Qualitative Analysis of the Interdisciplinary Interaction between Data Analysis Specialists and Novice Clinical Researchers

Background: The inherent complexity of statistical methods and clinical phenomena compel researchers with diverse domains of expertise to work in interdisciplinary teams, where none of them have a complete knowledge in their counterpart's field. As a result, knowledge exchange may often be characterized by miscommunication leading to misinterpretation, ultimately resulting in errors in research and even clinical practice. Though communication has a central role in interdisciplinary collaboration and since miscommunication can have a negative impact on research processes, to the best of our knowledge, no study has yet explored how data analysis specialists and clinical researchers communicate over time. Methods/Principal Findings: We conducted qualitative analysis of encounters between clinical researchers and data analysis specialists (epidemiologist, clinical epidemiologist, and data mining specialist). These encounters were recorded and systematically analyzed using a grounded theory methodology for extraction of emerging themes, followed by data triangulation and analysis of negative cases for validation. A policy analysis was then performed using a system dynamics methodology looking for potential interventions to improve this process. Four major emerging themes were found. Definitions using lay language were frequently employed as a way to bridge the language gap between the specialties. Thought experiments presented a series of ""what if'' situations that helped clarify how the method or information from the other field would behave, if exposed to alternative situations, ultimately aiding in explaining their main objective. Metaphors and analogies were used to translate concepts across fields, from the unfamiliar to the familiar. Prolepsis was used to anticipate study outcomes, thus helping specialists understand the current context based on an understanding of their final goal. Conclusion/Significance: The communication between clinical researchers and data analysis specialists presents multiple challenges that can lead to errors.

Size at birth and lipoprotein concentrations in adulthood: two prospective studies in Latin American cities

Background The relationship between birth weight and plasma lipoproteins is inconsistent. Aims To assess the association between birth weight and (1) body mass index (BMI) at birth and (2) lipoproteins in young adults, and also to explore the possible effect of current obesity as a possible effect modifier. Methods Two prospective studies based on representative samples of subjects born in the 1970s were carried out in Ribeirao Preto, Brazil (n = 2063) and Limache, Chile (n = 999). The surveys were carried out between 2001 and 2004. Results Mean birth weights were 3267 g and 3177 g and mean adult BMIs were 24.3 kg/m(2) and 25.8 kg/m(2) in the Brazilian and Chilean samples, respectively. Total adult cholesterol was 4.57 mmol/l in Chileans, 0.26 mmol/l higher than in Brazilians (p < 0.001). The main finding was an interaction between adult obesity (BMI 30 or over) and birth weight and also BMI at birth and low-density lipoprotein (LDL) and total cholesterol. A birth-weight increment of 1 kg was associated with a decrease in total cholesterol (-0.374 mmol/l, 95% CI -0.567 to -0.181) and LDL (-0.304 mmol/l (-0.479 to -0.129) in obese participants only. These associations persisted after allowing for gestational age in a smaller sample. This finding was consistent in separate analyses in the Brazilian and Chilean samples. No associations were found in relation to high-density lipoprotein and triglyceride concentrations. Conclusion The results suggest that those who were of low birth weight and are obese are more likely to have high cholesterol and LDL concentrations. Thus preventing obesity may be especially rewarding in subjects with a low birth weight.

Multifilter rotating shadowband radiometer calibration for spectral aerosol optical depth retrievals over Sao Paulo City, Brazil

Multifilter rotating shadowband radiometer (MFRSR) calibration values for aerosol optical depth (AOD) retrievals were determined by means of the general method formulated by Forgan [Appl. Opt. 33, 4841 (1994)] at a polluted urban site. The obtained precision is comparable with the classical method, the Langley plot, applied on clean mountaintops distant of pollution sources. The AOD retrieved over Sao Paulo City with both calibration procedures is compared with the Aerosol Robotic Network data. The observed results are similar, and, except for the shortest wavelength (415 nm), the MFRSR`s AOD is systematically overestimated by similar to 0.03. (c) 2008 Optical Society of America.

