Competition dynamics in a chemical system of self-replicating macrocycles

Central to the origin of life is the question how a chemical system transitioned from interacting molecules to an entity with the capacity for self-replication, diversification and adaptive evolution. Here, we study a chemical system that is comprised of macrocycles that have been shown to spontaneously give rise to self-replicating entities. By combining experimental and theoretical approaches, we strive to understand the evolutionary potential of this system. In particular, we apply eco-evolutionary reasoning to investigate whether and when this system of chemical replicators can diversify. Here, we report first results of a simplified stochastic chemical reaction model that is parameterized on the basis of experimental data. The model considers the competition of two replicators that do not interact directly but need similar building blocks for their growth and reproduction. Interestingly, the replicator that emerges first is being overtaken by the later one. By means of stochastic simulations, we will explore how the competitive ability of a replicator is determined by its chemical characteristics, and under which conditions replicators can coexist. The results will subsequently inform the design of future experiments

Chemical fingerprints of emotional body odor

Chemical communication is common among animals. In humans, the chemical basis of social communication has remained a black box, despite psychological and neural research showing distinctive physiological, behavioral, and neural consequences of body odors emitted during emotional states like fear and happiness. We used a multidisciplinary approach to examine whether molecular cues could be associated with an emotional state in the emitter. Our research revealed that the volatile molecules transmitting different emotions to perceivers also have objectively different chemical properties. Chemical analysis of underarm sweat collected from the same donors in fearful, happy, and emotionally neutral states was conducted using untargeted two-dimensional (GC×GC) coupled with time of flight (ToF) MS-based profiling. Based on the multivariate statistical analyses, we find that the pattern of chemical volatiles (N = 1655 peaks) associated with fearful state is clearly different from that associated with (pleasant) neutral state. Happy sweat is also significantly different from the other states, chemically, but shows a bipolar pattern of overlap with fearful as well as neutral state. Candidate chemical classes associated with emotional and neutral sweat have been identified, specifically, linear aldehydes, ketones, esters, and cyclic molecules (5 rings). This research constitutes a first step toward identifying the chemical fingerprints of emotion.info:eu-repo/semantics/publishedVersio

Caught in the Act:Mechanistic Insight into Supramolecular Polymerization-Driven Self-Replication from Real-Time Visualization

Self-assembly features prominently in fields ranging from materials science to biophysical chemistry. Assembly pathways, often passing through transient intermediates, can control the outcome of assembly processes. Yet, the mechanisms of self-assembly remain largely obscure due to a lack of experimental tools for probing these pathways at the molecular level. Here, the self-assembly of self-replicators into fibers is visualized in real-time by high-speed atomic force microscopy (HS-AFM). Fiber growth requires the conversion of precursor molecules into six-membered macrocycles, which constitute the fibers. HS-AFM experiments, supported by molecular dynamics simulations, revealed that aggregates of precursor molecules accumulate at the sides of the fibers, which then diffuse to the fiber ends where growth takes place. This mechanism of precursor reservoir formation, followed by one-dimensional diffusion, which guides the precursor molecules to the sites of growth, reduces the entropic penalty associated with colocalizing precursors and growth sites and constitutes a new mechanism for supramolecular polymerization

Perspective: science policy through public engagement

While tensions may lie between science and policy, we argue that dissemination and public engagement are key in alleviating those perceived tensions. Science being valued by society results in fact-based policy-making being demanded by constituents. Constituents’ demands will yield representatives who are familiar with the scientific process and research to inform policy decisions.https://academic.oup.com/spp/article/47/6/890/590080

Inappropriate use of the title 'chiropractor' and term 'chiropractic manipulation' in the peer-reviewed biomedical literature

