Measuring Lineup Difficulty By Matching Distance Metrics With Subject Choices in Crowd-Sourced Data

Graphics play a crucial role in statistical analysis and data mining. Being able to quantify structure in data that is visible in plots, and how people read the structure from plots is an ongoing challenge. The lineup protocol provides a formal framework for data plots, making inference possible. The data plot is treated like a test statistic, and lineup protocol acts like a comparison with the sampling distribution of the nulls. This article describes metrics for describing structure in data plots and evaluates them in relation to the choices that human readers made during several large Amazon Turk studies using lineups. The metrics that were more specific to the plot types tended to better match subject choices, than generic metrics. The process that we followed to evaluate metrics will be useful for general development of numerically measuring structure in plots, and also in future experiments on lineups for choosing blocks of pictures. Supplementary materials for this article are available online.     

The Cancer Genetics Network: recruitment results and pilot studies

OBJECTIVE: The National Cancer Institute established the Cancer Genetics Network (CGN) to support collaborative investigations into the genetic basis of cancer susceptibility, explore mechanisms to integrate this new knowledge into medical practice, and identify ways of addressing the associated psychosocial, ethical, legal, and public health issues. SUBJECTS AND METHODS: The CGN has developed the complex infrastructure required to support the projects, including the establishment of guidelines and policies, uniform methods, standard questionnaires to be used by all of the centers, and a standard format for submission of data to the Informatics Center. Cancer patients and their family members have been invited to enroll and be included in a pool of potential study participants. The Information Technology Group is responsible for support of the design, implementation, and maintenance of the multicenter Network-wide research protocols. RESULTS: As of January 2004, the CGN contained data on 23,995 probands (participants) and 425,798 family members. As a resource for cancer genetic studies, the CGN has a large number of probands and first-degree relatives with and without cancer and with multiple ethnicities. Different study designs can be used including case-control, case-case, and family studies. CONCLUSIONS: The unique resources of the CGN are available for studies on cancer genetic susceptibility, translational research, and behavioral research. The CGN is now at a point where approved collaborators may have access to enrolled patients and their families for special studies, as well as to the clinical, environmental and family cancer history data banked in the Informatics Center.     

Preservice Mathematics and Science Teachers' Case Studies of a Diverse Population of Workers

Sixteen preservice science and mathematics teachers in the last term of a Master of Arts in Teaching (MAT) program completed case studies of workers from a variety of settings including a radio station, department store, manufacturing plant, health care facility, water treatment plant, and engineering firm. These preservice teachers then examined their findings and reflected about the knowledge and skills necessary for high school graduates to be successful in the present day workplace. Finally, the preservice teachers examined how they could personally contribute to these desirable student outcomes within the high school science or mathematics curriculum for which they will eventually be responsible in their future teaching situations.     

Adaptive use of iterative methods in predictor–corrector interior point methods for linear programming

In this work we devise efficient algorithms for finding the search directions for interior point methods applied to linear programming problems. There are two innovations. The first is the use of updating of preconditioners computed for previous barrier parameters. The second is an adaptive automated procedure for determining whether to use a direct or iterative solver, whether to reinitialize or update the preconditioner, and how many updates to apply. These decisions are based on predictions of the cost of using the different solvers to determine the next search direction, given costs in determining earlier directions. We summarize earlier results using a modified version of the OB1-R code of Lustig, Marsten, and Shanno, and we present results from a predictor–corrector code PCx modified to use adaptive iteration. If a direct method is appropriate for the problem, then our procedure chooses it, but when an iterative procedure is helpful, substantial gains in efficiency can be obtained.     

The use of immobilised metal affinity chromatography (IMAC) to compare expression of copper-binding proteins in control and copper-exposed marine microalgae

Toxicity of metals to aquatic organisms is dependent on both external factors, such as exposure concentration and water quality parameters, and intracellular processes including specific metal-binding sites and detoxification. Current models used to predict copper toxicity in microalgae do not adequately consider these intracellular processes. This study compared the copper-binding proteins from four species of marine microalgae, Dunaliella tertiolecta, Tetraselmis sp., Phaedactylum tricornutum and Ceratoneis closterium, in controls (no added copper) and following a 72-h exposure to copper (sufficient to inhibit growth by approximately 50 %). Cells were lysed by sonication, which was optimised to obtain 54–94 % cell rupture for the different algae. Cell lysates were processed by immobilised metal affinity chromatography (IMAC) using Cu²⁺ as the bound metal (i.e. Cu-IMAC). Bound proteins were subsequently analysed by SDS-PAGE, comparing proteins recovered from algae that were exposed to copper versus untreated control cells. Individual proteins for which copper exposure resulted in changes to proteins present were excised from gels and further analysed by nano LC ESI-MS/MS; proteins were identified using the Mascot database. Proteins identified in this way included heat-shock proteins, rubisco, α- and β-tubulins and ATP synthase (β subunit). The results established that Cu-IMAC is a useful approach to identify proteins involved in copper binding in algae. This study identified several proteins that may play an active role in responses to copper toxicity in marine microalgae.

