PyPhi: A toolbox for integrated information theory

Integrated information theory provides a mathematical framework to fully characterize the cause-effect structure of a physical system. Here, we introduce PyPhi, a Python software package that implements this framework for causal analysis and unfolds the full cause-effect structure of discrete dynamical systems of binary elements. The software allows users to easily study these structures, serves as an up-to-date reference implementation of the formalisms of integrated information theory, and has been applied in research on complexity, emergence, and certain biological questions. We first provide an overview of the main algorithm and demonstrate PyPhi's functionality in the course of analyzing an example system, and then describe details of the algorithm's design and implementation. PyPhi can be installed with Python's package manager via the command 'pip install pyphi' on Linux and macOS systems equipped with Python 3.4 or higher. PyPhi is open-source and licensed under the GPLv3; the source code is hosted on GitHub at https://github.com/wmayner/pyphi . Comprehensive and continually-updated documentation is available at https://pyphi.readthedocs.io/ . The pyphi-users mailing list can be joined at https://groups.google.com/forum/#!forum/pyphi-users . A web-based graphical interface to the software is available at http://integratedinformationtheory.org/calculate.html .Comment: 22 pages, 4 figures, 6 pages of appendices. Supporting information "S1 Calculating Phi" can be found in the ancillary file

Measurement of vacuum pressure with a magneto-optical trap : a pressure-rise method

This research was supported by UK EPSRC grant GR/T08272/01, IOP Scotland and the Leverhulme Trust Research Project Grant RPG-2013-074.The lifetime of an atom trap is often limited by the presence of residual background gases in the vacuum chamber. This leads to the lifetime being inversely proportional to the pressure. Here we use this dependence to estimate the pressure and to obtain pressure rate-of-rise curves, which are commonly used in vacuum science to evaluate the performance of a system. We observe different rates of pressure increase in response to different levels of outgassing in our system. Therefore we suggest that this is a sensitive method which will find useful applications in cold atom systems, in particular where the inclusion of a standard vacuum gauge is impractical.Peer reviewe

Blood coagulation factor X exerts differential effects on adenovirus entry into human lymphocytes

It has been proposed that blood coagulation factors, principally factor X (FX), enhance the uptake of human adenovirus type 5 (Ad5) into cultured epithelial cells by bridging the viral hexon capsid protein and cell-surface heparan sulphate proteoglycans (HSPGs). We studied the effects of FX on Ad transduction of lymphoid cell lines (NK92MI, a natural killer cell line; Daudi, a B-cell line and Jurkat, a T-cell line) as well as primary peripheral blood lymphocytes (PBL) and HeLa epithelial cells using either replication-deficient Ad5, or a derivative in which the Ad5 fiber was replaced with that of another Ad type, Ad35, termed Ad5F35. PBL and NK92MI were resistant to Ad5 transduction. Transduction of Jurkat and Daudi cells by Ad5 was reduced by FX but without discernible effects on cell-surface Ad5 binding. FX reduced virus binding and transduction of all lymphoid cell lines by Ad5F35, as well as transduction of the T- and Natural Killer (NK)-cell populations of PBL. Flow cytometry analysis showed that all lymphoid cell lines were negative for HSPG components, in contrast to HeLa cells. FX reduced transduction of an HSPG-negative mutant Chinese hamster ovary cell line (CHOpgsA745) by Ad5 and Ad5F35, with Ad5F35 binding also being reduced by FX. These results point to fiber-dependent differences (Ad5 versus Ad35 fiber) in Ad binding to and transduction of human lymphoid and epithelial cells in the presence of FX

Detection of Estrogen Receptor Alpha and Assessment of Fulvestrant Activity in MCF-7 Tumor Spheroids Using Microfluidics and SERS

