Information Theory for Complex Systems Scientists

In the 21st century, many of the crucial scientific and technical issues facing humanity can be understood as problems associated with understanding, modelling, and ultimately controlling complex systems: systems comprised of a large number of non-trivially interacting components whose collective behaviour can be difficult to predict. Information theory, a branch of mathematics historically associated with questions about encoding and decoding messages, has emerged as something of a lingua franca for those studying complex systems, far exceeding its original narrow domain of communication systems engineering. In the context of complexity science, information theory provides a set of tools which allow researchers to uncover the statistical and effective dependencies between interacting components; relationships between systems and their environment; mereological whole-part relationships; and is sensitive to non-linearities missed by commonly parametric statistical models. In this review, we aim to provide an accessible introduction to the core of modern information theory, aimed specifically at aspiring (and established) complex systems scientists. This includes standard measures, such as Shannon entropy, relative entropy, and mutual information, before building to more advanced topics, including: information dynamics, measures of statistical complexity, information decomposition, and effective network inference. In addition to detailing the formal definitions, in this review we make an effort to discuss how information theory can be interpreted and develop the intuition behind abstract concepts like "entropy," in the hope that this will enable interested readers to understand what information is, and how it is used, at a more fundamental level

Next-to-Minimal Supersymmetric Model Higgs Scenarios for Partially Universal GUT Scale Boundary Conditions

We examine the extent to which it is possible to realize the NMSSM "ideal Higgs" models espoused in several papers by Gunion et al in the context of partially universal GUT scale boundary conditions. To this end we use the powerful methodology of nested sampling. We pay particular attention to whether ideal-Higgs-like points not only pass LEP constraints but are also acceptable in terms of the numerous constraints now available, including those from the Tevatron and $B$-factory data, $(g-2)_\mu$ and the relic density $\Omega h^2$. In general for this particular methodology and range of parameters chosen, very few points corresponding to said previous studies were found, and those that were found were at best $2\sigma$ away from the preferred relic density value. Instead, there exist a class of points, which combine a mostly singlet-like Higgs with a mostly singlino-like neutralino coannihilating with the lightest stau, that are able to effectively pass all implemented constraints in the region $80<m_h<100$. It seems that the spin-independent direct detection cross section acts as a key discriminator between ideal Higgs points and the hard to detect singlino-like points.Comment: 22 pages, 15 figure

Genome-wide association analysis and functional annotation of positional candidate genes for feed conversion efficiency and growth rate in pigs

This project has received funding from the European Union‘s Seventh Framework Programme for research, technological development and demonstration as part of the ECO-FCE project under grant agreement No. 311794.peer-reviewedFeed conversion efficiency is a measure of how well an animal converts feed into live weight and it is typically expressed as feed conversion ratio (FCR). FCR and related traits like growth rate (e.g. days to 110 kg—D110) are of high interest for animal breeders, farmers and society due to implications on animal performance, feeding costs and environmental sustainability. The objective of this study was to identify genomic regions associated with FCR and D110 in pigs. A total of 952 terminal line boars, showing an individual variation in FCR, were genotyped using 60K SNP-Chips. Markers were tested for associations with estimated breeding values (EBV) for FCR and D110. For FCR, the largest number of associated SNPs was located on chromosomes 4 (30 SNPs), 1 (25 SNPs), X (15 SNPs) and 6 (12 SNPs). The most prominent genomic regions for D110 were identified on chromosomes 15 (10 SNPs), 1 and 4 (both 9 SNPs). The most significantly associated SNPs for FCR and D110 mapped 129.8 Kb from METTL11B (chromosome 4) and 32Kb from MBD5 (chromosome 15), respectively. A list of positional genes, closest to significantly associated SNPs, was used to identify enriched pathways and biological functions related to the QTL for both traits. A number of candidate genes were significantly overrepresented in pathways of immune cell trafficking, lymphoid tissue structure, organ morphology, endocrine system function, lipid metabolism, and energy production. After resequencing the coding region of selected positional and functional candidate genes, six SNPs were genotyped in a subset of boars. SNPs in PRKDC, SELL, NR2E1 and AKRIC3 showed significant associations with EBVs for FCR/D110. The study revealed a number of chromosomal regions and candidate genes affecting FCR/D110 and pointed to corresponding biological pathways related to lipid metabolism, olfactory reception, and also immunological status.This project has received funding from the European Union‘s Seventh Framework Programme for research, technological development and demonstration as part of the ECO-FCE project under grant agreement No. 311794

