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

Prosomal-width-to-weight relationships in American horseshoe crabs (Limulus polyphemus): examining conversion factors used to estimate landings

Horseshoe crabs (Limulus polyphemus) are valued by many stakeholders, including the commercial fishing industry, biomedical companies, and environmental interest groups. We designed a study to test the accuracy of the conversion factors that were used by NOAA Fisheries and state agencies to estimate horseshoe crab landings before mandatory reporting that began in 1998. Our results indicate that the NOAA Fisheries conversion factor consistently overestimates the weight of male horseshoe crabs, particularly those from New England populations. Because of the inaccuracy of this and other conversion factors, states are now mandated to report the number (not biomass) and sex of landed horseshoe crabs. However, accurate estimates of biomass are still necessary for use in prediction models that are being developed to better manage the horseshoe crab fishery. We recommend that managers use the conversion factors presented in this study to convert current landing data from numbers to biomass of harvested horseshoe crabs for future assessments

Reversible conjugation of a CBASS nucleotide cyclase regulates bacterial immune response to phage infection

Funding: This work was funded by a European Research Council Advanced Grant (grant number 101018608) to M.F.W. L.K. was funded by an EMBO postdoctoral fellowship (grant number ALTF 234-2022). L.G.-M. was funded by the UKRI Biotechnology and Biological Sciences Research Council (BBSRC) (grant number BB/T00875X/1).Prokaryotic antiviral defence systems are frequently toxic for host cells and stringent regulation is required to ensure survival and fitness. These systems must be readily available in case of infection but tightly controlled to prevent activation of an unnecessary cellular response. Here we investigate how the bacterial cyclic oligonucleotide-based antiphage signalling system (CBASS) uses its intrinsic protein modification system to regulate the nucleotide cyclase. By integrating a type II CBASS system from Bacillus cereus into the model organism Bacillus subtilis, we show that the protein-conjugating Cap2 (CBASS associated protein 2) enzyme links the cyclase exclusively to the conserved phage shock protein A (PspA) in the absence of phage. The cyclase–PspA conjugation is reversed by the deconjugating isopeptidase Cap3 (CBASS associated protein 3). We propose a model in which the cyclase is held in an inactive state by conjugation to PspA in the absence of phage, with conjugation released upon infection, priming the cyclase for activation.Peer reviewe

Biobehavioral effects of Tai Chi Qigong in men with prostate cancer: Study design of a three-arm randomized clinical trial.

Fatigue is often one of the most commonly reported symptoms in prostate cancer survivors, but it is also one of the least understood cancer-related symptoms. Fatigue is associated with psychological distress, disruptions in sleep quality, and impairments in health-related quality of life. Moreover, inflammatory processes and changes related to the hypothalamic-pituitary-adrenal (HPA) axis and/or autonomic nervous system may also play a role in cancer-related fatigue. Thus, effective treatments for fatigue in prostate cancer survivors represent a current unmet need. Prior research has shown that Tai Chi Qigong, a mind-body exercise intervention, can improve physical and emotional health. Herein, we describe the protocol of the ongoing 3-arm randomized controlled Health Empowerment & Recovery Outcomes (HERO) clincal trial. One hundred sixty-six prostate cancer survivors with fatigue are randomized to a modified Tai Chi Qigong intervention (TCQ), intensity-matched body training intervention (BT), or usual care (UC) condition. Guided by biopsychosocial and psychoneuroimmunology models, we propose that TCQ, as compared to BT or UC will: i) reduce fatigue (primary outcome) in prostate cancer survivors; ii) reduce inflammation; and iii) regulate the expression of genes from two major functional clusters: a) inflammation, vasodilation and metabolite sensing and b) energy and adrenergic activation. Assessments are conducted at baseline, the 6-week midpoint of the intervention, and 1 week, 3 months, and 12 months post-intervention. If our findings show that TCQ promotes recovery from prostate cancer and its treatment, this type of intervention can be integrated into survivorship care plans as the standard of care. The study's findings will also provide novel information about underlying biobehavioral mechanisms of cancer-related fatigue. Trial registration number:NCT03326713; clinicaltrials.gov

Developing a business case for greening hard coastal and estuarine infrastructure: preliminary results

