Evolution from the ground up with Amee – From basic concepts to explorative modeling

Evolutionary theory has been the foundation of biological research for about a century now, yet over the past few decades, new discoveries and theoretical advances have rapidly transformed our understanding of the evolutionary process. Foremost among them are evolutionary developmental biology, epigenetic inheritance, and various forms of evolu- tionarily relevant phenotypic plasticity, as well as cultural evolution, which ultimately led to the conceptualization of an extended evolutionary synthesis. Starting from abstract principles rooted in complexity theory, this thesis aims to provide a unified conceptual understanding of any kind of evolution, biological or otherwise. This is used in the second part to develop Amee, an agent-based model that unifies development, niche construction, and phenotypic plasticity with natural selection based on a simulated ecology. Amee is implemented in Utopia, which allows performant, integrated implementation and simulation of arbitrary agent-based models. A phenomenological overview over Amee’s capabilities is provided, ranging from the evolution of ecospecies down to the evolution of metabolic networks and up to beyond-species-level biological organization, all of which emerges autonomously from the basic dynamics. The interaction of development, plasticity, and niche construction has been investigated, and it has been shown that while expected natural phenomena can, in principle, arise, the accessible simulation time and system size are too small to produce natural evo-devo phenomena and –structures. Amee thus can be used to simulate the evolution of a wide variety of processes

Combinatorial quantization of the Hamiltonian Chern-Simons theory I

Motivated by a recent paper of Fock and Rosly \cite{FoRo} we describe a mathematically precise quantization of the Hamiltonian Chern-Simons theory. We introduce the Chern-Simons theory on the lattice which is expected to reproduce the results of the continuous theory exactly. The lattice model enjoys the symmetry with respect to a quantum gauge group. Using this fact we construct the algebra of observables of the Hamiltonian Chern-Simons theory equipped with a *-operation and a positive inner product.Comment: 49 pages. Some minor corrections, discussion of positivity improved, a number of remarks and a reference added

Spatio-temporal dynamics of aerosol distribution in an urban environment recorded in situ by means of a bike based monitoring system

Aerosol pollution in urban areas is highly variable due to numerous single emission sources such as automobiles, industrial and commercial activities as well as domestic heating, but also due to complex building structures redirecting air mass flows, producing leeward and windward turbulences and resuspension effects. In this publication, it is shown that one or even few aerosol monitoring sites are not able to reflect these complex patterns. In summer 2019, aerosol pollution was recorded in high spatial resolution during six night and daytime tours with a mobile sensor platform on a trailer pulled by a bicycle. Particle mass loadings showed a high variability with PM$_{10}$ values ranging from 1.3 to 221 μg m$^{-3}$ and PM$_{2.5}$ values from 0.7 to 69.0 μg m$^{-3}$. Geostatistics were used to calculate respective models of the spatial distributions of PM$_{2.5}$ and PM10. The resulting maps depict the variability of aerosol concentrations within the urban space. These spatial distribution models delineate the distributions without cutting out the built-up structures. Elsewise, the overall spatial patterns do not become visible because of being sharply interrupted by those cutouts in the resulting maps. Thus, the spatial maps allow to identify most affected urban areas and are not restricted to the street space. Furthermore, this method provides an insight to potentially affected areas, and thus can be used to develop counter measures. It is evident that the spatial aerosol patterns cannot be directly derived from the main wind direction, but result far more from an interplay between main wind direction, built-up patterns and distribution of pollution sources. Not all pollution sources are directly obvious and more research has to be carried out to explain the micro-scale variations of spatial aerosol distribution patterns. In addition, since aerosol load in the atmosphere is a severe issue for health and wellbeing of city residents more attention has to be paid to these local inhomogeneities

TRY plant trait database – enhanced coverage and open access

Plant traits - the morphological, anatomical, physiological, biochemical and phenological characteristics of plants - determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait‐based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits - almost complete coverage for ‘plant growth form’. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait–environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Elective cancer surgery in COVID-19-free surgical pathways during the SARS-CoV-2 pandemic: An international, multicenter, comparative cohort study

PURPOSE As cancer surgery restarts after the first COVID-19 wave, health care providers urgently require data to determine where elective surgery is best performed. This study aimed to determine whether COVID-19–free surgical pathways were associated with lower postoperative pulmonary complication rates compared with hospitals with no defined pathway. PATIENTS AND METHODS This international, multicenter cohort study included patients who underwent elective surgery for 10 solid cancer types without preoperative suspicion of SARS-CoV-2. Participating hospitals included patients from local emergence of SARS-CoV-2 until April 19, 2020. At the time of surgery, hospitals were defined as having a COVID-19–free surgical pathway (complete segregation of the operating theater, critical care, and inpatient ward areas) or no defined pathway (incomplete or no segregation, areas shared with patients with COVID-19). The primary outcome was 30-day postoperative pulmonary complications (pneumonia, acute respiratory distress syndrome, unexpected ventilation). RESULTS Of 9,171 patients from 447 hospitals in 55 countries, 2,481 were operated on in COVID-19–free surgical pathways. Patients who underwent surgery within COVID-19–free surgical pathways were younger with fewer comorbidities than those in hospitals with no defined pathway but with similar proportions of major surgery. After adjustment, pulmonary complication rates were lower with COVID-19–free surgical pathways (2.2% v 4.9%; adjusted odds ratio [aOR], 0.62; 95% CI, 0.44 to 0.86). This was consistent in sensitivity analyses for low-risk patients (American Society of Anesthesiologists grade 1/2), propensity score–matched models, and patients with negative SARS-CoV-2 preoperative tests. The postoperative SARS-CoV-2 infection rate was also lower in COVID-19–free surgical pathways (2.1% v 3.6%; aOR, 0.53; 95% CI, 0.36 to 0.76). CONCLUSION Within available resources, dedicated COVID-19–free surgical pathways should be established to provide safe elective cancer surgery during current and before future SARS-CoV-2 outbreaks

Elective Cancer Surgery in COVID-19-Free Surgical Pathways During the SARS-CoV-2 Pandemic: An International, Multicenter, Comparative Cohort Study.

