Coulomb charging energy for arbitrary tunneling strength

The Coulomb energy of a small metallic island coupled to an electrode by a tunnel junction is investigated. We employ Monte Carlo simulations to determine the effective charging energy for arbitrary tunneling strength. For small tunneling conductance, the data agree with analytical results based on a perturbative treatment of electron tunneling, while for very strong tunneling recent semiclassical results for large conductance are approached. The data allow for an identification of the range of validity of various analytical predictions.Comment: 4 pages REVTeX, incl 3 figures, to appear in Europhys.Let

Path integrals, particular kinds, and strange things

This paper describes a path integral formulation of the free energy principle. The ensuing account expresses the paths or trajectories that a particle takes as it evolves over time. The main results are a method or principle of least action that can be used to emulate the behaviour of particles in open exchange with their external milieu. Particles are defined by a particular partition, in which internal states are individuated from external states by active and sensory blanket states. The variational principle at hand allows one to interpret internal dynamics - of certain kinds of particles - as inferring external states that are hidden behind blanket states. We consider different kinds of particles, and to what extent they can be imbued with an elementary form of inference or sentience. Specifically, we consider the distinction between dissipative and conservative particles, inert and active particles and, finally, ordinary and strange particles. Strange particles (look as if they) infer their own actions, endowing them with apparent autonomy or agency. In short - of the kinds of particles afforded by a particular partition - strange kinds may be apt for describing sentient behaviour.Comment: 31 pages (excluding references), 6 figure

Surmising synchrony of sound and sight: Factors explaining variance of audiovisual integration in hurdling, tap dancing and drumming.

Auditory and visual percepts are integrated even when they are not perfectly temporally aligned with each other, especially when the visual signal precedes the auditory signal. This window of temporal integration for asynchronous audiovisual stimuli is relatively well examined in the case of speech, while other natural action-induced sounds have been widely neglected. Here, we studied the detection of audiovisual asynchrony in three different whole-body actions with natural action-induced sounds-hurdling, tap dancing and drumming. In Study 1, we examined whether audiovisual asynchrony detection, assessed by a simultaneity judgment task, differs as a function of sound production intentionality. Based on previous findings, we expected that auditory and visual signals should be integrated over a wider temporal window for actions creating sounds intentionally (tap dancing), compared to actions creating sounds incidentally (hurdling). While percentages of perceived synchrony differed in the expected way, we identified two further factors, namely high event density and low rhythmicity, to induce higher synchrony ratings as well. Therefore, we systematically varied event density and rhythmicity in Study 2, this time using drumming stimuli to exert full control over these variables, and the same simultaneity judgment tasks. Results suggest that high event density leads to a bias to integrate rather than segregate auditory and visual signals, even at relatively large asynchronies. Rhythmicity had a similar, albeit weaker effect, when event density was low. Our findings demonstrate that shorter asynchronies and visual-first asynchronies lead to higher synchrony ratings of whole-body action, pointing to clear parallels with audiovisual integration in speech perception. Overconfidence in the naturally expected, that is, synchrony of sound and sight, was stronger for intentional (vs. incidental) sound production and for movements with high (vs. low) rhythmicity, presumably because both encourage predictive processes. In contrast, high event density appears to increase synchronicity judgments simply because it makes the detection of audiovisual asynchrony more difficult. More studies using real-life audiovisual stimuli with varying event densities and rhythmicities are needed to fully uncover the general mechanisms of audiovisual integration

Transport by molecular motors in the presence of static defects

The transport by molecular motors along cytoskeletal filaments is studied theoretically in the presence of static defects. The movements of single motors are described as biased random walks along the filament as well as binding to and unbinding from the filament. Three basic types of defects are distinguished, which differ from normal filament sites only in one of the motors' transition probabilities. Both stepping defects with a reduced probability for forward steps and unbinding defects with an increased probability for motor unbinding strongly reduce the velocities and the run lengths of the motors with increasing defect density. For transport by single motors, binding defects with a reduced probability for motor binding have a relatively small effect on the transport properties. For cargo transport by motors teams, binding defects also change the effective unbinding rate of the cargo particles and are expected to have a stronger effect.Comment: 20 pages, latex, 7 figures, 1 tabl

