Evaluation of Multiple Models to Distinguish Closely Related Forms of Disease Using DNA Microarray Data: an Application to Multiple Myeloma

Motivation: Standard laboratory classification of the plasma cell dyscrasia monoclonal gammopathy of undetermined significance (MGUS) and the overt plasma cell neoplasm multiple myeloma (MM) is quite accurate, yet, for the most part, biologically uninformative. Most, if not all, cancers are caused by inherited or acquired genetic mutations that manifest themselves in altered gene expression patterns in the clonally related cancer cells. Microarray technology allows for qualitative and quantitative measurements of the expression levels of thousands of genes simultaneously, and it has now been used both to classify cancers that are morphologically indistinguishable and to predict response to therapy. It is anticipated that this information can also be used to develop molecular diagnostic models and to provide insight into mechanisms of disease progression, e.g., transition from healthy to benign hyperplasia or conversion of a benign hyperplasia to overt malignancy. However, standard data analysis techniques are not trivial to employ on these large data sets. Methodology designed to handle large data sets (or modified to do so) is needed to access the vital information contained in the genetic samples, which in turn can be used to develop more robust and accurate methods of clinical diagnostics and prognostics.Results: Here we report on the application of a panel of statistical and data mining methodologies to classify groups of samples based on expression of 12,000 genes derived from a high density oligonucleotide microarray analysis of highly purified plasma cells from newly diagnosed MM, MGUS, and normal healthy donors. The three groups of samples are each tested against each other. The methods are found to be similar in their ability to predict group membership; all do quite well at predicting MM vs. normal and MGUS vs. normal. However, no method appears to be able to distinguish explicitly the genetic mechanisms between MM and MGUS. We believe this might be due to the lack of genetic differences between these two conditions, and may not be due to the failure of the models. We report the prediction errors for each of the models and each of the methods. Additionally, we report ROC curves for the results on group prediction.Availability: Logistic regression: standard software, available, for example in SAS. Decision trees and boosted trees: C5.0 from www.rulequest.com. SVM: SVM-light is publicly available from svmlight.joachims.org. Naïve Bayes and ensemble of voters are publicly available from www.biostat.wisc.edu/~mwaddell/eov.html. Nearest Shrunken Centroids is publicly available from http://www-stat.stanford.edu/~tibs/PAM

A preliminary investigation to group disparate batches of licit and illicit diazepam tablets using differential scanning calorimetry

Increasing numbers of illicit and unlicensed medicines are in general circulation and regularly seized by the police and other regulatory authorities. Forensic identification of seized tablets tends to focus on visual appearance and chromatographic identification of the contained drug. This process is relatively time consuming and places a strain on forensic laboratories. It was therefore of interest to investigate the possible application of differential scanning calorimetry (DSC) as a fast and efficient tool to facilitate the identification of contained drug/s and associated tablet excipients. Sixteen different cases (Cases A to P) of diazepam tablets obtained from Police Scotland were characterised based on visual appearance (colour and manufacturers' logos), physical attributes (size, weight and hardness), drug type, drug quantity (HPLC) and thermal properties (DSC). Raw DSC data was further processed using principal component analysis (PCA) as an objective assessment of the thermograms obtained with a view to statistical grouping of different cases. Cases J/K, M/O and L/P could be paired on visual appearance and Cases B/C/E/G and J/K/L/P on tablet hardness (17–23 and 80–89 N respectively). HPLC indicated that 75% of the cases examined contained diazepam but less than half of these contained the recognised amount (10 mg); Cases B/E/L/P contained phenazepam and J/K contained etizolam. The thermal signatures of individual tablets provided by DSC produced qualitative information about both drugs and excipients, indicating lactose in Cases D/F/H/I/J/K/M/N/O and Emcompress™ in B/E/L/P. In particular, DSC coupled with PCA provided confident groupings of A/C/G, B/E/L/P and H/I/J/K, and specific pairings of B/E, L/P and F/N

Coordinated and tailored work rehabilitation: a randomized controlled trial with economic evaluation undertaken with workers on sick leave due to musculoskeletal disorders