Populations III.1 and III.2 gamma-ray bursts: constraints on the event rate for future radio and X-ray surveys

Aims. We calculate the theoretical event rate of gamma-ray bursts (GRBs) from the collapse of massive first-generation (Population III; Pop III) stars. The Pop III GRBs could be super-energetic with the isotropic energy up to E(iso) greater than or similar to 10(55-57) erg, providing a unique probe of the high-redshift Universe. Methods. We consider both the so-called Pop III.1 stars (primordial) and Pop III.2 stars (primordial but affected by radiation from other stars). We employ a semi-analytical approach that considers inhomogeneous hydrogen reionization and chemical evolution of the intergalactic medium. Results. We show that Pop III.2 GRBs occur more than 100 times more frequently than Pop III.1 GRBs, and thus should be suitable targets for future GRB missions. Interestingly, our optimistic model predicts an event rate that is already constrained by the current radio transient searches. We expect similar to 10-10(4) radio afterglows above similar to 0.3 mJy on the sky with similar to 1 year variability and mostly without GRBs (orphans), which are detectable by ALMA, EVLA, LOFAR, and SKA, while we expect to observe maximum of N < 20 GRBs per year integrated over at z > 6 for Pop III.2 and N < 0.08 per year integrated over at z > 10 for Pop III.1 with EXIST, and N < 0.2 for Pop III.2 GRBs per year integrated over at z > 6 with Swift.

Mitotic crossing-over induced by two commercial herbicides in diploid strains of the fungus Aspergillus nidulans

Some herbicides are suspected of promoting teratogenic, carcinogenic and mutagenic events. Detection of induced mitotic crossing-over has proven to be an indirect way of testing the carcinogenic properties of suspicious substances, because mitotic crossing-over is involved in the multistep process of carcinogenesis. We examined mitotic crossing-over induced by two commercial herbicides (diuron and trifluralin) in diploid strains of Aspergillus nidulans based on the homozygotization index. Low doses (2.5 mu g/mL) of diuron were sufficient to increase the mean homozygotization index in 2.1 and 11.3 times for UT448//UT196 and Dp II-I//UT196, respectively, whereas the same dose of trifluralin increased this mean only 1.2 (UT448//UT196) and 3.5 (Dp II-I//UT196) times, respectively. The lower homozygotization index value found for trifluralin could be due to its interference with mitotic crossing-over in eukaryotic cells. We concluded that the diploid Dp II-I//UT196 of A. nidulans is more sensitive to organic compounds than UT448//UT196; these compounds cause recombinational events at a greater frequency in the latter diploid. This system holds promise as an initial test for carcino-genicity of organic compounds, including herbicides.

Induction of mitotic crossing-over in diploid strains of Aspergillus nidulans using low-dose X-rays

As a contribution towards detecting the genetic effects of low doses of genotoxic physical agents, this paper deals with the consequences of low-dose X-rays in the Aspergillus nidulans genome. The irradiation doses studied were those commonly used in dental clinics (1-5 cGy). Even very low doses promoted increased mitotic crossing-over frequencies in diploid strains heterozygous for several genetic markers including the ones involved in DNA repair and recombination mechanisms. Genetic markers of several heterozygous strains were individu`ally analyzed disclosing that some markers were especially sensitive to the treatments. These markers should be chosen as bio-indicators in the homozygotization index assay to better detect the recombinogenic/carcinogenic genomic effects of low-dose X-rays.

Analytical solutions for Tokamak equilibria with reversed toroidal current

In tokamaks, an advanced plasma confinement regime has been investigated with a central hollow electric current with negative density which gives rise to non-nested magnetic surfaces. We present analytical solutions for the magnetohydrodynamic equilibria of this regime in terms of non-orthogonal toroidal polar coordinates. These solutions are obtained for large aspect ratio tokamaks and they are valid for any kind of reversed hollow current density profiles. The zero order solution of the poloidal magnetic flux function describes nested toroidal magnetic surfaces with a magnetic axis displaced due to the toroidal geometry. The first order correction introduces a poloidal field asymmetry and, consequently, magnetic islands arise around the zero order surface with null poloidal magnetic flux gradient. An analytic expression for the magnetic island width is deduced in terms of the equilibrium parameters. We give examples of the equilibrium plasma profiles and islands obtained for a class of current density profile. (C) 2011 American Institute of Physics. [doi: 10.1063/1.3624551]

A high voltage pulse power supply for metal plasma immersion ion implantation and deposition

We describe the design and implementation of a high voltage pulse power supply (pulser) that supports the operation of a repetitively pulsed filtered vacuum arc plasma deposition facility in plasma immersion ion implantation and deposition (Mepiiid) mode. Negative pulses (micropulses) of up to 20 kV in magnitude and 20 A peak current are provided in gated pulse packets (macropulses) over a broad range of possible pulse width and duty cycle. Application of the system consisting of filtered vacuum arc and high voltage pulser is demonstrated by forming diamond-like carbon (DLC) thin films with and without substrate bias provided by the pulser. Significantly enhanced film/substrate adhesion is observed when the pulser is used to induce interface mixing between the DLC film and the underlying Si substrate. (C) 2010 American Institute of Physics. [doi:10.1063/1.3518969]

