Integration of bioinformatic predictions and experimental data to identify circRNA-miRNA associations

Circular RNAs (circRNAs) have recently emerged as a novel class of transcripts, characterized by covalently linked 3′–5′ ends that result in the so-called backsplice junction. During the last few years, thousands of circRNAs have been identified in different organisms. Yet, despite their role as disease biomarker started to emerge, depicting their function remains challenging. Different studies have shown that certain circRNAs act as miRNA sponges, but any attempt to generalize from the single case to the “circ-ome” has failed so far. In this review, we explore the potential to define miRNA “sponging” as a more general function of circRNAs and describe the different approaches to predict miRNA response elements (MREs) in known or novel circRNA sequences. Moreover, we discuss how experiments based on Ago2-IP and experimentally validated miRNA:target duplexes can be used to either prioritize or validate putative miRNA-circRNA associations

Computational Methods for the Integrative Analysis of Genomics and Pharmacological Data

Since the pioneering NCI-60 panel of the late'80's, several major screenings of genetic profiling and drug testing in cancer cell lines have been conducted to investigate how genetic backgrounds and transcriptional patterns shape cancer's response to therapy and to identify disease-specific genes associated with drug response. Historically, pharmacogenomics screenings have been largely heterogeneous in terms of investigated cell lines, assay technologies, number of compounds, type and quality of genomic data, and methods for their computational analysis. The analysis of this enormous and heterogeneous amount of data required the development of computational methods for the integration of genomic profiles with drug responses across multiple screenings. Here, we will review the computational tools that have been developed to integrate cancer cell lines' genomic profiles and sensitivity to small molecule perturbations obtained from different screenings

Preface

These proceedings contain the papers of the Third International Workshop on Recent Trends in News Informa-tion Retrieval (NewsIR\u201919) held in conjunction with the ACM SIGIR 2019 conference in Paris, France, on the25thof July 2019. Ten full papers and two short papers (one position paper and one demo paper) were selectedby the programme committee from a total of 21 submissions. Each submitted paper was reviewed by at leastthree members of an international programme committee. In addition to the selected papers, the workshopfeatures one keynote and one invited talk. The Keynote speech is given by Aron Pilhofer \u201cFrom Redlining toRobots: How newsrooms apply technology to the craft of journalism\u201d. The invited talk is given by FriedrichLindenberg \u201cMining Leaks and Open Data to Follow the Money\u201d. We would like to thank SIGIR for hostingus. Thanks also go to the keynote speakers, the program committee, the paper authors, and the participants,for without these people there would be no worksho

Composition of sands in cores along the high-speed rail (TAV): Preliminary indications on the sedimentary evolution of the Modena plain

The Modena alluvial plain has been geologically investigated in great detail and is characterized by a spectacular abundance of archaeological sites of various age. For this reasons the area may be considered a natural laboratory for the reconstruction of the recent sedimentary evolution of the Po Plain. The alluvial plain area examined for this study has an approximate extent of 150 km2 and is located at the northern side of the Northern Apennines thrust- and fold-belt, where streams draining the chain flow toward the northeast into the Po river. Detailed modal analyses by point-counting of thin sections show that modern stream sands in the Modena plain show similar overall compositional fields, but can be discriminated on the base of key-components, such as quartz, feldspar, carbonate and lithic fragments. The study of sand sediments indicates that the compositional fields have not varied significantly since the Neolithic. The only major diagenetic process is the formation of carbonate concretions (caliche), which can be easily recognized as secondary particles during point counting of thin sections. These results indicate that the reconstruction of the recent evolution of the local drainage system is possible by comparing ancient with modern fluvial sand compositions. The drilling of numerous wells along the new high speed train tract (TAV) provided us with new insight on the sedimentary evolution of the plain through time. The samples recovered from 6 wells reaching depths up to -50 m show that the sand sediments older than 10-12 kyr, have a significant shift in composition from the modern ones. This compositional change consists in a marked overall increase of quartz and feldspar components. The compositional variations can be explained by the combination of various factors: a) significant change in the bedrock lithology through time induced by tectonics and/or change in the local drainage pattern, and b) recycling of older fluvial sediments enriched in feldspar. Because the sands older than 10-12 kyr compared to the overlaying olocenic and modern sediments are enriched in feldspar, which is considered a particularly alterable component, the compositional differentiation can be related to effects induced to glacial-interglacial climate changes but not to post-depositional diagenetic processes. The considerable change in sand composition and the stratigraphy of the deposits suggest dramatic geographical, environmental and depositional variations supporting the observation that a regional unconformity separates the Late Pleistocene from the Olocene sediments

Pasos Hacia La Salud: a randomized controlled trial of an internet-delivered physical activity intervention for Latinas.

