Design and interpretation of cell trajectory assays

Cell trajectory data is often reported in the experimental cell biology literature to distinguish between different types of cell migration. Unfortunately, there is no accepted protocol for designing or interpreting such experiments and this makes it difficult to quantitatively compare different published data sets and to understand how changes in experimental design influence our ability to interpret different experiments. Here, we use an individual based mathematical model to simulate the key features of a cell trajectory experiment. This shows that our ability to correctly interpret trajectory data is extremely sensitive to the geometry and timing of the experiment, the degree of motility bias and the number of experimental replicates. We show that cell trajectory experiments produce data that is most reliable when the experiment is performed in a quasi 1D geometry with a large number of identically{prepared experiments conducted over a relatively short time interval rather than few trajectories recorded over particularly long time intervals.

Review : "Quality of life: the assessment, analysis and interpretation of patient-reported outcomes (2nd Ed.)" by Peter M. Fayers & David Machin

An updated version, this excellent text is a timely addition to the library of any nurse researching in oncology or other settings where individuals’ quality of life must be understood. Health-related quality of life should be a central aspect of studies concerned with health and illness. Indeed, considerable evidence has recently emerged in oncology and other research settings that selfreported quality of life is of great prognostic significance and may be the most reliable predictor of subsequent morbidity and mortality. From a nursing perspective, it is also gratifying to note that novel therapy and other oncology studies increasingly recognize the importance of understanding patients’ subjective experiences of an intervention over time and to ascertain whether patients perceive that a new intervention makes a difference to their quality of life and treatment outcomes. Measurements of quality of life are now routine in clinical trials of chemotherapy drugs and are often considered the prime outcome of interest in the cost/benefit analyses of these treatments. The authors have extensive experience in qualityof- life assessment in cancer clinical trials, where most of the pioneering work into quality of life has been conducted. That said, many of the health-related qualityof- life issues discussed are common to many illnesses, and researchers outside of cancer should find the book equally helpful.

The importance of good data, analysis and interpretation for showing the economics of reducing healthcare-associated infection

To the Editor—In a recent review article in Infection Control and Hospital Epidemiology, Umscheid et al1 summarized published data on incidence rates of catheter-associated bloodstream infection (CABSI), catheter-associated urinary tract infection (CAUTI), surgical site infection (SSI), and ventilator- associated pneumonia (VAP); estimated how many cases are preventable; and calculated the savings in hospital costs and lives that would result from preventing all preventable cases. Providing these estimates to policy makers, political leaders, and health officials helps to galvanize their support for infection prevention programs. Our concern is that important limitations of the published studies on which Umscheid and colleagues built their findings are incompletely addressed in this review. More attention needs to be drawn to the techniques applied to generate these estimates...

Measurement and Interpretation of Salinity Tolerance in Four Perennial Grasses

Whilst the topic of soil salinity has received a substantive research effort over the years, the accurate measurement and interpretation of salinity tolerance data remain problematic. The tolerance of four perennial grass species (non-halophytes) to sodium chloride (NaCl) dominated salinity was determined in a free-flowing sand culture system. Although the salinity tolerance of non-halophytes is often represented by the threshold salinity model (bent-stick model), none of the species in the current study displayed any observable salinity threshold. Further, the observed yield decrease was not linear as suggested by the model. On re-examination of earlier datasets, we conclude that the threshold salinity model does not adequately describe the physiological processes limiting growth of non-halophytes in saline soils. Therefore, the use of the threshold salinity model is not recommended for non-halophytes, but rather, a model which more accurately reflects the physiological response observed in these saline soils, such as an exponential regression curve.

Biphenyl ethers conjugated CdSe/ZnS core/shell quantum dots and interpretation of the mechanism of amyloid fibril disruption

The biphenyl ethers (BPEs) are the potent inhibitors of TTR fibril formation and are efficient fibril disrupter. However, the mechanism by which the fibril disruption occurs is yet to be fully elucidated. To gain insight into the mechanism, we synthesized and used a new QD labeled BPE to track the process of fibril disruption. Our studies showed that the new BPE-QDs bind to the fiber uniformly and has affinity and specificity for TTR fiber and disrupted the pre-formed fiber at a relatively slow rate. Based on these studies we put forth the probable mechanism of fiber disruption by BPEs. Also, we show here that the BPE-QDs interact with high affinity to the amyloids of A beta(42), lysozyme and insulin. The potential of BPE-QDs in the detection of senile plaque in the brain of transgenic Alzheimer's mice has also been explored. (C) 2010 Elsevier Ltd. All rights reserved.

Demixing of severely overlapped H-1 NMR resonances and interpretation of anomalous intensity pattern of dipolar coupled A(3) spins in a weakly aligning medium

We report a single C-13 spin edited selective proton-proton correlation experiment to decipher overcrowded 13C coupled proton NMR spectra of weakly dipolar coupled spin systems. The experiment unravels the masked C-13 satellites in proton spectrum and permits the measurement of one bond carbon-proton residual dipolar couplings in I3S and for each diastereotopic proton in I2S groups. It also provides all the possible homonuclear proton-proton residual couplings which are otherwise difficult to extract from the broad and featureless one dimensional H-1 spectrum, in addition to enantiodifferentiation in a chiral molecule. Employment of heteronuclear (C-13) decoupling in the evolution period results in complete demixing of overlapped signals from enantiomers. The observed anomalous intensity pattern in strongly dipolar coupled methyl protons in methyl selective correlation experiment has been interpreted using polarization operator formalism. (C) 2010 Elsevier Inc. All rights reserved.