PURPOSE: As cancer surgery restarts after the first COVID-19 wave, health care providers urgently require data to determine where elective surgery is best performed. This study aimed to determine whether COVID-19-free surgical pathways were associated with lower postoperative pulmonary complication rates compared with hospitals with no defined pathway. PATIENTS AND METHODS: This international, multicenter cohort study included patients who underwent elective surgery for 10 solid cancer types without preoperative suspicion of SARS-CoV-2. Participating hospitals included patients from local emergence of SARS-CoV-2 until April 19, 2020. At the time of surgery, hospitals were defined as having a COVID-19-free surgical pathway (complete segregation of the operating theater, critical care, and inpatient ward areas) or no defined pathway (incomplete or no segregation, areas shared with patients with COVID-19). The primary outcome was 30-day postoperative pulmonary complications (pneumonia, acute respiratory distress syndrome, unexpected ventilation). RESULTS: Of 9,171 patients from 447 hospitals in 55 countries, 2,481 were operated on in COVID-19-free surgical pathways. Patients who underwent surgery within COVID-19-free surgical pathways were younger with fewer comorbidities than those in hospitals with no defined pathway but with similar proportions of major surgery. After adjustment, pulmonary complication rates were lower with COVID-19-free surgical pathways (2.2% v 4.9%; adjusted odds ratio [aOR], 0.62; 95% CI, 0.44 to 0.86). This was consistent in sensitivity analyses for low-risk patients (American Society of Anesthesiologists grade 1/2), propensity score-matched models, and patients with negative SARS-CoV-2 preoperative tests. The postoperative SARS-CoV-2 infection rate was also lower in COVID-19-free surgical pathways (2.1% v 3.6%; aOR, 0.53; 95% CI, 0.36 to 0.76). CONCLUSION: Within available resources, dedicated COVID-19-free surgical pathways should be established to provide safe elective cancer surgery during current and before future SARS-CoV-2 outbreaks

“Help in a Heartbeat?”: A Systematic Evaluation of Mobile Health Applications (Apps) for Coronary Heart Disease

For patients with coronary heart disease (CHD) lifestyle changes and disease management are key aspects of treatment that could be facilitated by mobile health applications (MHA). However, the quality and functions of MHA for CHD are largely unknown, since reviews are missing. Therefore, this study assessed the general characteristics, quality, and functions of MHA for CHD. Hereby, the Google Play and Apple App stores were systematically searched using a web crawler. The general characteristics and quality of MHA were rated with the Mobile Application Rating Scale (MARS) by two independent raters. From 3078 identified MHA, 38 met the pre-defined criteria and were included in the assessment. Most MHA were affiliated with commercial companies (52.63%) and lacked an evidence-base. An overall average quality of MHA (M = 3.38, SD = 0.36) was found with deficiencies in information quality and engagement. The most common functions were provision of information and CHD risk score calculators. Further functions included reminders (e.g., for medication or exercises), feedback, and health management support. Most MHA (81.58%) had one or two functions and MHA with more features had mostly higher MARS ratings. In summary, this review demonstrated that a number of potentially helpful MHA for patients with CHD are commercially available. However, there is a lack of scientific evidence documenting their usability and clinical potential. Since it is difficult for patients and healthcare providers to find suitable and high-quality MHA, databases with professionally reviewed MHA are required

“Help in a Heartbeat?”: A Systematic Evaluation of Mobile Health Applications (Apps) for Coronary Heart Disease

For patients with coronary heart disease (CHD) lifestyle changes and disease management are key aspects of treatment that could be facilitated by mobile health applications (MHA). However, the quality and functions of MHA for CHD are largely unknown, since reviews are missing. Therefore, this study assessed the general characteristics, quality, and functions of MHA for CHD. Hereby, the Google Play and Apple App stores were systematically searched using a web crawler. The general characteristics and quality of MHA were rated with the Mobile Application Rating Scale (MARS) by two independent raters. From 3078 identified MHA, 38 met the pre-defined criteria and were included in the assessment. Most MHA were affiliated with commercial companies (52.63) and lacked an evidence-base. An overall average quality of MHA (M = 3.38, SD = 0.36) was found with deficiencies in information quality and engagement. The most common functions were provision of information and CHD risk score calculators. Further functions included reminders (e.g., for medication or exercises), feedback, and health management support. Most MHA (81.58) had one or two functions and MHA with more features had mostly higher MARS ratings. In summary, this review demonstrated that a number of potentially helpful MHA for patients with CHD are commercially available. However, there is a lack of scientific evidence documenting their usability and clinical potential. Since it is difficult for patients and healthcare providers to find suitable and high-quality MHA, databases with professionally reviewed MHA are required