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  1. Abstract Existing phenotype ontologies were originally developed to represent phenotypes that manifest as a character state in relation to a wild-type or other reference. However, these do not include the phenotypic trait or attribute categories required for the annotation of genome-wide association studies (GWAS), Quantitative Trait Loci (QTL) mappings or any population-focussed measurable trait data. The integration of trait and biological attribute information with an ever increasing body of chemical, environmental and biological data greatly facilitates computational analyses and it is also highly relevant to biomedical and clinical applications. The Ontology of Biological Attributes (OBA) is a formalised, species-independent collection of interoperable phenotypic trait categories that is intended to fulfil a data integration role. OBA is a standardised representational framework for observable attributes that are characteristics of biological entities, organisms, or parts of organisms. OBA has a modular design which provides several benefits for users and data integrators, including an automated and meaningful classification of trait terms computed on the basis of logical inferences drawn from domain-specific ontologies for cells, anatomical and other relevant entities. The logical axioms in OBA also provide a previously missing bridge that can computationally link Mendelian phenotypes with GWAS and quantitative traits. The term components in OBA provide semantic links and enable knowledge and data integration across specialised research community boundaries, thereby breaking silos. 
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  2. null (Ed.)
    Motivated by the increasing need to understand the distributed algorithmic foundations of large-scale graph computations, we study some fundamental graph problems in a message-passing model for distributed computing where k ≥ 2 machines jointly perform computations on graphs with n nodes (typically, n >> k). The input graph is assumed to be initially randomly partitioned among the k machines, a common implementation in many real-world systems. Communication is point-to-point, and the goal is to minimize the number of communication rounds of the computation. Our main contribution is the General Lower Bound Theorem , a theorem that can be used to show non-trivial lower bounds on the round complexity of distributed large-scale data computations. This result is established via an information-theoretic approach that relates the round complexity to the minimal amount of information required by machines to solve the problem. Our approach is generic, and this theorem can be used in a “cookbook” fashion to show distributed lower bounds for several problems, including non-graph problems. We present two applications by showing (almost) tight lower bounds on the round complexity of two fundamental graph problems, namely, PageRank computation and triangle enumeration . These applications show that our approach can yield lower bounds for problems where the application of communication complexity techniques seems not obvious or gives weak bounds, including and especially under a stochastic partition of the input. We then present distributed algorithms for PageRank and triangle enumeration with a round complexity that (almost) matches the respective lower bounds; these algorithms exhibit a round complexity that scales superlinearly in k , improving significantly over previous results [Klauck et al., SODA 2015]. Specifically, we show the following results: PageRank: We show a lower bound of Ὼ(n/k 2 ) rounds and present a distributed algorithm that computes an approximation of the PageRank of all the nodes of a graph in Õ(n/k 2 ) rounds. Triangle enumeration: We show that there exist graphs with m edges where any distributed algorithm requires Ὼ(m/k 5/3 ) rounds. This result also implies the first non-trivial lower bound of Ὼ(n 1/3 ) rounds for the congested clique model, which is tight up to logarithmic factors. We then present a distributed algorithm that enumerates all the triangles of a graph in Õ(m/k 5/3 + n/k 4/3 ) rounds. 
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  3. null (Ed.)