Introduction In Denmark, the magnitude and impact of work disability on the individual worker and society has prompted the development of a new "coordinated and tailored work rehabilitation" (CTWR) approach. The aim of this study was to compare the effects of CTWR with conventional case management (CCM) on return-to-work of workers on sick leave due to musculoskeletal disorders (MSDs). Methods The study was a randomized controlled trial with economic evaluation undertaken with workers on sick leave for 4-12 weeks due to MSDs. CTWR consists of a work disability screening by an interdisciplinary team followed by the collaborative development of a RTW plan. The primary outcome variable was registered cumulative sickness absence hours during 12 months follow-up. Secondary outcomes were work status as well as pain intensity and functional disability, measured at baseline, 3 and 12 months follow-up. The economic evaluation (intervention costs, productivity loss, and health care utilization costs) was based on administrative data derived from national registries. Results For the time intervals 0-6 months, 6-12 months, and the entire follow-up period, the number of sickness absence hours was significantly lower in the CTWR group as compared to the control group. The total costs saved in CTWR participants compared to controls were estimated at US $1,366 per person at 6 months follow-up and US$ 10,666 per person at 12 months follow-up. Conclusions Workers on sick leave for 4-12 weeks due to MSD who underwent "CTWR" by an interdisciplinary team had fewer sickness absence hours than controls. The economic evaluation showed that-in terms of productivity loss-CTWR seems to be cost saving for the society

HIV non-B subtype distribution: emerging trends and risk factors for imported and local infections newly diagnosed in South Australia

Monitoring HIV subtype distribution is important for understanding transmission dynamics. Subtype B has historically been dominant in Australia, but in recent years new clades have appeared. Since 2000, clade data have been collected as part of HIV surveillance in South Australia. The aim of this study was to evaluate the prevalence of and risk factors for HIV-1 non-B subtypes. The study population was composed of newly diagnosed, genotyped HIV subjects in South Australia between 2000 and 2010. We analyzed time trends and subtype patterns in this cohort; notification data were aggregated into three time periods (2000–2003, 2004–2006, and 2007–2010). Main outcome measures were number of new non-B infections by year, exposure route, and other demographic characteristics. There were 513 new HIV diagnoses; 425 had information on subtype. The majority (262/425) were in men who have sex with men (MSM), predominantly subtype B and acquired in Australia. Infections acquired in Australia decreased from 77% (2000–2003) to 64% (2007–2010) ( p = 0.007) and correspondingly the proportion of subtype B declined from 85% to 68% ( p = 0.002). Non-B infections were predominantly (83%) heterosexual contacts, mostly acquired overseas (74%). The majority (68%) of non-B patients were born outside of Australia. There was a non-significant increase from 1.6% to 4.2% in the proportion of locally transmitted non-B cases (p = 0.3). Three non-B subtypes and two circulating recombinant forms (CRFs) were identified: CRF_AE (n = 41), C (n = 36), CRF_AG (n = 13), A (n = 9), and D (n = 2). There has been a substantial increase over the past decade in diagnosed non-B infections, primarily through cases acquired overseas

Weak Lensing with SDSS Commissioning Data: The Galaxy-Mass Correlation Function To 1/h Mpc

(abridged) We present measurements of galaxy-galaxy lensing from early commissioning imaging data from the Sloan Digital Sky Survey (SDSS). We measure a mean tangential shear around a stacked sample of foreground galaxies in three bandpasses out to angular radii of 600'', detecting the shear signal at very high statistical significance. The shear profile is well described by a power-law. A variety of rigorous tests demonstrate the reality of the gravitational lensing signal and confirm the uncertainty estimates. We interpret our results by modeling the mass distributions of the foreground galaxies as approximately isothermal spheres characterized by a velocity dispersion and a truncation radius. The velocity dispersion is constrained to be 150-190 km/s at 95% confidence (145-195 km/s including systematic uncertainties), consistent with previous determinations but with smaller error bars. Our detection of shear at large angular radii sets a 95% confidence lower limit $s>140^{\prime\prime}$, corresponding to a physical radius of $260h^{-1}$ kpc, implying that galaxy halos extend to very large radii. However, it is likely that this is being biased high by diffuse matter in the halos of groups and clusters. We also present a preliminary determination of the galaxy-mass correlation function finding a correlation length similar to the galaxy autocorrelation function and consistency with a low matter density universe with modest bias. The full SDSS will cover an area 44 times larger and provide spectroscopic redshifts for the foreground galaxies, making it possible to greatly improve the precision of these constraints, measure additional parameters such as halo shape, and measure the properties of dark matter halos separately for many different classes of galaxies.Comment: 28 pages, 11 figures, submitted to A

The Discovery of a Second Field Methane Brown Dwarf from Sloan Digital Sky Survey Commissioning Data

