The organization of biological sequences into constrained and unconstrained parts determines fundamental properties of genotype–phenotype maps

Biological information is stored in DNA, RNA and protein sequences, which can be understood as genotypes that are translated into phenotypes. The properties of genotype–phenotype (GP) maps have been studied in great detail for RNA secondary structure. These include a highly biased distribution of genotypes per phenotype, negative correlation of genotypic robustness and evolvability, positive correlation of phenotypic robustness and evolvability, shape-space covering, and a roughly logarithmic scaling of phenotypic robustness with phenotypic frequency. More recently similar properties have been discovered in other GP maps, suggesting that they may be fundamental to biological GP maps, in general, rather than specific to the RNA secondary structure map. Here we propose that the above properties arise from the fundamental organization of biological information into ‘constrained'' and ‘unconstrained'' sequences, in the broadest possible sense. As ‘constrained'' we describe sequences that affect the phenotype more immediately, and are therefore more sensitive to mutations, such as, e.g. protein-coding DNA or the stems in RNA secondary structure. ‘Unconstrained'' sequences, on the other hand, can mutate more freely without affecting the phenotype, such as, e.g. intronic or intergenic DNA or the loops in RNA secondary structure. To test our hypothesis we consider a highly simplified GP map that has genotypes with ‘coding'' and ‘non-coding'' parts. We term this the Fibonacci GP map, as it is equivalent to the Fibonacci code in information theory. Despite its simplicity the Fibonacci GP map exhibits all the above properties of much more complex and biologically realistic GP maps. These properties are therefore likely to be fundamental to many biological GP maps.     

Stimuli-Responsive Nanocomposite Hydrogels for Biomedical Applications

The complex tissue-specific physiology that is orchestrated from the nano- to the macroscale, in conjugation with the dynamic biophysical/biochemical stimuli underlying biological processes, has inspired the design of sophisticated hydrogels and nanoparticle systems exhibiting stimuli-responsive features. Recently, hydrogels and nanoparticles have been combined in advanced nanocomposite hybrid platforms expanding their range of biomedical applications. The ease and flexibility of attaining modular nanocomposite hydrogel constructs by selecting different classes of nanomaterials/hydrogels, or tuning nanoparticle-hydrogel physicochemical interactions widely expands the range of attainable properties to levels beyond those of traditional platforms. This review showcases the intrinsic ability of hybrid constructs to react to external or internal/physiological stimuli in the scope of developing sophisticated and intelligent systems with application-oriented features. Moreover, nanoparticle-hydrogel platforms are overviewed in the context of encoding stimuli-responsive cascades that recapitulate signaling interplays present in native biosystems. Collectively, recent breakthroughs in the design of stimuli-responsive nanocomposite hydrogels improve their potential for operating as advanced systems in different biomedical applications that benefit from tailored single or multi-responsiveness.     

Improving Clairvoyant: reduction algorithm resilient to imbalanced process arrival patterns

The Journal of Supercomputing - The Clairvoyant algorithm proposed in “A novel MPI reduction algorithm resilient to imbalances in process arrival times” was analyzed, commented and...     

Measurement of Electrophysiological Signals In Vitro Using High-Performance Organic Electrochemical Transistors

Biological environments use ions in charge transport for information transmission. The properties of mixed electronic and ionic conductivity in organic materials make them ideal candidates to transduce physiological information into electronically processable signals. A device proven to be highly successful in measuring such information is the organic electrochemical transistor (OECT). Previous electrophysiological measurements performed using OECTs show superior signal-to-noise ratios than electrodes at low frequencies. Subsequent development has significantly improved critical performance parameters such as transconductance and response time. Here, interdigitated-electrode OECTs are fabricated on flexible substrates, with one such state-of-the-art device achieving a peak transconductance of 139 mS with a 138 µs response time. The devices are implemented into an array with interconnects suitable for micro-electrocorticographic application and eight architecture variations are compared. The two best-performing arrays are subject to the full electrophysiological spectrum using prerecorded signals. With frequency filtering, kHz-scale frequencies with 10 µV-scale voltages are resolved. This is supported by a novel quantification of the noise, which compares the gate voltage input and drain current output. These results demonstrate that high-performance OECTs can resolve the full electrophysiological spectrum and suggest that superior signal-to-noise ratios could be achieved in high frequency measurements of multiunit activity.     

Algorithmic Fairness in Mortgage Lending: from Absolute Conditions to Relational Trade-offs

Minds and Machines - To address the rising concern that algorithmic decision-making may reinforce discriminatory biases, researchers have proposed many notions of fairness and corresponding...     

Results of Studies on Strengthening Retaining Walls with Composite Materials

Power Technology and Engineering - The experimental results on retaining reinforced-concrete walls reinforced with anchor ties and carbon composite materials on the face side of hydraulic...     

The influence of sonication time on the biogenic amines formation as a critical point in uncured dry-fermented beef manufacturing

In this study, the influence of sonication time on the biogenic amines formation as a critical point in uncured dry-fermented beef manufacturing was studied. Samples of musculus semimembranosus were sonicated at different times (5 and 10 min) using ultrasound cold bath (4 °C) in acid whey (US 40 kHz and acoustic power 480 W). The effect of sonication on biogenic amine (BA) formation was investigated during 93 days of ripening period. Other parameters (pH value, water activity, microbial counts) that might provide further information on the product under study were also determined. The use of ultrasound during beef marinating in acid whey has a positive effect on retarding histamine (HIS), cadaverine (CAD), tyramine (TYR) and putrescine (PUT) formation. Moreover, the sonication treatment did not inhibit the growth of lactic acid bacteria (LAB) in dry-fermented beef during the whole ripening period. The pathogen bacteria (Staphylococcus aureus, Clostridium sp., Listeria monocytogenes) were not detected in all samples neither after 31 nor after 93 days of ripening period.