A Minimum-Labeling Approach for Reconstructing Protein Networks across Multiple Conditions

The sheer amounts of biological data that are generated in recent years have driven the development of network analysis tools to facilitate the interpretation and representation of these data. A fundamental challenge in this domain is the reconstruction of a protein-protein subnetwork that underlies a process of interest from a genome-wide screen of associated genes. Despite intense work in this area, current algorithmic approaches are largely limited to analyzing a single screen and are, thus, unable to account for information on condition-specific genes, or reveal the dynamics (over time or condition) of the process in question. Here we propose a novel formulation for network reconstruction from multiple-condition data and devise an efficient integer program solution for it. We apply our algorithm to analyze the response to influenza infection in humans over time as well as to analyze a pair of ER export related screens in humans. By comparing to an extant, single-condition tool we demonstrate the power of our new approach in integrating data from multiple conditions in a compact and coherent manner, capturing the dynamics of the underlying processes.Comment: Peer-reviewed and presented as part of the 13th Workshop on Algorithms in Bioinformatics (WABI2013

A game-theoretic model of interspecific brood parasitism with sequential decisions

The interaction between hosts and parasites in bird populations has been studied extensively. This paper uses game-theoretic methods to model this interaction. This has been done in previous papers but has not been studied taking into account the detailed sequential nature of this game. We introduce a model allowing the host and parasite to make a number of decisions which will depend on various natural factors. The sequence of events begins with the host forming a nest and laying a number of eggs, followed by the possibility that a parasite bird will arrive at the nest; if it does it can choose to destroy some of the host eggs and lay one of its own. A sequence of events follows, which is broken down into two key stages; firstly the interaction between the host and the parasite adult, and secondly that between the host and the parasite chick. The final decision involves the host choosing whether to raise or abandon the chicks that are in the nest. There are certain natural parameters and probabilities which are central to these various decisions; in particular the host is generally uncertain whether parasitism has taken place, but can assess the likelihood of parasitism based upon certain cues (e.g. how many eggs remain in its nest). We then use this methodology to model two real-world interactions, that of the Reed Warbler with the Common Cuckoo and also the Yellow Warbler with the Brown-headed Cowbird. These parasites have different methods in the way they parasitize the nests of their hosts, and the hosts can in turn have different reactions to these parasites. Our model predictions generally match the real results well, and the model also makes predictions of the effect of changes in various key parameters on the type of parasitic interactions that should occur

Cycle-centrality in complex networks

Networks are versatile representations of the interactions between entities in complex systems. Cycles on such networks represent feedback processes which play a central role in system dynamics. In this work, we introduce a measure of the importance of any individual cycle, as the fraction of the total information flow of the network passing through the cycle. This measure is computationally cheap, numerically well-conditioned, induces a centrality measure on arbitrary subgraphs and reduces to the eigenvector centrality on vertices. We demonstrate that this measure accurately reflects the impact of events on strategic ensembles of economic sectors, notably in the US economy. As a second example, we show that in the protein-interaction network of the plant Arabidopsis thaliana, a model based on cycle-centrality better accounts for pathogen activity than the state-of-art one. This translates into pathogen-targeted-proteins being concentrated in a small number of triads with high cycle-centrality. Algorithms for computing the centrality of cycles and subgraphs are available for download

Intra-arterial hepatic fotemustine for the treatment of liver metastases from uveal melanoma: experience in 101 patients

