Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m6A modification

Understanding genome organization and gene regulation requires insight into RNA transcription, processing and modification. We adapted nanopore direct RNA sequencing to examine RNA from a wild-type accession of the model plant Arabidopsis thaliana and a mutant defective in mRNA methylation (m6A). Here we show that m6A can be mapped in full-length mRNAs transcriptome-wide and reveal the combinatorial diversity of cap-associated transcription start sites, splicing events, poly(A) site choice and poly(A) tail length. Loss of m6A from 3’ untranslated regions is associated with decreased relative transcript abundance and defective RNA 30 end formation. A functional consequence of disrupted m6A is a lengthening of the circadian period. We conclude that nanopore direct RNA sequencing can reveal the complexity of mRNA processing and modification in full-length single molecule reads. These findings can refine Arabidopsis genome annotation. Further, applying this approach to less well-studied species could transform our understanding of what their genomes encode

Scaling of the conductance distribution near the Anderson transition

The single parameter scaling hypothesis is the foundation of our understanding of the Anderson transition. However, the conductance of a disordered system is a fluctuating quantity which does not obey a one parameter scaling law. It is essential to investigate the scaling of the full conductance distribution to establish the scaling hypothesis. We present a clear cut numerical demonstration that the conductance distribution indeed obeys one parameter scaling near the Anderson transition

Estimating Population Abundance with a Mixture of Physical Capture and PIT Tag Antenna Detection Data

The inclusion of passive interrogation antenna (PIA) detection data has promise to increase precision of population abundance estimates (Nˆ ). However, encounter probabilities are often higher for PIAs than for physical capture. If the difference is not accounted for, Nˆ may be biased. Using simulations, we estimated the magnitude of bias resulting from mixed capture and detection probabilities and evaluated potential solutions for removing the bias for closed capture models. Mixing physical capture and PIA detections (pdet) resulted in negative biases in Nˆ . However, using an individual covariate to model differences removed bias and improved precision. From a case study of fish making spawning migrations across a stream-wide PIA (pdet ≤ 0.9), the coefficient of variation (CV) of Nˆ declined 39%–82% when PIA data were included, and there was a dramatic reduction in time to detect a significant change in Nˆ . For a second case study, with modest pdet (≤0.2) using smaller PIAs, CV (Nˆ ) declined 4%–18%. Our method is applicable for estimating abundance for any situation where data are collected with methods having different capture–detection probabilities

(±)-2′-Phenyl­cyclo­hexa­nespiro-4′-(aze­pano[1,2-b]isoxazolidine)

In the crystal structure of the racemic title isoxazolidine, C19H27NO, the relative stereochemistry between the phenyl group and the bridgehead H atom is shown to be syn. There are two mol­ecules in the asymmetric unit, one of which is the 7R*,13R* enanti­omer, and one of which is the 7S*,13S* enanti­omer. These enanti­omers adopt different orientations of the phenyl ring with respect to the isoxazolidine ring, with C—C—C—C torsion angles of 63.6 (4) and 86.8 (4)°, respectively. In both enanti­omers, the six-membered ring adopts a chair conformation, while the seven-membered ring adopts a twist-chair conformation

Probability distribution of the conductance at the mobility edge

Distribution of the conductance P(g) at the critical point of the metal-insulator transition is presented for three and four dimensional orthogonal systems. The form of the distribution is discussed. Dimension dependence of P(g) is proven. The limiting cases $g\to\infty$ and $g\to 0$ are discussed in detail and relation $P(g)\to 0$ in the limit $g\to 0$ is proven.Comment: 4 pages, 3 .eps figure

Disordered Electrons in a Strong Magnetic Field: Transfer Matrix Approaches to the Statistics of the Local Density of States

We present two novel approaches to establish the local density of states as an order parameter field for the Anderson transition problem. We first demonstrate for 2D quantum Hall systems the validity of conformal scaling relations which are characteristic of order parameter fields. Second we show the equivalence between the critical statistics of eigenvectors of the Hamiltonian and of the transfer matrix, respectively. Based on this equivalence we obtain the order parameter exponent $\alpha_0\approx 3.4$ for 3D quantum Hall systems.Comment: 4 pages, 3 Postscript figures, corrected scale in Fig.

