Machine Science in Biomedicine: Practicalities, Pitfalls and Potential

Machine Science, or Data-driven Research, is a new and interesting scientific methodology that uses advanced computational techniques to identify, retrieve, classify and analyse data in order to generate hypotheses and develop models. In this paper we describe three recent biomedical Machine Science studies, and use these to assess the current state of the art with specific emphasis on data mining, data assessment, costs, limitations, skills and tool support

Molecular astronomy of cool stars and sub-stellar objects

The optical and infrared spectra of a wide variety of `cool' astronomical objects including the Sun, sunspots, K-, M- and S-type stars, carbon stars, brown dwarfs and extrasolar planets are reviewed. The review provides the necessary astronomical background for chemical physicists to understand and appreciate the unique molecular environments found in astronomy. The calculation of molecular opacities needed to simulate the observed spectral energy distributions is discussed

Evidence for Past Subduction Earthquakes at a Plate Boundary with Widespread Upper Plate Faulting: Southern Hikurangi Margin, New Zealand

At the southern Hikurangi margin, New Zealand, we use salt marsh stratigraphy, sedimentology, micropaleontology, and radiocarbon dating to document evidence of two earthquakes producing coseismic subsidence and (in one case) a tsunami over the past 1000 yrs. The earthquake at 520-470 yrs before present (B.P.) produced 0.25 +/- 0.1 m of subsidence at Big Lagoon. The earthquake at 880-800 yrs B.P. produced 0.45 +/- 0.1 m of subsidence at Big Lagoon and was accompanied by a tsunami that inundated >= 360 m inland with a probable height of >= 3.3 m. Distinguishing the effects of upper plate faulting from plate interface earthquakes is a significant challenge at this margin. We use correlation with regional upper plate paleoearthquake chronologies and elastic dislocation modeling to determine that the most likely cause of the subsidence and tsunami events is subduction interface rupture, although the older event may have been a synchronous subduction interface and upper plate fault rupture. The southern Hikurangi margin has had no significant (M > 6.5) documented subduction interface earthquakes in historic times, and previous assumptions that this margin segment is prone to rupture in large to great earthquakes were based on seismic and geodetic evidence of strong contemporary plate coupling. This is the first geologic evidence to confirm that the southern Hikurangi margin ruptures in large earthquakes. The relatively short-time interval between the two subduction earthquakes (similar to 350 yrs) is shorter than in current seismic-hazard models.GNSEQC Biennial ProjectNew Zealand Natural Hazards Research Platform and Foundation for Research Science and TechnologyInstitute for Geophysic

The Evolution of Optical Depth in the Ly-alpha Forest: Evidence Against Reionization at z~6

We examine the evolution of the IGM Ly-alpha optical depth distribution using the transmitted flux probability distribution function (PDF) in a sample of 63 QSOs spanning absorption redshifts 1.7 < z < 5.8. The data are compared to two theoretical optical depth distributions: a model distribution based on the density distribution of Miralda-Escude et al. (2000) (MHR00), and a lognormal distribution. We assume a uniform UV background and an isothermal IGM for the MHR00 model, as has been done in previous works. Under these assumptions, the MHR00 model produces poor fits to the observed flux PDFs at redshifts where the optical depth distribution is well sampled, unless large continuum corrections are applied. However, the lognormal optical depth distribution fits the data at all redshifts with only minor continuum adjustments. We use a simple parametrization for the evolution of the lognormal parameters to calculate the expected mean transmitted flux at z > 5.4. The lognormal optical depth distribution predicts the observed Ly-alpha and Ly-beta effective optical depths at z > 5.7 while simultaneously fitting the mean transmitted flux down to z = 1.6. If the evolution of the lognormal distribution at z < 5 reflects a slowly-evolving density field, temperature, and UV background, then no sudden change in the IGM at z ~ 6 due to late reionization appears necessary. We have used the lognormal optical depth distribution without any assumption about the underlying density field. If the MHR00 density distribution is correct, then a non-uniform UV background and/or IGM temperature may be required to produce the correct flux PDF. We find that an inverse temperature-density relation greatly improves the PDF fits, but with a large scatter in the equation of state index. [Abridged]Comment: 45 pages, 16 figures, submitted to Ap

Effects of Material Choice on Biocide Loss in Orion Water Storage Tanks

When preparing for long-duration spaceflight missions, maintaining a safe supply of potable water is of the utmost importance. One major aspect of that is ensuring that microbial growth is minimized. Historically, this challenge has been addressed through the use of biocides. When using biocides, the choice of materials for the storage containers is important, because surface reactions can reduce biocide concentrations below their effective range. In the water storage system baselined for the Orion vehicle, the primary wetted materials are stainless steel (316 L) and a titanium alloy (Ti6Al4V). Previous testing with these materials has shown that the biocide selected for use in the system (ionic silver) will plate out rapidly upon initial wetting of the system. One potential approach for maintaining an adequate biocide concentration is to spike the water supply with high levels of biocide in an attempt to passivate the surface. To evaluate this hypothesis, samples of the wetted materials were tested individually and together to determine the relative loss of biocide under representative surface area-to-volume ratios after 24 hours. Additionally, we have analyzed the efficacy of disinfecting a system containing these materials by measuring reductions in bacterial counts in the same test conditions. Preliminary results indicate that the use of titanium, either individually or in combination with stainless steel, can result in over 95% loss of biocide, while less than 5% is lost when using stainless steel. In bacterial testing, viable organisms were recovered from samples exposed to the titanium coupons after 24 hours. By comparison, no organisms were recovered from the test vessels containing only stainless steel. These results indicate that titanium, while possessing some favorable attributes, may pose additional challenges when used in water storage tanks with ionic silver biocide