Background: Exclusive liver metastases occur in up to 40% of patients with uveal melanoma associated with a median survival of 2-7 months. Single agent response rates with commonly available chemotherapy are below 10%. We have investigated the use of fotemustine via direct intra-arterial hepatic (i.a.h.) administration in patients with uveal melanoma metastases. Patients and methods: A total of 101 patients from seven centers were treated with i.a.h. fotemustine, administered intra-arterially weekly for a 4-week induction period, and then as a maintenance treatment every 3 weeks until disease progression, unacceptable toxicity or patient refusal. Results: A median of eight fotemustine infusions per patient were delivered (range 1-26). Catheter related complications occurred in 23% of patients; however, this required treatment discontinuation in only 10% of the patients. The overall response rate was 36% with a median overall survival of 15 months and a 2-year survival rate of 29%. LDH, time between diagnosis and treatment start and gender were significant predictors of survival. Conclusions: Locoregional treatment with fotemustine is well tolerated and seems to improve outcome of this poor prognosis patient population. Median survival rates are among the longest reported and one-third of the patients are still alive at 2 year

CRISPR-Cas9 screens in human cells and primary neurons identify modifiers of C9ORF72 dipeptide-repeat-protein toxicity.

Hexanucleotide-repeat expansions in the C9ORF72 gene are the most common cause of amyotrophic lateral sclerosis and frontotemporal dementia (c9ALS/FTD). The nucleotide-repeat expansions are translated into dipeptide-repeat (DPR) proteins, which are aggregation prone and may contribute to neurodegeneration. We used the CRISPR-Cas9 system to perform genome-wide gene-knockout screens for suppressors and enhancers of C9ORF72 DPR toxicity in human cells. We validated hits by performing secondary CRISPR-Cas9 screens in primary mouse neurons. We uncovered potent modifiers of DPR toxicity whose gene products function in nucleocytoplasmic transport, the endoplasmic reticulum (ER), proteasome, RNA-processing pathways, and chromatin modification. One modifier, TMX2, modulated the ER-stress signature elicited by C9ORF72 DPRs in neurons and improved survival of human induced motor neurons from patients with C9ORF72 ALS. Together, our results demonstrate the promise of CRISPR-Cas9 screens in defining mechanisms of neurodegenerative diseases

A centrality measure for cycles and subgraphs II

In a recent work we introduced a measure of importance for groups of vertices in a complex network. This centrality for groups is always between 0 and 1 and induces the eigenvector centrality over vertices. Furthermore, its value over any group is the fraction of all network flows intercepted by this group. Here we provide the rigorous mathematical constructions underpinning these results via a semi-commutative extension of a number theoretic sieve. We then established further relations between the eigenvector centrality and the centrality proposed here, showing that the latter is a proper extension of the former to groups of nodes. We finish by comparing the centrality proposed here with the notion of group-centrality introduced by Everett and Borgatti on two real-world networks: the Wolfe’s dataset and the protein-protein interaction network of the yeast Saccharomyces cerevisiae. In this latter case, we demonstrate that the centrality is able to distinguish protein complexe

Genome-wide differentiation in closely related populations: the roles of selection and geographic isolation.

Population divergence in geographic isolation is due to a combination of factors. Natural and sexual selection may be important in shaping patterns of population differentiation, a pattern referred to as 'Isolation by Adaptation' (IBA). IBA can be complementary to the well-known pattern of 'Isolation by Distance' (IBD), in which the divergence of closely related populations (via any evolutionary process) is associated with geographic isolation. The barn swallow Hirundo rustica complex comprises six closely related subspecies, where divergent sexual selection is associated with phenotypic differentiation among allopatric populations. To investigate the relative contributions of selection and geographic distance to genome-wide differentiation, we compared genotypic and phenotypic variation from 350 barn swallows sampled across eight populations (28 pairwise comparisons) from four different subspecies. We report a draft whole genome sequence for H. rustica, to which we aligned a set of 9,493 single nucleotide polymorphisms (SNPs). Using statistical approaches to control for spatial autocorrelation of phenotypic variables and geographic distance, we find that divergence in traits related to migratory behavior and sexual signaling, as well as geographic distance together, explain over 70% of genome-wide divergence among populations. Controlling for IBD, we find 42% of genome-wide divergence is attributable to IBA through pairwise differences in traits related to migratory behavior and sexual signaling alone. By (i) combining these results with prior studies of how selection shapes morphological differentiation and (ii) accounting for spatial autocorrelation, we infer that morphological adaptation plays a large role in shaping population-level differentiation in this group of closely related populations. This article is protected by copyright. All rights reserved

Ratings of age of acquisition of 299 words across 25 languages: Is there a cross-linguistic order of words?

