Basins of Attraction, Commitment Sets and Phenotypes of Boolean Networks

The attractors of Boolean networks and their basins have been shown to be highly relevant for model validation and predictive modelling, e.g., in systems biology. Yet there are currently very few tools available that are able to compute and visualise not only attractors but also their basins. In the realm of asynchronous, non-deterministic modeling not only is the repertoire of software even more limited, but also the formal notions for basins of attraction are often lacking. In this setting, the difficulty both for theory and computation arises from the fact that states may be ele- ments of several distinct basins. In this paper we address this topic by partitioning the state space into sets that are committed to the same attractors. These commitment sets can easily be generalised to sets that are equivalent w.r.t. the long-term behaviours of pre-selected nodes which leads us to the notions of markers and phenotypes which we illustrate in a case study on bladder tumorigenesis. For every concept we propose equivalent CTL model checking queries and an extension of the state of the art model checking software NuSMV is made available that is capa- ble of computing the respective sets. All notions are fully integrated as three new modules in our Python package PyBoolNet, including functions for visualising the basins, commitment sets and phenotypes as quotient graphs and pie charts

Creating Wealth and Welfare

Summaries This article examines the role of China's rural township and village governments in welfare provision. In it, I first describe the role of local officials in the promotion of collective and private enterprise, and the relationship between these entrepreneurial activities and more traditional responsibilities of government, particularly social assistance and welfare provision. The extraordinary development of China's township and village enterprises created resources which have frequently been channelled towards the provision of public goods and welfare. Examination of policy changes and budget allocations for rural welfare highlights the extent to which localities are dependent on their own funding sources. In conclusion, I suggest that new initiatives in fiscal reform may limit the entrepreneurial capacity of local governments, reducing their control over resources and thus their capacity to meet welfare responsibilities

Effects of Irritable Bowel Syndrome on Daily Activities Vary Among Subtypes Based on Results From the IBS in America Survey

Background & Aims Irritable bowel syndrome (IBS) is associated with significant disease burden and decreased quality of life (QOL). We investigated the effects of IBS on different areas of daily function and compared these among disease subtypes. Methods The Life with IBS survey was conducted by Gfk Public Affairs & Corporate Communications from September through October 2015. Respondents met Rome III criteria for constipation-predominant or diarrhea-predominant IBS (IBS-C and IBS-D, respectively). Data were collected from 3254 individuals (mean age, 47 years; 81% female; and 90% Caucasian) who met IBS criteria. Results Respondents who were employed or in school (n = 1885) reported that IBS symptoms affected their productivity an average of 8.0 days out of the month and they missed approximately 1.5 days of work/school per month because of IBS. More than half the individuals reported that their symptoms were very bothersome. Individuals with IBS-C were more likely than with IBS-D to report avoiding sex, difficulty concentrating, and feeling self-conscious. Individuals with IBS-D reported more avoidance of places without bathrooms, difficulty making plans, avoiding leaving the house, and reluctance to travel. These differences remained when controlling for symptom bothersomeness, age, sex, and employment status. In exchange for 1 month of relief from IBS, more than half of the sample reported they would be willing to give up caffeine or alcohol, 40% would give up sex, 24.5% would give up cell phones, and 21.5% would give up the internet for 1 month. Conclusions Although the perceived effects of IBS symptoms on productivity are similar among its subtypes, patients with IBS-C and IBS-D report differences in specific areas of daily function

Patients’ experiences treated with open-label placebo versus double-blind placebo: a mixed methods qualitative study

Background: There is increasing evidence suggesting that open-label placebo (OLP) is an effective treatment for several medical conditions defined by self-report. However, little is known about patients’ experiences with OLP, and no studies have directly compared patients’ experiences in double-blind placebo (DBP) conditions. Methods: This study was nested in a large randomized-controlled trial comparing the effects of OLP and DBP treatments in individuals with irritable bowel syndrome (IBS). We randomly selected 33 participants for interviews concerning their experiences in the parent trial. The data were qualitatively analyzed using an iterative immersion/crystallization approach. We then compared the qualitative interview data to the quantitative IBS severity data assessed during the parent trial, using a mixed methods approach. Results: Two prominent interview themes were identified: (1) the participants’ feelings about their treatment allocation and (2) their reflections about the treatment. Both OLP and DBP participants mentioned hope and curiosity as major feelings driving them to engage with their treatment. However, while DBP participants tended to be more enthusiastic about their allocation, OLP participants were more ambivalent. Furthermore, OLP participants reflected more on their treatment, often involving noticeable cognitive and emotional processes of self-reflection. They offered a variety of explanations for their symptom improvement and were significantly less likely to attribute it to the treatment itself than DBP participants (Χ2 [3] = 8.28; p =.041). Similarly, the participants’ retrospective narratives of symptom improvement were significantly correlated with their corresponding quantitative IBS severity scores only in DBP (p’s ≤.006) but not in OLP (p’s ≥.637). Conclusion: OLP and DBP participants share feelings of hope, uncertainty and curiosity but differ in the extent of conscious reflection. The counter-intuitive OLP prompts more self-examination, ambivalent feelings and active engagement compared to DBP. At the same time, OLP participants are more reluctant to attribute symptom improvement to their treatment. Our findings substantially add to the emerging picture of factors that distinguish OLP and DBP and their potential mechanisms

