Given frustrations with academic structures, how can we build a more human-centered open science?

Open science has finally hit the mainstream. Alex Lancaster looks at the emerging criticisms leveled against how we publish and disseminate science and argues it may be time to reframe the open science project. Rather than relying on instrumentalist language of “carrot-and-sticks” and “rewards-and-incentives” we should instead focus on the actual working conditions for scientists and the political economy in which they are embedded

Gigantic transmission band edge resonance in periodic stacks of anisotropic layers

We consider Fabry-Perot cavity resonance in periodic stacks of anisotropic layers with misaligned in-plane anisotropy at the frequency close to a photonic band edge. We show that in-plane dielectric anisotropy can result in a dramatic increase in field intensity and group delay associated with the transmission resonance. The field enhancement appears to be proportional to forth degree of the number N of layers in the stack. By contrast, in common periodic stacks of isotropic layers, those effects are much weaker and proportional to N^2. Thus, the anisotropy allows to drastically reduce the size of the resonance cavity with similar performance. The key characteristic of the periodic arrays with the gigantic transmission resonance is that the dispersion curve omega(k)at the photonic band edge has the degenerate form Delta(omega) ~ Delta(k)^4, rather than the regular form Delta(omega) ~ Delta(k)^2. This can be realized in specially arranged stacks of misaligned anisotropic layers. The degenerate band edge cavity resonance with similar outstanding properties can also be realized in a waveguide environment, as well as in a linear array of coupled multimode resonators, provided that certain symmetry conditions are in place.Comment: To be submitted to Phys. Re

Feed-forward regulation adaptively evolves via dynamics rather than topology when there is intrinsic noise

In transcriptional regulatory networks (TRNs), a canonical 3-node feed-forward loop (FFL) is hypothesized to evolve to filter out short spurious signals. We test this adaptive hypothesis against a novel null evolutionary model. Our mutational model captures the intrinsically high prevalence of weak affinity transcription factor binding sites. We also capture stochasticity and delays in gene expression that distort external signals and intrinsically generate noise. Functional FFLs evolve readily under selection for the hypothesized function but not in negative controls. Interestingly, a 4-node "diamond" motif also emerges as a short spurious signal filter. The diamond uses expression dynamics rather than path length to provide fast and slow pathways. When there is no idealized external spurious signal to filter out, but only internally generated noise, only the diamond and not the FFL evolves. While our results support the adaptive hypothesis, we also show that non-adaptive factors, including the intrinsic expression dynamics, matter.University of Arizona; Pew Scholarship; John Templeton Foundation [39667]; National Institutes of Health [R35GM118170, R01GM076041]Open access journalThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Luminidependens (LD) is an Arabidopsis protein with prion behavior

Prion proteins provide a unique mode of biochemical memory through self-perpetuating changes in protein conformation and function. They have been studied in fungi and mammals, but not yet identified in plants. Using a computational model, we identified candidate prion domains (PrDs) in nearly 500 plant proteins. Plant flowering is of particular interest with respect to biological memory, because its regulation involves remembering and integrating previously experienced environmental conditions. We investigated the prion-forming capacity of three prion candidates involved in flowering using a yeast model, where prion attributes are well defined and readily tested. In yeast, prions heritably change protein functions by templating monomers into higher-order assemblies. For most yeast prions, the capacity to convert into a prion resides in a distinct prion domain. Thus, new prion-forming domains can be identified by functional complementation of a known prion domain. The prion-like domains (PrDs) of all three of the tested proteins formed higher-order oligomers. Uniquely, the Luminidependens PrD (LDPrD) fully replaced the prion-domain functions of a well-characterized yeast prion, Sup35. Our results suggest that prion-like conformational switches are evolutionarily conserved and might function in a wide variety of normal biological processes.Howard Hughes Medical InstituteG. Harold and Leila Y. Mathers FoundationEleanor Schwartz Charitable FoundationNational Science Foundation (U.S.). Graduate Research Fellowship Progra

Maisonneuve Fracture

Download PD

Behavioural Indicators of Intra- and Inter-Specific Competition: Sheep Co-Grazing with Guanaco in the Patagonian Steppe

In extensive livestock production, high densities may inhibit regulation processes, main- taining high levels of intraspecific competition over time. During competition, individuals typically modify their behaviours, particularly feeding and bite rates, which can therefore be used as indicators of competition. Over eight consecutive seasons, we investigated if variation in herd density, food availability, and the presence of a potential competitor, the guanaco (Lama guanicoe), was related with behavioural changes in domestic sheep in Chilean Patagonia. Focal sampling, instantaneous scan sampling, measures of bite and movement rates were used to quantify behavioural changes in domestic sheep. We found that food availability increased time spent feeding, while herd density was associated with an increase in vigilant behaviour and a decrease in bite rate, but only when food availability was low. Guanaco presence appeared to have no impact on sheep behaviour. Our results suggest that the observed behavioural changes in domestic sheep are more likely due to intraspecific competition rather than interspecific competition. Consideration of intraspecific competition where guanaco and sheep co-graze on pastures could allow management strategies to focus on herd density, according to rangeland carrying capacity

Slow light in photonic crystals

The problem of slowing down light by orders of magnitude has been extensively discussed in the literature. Such a possibility can be useful in a variety of optical and microwave applications. Many qualitatively different approaches have been explored. Here we discuss how this goal can be achieved in linear dispersive media, such as photonic crystals. The existence of slowly propagating electromagnetic waves in photonic crystals is quite obvious and well known. The main problem, though, has been how to convert the input radiation into the slow mode without loosing a significant portion of the incident light energy to absorption, reflection, etc. We show that the so-called frozen mode regime offers a unique solution to the above problem. Under the frozen mode regime, the incident light enters the photonic crystal with little reflection and, subsequently, is completely converted into the frozen mode with huge amplitude and almost zero group velocity. The linearity of the above effect allows to slow light regardless of its intensity. An additional advantage of photonic crystals over other methods of slowing down light is that photonic crystals can preserve both time and space coherence of the input electromagnetic wave.Comment: 96 pages, 12 figure

Concert recording 2022-04-02b

[Track 1]. Act 1

Concert recording 2022-04-02b

[Track 1]. Act 1

COSMOS: Python library for massively parallel workflows

Summary: Efficient workflows to shepherd clinically generated genomic data through the multiple stages of a next-generation sequencing pipeline are of critical importance in translational biomedical science. Here we present COSMOS, a Python library for workflow management that allows formal description of pipelines and partitioning of jobs. In addition, it includes a user interface for tracking the progress of jobs, abstraction of the queuing system and fine-grained control over the workflow. Workflows can be created on traditional computing clusters as well as cloud-based services. Availability and implementation: Source code is available for academic non-commercial research purposes. Links to code and documentation are provided at http://lpm.hms.harvard.edu and http://wall-lab.stanford.edu. Contact: [email protected] or [email protected]. Supplementary information: Supplementary data are available at Bioinformatics online