Public engagement on global health challenges

<p>Abstract</p> <p>Background</p> <p>Experience with public engagement activities regarding the risks and benefits of science and technology (S&T) is growing, especially in the industrialized world. However, public engagement in the developing world regarding S&T risks and benefits to explore health issues has not been widely explored.</p> <p>Methods</p> <p>This paper gives an overview about public engagement and related concepts, with a particular focus on challenges and benefits in the developing world. We then describe an Internet-based platform, which seeks to both inform and engage youth and the broader public on global water issues and their health impacts. Finally, we outline a possible course for future action to scale up this and similar online public engagement platforms.</p> <p>Results</p> <p>The benefits of public engagement include creating an informed citizenry, generating new ideas from the public, increasing the chances of research being adopted, increasing public trust, and answering ethical research questions. Public engagement also fosters global communication, enables shared experiences and methodology, standardizes strategy, and generates global viewpoints. This is especially pertinent to the developing world, as it encourages previously marginalized populations to participate on a global stage. One of the core issues at stake in public engagement is global governance of science and technology. Also, beyond benefiting society at large, public engagement in science offers benefits to the scientific enterprise itself.</p> <p>Conclusion</p> <p>Successful public engagement with developing world stakeholders will be a critical part of implementing new services and technologies. Interactive engagement platforms, such as the Internet, have the potential to unite people globally around relevant health issues.</p

A Tribute to the Mind, Methodology and Mentoring of Wayne Velicer

Wayne Velicer is remembered for a mind where mathematical concepts and calculations intrigued him, behavioral science beckoned him, and people fascinated him. Born in Green Bay, Wisconsin on March 4, 1944, he was raised on a farm, although early influences extended far beyond that beginning. His Mathematics BS and Psychology minor at Wisconsin State University in Oshkosh, and his PhD in Quantitative Psychology from Purdue led him to a fruitful and far-reaching career. He was honored several times as a high-impact author, was a renowned scholar in quantitative and health psychology, and had more than 300 scholarly publications and 54,000+ citations of his work, advancing the arenas of quantitative methodology and behavioral health. In his methodological work, Velicer sought out ways to measure, synthesize, categorize, and assess people and constructs across behaviors and time, largely through principal components analysis, time series, and cluster analysis. Further, he and several colleagues developed a method called Testing Theory-based Quantitative Predictions, successfully applied to predicting outcomes and effect sizes in smoking cessation, diet behavior, and sun protection, with the potential for wider applications. With $60,000,000 in external funding, Velicer also helped engage a large cadre of students and other colleagues to study methodological models for a myriad of health behaviors in a widely applied Transtheoretical Model of Change. Unwittingly, he has engendered indelible memories and gratitude to all who crossed his path. Although Wayne Velicer left this world on October 15, 2017 after battling an aggressive cancer, he is still very present among us

Characteristics Associated with Citation Rate of the Medical Literature

BACKGROUND: The citation rate for articles is viewed as a measure of their importance and impact; however, little is known about what features of articles are associated with higher citation rate. METHODOLOGY/PRINCIPAL FINDINGS: We conducted a cohort study of all original articles, regardless of study methodology, published in the Lancet, JAMA, and New England Journal of Medicine, from October 1, 1999 to March 31, 2000. We identified 328 articles. Two blinded, independent reviewers extracted, in duplicate, nine variables from each article, which were analyzed in both univariable and multivariable linear least-squares regression models for their association with the annual rate of citations received by the article since publication. A two-way interaction between industry funding and an industry-favoring result was tested and found to be significant (p = 0.02). In our adjusted analysis, the presence of industry funding and an industry-favoring result was associated with an increase in annual citation rate of 25.7 (95% confidence interval, 8.5 to 42.8) compared to the absence of both industry funding and industry-favoring results. Higher annual rates of citation were also associated with articles dealing with cardiovascular medicine (13.3 more; 95% confidence interval, 3.9 to 22.3) and oncology (12.6 more; 95% confidence interval, 1.2 to 24.0), articles with group authorship (11.1 more; 95% confidence interval, 2.7 to 19.5), larger sample size and journal of publication. CONCLUSIONS/SIGNIFICANCE: Large trials, with group authorship, industry-funded, with industry-favoring results, in oncology or cardiology were associated with greater subsequent citations