A comparison of dry and wet season aerosol number fluxes over the Amazon rain forest

Vertical number fluxes of aerosol particles and vertical fluxes of CO(2) were measured with the eddy covariance method at the top of a 53 m high tower in the Amazon rain forest as part of the LBA (The Large Scale Biosphere Atmosphere Experiment in Amazonia) experiment. The observed aerosol number fluxes included particles with sizes down to 10 nm in diameter. The measurements were carried out during the wet and dry season in 2008. In this study focus is on the dry season aerosol fluxes, with significant influence from biomass burning, and these are compared with aerosol fluxes measured during the wet season. Net particle deposition fluxes dominated in daytime in both seasons and the deposition flux was considerably larger in the dry season due to the much higher dry season particle concentration. The particle transfer velocity increased linearly with increasing friction velocity in both seasons. The difference in transfer velocity between the two seasons was small, indicating that the seasonal change in aerosol number size distribution is not enough for causing any significant change in deposition velocity. In general, particle transfer velocities in this study are low compared to studies over boreal forests. The reasons are probably the high percentage of accumulation mode particles and the low percentage of nucleation mode particles in the Amazon boundary layer, both in the dry and wet season, and low wind speeds in the tropics compared to the midlatitudes. In the dry season, nocturnal particle fluxes behaved very similar to the nocturnal CO(2) fluxes. Throughout the night, the measured particle flux at the top of the tower was close to zero, but early in the morning there was an upward particle flux peak that is not likely a result of entrainment or local pollution. It is possible that these morning upward particle fluxes are associated with emission of primary biogenic particles from the rain forest. Emitted particles may be stored within the canopy during stable conditions at nighttime, similarly to CO(2), and being released from the canopy when conditions become more turbulent in the morning.

Aerosol number fluxes over the Amazon rain forest during the wet season

Number fluxes of particles with diameter larger than 10 nm were measured with the eddy covariance method over the Amazon rain forest during the wet season as part of the LBA (The Large Scale Biosphere Atmosphere Experiment in Amazonia) campaign 2008. The primary goal was to investigate whether sources or sinks dominate the aerosol number flux in the tropical rain forest-atmosphere system. During the measurement campaign, from 12 March to 18 May, 60% of the particle fluxes pointed downward, which is a similar fraction to what has been observed over boreal forests. The net deposition flux prevailed even in the absolute cleanest atmospheric conditions during the campaign and therefore cannot be explained only by deposition of anthropogenic particles. The particle transfer velocity v(t) increased with increasing friction velocity and the relation is described by the equation v(t) = 2.4x10(-3)xu(*) where u(*) is the friction velocity. Upward particle fluxes often appeared in the morning hours and seem to a large extent to be an effect of entrainment fluxes into a growing mixed layer rather than primary aerosol emission. In general, the number source of primary aerosol particles within the footprint area of the measurements was small, possibly because the measured particle number fluxes reflect mostly particles less than approximately 200 nm. This is an indication that the contribution of primary biogenic aerosol particles to the aerosol population in the Amazon boundary layer may be low in terms of number concentrations. However, the possibility of horizontal variations in primary aerosol emission over the Amazon rain forest cannot be ruled out.

Spectral dependence of aerosol light absorption over the Amazon Basin

In this study, we examine the spectral dependence of aerosol absorption at different sites and seasons in the Amazon Basin. The analysis is based on measurements performed during three intensive field experiments at a pasture site (Fazenda Nossa Senhora, Rondonia) and at a primary forest site (Cuieiras Reserve, Amazonas), from 1999 to 2004. Aerosol absorption spectra were measured using two Aethalometers: a 7-wavelength Aethalometer (AE30) that covers the visible (VIS) to near-infrared (NIR) spectral range, and a 2-wavelength Aethalometer (AE20) that measures absorption in the UV and in the NIR. As a consequence of biomass burning emissions, about 10 times greater absorption values were observed in the dry season in comparison to the wet season. Power law expressions were fitted to the measurements in order to derive the absorption Angstrom exponent, defined as the negative slope of absorption versus wavelength in a log-log plot. At the pasture site, about 70% of the absorption Angstrom exponents fell between 1.5 and 2.5 during the dry season, indicating that biomass burning aerosols have a stronger spectral dependence than soot carbon particles. Angstrom exponents decreased from the dry to the wet season, in agreement with the shift from biomass burning aerosols, predominant in the fine mode, to biogenic and dust aerosols, predominant in the coarse mode. The lowest absorption Angstrom exponents (90% of data below 1.5) were observed at the forest site during the dry season. Also, results indicate that low absorption coefficients were associated with low Angstrom exponents. This finding suggests that biogenic aerosols from Amazonia have a weaker spectral dependence for absorption than biomass burning aerosols, contradicting our expectations of biogenic particles behaving as brown carbon. In a first order assessment, results indicate a small (<1 %) effect of variations in absorption Angstrom exponents on 24-h aerosol forcings, at least in the spectral range of 450-880 nm. Further studies should be taken to assess the corresponding impact in the UV spectral range. The assumption that soot spectral properties represent all ambient light absorbing particles may cause a misjudgment of absorption towards the UV, especially in remote areas. Therefore, it is recommended to measure aerosol absorption at several wavelengths to accurately assess the impact of non-soot aerosols on climate and on photochemical atmospheric processes.