BackgroundInternet access has grown markedly in Latinos during the past decade. However, there have been no Internet-based physical activity interventions designed for Latinos, despite large disparities in lifestyle-related conditions, such as obesity and diabetes, particularly in Latina women. The current study tested the efficacy of a 6-month culturally adapted, individually tailored, Spanish-language Internet-based physical activity intervention.MethodsInactive Latinas (N = 205) were randomly assigned to the Tailored Physical Activity Internet Intervention or the Wellness Contact Control Internet Group. Participants in both groups received emails on a tapered schedule over 6 months to alert them to new content on the website. The primary outcome was minutes/week of moderate to vigorous physical activity (MVPA) at 6 months as measured by the 7-Day Physical Activity Recall; activity was also measured by accelerometers. Data were collected between 2011 and 2014 and analyzed in 2015 at the University of California, San Diego.ResultsIncreases in minutes/week of MVPA were significantly greater in the Intervention Group compared to the Control Group (mean difference = 50.00, SE = 9.5, p < 0.01). Increases in objectively measured MVPA were also significantly larger in the Intervention Group (mean differences = 31.0, SE = 10.7, p < .01). The Intervention Group was also significantly more likely to meet national physical activity guidelines at 6 months (OR = 3.12, 95% CI 1.46-6.66, p < .05).ConclusionFindings from the current study suggest that this Internet-delivered individually tailored intervention successfully increased MVPA in Latinas compared to a Wellness Contact Control Internet Group.Trial registrationNCT01834287

Computational Controversy

Climate change, vaccination, abortion, Trump: Many topics are surrounded by fierce controversies. The nature of such heated debates and their elements have been studied extensively in the social science literature. More recently, various computational approaches to controversy analysis have appeared, using new data sources such as Wikipedia, which help us now better understand these phenomena. However, compared to what social sciences have discovered about such debates, the existing computational approaches mostly focus on just a few of the many important aspects around the concept of controversies. In order to link the two strands, we provide and evaluate here a controversy model that is both, rooted in the findings of the social science literature and at the same time strongly linked to computational methods. We show how this model can lead to computational controversy analytics that have full coverage over all the crucial aspects that make up a controversy.Comment: In Proceedings of the 9th International Conference on Social Informatics (SocInfo) 201

A Fermi Surface Model for Large Supersymmetric AdS_5 Black Holes

We identify a large family of 1/16 BPS operators in N=4 SYM that qualitatively reproduce the relations between charge, angular momentum and entropy in regular supersymmetric AdS_5 black holes when the main contribution to their masses is given by their angular momentum.Comment: 32 pages, 6 figures, LaTeX uses JHEP3 class; ver 2- added acknowledgment, minor change

De novo identification of universal cell mechanics regulators

Mechanical proprieties determine many cellular functions, such as cell fate specification, migration, or circulation through vasculature. Identifying factors governing cell mechanical phenotype is therefore a subject of great interest. Here we present a mechanomics approach for establishing links between mechanical phenotype changes and the genes involved in driving them. We employ a machine learning-based discriminative network analysis method termed PC-corr to associate cell mechanical states, measured by real-time deformability cytometry (RT-DC), with large-scale transcriptome datasets ranging from stem cell development to cancer progression, and originating from different murine and human tissues. By intersecting the discriminative networks inferred from two selected datasets, we identify a conserved module of five genes with putative roles in the regulation of cell mechanics. We validate the power of the individual genes to discriminate between soft and stiff cell states in silico, and demonstrate experimentally that the top scoring gene, CAV1, changes the mechanical phenotype of cells when silenced or overexpressed. The data-driven approach presented here has the power of de novo identification of genes involved in cell mechanics regulation and paves the way towards engineering cell mechanical properties on demand to explore their impact on physiological and pathological cell functions