Magnitude effects for experienced rewards at short delays in the escalating interest task

A first-person shooter video game was adapted for the study of choice between smaller sooner and larger later rewards. Participants chose when to fire a weapon that increased in damage potential over a short interval. When the delay to maximum damage was shorter (5 – 8 s), people showed greater sensitivity to the consequences of their choices than when the delay was longer (17 – 20 s). Participants also evidenced a magnitude effect by waiting proportionally longer when the damage magnitudes were doubled for all rewards. The experiment replicated the standard magnitude effect with this new video game preparation over time scales similar to those typically used in nonhuman animal studies and without complications due to satiation or cost

Outcome probability versus magnitude: When waiting benefits one at the cost of the other

Citation: Young, M. E., Webb, T. L., Rung, J. M., & McCoy, A. W. (2014). Outcome Probability versus Magnitude: When Waiting Benefits One at the Cost of the Other. PLOS ONE, 9(6), e98996. https://doi.org/10.1371/journal.pone.0098996Using a continuous impulsivity and risk platform (CIRP) that was constructed using a video game engine, choice was assessed under conditions in which waiting produced a continuously increasing probability of an outcome with a continuously decreasing magnitude (Experiment 1) or a continuously increasing magnitude of an outcome with a continuously decreasing probability (Experiment 2). Performance in both experiments reflected a greater desire for a higher probability even though the corresponding wait times produced substantive decreases in overall performance. These tendencies are considered to principally reflect hyperbolic discounting of probability, power discounting of magnitude, and the mathematical consequences of different response rates. Behavior in the CIRP is compared and contrasted with that in the Balloon Analogue Risk Task (BART)

Targeted sequence design within the coarse-grained polymer genome

The chemical design of polymers with target structural and/or functional properties represents a grand challenge in materials science. While data-driven design approaches are promising, success with polymers has been limited, largely due to limitations in data availability. Here, we demonstrate the targeted sequence design of single-chain structure in polymers by combining coarse-grained modeling, machine learning, and model optimization. Nearly 2000 unique coarse-grained polymers are simulated to construct and analyze machine learning models. We find that deep neural networks inexpensively and reliably predict structural properties with limited sequence information as input. By coupling trained ML models with sequential model-based optimization, polymer sequences are proposed to exhibit globular, swollen, or rod-like behaviors, which are verified by explicit simulations. This work highlights the promising integration of coarse-grained modeling with data-driven design and represents a necessary and crucial step toward more complex polymer design efforts

Transmembrane Domains of Highly Pathogenic Viral Fusion Proteins Exhibit Trimeric Association \u3cem\u3eIn Vitro\u3c/em\u3e

Enveloped viruses require viral fusion proteins to promote fusion of the viral envelope with a target cell membrane. To drive fusion, these proteins undergo large conformational changes that must occur at the right place and at the right time. Understanding the elements which control the stability of the prefusion state and the initiation of conformational changes is key to understanding the function of these important proteins. The construction of mutations in the fusion protein transmembrane domains (TMDs) or the replacement of these domains with lipid anchors has implicated the TMD in the fusion process. However, the structural and molecular details of the role of the TMD in these fusion events remain unclear. Previously, we demonstrated that isolated paramyxovirus fusion protein TMDs associate in a monomer-trimer equilibrium, using sedimentation equilibrium analytical ultracentrifugation. Using a similar approach, the work presented here indicates that trimeric interactions also occur between the fusion protein TMDs of Ebola virus, influenza virus, severe acute respiratory syndrome coronavirus (SARS CoV), and rabies virus. Our results suggest that TM-TM interactions are important in the fusion protein function of diverse viral families

The Theory of the Interleaving Distance on Multidimensional Persistence Modules

In 2009, Chazal et al. introduced $\epsilon$-interleavings of persistence modules. $\epsilon$-interleavings induce a pseudometric $d_I$ on (isomorphism classes of) persistence modules, the interleaving distance. The definitions of $\epsilon$-interleavings and $d_I$ generalize readily to multidimensional persistence modules. In this paper, we develop the theory of multidimensional interleavings, with a view towards applications to topological data analysis. We present four main results. First, we show that on 1-D persistence modules, $d_I$ is equal to the bottleneck distance $d_B$. This result, which first appeared in an earlier preprint of this paper, has since appeared in several other places, and is now known as the isometry theorem. Second, we present a characterization of the $\epsilon$-interleaving relation on multidimensional persistence modules. This expresses transparently the sense in which two $\epsilon$-interleaved modules are algebraically similar. Third, using this characterization, we show that when we define our persistence modules over a prime field, $d_I$ satisfies a universality property. This universality result is the central result of the paper. It says that $d_I$ satisfies a stability property generalizing one which $d_B$ is known to satisfy, and that in addition, if $d$ is any other pseudometric on multidimensional persistence modules satisfying the same stability property, then $d\leq d_I$. We also show that a variant of this universality result holds for $d_B$, over arbitrary fields. Finally, we show that $d_I$ restricts to a metric on isomorphism classes of finitely presented multidimensional persistence modules.Comment: Major revision; exposition improved throughout. To appear in Foundations of Computational Mathematics. 36 page

