Gene Function Classification Using Bayesian Models with Hierarchy-Based Priors

We investigate the application of hierarchical classification schemes to the annotation of gene function based on several characteristics of protein sequences including phylogenic descriptors, sequence based attributes, and predicted secondary structure. We discuss three Bayesian models and compare their performance in terms of predictive accuracy. These models are the ordinary multinomial logit (MNL) model, a hierarchical model based on a set of nested MNL models, and a MNL model with a prior that introduces correlations between the parameters for classes that are nearby in the hierarchy. We also provide a new scheme for combining different sources of information. We use these models to predict the functional class of Open Reading Frames (ORFs) from the E. coli genome. The results from all three models show substantial improvement over previous methods, which were based on the C5 algorithm. The MNL model using a prior based on the hierarchy outperforms both the non-hierarchical MNL model and the nested MNL model. In contrast to previous attempts at combining these sources of information, our approach results in a higher accuracy rate when compared to models that use each data source alone. Together, these results show that gene function can be predicted with higher accuracy than previously achieved, using Bayesian models that incorporate suitable prior information

Evaluating the Quality of Research into a Single Prognostic Biomarker: A Systematic Review and Meta-analysis of 83 Studies of C-Reactive Protein in Stable Coronary Artery Disease

Background Systematic evaluations of the quality of research on a single prognostic biomarker are rare. We sought to evaluate the quality of prognostic research evidence for the association of C-reactive protein (CRP) with fatal and nonfatal events among patients with stable coronary disease. Methods and Findings We searched MEDLINE (1966 to 2009) and EMBASE (1980 to 2009) and selected prospective studies of patients with stable coronary disease, reporting a relative risk for the association of CRP with death and nonfatal cardiovascular events. We included 83 studies, reporting 61,684 patients and 6,485 outcome events. No study reported a prespecified statistical analysis protocol; only two studies reported the time elapsed (in months or years) between initial presentation of symptomatic coronary disease and inclusion in the study. Studies reported a median of seven items (of 17) from the REMARK reporting guidelines, with no evidence of change over time. The pooled relative risk for the top versus bottom third of CRP distribution was 1.97 (95% confidence interval [CI] 1.78–2.17), with substantial heterogeneity (I2 = 79.5). Only 13 studies adjusted for conventional risk factors (age, sex, smoking, obesity, diabetes, and low-density lipoprotein [LDL] cholesterol) and these had a relative risk of 1.65 (95% CI 1.39–1.96), I2 = 33.7. Studies reported ten different ways of comparing CRP values, with weaker relative risks for those based on continuous measures. Adjusting for publication bias (for which there was strong evidence, Egger's p<0.001) using a validated method reduced the relative risk to 1.19 (95% CI 1.13–1.25). Only two studies reported a measure of discrimination (c-statistic). In 20 studies the detection rate for subsequent events could be calculated and was 31% for a 10% false positive rate, and the calculated pooled c-statistic was 0.61 (0.57–0.66). Conclusion Multiple types of reporting bias, and publication bias, make the magnitude of any independent association between CRP and prognosis among patients with stable coronary disease sufficiently uncertain that no clinical practice recommendations can be made. Publication of prespecified statistical analytic protocols and prospective registration of studies, among other measures, might help improve the quality of prognostic biomarker research

Nucleotide Polymorphisms in the Canine Noggin Gene and Their Distribution Among Dog (Canis lupus familiaris) Breeds

Noggin (NOG) is an important regulator for the signaling of bone morphogenetic proteins. In this study, we sequenced the complete coding sequence of the canine NOG gene and characterized the nucleotide polymorphisms. The sequence length varied from 717 to 729 bp, depending on the number of a 6-bp tandem repeat unit (GGCGCG), an insertion that has not been observed in other mammalian NOG genes investigated to date. It results in extensions of (Gly–Ala)3–5 in the putative NOG protein. To survey the distribution of these tandem repeat polymorphisms, we analyzed 126 individuals in seven dog breeds. We identified only three alleles: (GGCGCG)3, (GGCGCG)4, and (GGCGCG)5. Although the allele frequencies were remarkably different among the breeds, the three alleles were present in all seven of the breeds and did not show any deviation from Hardy–Weinberg equilibrium

Sugarcane stem borers of the Colombian Cauca River Valley: current pest status, biology, and control