We report the discovery of a second field methane brown dwarf from the commissioning data of the Sloan Digital Sky Survey (SDSS). The object, SDSS J134646.45-003150.4 (SDSS 1346-00), was selected because of its very red color and stellar appearance. Its spectrum between 0.8-2.5 mic is dominated by strong absorption bands of H_2O and CH_4 and closely mimics those of Gliese 229B and SDSS 162414.37+002915.6 (SDSS 1624+00), two other known methane brown dwarfs. SDSS 1346-00 is approximately 1.5 mag fainter than Gliese 229B, suggesting that it lies about 11 pc from the sun. The ratio of flux at 2.1 mic to that at 1.27 mic is larger for SDSS 1346-00 than for Gliese 229B and SDSS 1624+00, which suggests that SDSS 1346-00 has a slightly higher effective temperature than the others. Based on a search area of 130 sq. deg. and a detection limit of z* = 19.8, we estimate a space density of 0.05 pc^-3 for methane brown dwarfs with T_eff ~ 1000 K in the 40 pc^3 volume of our search. This estimate is based on small-sample statistics and should be treated with appropriate caution.Comment: 9 pages, 3 figures, AASTeX, to appear in ApJ Letters, authors list update

Structurally optimised BODIPY derivatives for imaging of mitochondrial dysfunction in cancer and heart cells

The structural features required for mitochondrial uptake of BODIPY-based optical imaging agents have been explored. The first derivatives of this class of dyes shown to have mitochondrial membrane potential-dependent uptake in both cancer and heart cells have been developed

The Sloan Digital Sky Survey Quasar Catalog I. Early Data Release

We present the first edition of the Sloan Digital Sky Survey (SDSS) Quasar Catalog. The catalog consists of the 3814 objects (3000 discovered by the SDSS) in the initial SDSS public data release that have at least one emission line with a full width at half maximum larger than 1000 km/s, luminosities brighter than M_i^* = -23, and highly reliable redshifts. The area covered by the catalog is 494 square degrees; the majority of the objects were found in SDSS commissioning data using a multicolor selection technique. The quasar redshifts range from 0.15 to 5.03. For each object the catalog presents positions accurate to better than 0.2" rms per coordinate, five band (ugriz) CCD-based photometry with typical accuracy of 0.05 mag, radio and X-ray emission properties, and information on the morphology and selection method. Calibrated spectra of all objects in the catalog, covering the wavelength region 3800 to 9200 Angstroms at a spectral resolution of 1800-2100, are also available. Since the quasars were selected during the commissioning period, a time when the quasar selection algorithm was undergoing frequent revisions, the sample is not homogeneous and is not intended for statistical analysis.Comment: 27 pages, 4 figures, 4 tables, accepted by A

Alternate transcription of the Toll-like receptor signaling cascade

BACKGROUND: Alternate splicing of key signaling molecules in the Toll-like receptor (Tlr) cascade has been shown to dramatically alter the signaling capacity of inflammatory cells, but it is not known how common this mechanism is. We provide transcriptional evidence of widespread alternate splicing in the Toll-like receptor signaling pathway, derived from a systematic analysis of the FANTOM3 mouse data set. Functional annotation of variant proteins was assessed in light of inflammatory signaling in mouse primary macrophages, and the expression of each variant transcript was assessed by splicing arrays. RESULTS: A total of 256 variant transcripts were identified, including novel variants of Tlr4, Ticam1, Tollip, Rac1, Irak1, 2 and 4, Mapk14/p38, Atf2 and Stat1. The expression of variant transcripts was assessed using custom-designed splicing arrays. We functionally tested the expression of Tlr4 transcripts under a range of cytokine conditions via northern and quantitative real-time polymerase chain reaction. The effects of variant Mapk14/p38 protein expression on macrophage survival were demonstrated. CONCLUSION: Members of the Toll-like receptor signaling pathway are highly alternatively spliced, producing a large number of novel proteins with the potential to functionally alter inflammatory outcomes. These variants are expressed in primary mouse macrophages in response to inflammatory mediators such as interferon-γ and lipopolysaccharide. Our data suggest a surprisingly common role for variant proteins in diversification/repression of inflammatory signaling

Ampullary cancers harbor ELF3 tumor suppressor gene mutations and exhibit frequent WNT dysregulation

The ampulla of Vater is a complex cellular environment from which adenocarcinomas arise to form a group of histopathologically heterogenous tumors. To evaluate the molecular features of these tumors, 98 ampullary adenocarcinomas were evaluated and compared to 44 distal bile duct and 18 duodenal adenocarcinomas. Genomic analyses revealed mutations in the WNT signaling pathway among half of the patients and in all three adenocarcinomas irrespective of their origin and histological morphology. These tumors were characterized by a high frequency of inactivating mutations of ELF3, a high rate of microsatellite instability, and common focal deletions and amplifications, suggesting common attributes in the molecular pathogenesis are at play in these tumors. The high frequency of WNT pathway activating mutation, coupled with small-molecule inhibitors of β-catenin in clinical trials, suggests future treatment decisions for these patients may be guided by genomic analysis