Breast cancer is one of the leading causes of cancer death in women. Novel in vitro tools that integrate three-dimensional (3D) tumor models with highly sensitive chemical reporters can provide useful information to aid biological characterization of cancer phenotype and understanding of drug activity. The combination of surface-enhanced Raman scattering (SERS) techniques with microfluidic technologies offers new opportunities for highly selective, specific, and multiplexed nanoparticle-based assays. Here, we explored the use of functionalized nanoparticles for the detection of estrogen receptor alpha (ERα) expression in a 3D tumor model, using the ERα-positive human breast cancer cell line MCF-7. This approach was used to compare targeted versus nontargeted nanoparticle interactions with the tumor model to better understand whether targeted nanotags are required to efficiently target ERα. Mixtures of targeted anti-ERα antibody-functionalized nanotags (ERα-AuNPs) and nontargeted (against ERα) anti-human epidermal growth factor receptor 2 (HER2) antibody-functionalized nanotags (HER2-AuNPs), with different Raman reporters with a similar SERS signal intensity, were incubated with MCF-7 spheroids in microfluidic devices and spectroscopically analyzed using SERS. MCF-7 cells express high levels of ERα and no detectable levels of HER2. 2D and 3D SERS measurements confirmed the strong targeting effect of ERα-AuNP nanotags to the MCF-7 spheroids in contrast to HER2-AuNPs (63% signal reduction). Moreover, 3D SERS measurements confirmed the differentiation between the targeted and the nontargeted nanotags. Finally, we demonstrated how nanotag uptake by MCF-7 spheroids was affected by the drug fulvestrant, the first-in-class approved selective estrogen receptor degrader (SERD). These results illustrate the potential of using SERS and microfluidics as a powerful in vitro platform for the characterization of 3D tumor models and the investigation of SERD activity

A simple method for estimating larval supply in reef fishes and a preliminary test of population limitation by larval delivery in the kelp bass \u3cem\u3eParalabrax clathratus\u3c/em\u3e

This paper describes a method for estimating larval supply of a temperate reef fish, the kelp bass Paralabrax clathratus, that is simple, inexpensive, requires relatively low effort, and integrates larval supply over time. Using this method, we sampled larval supply concurrently at 4 sites spread over about 35 km for nearly an entire settlement season. With these data and visual estimates of recruitment (the density of young-of-the-year after the end of the settlement season), we tested the hypothesis that spatial patterns in recruitment were set by larval supply. This hypothesis was rejected: kelp bass recruitment to the 4 sites was not related to patterns of larval supply. Furthermore, in contrast to the findings of an earlier study, recruitment was not related to the density of the macroalga Macrocystis pyrifera. Recruitment was, however, strongly correlated with the density of 1 yr old kelp bass, suggesting that spatial patterns of recruitment were consistent between the 2 cohorts. Recruitment, however, was not correlated with the density of bass 2+ yr old. We also measured larval supply in a second year and found that spatial patterns of supply were strongly correlated between years at a relatively small scale of 10s to 100s m, but not at a larger scale of several km. This finding suggests that some deterministic process (or set of processes) sets spatial patterns of larval supply at small, but not large scales. At large scales, consistent patterns of recruitment between 2 cohorts in the face of variable larval supply suggest that deterministic, postsettlement processes may generate predictable patterns of recruitment even when the supply of larvae is variable. In addition to demonstrating that spatial patterns in the abundance of demersal fish are not always well predicted by larval supply, this study introduces a technique that may facilitate more thorough exploration of the role of larval supply in determining the dynamics of populations of reef fishes

A review of independent living adaptations

This study will explore and test potential changes to the structural and delivery mechanisms for independent living adaptations. This is in order to move towards the Welsh Government goal of ensuring that adaptations can be delivered more speedily to those who need them. In doing so, it will help reduce inherent inequalities in the current system by ensuring joined up solutions, prevention and early intervention activity. This Review was commissioned in the light of some £35 million being spent annually by local authorities in Wales on Disabled Facilities Grants (DFGs) and the Welsh Government’s own spending of approximately £8 million on Physical Adaptations Grants (PAG) for social tenants. The Review was carried out between May and November 2014 and addressed three aims: mapping the current system performance Indicators testing the feasibility of options for change