Citation: Vargas, G., Gomez, L. A., & Michaud, J. P. (2015). Sugarcane stem borers of the Colombian Cauca River Valley: current pest status, biology, and control. Florida Entomologist, 98(2), 728-735. Retrieved from ://WOS:000356451400049Sugarcane stem borers of the genus of Diatraea (Lepidoptera: Crambidae) form a species complex that causes serious economic losses to sugarcane production in the Cauca River Valley and other regions of Colombia. Two primary species, Diatraea saccharalis (F.) and D. indigenella Dyar and Heinrich, have been effectively managed for more than 4 decades through augmentative releases of the tachinid flies Lydella minense (Townsend) and Billaea claripalpis (Wulp) (Diptera: Tachinidae) and the egg parasitoid Trichogramma exiguum Pinto & Platner (Hymenoptera: Trichogrammatidae). Here we review the current pest status of Diatraea species, damage assessment protocols, management tactics, and the environmental factors and cultural practices that can affect biological control outcomes. Recent changes in the cultivars grown have the potential to increase pest populations and diminish biological control efficacy. Additionally, recent outbreaks of new Diatraea species may further increase overall pest pressure. Thus, there is a need to develop supplementary tactics for the management of these pests that will be compatible with biological control, as well as more reliable protocols for assessing host plant resistance against the increase in infestation intensity

Hadronic Mass Moments in Inclusive Semileptonic B Meson Decays

We have measured the first and second moments of the hadronic mass-squared distribution in B -> X_c l nu, for P(lepton) > 1.5 GeV/c. We find <M_X^2 - M_D[Bar]^2> = 0.251 +- 0.066 GeV^2, )^2 > = 0.576 +- 0.170 GeV^4, where M_D[Bar] is the spin-averaged D meson mass. From that first moment and the first moment of the photon energy spectrum in b -> s gamma, we find the HQET parameter lambda_1 (MS[Bar], to order 1/M^3 and beta_0 alpha_s^2) to be -0.24 +- 0.11 GeV^2. Using these first moments and the B semileptonic width, and assuming parton-hadron duality, we obtain |V_cb| = 0.0404 +- 0.0013.Comment: 11 pages postscript, also available through http://w4.lns.cornell.edu/public/CLNS, submitted to PR

Quasi-Elastic Charge-Exchange in Nh-2-]Pnn at 794 Mev

Journals published by the American Physical Society can be found at http://publish.aps.org

Observation of the Ωc0\Omega_{c}^{0} Charmed Baryon at CLEO

The CLEO experiment at the CESR collider has used 13.7 fb$^{-1}$ of data to search for the production of the $\Omega_c^0$ (css-ground state) in $e^{+}e^{-}$ collisions at $\sqrt{s} \simeq 10.6$ {\rm GeV}. The modes used to study the $\Omega_c^0$ are $\Omega^- \pi^+$, $\Omega^- \pi^+ \pi^0$, $\Xi^- K^- pi^+ \pi^+$, $\Xi^0 K^- pi^+$, and $\Omega^- \pi^+ \pi^- \pi^+$. We observe a signal of 40.4$\pm$9.0(stat) events at a mass of 2694.6$\pm$2.6(stat)$\pm$1.9(syst) {\rm MeV/$c^2$}, for all modes combined.Comment: 10 pages postscript, also available through http://w4.lns.cornell.edu/public/CLN

Zero-Crossing Angle in the Np Analyzing Power at Medium Energies and its Relation to Charge Symmetry

Journals published by the American Physical Society can be found at http://publish.aps.org

Evidence of New States Decaying into Ξc′π\Xi^{\prime}_{c}\pi

Using 13.7 $fb^{-1}$ of data recorded by the CLEO detector at CESR, we report evidence for two new charmed baryons: one decaying into $\Xi_c^{0 \prime}\pi^+$ with the subsequent decay $\Xi_c^{0 \prime} \to \Xi_c^0 \gamma$, and its isospin partner decaying into $\Xi_c^{+ \prime} \pi^-$ followed by $\Xi_c^{+\prime} \to \Xi_c^+\gamma$. We measure the following mass differences for the two states: $M(\Xi_c^0 \gamma \pi^+)-M(\Xi_c^0)$=318.2+-1.3+-2.9 MeV, and $M(\Xi_c^+ \gamma \pi^-)-M(\Xi_c^+)$=324.0+-1.3+-3.0 MeV. We interpret these new states as the $J^P = 1/2^- \Xi_{c1}$ particles, the charmed-strange analogs of the $\Lambda_{c1}^+(2593)$.Comment: 10 pages postscript, also available through http://w4.lns.cornell.edu/public/CLN