I paid a bribe: An experiment on information sharing and extortionary corruption

Theoretical and empirical research on corruption has flourished in the last three decades; however, identifying successful anti-corruption policies remains a challenge. In this paper we ask whether bottom-up institutions that rely on voluntary and anonymous reports of bribe demands, such as the I paid a bribe website first launched in India in 2010, could act as effective anti-corruption tools, and, if this is the case, whether and how their effectiveness could be improved. We overcome measurement and identification problems by addressing our research questions in the laboratory. Our results show that the presence of a reporting platform like the I paid a bribe website may be insufficient to systematically lower bribery. A more effective platform is one where posts disclose specific information about the size of the bribes and the location of their requestors, i.e., a platform that could serve as a search engine for the least corrupt officials, especially if posting is restricted to service recipients. Our results also show that while citizens rarely post false information, lying by officials, when allowed to post on the platform, is widespread. (C) 2017 Elsevier B.V. All rights reserved

Photoinduced absorption from localized intra-gap states

A model is developed for photoinduced absorption from localized states observed in femtosecond pump-probe experiments in high-Tc superconductors and other materials. The dynamics of localized carriers are described in terms of phenomenological approach similar to that originaly proposed by Rothwarf and Taylor. Expanding the relaxation rate in powers of the order parameter we have shown that density of localized carriers is sensitive to Tc. From the analysis of the experimental data on YBa2Cu3O(7-x) and K0.3MoO3 we conclude that significant intra-gap density of localized states exists in these materials. Temperature dependence of the density of photoexcited localized carriers in underdoped YBa2Cu3O(7-x) and in K0.3MoO3 is consistent with the observation of the pseudogap above Tc.Comment: 4 pages, 2 figures, acepted for publication in Physica C, invited poster presented at M2S, Feb. 20 - 25, 2000, Houston, US

Spatial distribution of Pleistocene/Holocene warming amplitudes in Northern Eurasia inferred from geothermal data

International audienceWe analyze 48 geothermal estimates of Pleistocene/Holocene warming amplitudes from various locations in Greenland, Europe, Arctic regions of Western Siberia, and Yakutia. The spatial distribution of these estimates exhibits two remarkable features. (i) In Europe and part of Asia the amplitude of warming increases toward the northwest and displays clear asymmetry with respect to the North Pole. The region of maximal warming is close to the North Atlantic. A simple parametric dependence of the warming amplitudes on the distance to the warming center explains 91% of the amplitude variation. The Pleistocene/Holocene warming center is located northeast of Iceland. We claim that the Holocene warming is primarily related to the formation (or resumption) of the modern system of currents in the North Atlantic. (ii) In Arctic Asia, north of the 68-th parallel, the amplitude of temperature change sharply decreases from South to North, reaching zero and even negative values. These small or negative amplitudes could be attributed partially to a joint influence of Late Pleistocene ice sheets. Using a simple model of the temperature regime underneath the ice sheet we show that, depending on the relationship between the heat flow and the vertical ice advection velocity, the base of the glacier can either warm up or cool down. Nevertheless, we speculate that the more likely explanation of these observations are warm-water lakes thought of have formed in the Late Pleistocene by the damming of the Ob, Yenisei and Lena Rivers

CoRAL: Predicting Non-Coding RNAs from Small RNA-Sequencing Data

The surprising observation that virtually the entire human genome is transcribed means we know little about the function of many emerging classes of RNAs, except their astounding diversities. Traditional RNA function prediction methods rely on sequence or alignment information, which are limited in their abilities to classify the various collections of non-coding RNAs (ncRNAs). To address this, we developed Classification of RNAs by Analysis of Length (CoRAL), a machine learning-based approach for classification of RNA molecules. CoRAL uses biologically interpretable features including fragment length and cleavage specificity to distinguish between different ncRNA populations. We evaluated CoRAL using genome-wide small RNA sequencing data sets from four human tissue types and were able to classify six different types of RNAs with ∼80% cross-validation accuracy. Analysis by CoRAL revealed that microRNAs, small nucleolar and transposon-derived RNAs are highly discernible and consistent across all human tissue types assessed, whereas long intergenic ncRNAs, small cytoplasmic RNAs and small nuclear RNAs show less consistent patterns. The ability to reliably annotate loci across tissue types demonstrates the potential of CoRAL to characterize ncRNAs using small RNA sequencing data in less well-characterized organisms

