Errors in CGAP xProfiler and cDNA DGED: the importance of library parsing and gene selection algorithms

<p>Abstract</p> <p>Background</p> <p>The Cancer Genome Anatomy Project (CGAP) xProfiler and cDNA Digital Gene Expression Displayer (DGED) have been made available to the scientific community over a decade ago and since then were used widely to find genes which are differentially expressed between cancer and normal tissues. The tissue types are usually chosen according to the ontology hierarchy developed by NCBI. The xProfiler uses an internally available flat file database to determine the presence or absence of genes in the chosen libraries, while cDNA DGED uses the publicly available UniGene Expression and Gene relational databases to count the sequences found for each gene in the presented libraries.</p> <p>Results</p> <p>We discovered that the CGAP approach often includes libraries from dependent or irrelevant tissues (one third of libraries were incorrect on average, with some tissue searches no correct libraries being selected at all). We also discovered that the CGAP approach reported genes from outside the selected libraries and may omit genes found within the libraries. Other errors include the incorrect estimation of the significance values and inaccurate settings for the library size cut-off values. We advocated a revised approach to finding libraries associated with tissues. In doing so, libraries from dependent or irrelevant tissues do not get included in the final library pool. We also revised the method for determining the presence or absence of a gene by searching the UniGene relational database, revised calculation of statistical significance and sorted the library cut-off filter.</p> <p>Conclusion</p> <p>Our results justify re-evaluation of all previously reported results where NCBI CGAP expression data and tools were used.</p

High school drinking mediates the relationship between parental monitoring and college drinking: A longitudinal analysis

<p>Abstract</p> <p>Background</p> <p>College drinking is a significant public health problem. Although parental monitoring and supervision reduces the risk for alcohol consumption among younger adolescents, few studies have investigated the impact of earlier parental monitoring on later college drinking. This study examined whether parental monitoring indirectly exerts a protective effect on college drinking by reducing high school alcohol consumption.</p> <p>Methods</p> <p>A longitudinal cohort of 1,253 male and female students, ages 17 to 19, attending a large, public, mid-Atlantic university was studied at two time points. First, data on high school parental monitoring and alcohol consumption were gathered via questionnaire during the summer prior to college entry. Second, during the first year of college, past-year alcohol consumption was measured via a personal interview. Multiple regression models tested the relationship between parental monitoring and past year alcohol use (i.e., number of drinks per drinking day).</p> <p>Results</p> <p>Holding constant demographics, SAT score, and religiosity, parental monitoring had a significant protective effect on both high school and college drinking level. However, the association between parental monitoring and college drinking level became non-significant once high school drinking level was held constant.</p> <p>Conclusion</p> <p>While parental monitoring did not directly influence college alcohol consumption, evidence for mediation was observed, whereby parental monitoring had an indirect influence on college drinking through reductions in high school drinking. Initiatives that promote effective parenting might be an important strategy to curb high-risk drinking among older adolescents. More research is needed to understand the nature and degree of parent-child communication that is necessary to extend the protective influence of parents into the college years.</p

Measurement of single π0 production by coherent neutral-current ν Fe interactions in the MINOS Near Detector

Forward single π0 production by coherent neutral-current interactions, νA→νAπ0, is investigated using a 2.8×1020 protons-on-target exposure of the MINOS Near Detector. For single-shower topologies, the event distribution in production angle exhibits a clear excess above the estimated background at very forward angles for visible energy in the range 1-8 GeV. Cross sections are obtained for the detector medium comprised of 80% iron and 20% carbon nuclei with =48, the highest- target used to date in the study of this coherent reaction. The total cross section for coherent neutral-current single π0 production initiated by the νμ flux of the NuMI low-energy beam with mean (mode) Eν of 4.9 GeV (3.0 GeV), is 77.6±5.0(stat)-16.8+15.0(syst)×10-40 cm2 pernucleus. The results are in good agreement with predictions of the Berger-Sehgal model

Search for Sterile Neutrinos Mixing with Muon Neutrinos in MINOS

We report results of a search for oscillations involving a light sterile neutrino over distances of 1.04 and 735 km in a νμ-dominated beam with a peak energy of 3 GeV. The data, from an exposure of 10.56 × 10^20 protons on target, are analyzed using a phenomenological model with one sterile neutrino. We constrain the mixing parameters θ24 and Δm41^2 and set limits on parameters of the four-dimensional Pontecorvo-Maki- Nakagawa-Sakata matrix, |Uμ4|2 and |Uτ4|2, under the assumption that mixing between νe and νs is negligible (|Ue4|^2 = 0). No evidence for νμ → νs transitions is found and we set a world-leading limit on θ24 for values of Δm41^2 ≲ 1 eV^2

Search for flavor-changing nonstandard neutrino interactions using nu(e) appearance in MINOS

We report new constraints on flavor-changing nonstandard neutrino interactions from the MINOS long-baseline experiment using νe and ¯νe appearance candidate events from predominantly νμ and ¯νμ beams. We used a statistical selection algorithm to separate νe candidates from background events, enabling an analysis of the combined MINOS neutrino and antineutrino data. We observe no deviations from standard neutrino mixing, and thus place constraints on the nonstandard interaction matter effect, |ϵeτ|, and phase, (δCP+δeτ), using a 30-bin likelihood fit

Measurement of the multiple-muon charge ratio in the MINOS Far Detector

The charge ratio, Rμ=Nμ+/Nμ−, for cosmogenic multiple-muon events observed at an underground depth of 2070 mwe has been measured using the magnetized MINOS Far Detector. The multiple-muon events, recorded nearly continuously from August 2003 until April 2012, comprise two independent data sets imaged with opposite magnetic field polarities, the comparison of which allows the systematic uncertainties of the measurement to be minimized. The multiple-muon charge ratio is determined to be Rμ=1.104±0.006(stat)+0.009−0.010(syst). This measurement complements previous determinations of single-muon and multiple-muon charge ratios at underground sites and serves to constrain models of cosmic-ray interactions at TeV energies

Measurement of Neutrino and Antineutrino Oscillations Using Beam and Atmospheric Data in MINOS

We report measurements of oscillation parameters from νμ and ν̅ μ disappearance using beam and atmospheric data from MINOS. The data comprise exposures of 10.71×1020 protons on target in the νμ-dominated beam, 3.36×1020 protons on target in the ν̅ μ-enhanced beam, and 37.88 kton yr of atmospheric neutrinos. Assuming identical ν and ν̅ oscillation parameters, we measure |Δm2|=(2.41-0.10+0.09)×10-3  eV2 and sin⁡2(2θ)=0.950-0.036+0.035. Allowing independent ν and ν̅ oscillations, we measure antineutrino parameters of |Δm̅ 2|=(2.50-0.25+0.23)×10-3  eV2 and sin⁡2(2θ̅ )=0.97-0.08+0.03, with minimal change to the neutrino parameters