Variations in hypoxia impairs muscle oxygenation and performance during simulated team-sport running

Purpose: To quantify the effect of acute hypoxia on muscle oxygenation and power during simulated team-sport running. Methods: Seven individuals performed repeated and single sprint efforts, embedded in a simulated team-sport running protocol, on a non-motorized treadmill in normoxia (sea-level), and acute normobaric hypoxia (simulated altitudes of 2,000 and 3,000 m). Mean and peak power was quantified during all sprints and repeated sprints. Mean total work, heart rate, blood oxygen saturation, and quadriceps muscle deoxyhaemoglobin concentration (assessed via near-infrared spectroscopy) were measured over the entire protocol. A linear mixed model was used to estimate performance and physiological effects across each half of the protocol. Changes were expressed in standardized units for assessment of magnitude. Uncertainty in the changes was expressed as a 90% confidence interval and interpreted via non-clinical magnitude-based inference. Results: Mean total work was reduced at 2,000 m (−10%, 90% confidence limits ±6%) and 3,000 m (−15%, ±5%) compared with sea-level. Mean heart rate was reduced at 3,000 m compared with 2,000 m (−3, ±3 min(−1)) and sea-level (−3, ±3 min(−1)). Blood oxygen saturation was lower at 2,000 m (−8, ±3%) and 3,000 m (−15, ±2%) compared with sea-level. Sprint mean power across the entire protocol was reduced at 3,000 m compared with 2,000 m (−12%, ±3%) and sea-level (−14%, ±4%). In the second half of the protocol, sprint mean power was reduced at 3,000 m compared to 2,000 m (−6%, ±4%). Sprint mean peak power across the entire protocol was lowered at 2,000 m (−10%, ±6%) and 3,000 m (−16%, ±6%) compared with sea-level. During repeated sprints, mean peak power was lower at 2,000 m (−8%, ±7%) and 3,000 m (−8%, ±7%) compared with sea-level. In the second half of the protocol, repeated sprint mean power was reduced at 3,000 m compared to 2,000 m (−7%, ±5%) and sea-level (−9%, ±5%). Quadriceps muscle deoxyhaemoglobin concentration was lowered at 3,000 m compared to 2,000 m (−10, ±12%) and sea-level (−11, ±12%). Conclusions: Simulated team-sport running is impaired at 3,000 m compared to 2,000 m and sea-level, likely due to a higher muscle deoxygenation

Hybrid Adaptive Filter development for the minimisation of transient fluctuations superimposed on electrotelluric field recordings mainly by magnetic storms

The method of Hybrid Adaptive Filtering (HAF) aims to recover the recorded electric field signals from anomalies of magnetotelluric origin induced mainly by magnetic storms. An adaptive filter incorporating neuro-fuzzy technology has been developed to remove any significant distortions from the equivalent magnetic field signal, as retrieved from the original electric field signal by reversing the magnetotelluric method. Testing with further unseen data verifies the reliability of the model and demonstrates the effectiveness of the HAF method

Serotonergic psychedelics LSD & psilocybin increase the fractal dimension of cortical brain activity in spatial and temporal domains.

Psychedelic drugs, such as psilocybin and LSD, represent unique tools for researchers investigating the neural origins of consciousness. Currently, the most compelling theories of how psychedelics exert their effects is by increasing the complexity of brain activity and moving the system towards a critical point between order and disorder, creating more dynamic and complex patterns of neural activity. While the concept of criticality is of central importance to this theory, few of the published studies on psychedelics investigate it directly, testing instead related measures such as algorithmic complexity or Shannon entropy. We propose using the fractal dimension of functional activity in the brain as a measure of complexity since findings from physics suggest that as a system organizes towards criticality, it tends to take on a fractal structure. We tested two different measures of fractal dimension, one spatial and one temporal, using fMRI data from volunteers under the influence of both LSD and psilocybin. The first was the fractal dimension of cortical functional connectivity networks and the second was the fractal dimension of BOLD time-series. In addition to the fractal measures, we used a well-established, non-fractal measure of signal complexity and show that they behave similarly. We were able to show that both psychedelic drugs significantly increased the fractal dimension of functional connectivity networks, and that LSD significantly increased the fractal dimension of BOLD signals, with psilocybin showing a non-significant trend in the same direction. With both LSD and psilocybin, we were able to localize changes in the fractal dimension of BOLD signals to brain areas assigned to the dorsal-attenion network. These results show that psychedelic drugs increase the fractal dimension of activity in the brain and we see this as an indicator that the changes in consciousness triggered by psychedelics are associated with evolution towards a critical zone.NIHR Wellcome NSF-NRT MRC Beckley Foundation Alex Mosley Charitable Trust Ad Astria Chandaria Foundation. Neuro-psychoanalysis Foundation Multidisplinary Association for Psychedelic Studies The Heffter Research Institut