Challenges in the quantification and interpretation of spike-LFP relationships

Brain signals often show fluctuations in particular frequency bands, which are highly conserved across species and are associated with specific behavioural states. Such rhythmic patterns can be captured in the local field potential (LFP), which is obtained by low-pass filtering the extracellular signal recorded from microelectrodes. However, LFP also captures other neural processes that are associated with spikes, such as synaptic events preceding a spike, low-frequency component of the action potential (spike bleed-through'') and spike afterhyperpolarization, which pose difficulties in the estimation of the amplitude and phase of the rhythm with respect to spikes. Here we discuss these issues and different techniques that have been used to dissociate the rhythm from other neural events in the LFP.

Asymptotic behavior and interpretation of virtual states: The effects of confinement and of basis sets

A real-space high order finite difference method is used to analyze the effect of spherical domain size on the Hartree-Fock (and density functional theory) virtual eigenstates. We show the domain size dependence of both positive and negative virtual eigenvalues of the Hartree-Fock equations for small molecules. We demonstrate that positive states behave like a particle in spherical well and show how they approach zero. For the negative eigenstates, we show that large domains are needed to get the correct eigenvalues. We compare our results to those of Gaussian basis sets and draw some conclusions for real-space, basis-sets, and plane-waves calculations. (C) 2016 AIP Publishing LLC.

An investigation of techniques for the measurement and interpretation of cosmic ray isotopic abundances

An instrument, the Caltech High Energy Isotope Spectrometer Telescope (HEIST), has been developed to measure isotopic abundances of cosmic ray nuclei in the charge range 3 ≤ Z ≤ 28 and the energy range between 30 and 800 MeV/nuc by employing an energy loss -- residual energy technique. Measurements of particle trajectories and energy losses are made using a multiwire proportional counter hodoscope and a stack of CsI(TI) crystal scintillators, respectively. A detailed analysis has been made of the mass resolution capabilities of this instrument.

Landau fluctuations set a fundamental limit on the attainable mass resolution, which for this instrument ranges between ~.07 AMU for z~3 and ~.2 AMU for z~2b. Contributions to the mass resolution due to uncertainties in measuring the path-length and energy losses of the detected particles are shown to degrade the overall mass resolution to between ~.1 AMU (z~3) and ~.3 AMU (z~2b).

A formalism, based on the leaky box model of cosmic ray propagation, is developed for obtaining isotopic abundance ratios at the cosmic ray sources from abundances measured in local interstellar space for elements having three or more stable isotopes, one of which is believed to be absent at the cosmic ray sources. This purely secondary isotope is used as a tracer of secondary production during propagation. This technique is illustrated for the isotopes of the elements O, Ne, S, Ar and Ca.

The uncertainties in the derived source ratios due to errors in fragmentation and total inelastic cross sections, in observed spectral shapes, and in measured abundances are evaluated. It is shown that the dominant sources of uncertainty are uncorrelated errors in the fragmentation cross sections and statistical uncertainties in measuring local interstellar abundances.

These results are applied to estimate the extent to which uncertainties must be reduced in order to distinguish between cosmic ray production in a solar-like environment and in various environments with greater neutron enrichments.

Observation and interpretation of tectonic strain release mechanisms

In four chapters various aspects of earthquake source are studied.

Chapter I

Surface displacements that followed the Parkfield, 1966, earthquakes were measured for two years with six small-scale geodetic networks straddling the fault trace. The logarithmic rate and the periodic nature of the creep displacement recorded on a strain meter made it possible to predict creep episodes on the San Andreas fault. Some individual earthquakes were related directly to surface displacement, while in general, slow creep and aftershock activity were found to occur independently. The Parkfield earthquake is interpreted as a buried dislocation.

Chapter II

The source parameters of earthquakes between magnitude 1 and 6 were studied using field observations, fault plane solutions, and surface wave and S-wave spectral analysis. The seismic moment, M_O, was found to be related to local magnitude, M_L, by log M_O = 1.7 M_L + 15.1. The source length vs magnitude relation for the San Andreas system found to be: M_L = 1.9 log L - 6.7. The surface wave envelope parameter AR gives the moment according to log M_O = log AR₃₀₀ + 30.1, and the stress drop, τ, was found to be related to the magnitude by τ = 0.54 M - 2.58. The relation between surface wave magnitude M_S and M_L is proposed to be M_S = 1.7 M_L - 4.1. It is proposed to estimate the relative stress level (and possibly the strength) of a source-region by the amplitude ratio of high-frequency to low-frequency waves. An apparent stress map for Southern California is presented.

Chapter III

Seismic triggering and seismic shaking are proposed as two closely related mechanisms of strain release which explain observations of the character of the P wave generated by the Alaskan earthquake of 1964, and distant fault slippage observed after the Borrego Mountain, California earthquake of 1968. The Alaska, 1964, earthquake is shown to be adequately described as a series of individual rupture events. The first of these events had a body wave magnitude of 6.6 and is considered to have initiated or triggered the whole sequence. The propagation velocity of the disturbance is estimated to be 3.5 km/sec. On the basis of circumstantial evidence it is proposed that the Borrego Mountain, 1968, earthquake caused release of tectonic strain along three active faults at distances of 45 to 75 km from the epicenter. It is suggested that this mechanism of strain release is best described as "seismic shaking."

Chapter IV

The changes of apparent stress with depth are studied in the South American deep seismic zone. For shallow earthquakes the apparent stress is 20 bars on the average, the same as for earthquakes in the Aleutians and on Oceanic Ridges. At depths between 50 and 150 km the apparent stresses are relatively high, approximately 380 bars, and around 600 km depth they are again near 20 bars. The seismic efficiency is estimated to be 0.1. This suggests that the true stress is obtained by multiplying the apparent stress by ten. The variation of apparent stress with depth is explained in terms of the hypothesis of ocean floor consumption.