Nature of the X(3872) from QCD

We have studied some possible four-quark and molecule configurations of the X(3872) using double ratios of sum rules, which are more accurate than the usual simple ratios often used in the literature to obtain hadron masses. We found that the different structures ((3) over bar - (3) over bar and (6) over bar - 6 tetraquarks and D - D(*) molecule) lead to the same prediction for the mass (within the accuracy of the method), indicating that the alone prediction of the X mass may not be sufficient to reveal its nature. In doing these analyses, we also find that (within our approximation) the use of the (MS) over bar running (m) over bar (c)(m(c)(2)), rather than the on-shell mass, is more appropriate to obtain the J/psi and X meson masses. Using vertex sum rules to roughly estimate the X(3872) hadronic and radiative widths, we found that the available experimental data does not exclude a lambda - J/psi-like molecule current.

Search for Lorentz Invariance and CPT Violation with the MINOS Far Detector

We searched for a sidereal modulation in the MINOS far detector neutrino rate. Such a signal would be a consequence of Lorentz and CPT violation as described by the standard-model extension framework. It also would be the first detection of a perturbative effect to conventional neutrino mass oscillations. We found no evidence for this sidereal signature, and the upper limits placed on the magnitudes of the Lorentz and CPT violating coefficients describing the theory are an improvement by factors of 20-510 over the current best limits found by using the MINOS near detector.

Search for sterile neutrino mixing in the MINOS long-baseline experiment

A search for depletion of the combined flux of active neutrino species over a 735 km baseline is reported using neutral-current interaction data recorded by the MINOS detectors in the NuMI neutrino beam. Such a depletion is not expected according to conventional interpretations of neutrino oscillation data involving the three known neutrino flavors. A depletion would be a signature of oscillations or decay to postulated noninteracting sterile neutrinos, scenarios not ruled out by existing data. From an exposure of 3.18 x 10(20) protons on target in which neutrinos of energies between similar to 500 MeV and 120 GeV are produced predominantly as nu(mu), the visible energy spectrum of candidate neutral-current reactions in the MINOS far detector is reconstructed. Comparison of this spectrum to that inferred from a similarly selected near-detector sample shows that of the portion of the nu(mu) flux observed to disappear in charged-current interaction data, the fraction that could be converting to a sterile state is less than 52% at 90% confidence level (C. L.). The hypothesis that active neutrinos mix with a single sterile neutrino via oscillations is tested by fitting the data to various models. In the particular four-neutrino models considered, the mixing angles theta(24) and theta(34) are constrained to be less than 11 degrees and 56 degrees at 90% C. L., respectively. The possibility that active neutrinos may decay to sterile neutrinos is also investigated. Pure neutrino decay without oscillations is ruled out at 5.4 standard deviations. For the scenario in which active neutrinos decay into sterile states concurrently with neutrino oscillations, a lower limit is established for the neutrino decay lifetime tau(3)/m(3) > 2.1 x 10(-12) s/eV at 90% C.L.

First Direct Observation of Muon Antineutrino Disappearance

This Letter reports the first direct observation of muon antineutrino disappearance. The MINOS experiment has taken data with an accelerator beam optimized for (nu) over bar (mu) production, accumulating an exposure of 1.71 x 10(20) protons on target. In the Far Detector, 97 charged current (nu) over bar (mu) events are observed. The no-oscillation hypothesis predicts 156 events and is excluded at 6.3 sigma. The best fit to oscillation yields vertical bar Delta(m) over bar (2)vertical bar = [3.36(-0.40)(+0.46)(stat) +/- 0.06(sys)] x 10(-3) eV(2), sin(2)(2 (theta) over bar) = 0.86(-0.12)(+0.11)(stat) +/- 0.01(syst). The MINOS nu(mu) and (nu) over bar (mu) measurements are consistent at the 2.0% confidence level, assuming identical underlying oscillation parameters.