Aortic intima media thickness in children and adolescents with type 1 diabetes : A systematic review

Aims Greater aortic intima media thickness (aIMT), a marker of subclinical atherosclerosis, can identify individuals at risk of CVD. This systematic review with meta-analysis compared aIMT in youth with type 1 diabetes and healthy controls. Methods A systematic search of published literature (to July 2021) was undertaken using electronic databases MEDLINE, EMBASE, Scopus, CINAHL and AMED. Eligible studies reported aIMT in participants aged <20 years with type 1 diabetes and healthy controls. Meta-analysis was used to combine outcome data, presented as forest plots. Moderator analysis and metaregression were conducted to identify study and participant characteristics associated with aIMT. Publication bias was assessed by funnel plot inspection. Results Meta-analysis of nine studies (n = 1030 with type 1 diabetes and n = 498 healthy control participants) indicated, with high heterogeneity (I2 98%), that youth with type 1 diabetes have higher aIMT compared with healthy controls (mean difference [95% CIs]: 0.11 [0.04, 0.18] mm, P = 0.003). Factors associated with greater aIMT in type 1 diabetes compared to controls included: use of a phased array probe versus linear array probe; longer diabetes duration; higher insulin dose; higher BMI z score and waist circumference; higher LDL cholesterol; higher triglycerides; and higher diastolic blood pressure. Conclusions Type 1 diabetes in youth is associated with higher aIMT compared with healthy control individuals. Longer duration of diabetes and major CVD risk factors were also associated with higher aIMT. Together, these findings provide a strong rationale for targeting modifiable risk factors in CVD prevention. Registered in PROSPERO on 8 August 2019 (CRD42019137559)

External load differences between elite youth and professional football players:ready for take-off?

This study examines differences in weekly load between the first (FT) and the under 19 team (U19) within a professional football setting. Data were collected in 11 FT and 9 U19 players (2016-2017 season). FT data was divided into weeks with (FT-M1) or without (FT-M0) a mid-week match. Indicators were total distance (TD) and TD at 12-15, 15-20, 20-25 and >25 km‧h-1 and were analysed as external load (m), intensity (m‧min-1) and load monotony (a.u.). TD-based load was higher for U19 compared to FT-M0 (very likely moderate) and FT-M1 (likely large). Differences at higher velocities were substantially less (trivial to possibly small), with TD >25 km‧h-1 being lower than FT-M0 (very likely moderate) and FT-M1 (likely small). All intensity indicators were lower for U19 (likely small to almost certainly large). Load monotony was higher compared to FT-M1 (possibly small to almost certainly very large). Compared to FT-M0, monotony was higher for TD (possibly very large) and TD >25 km‧h‑1 (possibly moderate) but lower for TD 12-15 (possibly small) and 15-20 km‧h‑1 (likely moderate). So, despite higher weekly external loads at low velocity for elite youth players, external intensity and load variation increases when these players may transition to professional football. 

Identification of genetic changes associated with drug resistance by reverse in situ hybridization.

The molecular cytogenetic techniques of comparative genomic hybridization (CGH) and reverse in situ hybridization (REVISH) allow the entire genomes of tumours to be screened for genetic changes without the requirement for specific probes or markers. In order to define the ability of REVISH to detect and map regions of amplification associated with drug resistance, we investigated a panel of cell lines selected for resistance to doxorubicin and intrinsic sensitivity to topoisomerase II-inhibitory drugs. We have defined a modified REVISH protocol, which involves double hybridizations with genomic DNA from the test cell lines and chromosome-specific whole chromosome paints to identify the chromosomes to which the amplicons localize. Sites of amplification are then mapped by fractional length measurements (Flpter), using published genome databases. Our findings show that amplification of the topoisomerase II alpha gene is readily detected and mapped, as is amplification of the MDR and MRP loci. Interestingly, REVISH detected a new amplicon in the doxorubicin-resistant lung cancer cell line, GLC4-ADR, which mapped to chromosome 1q. REVISH is therefore ideally suited to characterize genetic changes specific for drug resistance within a background of genetic anomalies associated with tumour progression