Randomly Amplified DNA Fingerprinting: A Culmination of DNA Marker Technologies Based on Arbitrarily-Primed PCR Amplification

Arbitrarily-primed DNA markers can be very useful for genetic fingerprinting and for facilitating positional cloning of genes. This class of technologies is particularly important for less studied species, for which genome sequence information is generally not known. The technologies include Randomly Amplified Polymorphic DNA (RAPD), DNA Amplification Fingerprinting (DAF), and Amplified Fragment Length Polymorphism (AFLP). We have modified the DAF protocol to produce a robust PCR-based DNA marker technology called Randomly Amplified DNA Fingerprinting (RAF). While the protocol most closely resembles DAF, it is much more robust and sensitive because amplicons are labelled with either radioactive (33)P or fluorescence in a 30-cycle PCR, and then separated and detected on large polyacrylamide sequencing gels. Highly reproducible RAF markers were readily amplified from either purified DNA or alkali-treated intact leaf tissue. RAF markers typically display dominant inheritance. However, a small but significant portion of the RAF markers exhibit codominant inheritance and represent microsatellite loci. RAF compares favorably with AFLP for efficiency and reliability on many plant genomes, including the very large and complex genomes of sugarcane and wheat. While the two technologies detect about the same number of markers per large polyacrylamide gel, advantages of RAF over AFLP include: (i) no requirement for enzymatic template preparation, (ii) one instead of two PCRs, and (iii) overall cost. RAF and AFLP were shown to differ in the selective basis of amplification of markers from genomes and could therefore be used in complementary fashion for some genetic studies

Grazing in a megagrazer-dominated savanna does not reduce soil carbon stocks, even at high intensities

Recent studies suggest that wild animals can promote ecosystem carbon sinks through their impacts on vegetation and soils. However, livestock studies show that intense levels of grazing reduce soil organic carbon (SOC), leading to concerns that rewilding with large grazers may compromise ecosystem carbon storage. Furthermore, wild grazers can both limit and promote woody plant recruitment and survival on savanna grasslands, with both positive and negative impacts on SOC, depending on the rainfall and soil texture contexts. We used grazing lawns in one of the few African protected savannas that are still dominated by megagrazers (> 1000 kg), namely white rhinoceros Ceratotherium simum, as a model to study the impact of prolonged and intense wild grazing on SOC stocks. We contrasted SOC stocks between patches of varying grazing intensity and woody plant encroachment in sites across different rhino habitat types. We found no differences in SOC stocks between the most- and least grazed plots in any of the habitats. Intermediately grazed plots, however, had higher SOC stocks in the top 5 cm compared to most and least grazed plots, but only in the closed-canopy woodland habitat and not in the open habitats. Importantly, we found no evidence to support the hypothesis that wild grazing reduces SOC, even at high grazing intensities by the world's largest megagrazer. Compared to the non-encroached reference plots, woody encroached plots had higher SOC stocks in soils with low clay content and lower SOC stocks in soils with high clay content, although only in the top 5 cm. Accordingly, our study highlights that wild grazers may influence SOC indirectly through their impact on tree-grass ratios in grassy ecosystems. Our study thus provides important insights for future natural climate solutions that focus on wild grazer conservation and restoration.Keywords: fire, grazing impact, rewilding, soil carbon, white rhinoceros, woody encroachmen

A review of independent living adaptations

This study will explore and test potential changes to the structural and delivery mechanisms for independent living adaptations. This is in order to move towards the Welsh Government goal of ensuring that adaptations can be delivered more speedily to those who need them. In doing so, it will help reduce inherent inequalities in the current system by ensuring joined up solutions, prevention and early intervention activity. This Review was commissioned in the light of some £35 million being spent annually by local authorities in Wales on Disabled Facilities Grants (DFGs) and the Welsh Government’s own spending of approximately £8 million on Physical Adaptations Grants (PAG) for social tenants. The Review was carried out between May and November 2014 and addressed three aims: mapping the current system performance Indicators testing the feasibility of options for change