This paper presents a new framework of critical success factors (CSF) that is being developed to aid approval of ecological enhancements and green engineering options in cities, historic conservation areas, estuaries and at the coast. This is intended to support asset managers, engineers, conservation and biodiversity teams, decision-makers, and other end-users. The CSF framework is outlined and demonstrated by assessing the engineering performance and ecosystem services benefits of ecological enhancements used in specific operational scale case studies. Where data availability permits, the costs and benefits of different greening approaches compared to ‘business as usual’ are assessed. Three coastal and estuarine case studies are presented to demonstrate how the framework can be applied to compare traditional engineering solutions to green-grey options. Results show that simple, inexpensive ecological enhancement and green engineering solutions can deliver more multifunctional benefits than business as usual solutions for similar or reduced costs. They also demonstrate that the CSF framework will be a powerful tool that can aid practitioners in evaluating green engineering solutions compared with business as usual

Multiple-University Extension Program Addresses Postdisaster Oil Spill Needs Through Private Funding Partnership

In response to the Deepwater Horizon Oil Spill, the Gulf of Mexico Research Initiative (GoMRI) was formed to answer oil spill–related scientific questions. However, peer-reviewed scientific discoveries were not reaching people whose livelihoods depended on a healthy Gulf of Mexico. GoMRI and the four Gulf of Mexico Sea Grant programs partnered to develop a regional Extension program with a team of multidisciplinary specialists and a regional manager embedded within the Sea Grant programs. The team answered oil spill science questions from target audiences. The program leaders also identified the value of adding a regional Extension communicator to enhance their Extension products

Pulmonary Disease and Age at Immigration among Hispanics. Results from the Hispanic Community Health Study/Study of Latinos

Rationale: Asthma has been reported to be more prevalent among Hispanics of Puerto Rican heritage than among other Hispanics and among Hispanics born in the United States or who immigrated as children than among those who came as adults; however, direct comparisons across Hispanic groups are lacking

A longitudinal analysis of urological chronic pelvic pain syndrome flares in the Multidisciplinary Approach to the Study of Chronic Pelvic Pain (MAPP) Research Network

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/151272/1/bju14783.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/151272/2/bju14783_am.pd

SIR AUSTIN BRADFORD HILL

CD40L/interleukin-4 (IL-4) stimulation occurs in vivo in the tumor microenvironment and induces global translation to varying degrees in individuals with chronic lymphocytic leukemia (CLL) in vitro. However, the implications of CD40L/IL-4 for the translation of specific genes is not known. To determine the most highly translationally regulated genes in response to CD40L/IL-4, we carried out ribosome profiling, a next-generation sequencing method. Significant differences in the translational efficiency of DNA damage response genes, specifically ataxia‐telangiectasia–mutated kinase (ATM) and the MRE11/RAD50/NBN (MRN) complex, were observed between patients, suggesting different patterns of translational regulation. We confirmed associations between CD40L/IL-4 response and baseline ATM levels, induction of ATM, and phosphorylation of the ATM targets, p53 and H2AX. X-irradiation was used to demonstrate that CD40L/IL-4 stimulation tended to improve DNA damage repair. Baseline ATM levels, independent of the presence of 11q deletion, correlated with overall survival (OS). Overall, we suggest that there are individual differences in translation of specific genes, including ATM, in response to CD40L/IL-4 and that these interpatient differences might be clinically important

(Not) being at home: Hsu Ming Teo's Behind the Moon (2005) and Michelle de Kretser's Questions of Travel (2012)

This article examines some interventions of Asian Australian writing into the debate over multiculturalism, and the shift from negative stereotyping of Asian migrants, to reification of racial divisions and propagation of a masked racism, to the creation of new alignments and the revival of pre-existing affiliations by migrant and second generation subjects. It compares the practices of not-at-homeness by Asian migrants and their descendants and white Australians in Hsu Ming Teo’s Behind the Moon with those of a Sri Lankan refugee and a white Australian traveller in Michelle de Kretser’s Questions of Travel. The changing concepts of belonging in the novels show a realignment of core and periphery relations within the nation state under the pressures of multiculturalism and globalization: where home is and how it is configured are questions as important for white Australians whose sense of territory is challenged as they are for Asian migrants who seek to establish a new belonging