A comprehensive program for textual concordances and statistics

Literary research tool can provide concordance and many other textual statistics relating to authorship or sequence of composition. Mechanical text manipulation provides wide variety of text formats and conventions (such as upper case). This program is written in FORTRAN H for use on IBM-360 computer

In search of stars: network formation among heterogeneous agents

This paper reports results from a laboratory experiment on network formation among heterogeneous agents. The experimental design extends the Bala-Goyal [Bala, V., Goyal, S., 2000. A non-cooperative model of network formation, Econometrica 68, 1131-1230] model of network formation with decay and two-way flow of benefits by introducing agents with lower linking costs or higher benefits to others. Furthermore, agents' types may be common knowledge or private information. In all treatments, the (efficient) equilibrium network has a "star" structure. While equilibrium predictions fail completely with homogeneous agents, star networks frequently occur with heterogeneous agents. Stars are not born but rather develop: with a high-value agent, the network's centrality, stability, and efficiency all increase over time. A structural econometric model based on best response dynamics and other-regarding preferences is used to analyze individual linking behavior. Maximum-likelihood estimates of the underlying structural parameters, obtained by pooling data from several treatments, allow us to explain the main treatment effects. © 2008 Elsevier Inc. All rights reserved

Indirect punishment and generosity towards strangers

Many people incur costs to reward strangers who have been kind to others. Theoretical and experimental evidence suggests that such "indirect rewarding" sustains cooperation between unrelated humans. Its emergence is surprising, because rewarders incur costs but receive no immediate benefits. It can prevail in the long run only if rewarders earn higher payoffs than "defectors" who ignore strangers' kindness. We provide experimental evidence regarding the payoffs received by individuals who employ these and other strategies, such as "indirect punishment" by imposing costs on unkind strangers. We find that if unkind strangers cannot be punished, defection earns most. If they can be punished, however, then indirect rewarding earns most. Indirect punishment plays this important role, even if it gives a low payoff and is rarely implemented

TDP-43 condensation properties specify its RNA binding and regulation

Summary: Mutations causing amyotrophic lateral sclerosis (ALS) often affect the condensation properties of RNA-binding proteins (RBPs). However, the role of RBP condensation in the specificity and function of protein-RNA complexes remains unclear. We created a series of TDP-43 C-terminal domain (CTD) variants that exhibited a gradient of low to high condensation propensity, as observed in vitro and by nuclear mobility and foci formation. Notably, a capacity for condensation was required for efficient TDP-43 assembly on subsets of RNA-binding regions, which contain unusually long clusters of motifs of characteristic types and density. These “binding-region condensates” are promoted by homomeric CTD-driven interactions and required for efficient regulation of a subset of bound transcripts, including autoregulation of TDP-43 mRNA. We establish that RBP condensation can occur in a binding-region-specific manner to selectively modulate transcriptome-wide RNA regulation, which has implications for remodeling RNA networks in the context of signaling, disease, and evolution

A computationally-enhanced hiCLIP atlas reveals Staufen1-RNA binding features and links 3′ UTR structure to RNA metabolism

The structure of mRNA molecules plays an important role in its interactions with trans-acting factors, notably RNA binding proteins (RBPs), thus contributing to the functional consequences of this interplay. However, current transcriptome-wide experimental methods to chart these interactions are limited by their poor sensitivity. Here we extend the hiCLIP atlas of duplexes bound by Staufen1 (STAU1) ∼10-fold, through careful consideration of experimental assumptions, and the development of bespoke computational methods which we apply to existing data. We present Tosca, a Nextflow computational pipeline for the processing, analysis and visualisation of proximity ligation sequencing data generally. We use our extended duplex atlas to discover insights into the RNA selectivity of STAU1, revealing the importance of structural symmetry and duplex-span-dependent nucleotide composition. Furthermore, we identify heterogeneity in the relationship between transcripts with STAU1-bound 3' UTR duplexes and metabolism of the associated RNAs that we relate to RNA structure: transcripts with short-range proximal 3' UTR duplexes have high degradation rates, but those with long-range duplexes have low rates. Overall, our work enables the integrative analysis of proximity ligation data delivering insights into specific features and effects of RBP-RNA structure interactions

Pregled slitina otpornih na puzanje za uporabu u energetskim postrojenjima

A paper describes the most popular alloys for power plant application as well as the most promising alloys for future application in that technology. The components in power plants operate in severe conditions (high temperatures and pressures) and they are expected reliable service for 30 years and more. The correct choice of the material is, thus, of a very importance. The paper describes the development as well as advantages and disadvantages of convenient ferritic/martensitic steels, ferritic/bainitic steels, austenitic stainless steels and the new alloys for the application at temperatures of 650°C and more.Članak opisuje najzastupljenije slitine za uporabu u energetici kao i slitine koje najviše obećavaju za uporabu u toj tehnologiji. Komponente u termoenergetskim postrojenjima rade u oštrim uvjetima (visoke temperature i tlakovi) i očekuje se da budu u radu 30 i više godina. Stoga je izbor materijala veoma važan. Članak opisuje razvoj te prednosti i nedostatke uobičajenih feritno/martenzitnih, feritno/bainitnih i austenitnih čelika kao i novih slitina za uporabu na temperaturama 650°C i više

Data Science Issues in Understanding Protein-RNA Interactions

An interplay of experimental and computational methods is required to achieve a comprehensive understanding of protein–RNA interactions. UV crosslinking and immunoprecipitation (CLIP) identifies endogenous interactions by sequencing RNA fragments that copurify with a selected RNA-binding protein under stringent conditions. Here we focus on approaches for the analysis of the resulting data and appraise the methods for peak calling, visualization, analysis, and computational modeling of protein–RNA binding sites. We advocate that the sensitivity and specificity of data be assessed in combination for computational quality control. Moreover, we demonstrate the value of analyzing sequence motif enrichment in peaks assigned from CLIP data and of visualizing RNA maps, which examine the positional distribution of peaks around regulated landmarks in transcripts. We use these to assess how variations in CLIP data quality and in different peak calling methods affect the insights into regulatory mechanisms. We conclude by discussing future opportunities for the computational analysis of protein–RNA interaction experiments