We present a new set of subjective age-of-acquisition (AoA) ratings for 299 words (158 nouns, 141 verbs) in 25 languages from five language families (Afro-Asiatic: Semitic languages; Altaic: one Turkic language: Indo-European: Baltic, Celtic, Germanic, Hellenic, Slavic, and Romance languages; Niger-Congo: one Bantu language; Uralic: Finnic and Ugric languages). Adult native speakers reported the age at which they had learned each word. We present a comparison of the AoA ratings across all languages by contrasting them in pairs. This comparison shows a consistency in the orders of ratings across the 25 languages. The data were then analyzed (1) to ascertain how the demographic characteristics of the participants influenced AoA estimations and (2) to assess differences caused by the exact form of the target question (when did you learn vs. when do children learn this word); (3) to compare the ratings obtained in our study to those of previous studies; and (4) to assess the validity of our study by comparison with quasi-objective AoA norms derived from the MacArthur–Bates Communicative Development Inventories (MB-CDI). All 299 words were judged as being acquired early (mostly before the age of 6 years). AoA ratings were associated with the raters’ social or language status, but not with the raters’ age or education. Parents reported words as being learned earlier, and bilinguals reported learning them later. Estimations of the age at which children learn the words revealed significantly lower ratings of AoA. Finally, comparisons with previous AoA and MB-CDI norms support the validity of the present estimations. Our AoA ratings are available for research or other purposes

Dispersion of the second-order nonlinear susceptibility in ZnTe, ZnSe, and ZnS

We have measured the absolute values of the second-harmonic generation (SHG) coefficient |d| for the zinc-blende II-VI semiconductors ZnTe, ZnSe, and ZnS at room temperature. The investigated spectral region of the fundamental radiation λF ranges from 520 to 1321 nm using various pulsed laser sources. In the transparent region of the II-VI semiconductors, the SHG coefficient exceeds the values of birefringent materials as ammonium dihydrogen phosphate (ADP) and potassium dihydrogen phosphate (KDP) by one or two orders of magnitudes. Above the E0 band gap a strong dispersion of |d| is observed, showing a maximum for a second-harmonic frequency close to the E1 gap. The experimental results are compared to calculated values using a simple three-band model including spin-orbit splitting. Substantial agreement is found to the experimentally observed dispersion of the second-order nonlinear susceptibility

Noun and verb knowledge in monolingual preschool children across 17 languages: Data from cross-linguistic lexical tasks (LITMUS-CLT)

This article investigates the cross-linguistic comparability of the newly developed lexical assessment tool Cross-linguistic Lexical Tasks (LITMUS-CLT). LITMUS-CLT is a part the Language Impairment Testing in Multilingual Settings (LITMUS) battery (Armon-Lotem, de Jong & Meir, 2015). Here we analyse results on receptive and expressive word knowledge tasks for nouns and verbs across 17 languages from eight different language families: Baltic (Lithuanian), Bantu (isiXhosa), Finnic (Finnish), Germanic (Afrikaans, British English, South African English, German, Luxembourgish, Norwegian, Swedish), Romance (Catalan, Italian), Semitic (Hebrew), Slavic (Polish, Serbian, Slovak) and Turkic (Turkish). The participants were 639 monolingual children aged 3;0-6;11 living in 15 different countries. Differences in vocabulary size were small between 16 of the languages; but isiXhosa-speaking children knew significantly fewer words than speakers of the other languages. There was a robust effect of word class: accuracy was higher for nouns than verbs. Furthermore, comprehension was more advanced than production. Results are discussed in the context of cross-linguistic comparisons of lexical development in monolingual and bilingual populations