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types

Designing Ecosystems of Intelligence from First Principles

This white paper lays out a vision of research and development in the field of artificial intelligence for the next decade (and beyond). Its denouement is a cyber-physical ecosystem of natural and synthetic sense-making, in which humans are integral participants -- what we call ''shared intelligence''. This vision is premised on active inference, a formulation of adaptive behavior that can be read as a physics of intelligence, and which inherits from the physics of self-organization. In this context, we understand intelligence as the capacity to accumulate evidence for a generative model of one's sensed world -- also known as self-evidencing. Formally, this corresponds to maximizing (Bayesian) model evidence, via belief updating over several scales: i.e., inference, learning, and model selection. Operationally, this self-evidencing can be realized via (variational) message passing or belief propagation on a factor graph. Crucially, active inference foregrounds an existential imperative of intelligent systems; namely, curiosity or the resolution of uncertainty. This same imperative underwrites belief sharing in ensembles of agents, in which certain aspects (i.e., factors) of each agent's generative world model provide a common ground or frame of reference. Active inference plays a foundational role in this ecology of belief sharing -- leading to a formal account of collective intelligence that rests on shared narratives and goals. We also consider the kinds of communication protocols that must be developed to enable such an ecosystem of intelligences and motivate the development of a shared hyper-spatial modeling language and transaction protocol, as a first -- and key -- step towards such an ecology.Comment: 23+18 pages, one figure, one six page appendi

The masked demos: Associational anonymity and democratic practice

The increased use of anonymous digital platforms raises substantive concerns about accountability in digital spaces. However, contemporary evaluations of anonymity focus too narrowly on its protective function: its ability to protect a diversity of speakers and ideas. Drawing on two examples of anonymous political engagements – Publius’s writing of the Federalist Papers and college students’ use of the social media platform Yik Yak – we develop an account of anonymity’s associational function: the processes by which people generate and negotiate collective identities, discussions, and actions in wider publics. As we argue, anonymity’s associational function can (1) generate conditions under which individuals develop collective interests and identities to foster collective action, and (2) enable novel interactions between these individuals and communities and the larger publics of which they are part. We conclude with a discussion of how attention to associational anonymity can contribute to a more nuanced account of democracy in practice

Directing Astroglia from the Cerebral Cortex into Subtype Specific Functional Neurons

Forced expression of single defined transcription factors can selectively and stably convert cultured astroglia into synapse-forming excitatory and inhibitory neurons

Nanopore-based kinetics analysis of individual antibody-channel and antibody-antigen interactions

<p>Abstract</p> <p>Background</p> <p>The UNO/RIC Nanopore Detector provides a new way to study the binding and conformational changes of individual antibodies. Many critical questions regarding antibody function are still unresolved, questions that can be approached in a new way with the nanopore detector.</p> <p>Results</p> <p>We present evidence that different forms of channel blockade can be associated with the same antibody, we associate these different blockades with different orientations of "capture" of an antibody in the detector's nanometer-scale channel. We directly detect the presence of antibodies via reductions in channel current. Changes to blockade patterns upon addition of antigen suggest indirect detection of antibody/antigen binding. Similarly, DNA-hairpin anchored antibodies have been studied, where the DNA linkage is to the carboxy-terminus at the base of the antibody's Fc region, with significantly fewer types of (lengthy) capture blockades than was observed for free (un-bound) IgG antibody. The introduction of chaotropic agents and its effects on protein-protein interactions have also been observed.</p> <p>Conclusion</p> <p>Nanopore-based approaches may eventually provide a direct analysis of the complex conformational "negotiations" that occur upon binding between proteins.</p