Dynamic mean-field and cavity methods for diluted Ising systems

We compare dynamic mean-field and dynamic cavity as methods to describe the stationary states of dilute kinetic Ising models. We compute dynamic mean-field theory by expanding in interaction strength to third order, and compare to the exact dynamic mean-field theory for fully asymmetric networks. We show that in diluted networks the dynamic cavity method generally predicts magnetizations of individual spins better than both first order ("naive") and second order ("TAP") dynamic mean field theory

Superconducting film with randomly magnetized dots: A realization of the 2D XY model with random phase shifts

We consider a thin superconducting film with randomly magnetized dots on top of it. The dots produce a disordered pinning potential for vortices in the film. We show that for dots with permanent and random magnetization normal or parallel to the film surface, our system is an experimental realization of the two-dimensional XY model with random phase shifts. The low-temperature superconducting phase, that exists without magnetic dots, survives in the presence of magnetic dots for sufficiently small disorder.Comment: 5 pages, 1 figur

Self-administering arithmetic enrichment activities for the more rapid learner

Thesis (Ed.M.)--Boston Universit

Specific recognition of a multiply phosphorylated motif in the DNA repair scaffold XRCC1 by the FHA domain of human PNK.

Short-patch repair of DNA single-strand breaks and gaps (SSB) is coordinated by XRCC1, a scaffold protein that recruits the DNA polymerase and DNA ligase required for filling and sealing the damaged strand. XRCC1 can also recruit end-processing enzymes, such as PNK (polynucleotide kinase 3'-phosphatase), Aprataxin and APLF (aprataxin/PNK-like factor), which ensure the availability of a free 3'-hydroxyl on one side of the gap, and a 5'-phosphate group on the other, for the polymerase and ligase reactions respectively. PNK binds to a phosphorylated segment of XRCC1 (between its two C-terminal BRCT domains) via its Forkhead-associated (FHA) domain. We show here, contrary to previous studies, that the FHA domain of PNK binds specifically, and with high affinity to a multiply phosphorylated motif in XRCC1 containing a pSer-pThr dipeptide, and forms a 2:1 PNK:XRCC1 complex. The high-resolution crystal structure of a PNK-FHA-XRCC1 phosphopeptide complex reveals the basis for this unusual bis-phosphopeptide recognition, which is probably a common feature of the known XRCC1-associating end-processing enzymes

RankPL: A Qualitative Probabilistic Programming Language

In this paper we introduce RankPL, a modeling language that can be thought of as a qualitative variant of a probabilistic programming language with a semantics based on Spohn's ranking theory. Broadly speaking, RankPL can be used to represent and reason about processes that exhibit uncertainty expressible by distinguishing "normal" from" surprising" events. RankPL allows (iterated) revision of rankings over alternative program states and supports various types of reasoning, including abduction and causal inference. We present the language, its denotational semantics, and a number of practical examples. We also discuss an implementation of RankPL that is available for download

Genetic analysis of safflower domestication.

BackgroundSafflower (Carthamus tinctorius L.) is an oilseed crop in the Compositae (a.k.a. Asteraceae) that is valued for its oils rich in unsaturated fatty acids. Here, we present an analysis of the genetic architecture of safflower domestication and compare our findings to those from sunflower (Helianthus annuus L.), an independently domesticated oilseed crop within the same family.We mapped quantitative trait loci (QTL) underlying 24 domestication-related traits in progeny from a cross between safflower and its wild progenitor, Carthamus palaestinus Eig. Also, we compared QTL positions in safflower against those that have been previously identified in cultivated x wild sunflower crosses to identify instances of colocalization.ResultsWe mapped 61 QTL, the vast majority of which (59) exhibited minor or moderate phenotypic effects. The two large-effect QTL corresponded to one each for flower color and leaf spininess. A total of 14 safflower QTL colocalized with previously reported sunflower QTL for the same traits. Of these, QTL for three traits (days to flower, achene length, and number of selfed seed) had cultivar alleles that conferred effects in the same direction in both species.ConclusionsAs has been observed in sunflower, and unlike many other crops, our results suggest that the genetics of safflower domestication is quite complex. Moreover, our comparative mapping results indicate that safflower and sunflower exhibit numerous instances of QTL colocalization, suggesting that parallel trait transitions during domestication may have been driven, at least in part, by parallel genotypic evolution at some of the same underlying genes

Gaussian Belief with dynamic data and in dynamic network

In this paper we analyse Belief Propagation over a Gaussian model in a dynamic environment. Recently, this has been proposed as a method to average local measurement values by a distributed protocol ("Consensus Propagation", Moallemi & Van Roy, 2006), where the average is available for read-out at every single node. In the case that the underlying network is constant but the values to be averaged fluctuate ("dynamic data"), convergence and accuracy are determined by the spectral properties of an associated Ruelle-Perron-Frobenius operator. For Gaussian models on Erdos-Renyi graphs, numerical computation points to a spectral gap remaining in the large-size limit, implying exceptionally good scalability. In a model where the underlying network also fluctuates ("dynamic network"), averaging is more effective than in the dynamic data case. Altogether, this implies very good performance of these methods in very large systems, and opens a new field of statistical physics of large (and dynamic) information systems.Comment: 5 pages, 7 figure

Cross-age friendship in 25 European countries

This paper focuses on individual and country-level circumstances shaping friendships between young and old to gain insight into conditions for intergenerational solidarity. Using European Social Survey data, findings show that relatively few people have cross-age friendships (18% of the young and 31% of the old). As predicted by the “meeting principle”, individuals who operate in settings where there are opportunities for meaningful interactions with people belonging to a different age group are more likely to have cross-age friendships. As predicted by the “disposition principle”, individuals with more favourable attitudes towards other age groups are more likely to have cross-age friendships. Neither the Active Ageing Index nor macro-level trust show significant associations with the likelihood of having cross-age friendships. Apparently, conditions that bring generations together are at the local level, underscoring the importance of decentralized initiatives aimed at increased contact and co-operation across age groups

Common Causes and The Direction of Causation

Is the common cause principle merely one of a set of useful heuristics for discovering causal relations, or is it rather a piece of heavy duty metaphysics, capable of grounding the direction of causation itself? Since the principle was introduced in Reichenbach’s groundbreaking work The Direction of Time (1956), there have been a series of attempts to pursue the latter program—to take the probabilistic relationships constitutive of the principle of the common cause and use them to ground the direction of causation. These attempts have not all explicitly appealed to the principle as originally formulated; it has also appeared in the guise of independence conditions, counterfactual overdetermination, and, in the causal modelling literature, as the causal markov condition. In this paper, I identify a set of difficulties for grounding the asymmetry of causation on the principle and its descendents. The first difficulty, concerning what I call the vertical placement of causation, consists of a tension between considerations that drive towards the macroscopic scale, and considerations that drive towards the microscopic scale—the worry is that these considerations cannot both be comfortably accommodated. The second difficulty consists of a novel potential counterexample to the principle based on the familiar Einstein Podolsky Rosen (EPR) cases in quantum mechanics