Serial lung ultrasounds in pediatric pneumonia in Mozambique and Pakistan

Lung ultrasound (LUS) is a promising point-of-care imaging technology for diagnosing and managing pneumonia. We sought to explore serial LUS examinations in children with chest-indrawing pneumonia in resource-constrained settings and compare their clinical and LUS imaging courses longitudinally. We conducted a prospective, observational study among children aged 2 through 23 months with World Health Organization Integrated Management of Childhood Illness chest-indrawing pneumonia and among children without fast breathing, chest indrawing or fever (no pneumonia cohort) at 2 district hospitals in Mozambique and Pakistan. We assessed serial LUS at enrollment, 2, 6, and 14 days, and performed a secondary analysis of enrolled children\u27s longitudinal clinical and imaging courses. By Day 14, the majority of children with chest-indrawing pneumonia and consolidation on enrollment LUS showed improvement on follow-up LUS (100% in Mozambique, 85.4% in Pakistan) and were clinically cured (100% in Mozambique, 78.0% in Pakistan). In our cohort of children with chest-indrawing pneumonia, LUS imaging often reflected the clinical course; however, it is unclear how serial LUS would inform the routine management of non-severe chest-indrawing pneumonia

Electrical conduction by interface states in semiconductor heterojunctions

peer reviewedaudience: researcher, professionalElectrical conduction in semiconductor heterojunctions containing defect states in the interface region is studied. As the classical drift-diffusion mechanism cannot in any case explain electrical conduction in semiconductor heterojunctions, tunnelling involving interface states is often considered as a possible conduction path. A theoretical treatment is made where defect states in the interface region with a continuous energy distribution are included. Electrical conduction through this defect band then allows the transit of electrons from the conduction band of one semiconductor to the valence band of the second component. The analysis is initiated by electrical measurements on n-CdS/p-CdTe heterojunctions obtained by chemical vapour deposition of CdS on (111) oriented CdTe single crystals, for which current--voltage and capacitance--frequency results are shown. The theoretical analysis is based on the numerical resolution of Poisson's equation and the continuity equations of electrons, holes and defect states, where a current component corresponding to the defect band conduction is explicitly included. Comparison with the experimental curves shows that this formalism yields an efficient tool to model the conduction process through the interface region. It also allows us to determine critical values of the physical parameters when a particular step in the conduction mechanism becomes dominant

Development of reverse-transcription PCR techniques to analyse the density and sex ratio of gametocytes in genetically diverse Plasmodium chabaudi infections

We have developed cross-genotype and genotype-specific quantitative reverse-transcription PCR (qRT-PCR) assays to detect and quantify the number of parasites, transmission stages (gametocytes) and male gametocytes in blood stage Plasmodium chabaudi infections. Our cross-genotype assays are reliable, repeatable and generate counts that correlate strongly (R(2)s > 90%) with counts expected from blood smears. Our genotype-specific assays can distinguish and quantify different stages of genetically distinct parasite clones (genotypes) in mixed infections and are as sensitive as our cross-genotype assays. Using these assays we show that gametocyte density and gametocyte sex ratios vary during infections for two genetically distinct parasite lines (genotypes) and present the first data to reveal how sex ratio is affected when each genotype experiences competition in mixed-genotype infections. Successful infection of mosquito vectors depends on both gametocyte density and their sex ratio and we discuss the implications of competition in genetically diverse infections for transmission success

Gametocytes: insights gained during a decade of molecular monitoring

In vertebrate hosts, malaria parasites produce specialized male and female sexual stages (gametocytes). Soon after being taken up by a mosquito, gametocytes rapidly produce gametes and, once mated, they infect their vector and can be transmitted to new hosts. Despite being the parasite stages that were first identified (over a century ago), gametocytes have remained elusive, and basic questions remain concerning their biology. However, the postgenomic era has substantiated information on the specialized molecular machinery of gametocytogenesis and expedited the development of molecular tools to detect and quantify gametocytes. The application of such highly sensitive and specific tools has opened up novel approaches and provided new insights into gametocyte biology. Here, we review the discoveries made during the past decade, highlight unanswered questions and suggest new directions

Bringing down barriers to children’s healthy eating: a critical review of opportunities, within a complex food system

This narrative review revises the scientific evidence of recent years on healthy eating in children and adolescents, making sense of promising avenues of action, from a food system perspective. A conceptual framework is provided to better understand how eating habits of children and adolescents are shaped to identify key multisectoral approaches that should be implemented to promote healthier diets. The following influencing factors are discussed: individual factors (physiological and psychological factors, food preferences and food literacy competencies), factors within the personal and socio-cultural food environments, external food environments, and the supply chain. In each section, the main barriers to healthy eating are briefly discussed focusing on how to overcome them. Finally, a discussion with recommendations of actions is provided, anchored in scientific knowledge, and transferable to the general public, industry, and policymakers. We highlight that multidisciplinary approaches are not enough, a systems approach, with a truly holistic view is needed. Apart from introducing systemic changes, a variety of interventions can be implemented at different levels to foster healthier diets in children, through fostering healthier and more sustainable food environments, facilitating pleasurable sensory experiences, increasing their food literacy, and enhancing their agency by empowering them to make better food related decisions. Acknowledging children as unique individuals is required, through interpersonal interactions, as well as their role in their environments. Actions should aim to enable children and adolescents as active participants within sustainable food systems, to support healthier dietary behaviours that can be sustained throughout life, impacting health at a societal level