sheep.

BackgroundThe present preliminary study describes concentration time courses of the NSAID carprofen in the plasma and synovial fluid in a microfrature sheep model after transcutaneous treatments with a novel application device (Vetdrop®). To treat circumscribed inflammatory processes a transcutaneous application device could potentially be beneficial. After transcutaneous application normally lower systemic concentrations are measured which may reduce the incidence of side effects, whereas efficacy is still maintained.In this study carprofen was used based on its capacity to provide analgesia after orthopaedic procedures in sheep and it is considered that it may have a positive influence on the healing of cartilage in low concentrations.ResultsIn all transcutaneously treated animals, carprofen plasma concentrations exceeded those of synovial fluid, although plasma levels remained significantly reduced (300-fold) as compared to carprofen administered intravenously. Furthermore, in contrast to the intravenously treated animals, a modest accumulation of carprofen in plasma and synovial fluid was observed in the transcutaneously treated animals over the 6-week treatment period.ConclusionsThe transcutaneously administered carprofen using the Vetdrop® device penetrated the skin and both, plasma- and synovial concentrations could be measured repeatedly over time. This novel device may be considered a valuable transcutaneous drug delivery system.

A Time-based Passive Source Localization System for Narrow-band Signal

Time-based indoor localization has been investigated for several years but the accuracy of existing solutions is limited by several factors, e.g., imperfect synchronization, signal bandwidth and indoor environment. In this paper, we compare two time-based localization algorithms for narrow-band signals, i.e., multilateration and fingerprinting. First, we develop a new Linear Least Square (LLS) algorithm for Differential Time Difference Of Arrival (DTDOA). Second, fingerprinting is among the most successful approaches used for indoor localization and typically relies on the collection of measurements on signal strength over the area of interest. We propose an alternative by constructing fingerprints of fine-grained time information of the radio signal. We offer comprehensive analytical discussions on the feasibility of the approaches, which are backed up by evaluations in a software defined radio based IEEE 802.15.4 testbed. Our work contributes to research on localization with narrow-band signals. The results show that our proposed DTDOA-based LLS algorithm obviously improves the localization accuracy compared to traditional TDOA-based LLS algorithm but the accuracy is still limited because of the complex indoor environment. Furthermore, we show that time-based fingerprinting is a promising alternative to power-based fingerprinting.

Retinal layer measurements after successful macula-off retinal detachment repair using optical coherence tomography

PURPOSE Optical coherence tomography (OCT) was used to analyze the thickness of various retinal layers of patients following successful macula-off retinal detachment (RD) repair. METHODS Optical coherence tomography scans of patients after successful macula-off RD repair were reanalyzed with a subsegmentation algorithm to measure various retinal layers. Regression analysis was performed to correlate time after surgery with changes in layer thickness. In addition, patients were divided in two groups. Group 1 had a follow-up period after surgery of up to 7 weeks (range, 21-49 days). In group 2, the follow-up period was >8 weeks (range, 60-438 days). Findings were compared to a group of age-matched healthy controls. RESULTS Correlation analysis showed a significant positive correlation between inner nuclear-outer plexiform layer (INL-OPL) thickness and time after surgery (P=0.0212; r2=0.1551). Similar results were found for the ellipsoid zone-retinal pigment epithelium complex (EZ-RPE) thickness (P=0.005; r2=0.2215). Ganglion cell-inner plexiform layer thickness (GCL-IPL) was negatively correlated with time after surgery (P=0.0064; r2=0.2101). For group comparison, the retinal nerve fiber layer in both groups was thicker compared to controls. The GCL-IPL showed significant thinning in group 2. The outer nuclear layer was significantly thinner in groups 1 and 2 compared to controls. The EZ-RPE complex was significantly thinner in groups 1 and 2 compared to controls. In addition, values in group 1 were significantly thinner than in group 2. CONCLUSIONS Optical coherence tomography retinal layer thickness measurements after successful macular-off RD repair revealed time-dependent thickness changes. Inner nuclear-outer plexiform layer thickness and EZ-RPE thickness was positively correlated with time after surgery. Ganglion cell-inner plexiform layer thickness was negatively correlated with time after surgery.