SAVoR: A Server for Sequencing Annotation and Visualization of RNA Structures

RNA secondary structure is required for the proper regulation of the cellular transcriptome. This is because the functionality, processing, localization and stability of RNAs are all dependent on the folding of these molecules into intricate structures through specific base pairing interactions encoded in their primary nucleotide sequences. Thus, as the number of RNA sequencing (RNA-seq) data sets and the variety of protocols for this technology grow rapidly, it is becoming increasingly pertinent to develop tools that can analyze and visualize this sequence data in the context of RNA secondary structure. Here, we present Sequencing Annotation and Visualization of RNA structures (SAVoR), a web server, which seamlessly links RNA structure predictions with sequencing data and genomic annotations to produce highly informative and annotated models of RNA secondary structure. SAVoR accepts read alignment data from RNA-seq experiments and computes a series of per-base values such as read abundance and sequence variant frequency. These values can then be visualized on a customizable secondary structure model. SAVoR is freely available at http://tesla.pcbi.upenn.edu/savor

HAMR: High-Throughput Annotation of Modified Ribonucleotides

RNA is often altered post-transcriptionally by the covalent modification of particular nucleotides; these modifications are known to modulate the structure and activity of their host RNAs. The recent discovery that an RNA methyl-6 adenosine demethylase (FTO) is a risk gene in obesity has brought to light the significance of RNA modifications to human biology. These noncanonical nucleotides, when converted to cDNA in the course of RNA sequencing, can produce sequence patterns that are distinguishable from simple base-calling errors. To determine whether these modifications can be detected in RNA sequencing data, we developed a method that can not only locate these modifications transcriptome-wide with single nucleotide resolution, but can also differentiate between different classes of modifications. Using small RNA-seq data we were able to detect 92% of all known human tRNA modification sites that are predicted to affect RT activity. We also found that different modifications produce distinct patterns of cDNA sequence, allowing us to differentiate between two classes of adenosine and two classes of guanine modifications with 98% and 79% accuracy, respectively. To show the robustness of this method to sample preparation and sequencing methods, as well as to organismal diversity, we applied it to a publicly available yeast data set and achieved similar levels of accuracy. We also experimentally validated two novel and one known 3-methylcytosine (3mC) sites predicted by HAMR in human tRNAs. Researchers can now use our method to identify and characterize RNA modifications using only RNA-seq data, both retrospectively and when asking questions specifically about modified RNA

Genome-Wide Double-Stranded RNA Sequencing Reveals the Functional Significance of Base-Paired RNAs in \u3cem\u3eArabidopsis\u3c/em\u3e

The functional structure of all biologically active molecules is dependent on intra- and inter-molecular interactions. This is especially evident for RNA molecules whose functionality, maturation, and regulation require formation of correct secondary structure through encoded base-pairing interactions. Unfortunately, intra- and inter-molecular base-pairing information is lacking for most RNAs. Here, we marry classical nuclease-based structure mapping techniques with high-throughput sequencing technology to interrogate all base-paired RNA in Arabidopsis thaliana and identify ∼200 new small (sm)RNA–producing substrates of RNA–DEPENDENT RNA POLYMERASE6. Our comprehensive analysis of paired RNAs reveals conserved functionality within introns and both 5′ and 3′ untranslated regions (UTRs) of mRNAs, as well as a novel population of functional RNAs, many of which are the precursors of smRNAs. Finally, we identify intra-molecular base-pairing interactions to produce a genome-wide collection of RNA secondary structure models. Although our methodology reveals the pairing status of RNA molecules in the absence of cellular proteins, previous studies have demonstrated that structural information obtained for RNAs in solution accurately reflects their structure in ribonucleoprotein complexes. Furthermore, our identification of RNA–DEPENDENT RNA POLYMERASE6 substrates and conserved functional RNA domains within introns and both 5′ and 3′ untranslated regions (UTRs) of mRNAs using this approach strongly suggests that RNA molecules are correctly folded into their secondary structure in solution. Overall, our findings highlight the importance of base-paired RNAs in eukaryotes and present an approach that should be widely applicable for the analysis of this key structural feature of RNA

Global Analysis of RNA Secondary Structure in Two Metazoans

The secondary structure of RNA is necessary for its maturation, regulation, processing, and function. However, the global influence of RNA folding in eukaryotes is still unclear. Here, we use a high-throughput, sequencing-based, structure-mapping approach to identify the paired (double-stranded RNA [dsRNA]) and unpaired (single-stranded RNA [ssRNA]) components of the Drosophila melanogaster and Caenorhabditis elegans transcriptomes, which allows us to identify conserved features of RNA secondary structure in metazoans. From this analysis, we find that ssRNAs and dsRNAs are significantly correlated with specific epigenetic modifications. Additionally, we find key structural patterns across protein-coding transcripts that indicate that RNA folding demarcates regions of protein translation and likely affects microRNA-mediated regulation of mRNAs in animals. Finally, we identify and characterize 546 mRNAs whose folding pattern is significantly correlated between these metazoans, suggesting that their structure has some function. Overall, our findings provide a global assessment of RNA folding in animals