Phylotastic! Making Tree-of-Life Knowledge Accessible, Reusable and Convenient

Scientists rarely reuse expert knowledge of phylogeny, in spite of years of effort to assemble a great "Tree of Life" (ToL). A notable exception involves the use of Phylomatic, which provides tools to generate custom phylogenies from a large, pre-computed, expert phylogeny of plant taxa. This suggests great potential for a more generalized system that, starting with a query consisting of a list of any known species, would rectify non-standard names, identify expert phylogenies containing the implicated taxa, prune away unneeded parts, and supply branch lengths and annotations, resulting in a custom phylogeny suited to the user's needs. Such a system could become a sustainable community resource if implemented as a distributed system of loosely coupled parts that interact through clearly defined interfaces. Results: With the aim of building such a "phylotastic" system, the NESCent Hackathons, Interoperability, Phylogenies (HIP) working group recruited 2 dozen scientist-programmers to a weeklong programming hackathon in June 2012. During the hackathon (and a three-month follow-up period), 5 teams produced designs, implementations, documentation, presentations, and tests including: (1) a generalized scheme for integrating components; (2) proof-of-concept pruners and controllers; (3) a meta-API for taxonomic name resolution services; (4) a system for storing, finding, and retrieving phylogenies using semantic web technologies for data exchange, storage, and querying; (5) an innovative new service, DateLife.org, which synthesizes pre-computed, time-calibrated phylogenies to assign ages to nodes; and (6) demonstration projects. These outcomes are accessible via a public code repository (GitHub.com), a website (www.phylotastic.org), and a server image. Conclusions: Approximately 9 person-months of effort (centered on a software development hackathon) resulted in the design and implementation of proof-of-concept software for 4 core phylotastic components, 3 controllers, and 3 end-user demonstration tools. While these products have substantial limitations, they suggest considerable potential for a distributed system that makes phylogenetic knowledge readily accessible in computable form. Widespread use of phylotastic systems will create an electronic marketplace for sharing phylogenetic knowledge that will spur innovation in other areas of the ToL enterprise, such as annotation of sources and methods and third-party methods of quality assessment.NESCent (the National Evolutionary Synthesis Center)NSF EF-0905606iPlant Collaborative (NSF) DBI-0735191Biodiversity Synthesis Center (BioSync) of the Encyclopedia of LifeComputer Science

Descriptions of Two New Species, and a Catalog of the Species 1

Abstract: We review the West Indian species of Arachnocoris, a genus of spider-web dwelling kleptoparasitic nabids. We recognize five species: A. berytoides Uhler from Grenada, A. darlingtoni n. sp. from Hispaniola, A. karukerae Lopez-Moncet from Guadeloupe, A. portoricensis n. sp. from Puerto Rico, and A. trinitatis Bergroth from Trinidad. West Indian Arachnocoris antennal and profemoral color banding patterns are useful diagnostic characters and may have evolved to mimic their spider hosts, which are often island endemic spiders in the family Pholcidae. We provide a simplified and illustrated key to the species based on external characters. A catalog for the 16 recognized species of Arachnocoris is presented

Measuring quality of general reasoning

Machine learning models that automatically assess reasoning quality are trained on human-annotated written products. These “gold-standard” corpora are typically created by prompting annotators to choose, using a forced choice design, which of two products presented side by side is the most convincing, contains the strongest evidence or would be adopted by more people. Despite the increase in popularity of using a forced choice design for assessing quality of reasoning (QoR), no study to date has established the validity and reliability of such a method. In two studies, we simultaneously presented two products of reasoning to participants and asked them to identify which product was ‘better justified’ through a forced choice design. We investigated the criterion validity and inter-rater reliability of the forced choice protocol by assessing the relationship between QoR, measured using the forced choice protocol, and accuracy in objectively answerable problems using naive raters sampled from MTurk (Study 1) and experts (Study 2), respectively. In both studies products that were closer to the correct answer and products generated by larger teams were consistently preferred. Experts were substantially better at picking the reasoning products that corresponded to accurate answers. Perhaps the most surprising finding was just how rapidly raters made judgements regarding reasoning: On average, both novices and experts made reliable decisions in under 15 seconds. We conclude that forced choice is a valid and reliable method of assessing QoR

Cell imaging by phonon microscopy: sub-optical wavelength ultrasound for non-invasive imaging

The mechanical properties of cells play an important role in cell function and behavior. This paper presents recent developments that have enabled the use of laser-generated phonons (ultrasound) with sub-optical wavelengths to look inside living cells. The phonons reveal contrast from changes in the elasticity of the cell and can provide high resolution three dimensional images

A Search for Time Variation of the Fine Structure Constant

A method offering an order of magnitude sensitivity gain is described for using quasar spectra to investigate possible time or space variation in the fine structure constant, alpha. Applying the technique to a sample of 30 absorption systems, spanning redshifts 0.5 < z< 1.6, obtained with the Keck I telescope, we derive limits on variations in alpha over a wide range of epochs. For the whole sample Delta(alpha)/alpha = -1.1 +/- 0.4 x 10^{-5}. This deviation is dominated by measurements at z > 1, where Delta(alpha)/alpha = -1.9 +/- 0.5 x 10^{-5}. For z < 1, Delta(alpha)/alpha = -0.2 +/- 0.4 x 10^{-5}, consistent with other known constraints. Whilst these results are consistent with a time-varying alpha, further work is required to explore possible systematic errors in the data, although careful searches have so far not revealed any.Comment: 4 pages, 1 figure, accepted for publication in Physical Review Letter