BACKGROUND: The misuse of the title 'chiropractor' and term 'chiropractic manipulation', in relation to injury associated with cervical spine manipulation, have previously been reported in the peer-reviewed literature. The objectives of this study were to - 1) Prospectively monitor the peer-reviewed literature for papers reporting an association between chiropractic, or chiropractic manipulation, and injury; 2) Contact lead authors of papers that report such an association in order to determine the basis upon which the title 'chiropractor' and/or term 'chiropractic manipulation' was used; 3) Document the outcome of submission of letters to the editors of journals wherein the title 'chiropractor', and/or term 'chiropractic manipulation', had been misused and resulted in the over-reporting of chiropractic induced injury. METHODS: One electronic database (PubMed) was monitored prospectively, via monthly PubMed searches, during a 12 month period (June 2003 to May 2004). Once relevant papers were located, they were reviewed. If the qualifications and/or profession of the care provider/s were not apparent, an attempt was made to confirm them via direct e-mail communication with the principal researcher of each respective paper. A letter was then sent to the editor of each involved journal. RESULTS: A total of twenty four different cases, spread across six separate publications, were located via the monthly PubMed searches. All twenty four cases took place in one of two European countries. The six publications consisted of four case reports, each containing one patient, one case series, involving twenty relevant cases, and a secondary report that pertained to one of the four case reports. In each of the six publications the authors suggest the care provider was a chiropractor and that each patient received chiropractic manipulation of the cervical spine prior to developing symptoms suggestive of traumatic injury. In two of the four case reports contact with the principal researcher revealed that the care provider was not a chiropractor, as defined by the World Federation of Chiropractic. The authors of the other two case reports did not respond to my communications. In the case series, which involved twenty relevant cases, the principal researcher conceded that the term chiropractor had been inappropriately used and that his case series did not relate to chiropractors who had undergone appropriate formal training. The author of the secondary report, a British Medical Journal editor, conceded that he had misused the title chiropractor. Letters to editors were accepted and published by all four journals to which they were sent. To date one of the four journals has published a correction. CONCLUSION: The results of this year-long prospective review suggests that the words 'chiropractor' and 'chiropractic manipulation' are often used inappropriately by European biomedical researchers when reporting apparent associations between cervical spine manipulation and symptoms suggestive of traumatic injury. Furthermore, in those cases reported here, the spurious use of terminology seems to have passed through the peer-review process without correction. Additionally, these findings provide further preliminary evidence, beyond that already provided by Terrett, that the inappropriate use of the title 'chiropractor' and term 'chiropractic manipulation' may be a significant source of over-reporting of the link between the care provided by chiropractors and injury. Finally, editors of peer-reviewed journals were amenable to publishing 'letters to editors', and to a lesser extent 'corrections', when authors had inappropriately used the title 'chiropractor' and/or term 'chiropractic manipulation'

A framework for feature extraction from hospital medical data with applications in risk prediction

Background: Feature engineering is a time consuming component of predictive modeling. We propose a versatile platform to automatically extract features for risk prediction, based on a pre-defined and extensible entity schema. The extraction is independent of disease type or risk prediction task. We contrast auto-extracted features to baselines generated from the Elixhauser comorbidities. Results: Hospital medical records was transformed to event sequences, to which filters were applied to extract feature sets capturing diversity in temporal scales and data types. The features were evaluated on a readmission prediction task, comparing with baseline feature sets generated from the Elixhauser comorbidities. The prediction model was through logistic regression with elastic net regularization. Predictions horizons of 1, 2, 3, 6, 12 months were considered for four diverse diseases: diabetes, COPD, mental disorders and pneumonia, with derivation and validation cohorts defined on non-overlapping data-collection periods. For unplanned readmissions, auto-extracted feature set using socio-demographic information and medical records, outperformed baselines derived from the socio-demographic information and Elixhauser comorbidities, over 20 settings (5 prediction horizons over 4 diseases). In particular over 30-day prediction, the AUCs are: COPD-baseline: 0.60 (95% CI: 0.57, 0.63), auto-extracted: 0.67 (0.64, 0.70); diabetes-baseline: 0.60 (0.58, 0.63), auto-extracted: 0.67 (0.64, 0.69); mental disorders-baseline: 0.57 (0.54, 0.60), auto-extracted: 0.69 (0.64,0.70); pneumonia-baseline: 0.61 (0.59, 0.63), auto-extracted: 0.70 (0.67, 0.72). Conclusions: The advantages of auto-extracted standard features from complex medical records, in a disease and task agnostic manner were demonstrated. Auto-extracted features have good predictive power over multiple time horizons. Such feature sets have potential to form the foundation of complex automated analytic tasks

No short-cut in assessing trial quality: a case study

Assessing the quality of included trials is a central part of a systematic review. Many check-list type of instruments for doing this exist. Using a trial of antibiotic treatment for acute otitis media, Burke et al., BMJ, 1991, as the case study, this paper illustrates some limitations of the check-list approach to trial quality assessment. The general verdict from the check list type evaluations in nine relevant systematic reviews was that Burke et al. (1991) is a good quality trial. All relevant meta-analyses extensively used its data to formulate therapeutic evidence. My comprehensive evaluation, on the other hand, brought to the surface a series of serious problems in the design, conduct, analysis and report of this trial that were missed by the earlier evaluations. A check-list or instrument based approach, if used as a short-cut, may at times rate deeply flawed trials as good quality trials. Check lists are crucial but they need to be augmented with an in-depth review, and where possible, a scrutiny of the protocol, trial records, and original data. The extent and severity of the problems I uncovered for this particular trial warrant an independent audit before it is included in a systematic review

Surface Affinity of the Hydronium Ion: The Effective Fragment Potential and Umbrella Sampling

The surface affinity of the hydronium ion in water is investigated with umbrella sampling and classical molecular dynamics simulations, in which the system is described with the effective fragment potential (EFP). The solvated hydronium ion is also explored using second order perturbation theory for the hydronium ion and the empirical TIP5P potential for the waters. Umbrella sampling is used to analyze the surface affinity of the hydronium ion, varying the number of solvent water molecules from 32 to 256. Umbrella sampling with the EFP method predicts the hydronium ion to most probably lie about halfway between the center and edge of the water cluster, independent of the cluster size. Umbrella sampling using MP2 for the hydronium ion and TIP5P for the solvating waters predicts that the solvated proton most probably lies about 0.5–2.0 Å from the edge of the water cluster independent of the cluster size