NON-NUCLEAR DAMAGE AND CELL LYSIS ARE INDUCED BY UVA, BUT NOT UVB OR UVC, RADIATION IN THREE STRAINS OF L5178Y CELLS

The potential to induce non-nuclear changes in mammalian cells has been examined for (1) UVA1 radiation (340–400 nm, UVASUN 2000 lamp), (2) UVA + UVB (peak at 313 nm) radiation (FS20 lamp), and (3) UVC (254 nm) radiation (GI5T8 lamp). The effects of irradiation were monitored in vitro using three strains of L5178Y (LY) mouse lymphoma cells that markedly differ in sensitivity to UV radiation. Comparisons were made for the effects of approximately equitoxic fluences that reduced cell survival to 1–15%. Depending on the cell strain, the fluences ranged from 830 to 1600 kJ/m² for the UVASUN lamp, 75 to 390 J/m² for the FS20 lamp and 3.8 to 17.2 J/m² for the G15T8 lamp. At the exposure level used in this study, irradiation with the UVASUN, but not the FS20 or G15T8, lamp induced a variety of non-nuclear changes including damage to cytoplasmic organelles and increased plasma membrane permeability and cell lysis. Cell lysis and membrane permeabilization were induced by the UVA1 emission of the UVASUN lamp, but not by its visible + IR components (>400 nm). The results show that the plasma membrane and other organelles of LY cells are highly sensitive to UVA1 but not to UVB or UVC radiation. Also UVA1, but not UVB or UVC radiation, causes rapid and extensive lysis of LY cells. In conclusion, non-nuclear damage contributes substantially to UVA cytotoxicity in all three strains of LY cells.     

Improved curve fitting procedures to determine equilibrium binding constants

For ligand-biomacromolecule titration experiments it has been traditional practice to extract parameters such as the equilibrium binding constant K and the number of bases per ligand binding site n with relatively labour intensive methods, usually based on single wavelength data, such as the difference method by Rodger and Nordén coupled together with a Scatchard plot. Presented in this paper are both the theory and a least squares fitting method to derive parameters such as K and n more directly from all spectral non-linear experimental data. Both the case of non competitive binding of a metal complex ligand to DNA and the case of displacement by a metal complex ligand of an ethidium marker attached to the DNA are considered. This work may be applied directly to reduce experimental data produced by a spectropolarimeter (for circular or linear dichroism) or a spectrophotometer (for fluorescence or UV-Vis spectroscopy).     

Analysis of polycyclic aromatic hydrocarbons (PAHs) in environmental samples: a critical review of gas chromatographic (GC) methods

Polycyclic aromatic hydrocarbons (PAHs) are frequently measured in the atmosphere for air quality assessment, in biological tissues for health-effects monitoring, in sediments and mollusks for environmental monitoring, and in foodstuffs for safety reasons. In contemporary analysis of these complex matrices, gas chromatography (GC), rather than liquid chromatography (LC), is often the preferred approach for separation, identification, and quantification of PAHs, largely because GC generally affords greater selectivity, resolution, and sensitivity than LC. This article reviews modern-day GC and state-of-the-art GC techniques used for the determination of PAHs in environmental samples. Standard test methods are discussed. GC separations of PAHs on a variety of capillary columns are examined, and the properties and uses of selected mass spectrometric (MS) techniques are presented. PAH literature on GC with MS techniques, including chemical ionization, ion-trap MS, time-of-flight MS (TOF-MS), and isotope-ratio mass spectrometry (IRMS), is reviewed. Enhancements to GC, for example large-volume injection, thermal desorption, fast GC, and coupling of GC to LC, are also discussed with regard to the determination of PAHs in an effort to demonstrate the vigor and robustness GC continues to achieve in the analytical sciences.     

Chloro­bis­(tri­phenyl­phosphine)­nickel(I) tetra­hydro­furan solvate and an unsolvated trigonal phase of chloro­tris­(tri­phenyl­phosphine)­nickel(I)

In [NiCl(C₁₈H₁₅P)₂]·C₄H₈O, the Ni atom is coordinated by three ligands in a distorted trigonal–planar configuration, with a P—Ni—P angle of 111.52 (2)°. In [NiCl(C₁₈H₁₅P)₃], there are three independent mol­ecules in the asymmetric unit, with each Ni—Cl bond on a crystallographic threefold rotation axis. Each Ni centre is tetrahedrally bound. The Ni atoms in both compounds have a d⁹ configuration and a formal oxidation state of Ni^I. A comparison is made between the form of [NiCl(PPh₃)₃] presented here and that of a known toluene solvate.     

Action spectrum conversion factors that change erythemally weighted to previtamin D3-weighted UV doses

Abstract Many solar UV measurements, either terrestrial or personal, weight the raw data by the erythemal action spectrum. However, a problem arises when one tries to estimate the benefit of vitamin D(3) production based on erythemally weighted outdoor doses, like those measured by calibrated R-B meters or polysulphone badges, because the differences between action spectra give dissimilar values. While both action spectra peak in the UVB region, the erythemal action spectrum continues throughout the UVA region while the previtamin D(3) action spectrum stops near that boundary. When one uses the previtamin D(3) action spectrum to weight the solar spectra (D(eff)), one gets a different contribution in W m(-2) than what the erythemally weighted data predicts (E(eff)). Thus, to do proper benefit assessments, one must incorporate action spectrum conversion factors (ASCF) into the calculations to change erythemally weighted to previtamin D(3)-weighted doses. To date, all benefit assessments for vitamin D(3) production in human skin from outdoor exposures are overestimates because they did not account for the different contributions of each action spectrum with changing solar zenith angle and ozone and they did not account for body geometry. Here we describe how to normalize the ratios of the effective irradiances (D(eff)/E(eff)) to get ASCF that change erythemally weighted to previtamin D(3)-weighted doses. We also give the ASCF for each season of the year in the northern hemisphere every 5 degrees from 30 degrees N to 60 degrees N, based on ozone values. These ASCF, along with geometry conversion factors and other information, can give better vitamin D(3) estimates from erythemally weighted outdoor doses.