    We study the communication cost (or message complexity) of fundamental distributed symmetry breaking problems, namely, coloring and MIS. While significant progress has been made in understanding and improving the running time of such problems, much less is known about the message complexity of these problems. In fact, all known algorithms need at least Ω(m) communication for these problems, where m is the number of edges in the graph. We addressthe following question in this paper: can we solve problems such as coloring and MIS using sublinear, i.e., o(m) communication, and if sounder what conditions? In a classical result, Awerbuch, Goldreich, Peleg, and Vainish [JACM 1990] showed that fundamental global problems such asbroadcast and spanning tree construction require at least o(m) messages in the KT-1 Congest model (i.e., Congest model in which nodes have initial knowledge of the neighbors' ID's) when algorithms are restricted to be comparison-based (i.e., algorithms inwhich node ID's can only be compared). Thirty five years after this result, King, Kutten, and Thorup [PODC 2015] showed that onecan solve the above problems using Õ(n) messages (n is the number of nodes in the graph) in Õ(n) rounds in the KT-1 Congest model if non-comparison-based algorithms are permitted. An important implication of this result is that one can use the synchronous nature of the KT-1 Congest model, using silence to convey information,and solve any graph problem using non-comparison-based algorithms with Õ(n) messages, but this takes an exponential number of rounds. In the asynchronous model, even this is not possible. In contrast, much less is known about the message complexity of local symmetry breaking problems such as coloring and MIS. Our paper fills this gap by presenting the following results. Lower bounds: In the KT-1 CONGEST model, we show that any comparison-based algorithm, even a randomized Monte Carlo algorithm with constant success probability, requires Ω(n 2) messages in the worst case to solve either (△ + 1)-coloring or MIS, regardless of the number of rounds. We also show that Ω(n) is a lower bound on the number ofmessages for any (△ + 1)-coloring or MIS algorithm, even non-comparison-based, and even with nodes having initial knowledge of up to a constant radius. Upper bounds: In the KT-1 CONGEST model, we present the following randomized non-comparison-based algorithms for coloring that, with high probability, use o(m) messages and run in polynomially many rounds.(a) A (△ + 1)-coloring algorithm that uses Õ(n1.5) messages, while running in Õ(D + √ n) rounds, where D is the graph diameter. Our result also implies an asynchronous algorithm for (△ + 1)-coloring with the same message bound but running in Õ(n) rounds. (b) For any constantε > 0, a (1+ε)△-coloring algorithm that uses Õ(n/ε 2 ) messages, while running in Õ(n) rounds. If we increase our input knowledge slightly to radius 2, i.e.,in the KT-2 CONGEST model, we obtain:(c) A randomized comparison-based MIS algorithm that uses Õ(n 1.5) messages. while running in Õ( √n) rounds. While our lower bound results can be viewed as counterparts to the classical result of Awerbuch, Goldreich, Peleg, and Vainish [JACM 90], but for local problems, our algorithms are the first-known algorithms for coloring and MIS that take o(m) messages and run in polynomially many rounds. 
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  4. SUMMARY Lamellar magnetism is a source of remanent magnetization in natural rocks different from common bulk magnetic moments in ferrimagnetic minerals. It has been found to be a source for a wide class of magnetic anomalies with extremely high Koenigsberger ratio. Its physical origin are uncompensated interface moments in contact layers of nanoscale ilmenite lamellae inside an hematite host, which also generate unusual low-temperature (low-T) magnetic properties, such as shifted low-T hysteresis loops due to exchange bias. The atomic-magnetic basis for the exchange bias discovered in the hematite-ilmenite system is explored in a series of papers. In this third article of the series, simple models are developed for lamellae interactions of different structures when samples are either cooled in zero-field, or field-cooled in 5 T to temperatures below the ordering temperature of ilmenite. These models are built on the low-temperature measurements described earlier in Paper II. The important observations include: (i) the effects of lamellar shapes on magnetic coupling, (ii) the high-T acquisition of lamellar magnetism and low-T acquisition of magnetization of ilmenite lamellae, (iii) the intensity of lamellar magnetism and the consequent ilmenite magnetism in populations of randomly oriented crystals, (iv) lattice-preferred orientation of the titanohematite host crystal populations and (v) the effects of magnetic domain walls in the host on hysteresis properties. Based on exemplary growth models of lamellae with different geometries and surface couplings we here provide simple models to assess and explain the different observations listed above. Already the simplified models show that the shapes of the edges of ilmenite lamellae against their hematite hosts can control the degree of low-T coupling between ilmenite, and the lamellar magnetic moments. The models also explain certain features of the low-T exchange bias in the natural samples and emphasize the role of lattice-preferred orientation upon the intensity of remanent magnetization. The inverse link between ilmenite remanence and exchange-bias shift in bimodal low-T ilmenite lamellae is related to different densities of hematite domain walls induced by the clusters of ilmenite lamellae. 
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  5. In this paper, we study fault-tolerant distributed consensus in wireless systems. In more detail, we produce two new randomized algorithms that solve this problem in the abstract MAC layer model, which captures the basic interface and communication guarantees provided by most wireless MAC layers. Our algorithms work for any number of failures, require no advance knowledge of the network participants or network size, and guarantee termination with high probability after a number of broadcasts that are polynomial in the network size. Our first algorithm satisfies the standard agreement property, while our second trades a faster termination guarantee in exchange for a looser agreement property in which most nodes agree on the same value. These are the first known fault-tolerant consensus algorithms for this model. In addition to our main upper bound results, we explore the gap between the abstract MAC layer and the standard asynchronous message passing model by proving fault-tolerant consensus is impossible in the latter in the absence of information regarding the network participants, even if we assume no faults, allow randomized solutions, and provide the algorithm a constant-factor approximation of the network size. 
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