Lunar Dust and Lunar Simulant Activation and Monitoring

Prior to returning to the moon, understanding the effects of lunar dust on both human physiology and mechanical equipment is a pressing concern, as problems related to lunar dust during the Apollo missions have been well documented (J.R. Gaier, The Effects of Lunar Dust on EVA Systems During the Apollo Missions. 2005, NASA-Glenn Research Center. p. 65). While efforts were made to remove the dust before reentering the lunar module, via brushing of the suits or vacuuming, a significant amount of dust was returned to the spacecraft, causing various problems. For instance, astronaut Harrison Schmitt complained of hay fever effects caused by the dust, and the abrasive nature of the material was found to cause problems with various joints and seals of the spacecraft and suits. It is clear that, in order to avoid potential health and performance problems while on the lunar surface, the reactive properties of lunar dust must be quenched. It is likely that soil on the lunar surface is in an activated form, i.e. capable of producing oxygen-based radicals in a humidified air environment, due to constant exposure to meteorite impacts, UV radiation, and elements of the solar wind. An activated silica surface serves as a good example. An oxygen-based radical species arises from the breaking of Si-OSi bonds. This system is comparable to that expected for the lunar dust system due to the large amounts of agglutinic glass and silicate vapor deposits present in lunar soil. Unfortunately, exposure to the Earth s atmosphere has passivated the active species on lunar dust, leading to efforts to reactivate the dust in order to understand the true effects that will be experienced by astronauts and equipment on the moon. Electron spin resonance (ESR) spectroscopy is commonly used for the study of radical species, and has been used previously to study silicon- and oxygen-based radicals, as well as the hydroxyl radicals produced by these species in solution (V. Vallyathan, et al., Am. Rev. Respir. Dis. 138 (1988) 1213-1219). The size and cost of these instruments makes them unattractive for the monitoring of lunar dust activity. A more suitable technique is based on the change in fluorescence of a molecule upon reaction with a hydroxyl radical (or other radical species). Fluorescence instruments are much less costly and bulky than ESR spectrometers, and small fluorescence sensors for space missions have already been developed (F. Gao, et al., J. Biomed. Opt. 10 (2005) 054005). For the current fluorescence studies, the terephthalate molecule has been chosen for monitoring the production of hydroxyl radicals in solution. As shown in Scheme 1, the reaction between the non-fluorescent terephthalate molecule and a hydroxyl radical produces the highly-fluorescent 2-hydroxyterephthalate molecule

Mean-atom-trajectory model for the velocity autocorrelation function of monatomic liquids

We present a model for the motion of an average atom in a liquid or supercooled liquid state and apply it to calculations of the velocity autocorrelation function $Z(t)$ and diffusion coefficient $D$. The model trajectory consists of oscillations at a distribution of frequencies characteristic of the normal modes of a single potential valley, interspersed with position- and velocity-conserving transits to similar adjacent valleys. The resulting predictions for $Z(t)$ and $D$ agree remarkably well with MD simulations of Na at up to almost three times its melting temperature. Two independent processes in the model relax velocity autocorrelations: (a) dephasing due to the presence of many frequency components, which operates at all temperatures but which produces no diffusion, and (b) the transit process, which increases with increasing temperature and which produces diffusion. Because the model provides a single-atom trajectory in real space and time, including transits, it may be used to calculate all single-atom correlation functions.Comment: LaTeX, 8 figs. This is an updated version of cond-mat/0002057 and cond-mat/0002058 combined Minor changes made to coincide with published versio

Evaluation of the ALMA Prototype Antennas

The ALMA North American and European prototype antennas have been evaluated by a variety of measurement systems to quantify the major performance specifications. Nearfield holography was used to set the reflector surfaces to 17 microns RMS. Pointing and fast switching performance was determined with an optical telescope and by millimeter wavelength radiometry, yielding 2 arcsec absolute and 0.6 arcsec offset pointing accuracies. Path length stability was measured to be less than or approximately equal to 20 microns over 10 minute time periods using optical measurement devices. Dynamical performance was studied with a set of accelerometers, providing data on wind induced tracking errors and structural deformation. Considering all measurements made during this evaluation, both prototype antennas meet the major ALMA antenna performance specifications.Comment: 83 pages, 36 figures, AASTex format, to appear in PASP September 2006 issu