Dinosaur fossils predict body temperatures

Perhaps the greatest mystery surrounding dinosaurs concerns whether they were endotherms, ectotherms, or some unique intermediate form. Here we present a model that yields estimates of dinosaur body temperature based on ontogenetic growth trajectories obtained from fossil bones. The model predicts that dinosaur body temperatures increased with body mass from approximately 25 °C at 12 kg to approximately 41 °C at 13,000 kg. The model also successfully predicts observed increases in body temperature with body mass for extant crocodiles. These results provide direct evidence that dinosaurs were reptiles that exhibited inertial homeothermy.     

Imitation dynamics predict vaccinating behaviour

There exists an interplay between vaccine coverage, disease prevalence and the vaccinating behaviour of individuals. Moreover, because of herd immunity, there is also a strategic interaction between individuals when they are deciding whether or not to vaccinate, because the probability that an individual becomes infected depends upon how many other individuals are vaccinated. To understand this potentially complex interplay, a game dynamic model is developed in which individuals adopt strategies according to an imitation dynamic (a learning process), and base vaccination decisions on disease prevalence and perceived risks of vaccines and disease. The model predicts that oscillations in vaccine uptake are more likely in populations where individuals imitate others more readily or where vaccinating behaviour is more sensitive to changes in disease prevalence. Oscillations are also more likely when the perceived risk of vaccines is high. The model reproduces salient features of the time evolution of vaccine uptake and disease prevalence during the whole-cell pertussis vaccine scare in England and Wales during the 1970s. This suggests that using game theoretical models to predict, and even manage, the population dynamics of vaccinating behaviour may be feasible.     

Eye movements predict recollective experience

Previously encountered stimuli can bring to mind a vivid memory of the episodic context in which the stimulus was first experienced ("remembered" stimuli), or can simply seem familiar ("known" stimuli). Past studies suggest that more attentional resources are required to encode stimuli that are subsequently remembered than known. However, it is unclear if the attentional resources are distributed differently during encoding and recognition of remembered and known stimuli. Here, we record eye movements while participants encode photos, and later while indicating whether the photos are remembered, known or new. Eye fixations were more clustered during both encoding and recognition of remembered photos relative to known photos. Thus, recognition of photos that bring to mind a vivid memory for the episodic context in which they were experienced is associated with less distributed overt attention during encoding and recognition. The results suggest that remembering is related to encoding of a few distinct details of a photo rather than the photo as a whole. In turn, during recognition remembering may be trigged by enhanced memory for the salient details of the photos.     

Scoring function to predict solubility mutagenesis

Background  

Mutagenesis is commonly used to engineer proteins with desirable properties not present in the wild type (WT) protein, such as increased or decreased stability, reactivity, or solubility. Experimentalists often have to choose a small subset of mutations from a large number of candidates to obtain the desired change, and computational techniques are invaluable to make the choices. While several such methods have been proposed to predict stability and reactivity mutagenesis, solubility has not received much attention.     

Cytokine analysis to predict immunosuppression.

BACKGROUND: Recently, it has been realized that TH1/TH2 cytokine production offer the unique possibility to predict drug efficacy. However, there is still an incessant need to explore assay conditions and techniques of analyzing cytokines, which are specific and reliable for monitoring drug efficacy. METHODS: In this study we used the multiplex bead array technique to detect cytokines of TH1/TH2 cells in whole blood of heart transplanted (HTx) recipients. RESULTS: We found significantly different levels of cytokine expression in HTx recipients compared with cytokine levels in patients prior to HTx. Furthermore, particular cytokine levels were significantly decreased 2 h after drug dosing, compared with cytokine levels before dosing in mitogen-stimulated whole blood. CONCLUSIONS: Cytokine analysis with the multiplex array technique in mitogen-stimulated whole blood provides the possibility to predict immunosuppression.     

Computational methods to predict protein aggregation

In most cases, protein aggregation stems from the establishment of non-native intermolecular contacts. The formation of insoluble protein aggregates is associated with many human diseases and is a major bottleneck for the industrial production of protein-based therapeutics. Strikingly, fibrillar aggregates are naturally exploited for structural scaffolding or to generate molecular switches and can be artificially engineered to build up multi-functional nanomaterials. Thus, there is a high interest in rationalizing and forecasting protein aggregation. Here, we review the available computational toolbox to predict protein aggregation propensities, identify sequential or structural aggregation-prone regions, evaluate the impact of mutations on aggregation or recognize prion-like domains. We discuss the strengths and limitations of these algorithms and how they can evolve in the next future.     

Fixational eye movements predict visual sensitivity

During steady fixation, observers make small fixational saccades at a rate of around 1–2 per second. Presentation of a visual stimulus triggers a biphasic modulation in fixational saccade rate—an initial inhibition followed by a period of elevated rate and a subsequent return to baseline. Here we show that, during passive viewing, this rate signature is highly sensitive to small changes in stimulus contrast. By training a linear support vector machine to classify trials in which a stimulus is either present or absent, we directly compared the contrast sensitivity of fixational eye movements with individuals'' psychophysical judgements. Classification accuracy closely matched psychophysical performance, and predicted individuals'' threshold estimates with less bias and overall error than those obtained using specific features of the signature. Performance of the classifier was robust to changes in the training set (novel subjects and/or contrasts) and good prediction accuracy was obtained with a practicable number of trials. Our results indicate a tight coupling between the sensitivity of visual perceptual judgements and fixational eye control mechanisms. This raises the possibility that fixational saccades could provide a novel and objective means of estimating visual contrast sensitivity without the need for observers to make any explicit judgement.     

Electrical impedance measurements predict cellular transformation

Cellular transformation is the first step in cancer development. Two features of cellular transformation are proliferation in reduced serum and loss of contact inhibition. Electronic Cell-Substrate Impedance Sensing (ECIS) measurements have been used to measure cellular proliferation, cytotoxicity, apoptosis, and attachment. We have used impedance measurements to distinguish normal cells from cells transformed with a constitutively active chemokine receptor, CXCR2. CXCR2, a member of the G-protein coupled receptor (GPCR) family, is normally involved in cellular activation and migration, but a single amino acid substitution leads to constitutive activity. NIH3T3 cells were transformed with a constitutively active CXCR2 (D143V_CXCR2) and growth in reduced serum and foci formation were measured using established biological assays and compared to data from ECIS. The results of this study show that impedance measurements provide a quick and reliable way of measuring cellular transformation and provide real time assessment of transformed cellular parameters. Use of the ECIS system could allow a rapid screening of anti-cancer drugs that alter cellular transformation.     

Mathematical model to predict drivers' reaction speeds

Mental distractions and physical impairments can increase the risk of accidents by affecting a driver's ability to control the vehicle. In this article, we developed a linear mathematical model that can be used to quantitatively predict drivers' performance over a variety of possible driving conditions. Predictions were not limited only to conditions tested, but also included linear combinations of these tests conditions. Two groups of 12 participants were evaluated using a custom drivers' reaction speed testing device to evaluate the effect of cell phone talking, texting, and a fixed knee brace on the components of drivers' reaction speed. Cognitive reaction time was found to increase by 24% for cell phone talking and 74% for texting. The fixed knee brace increased musculoskeletal reaction time by 24%. These experimental data were used to develop a mathematical model to predict reaction speed for an untested condition, talking on a cell phone with a fixed knee brace. The model was verified by comparing the predicted reaction speed to measured experimental values from an independent test. The model predicted full braking time within 3% of the measured value. Although only a few influential conditions were evaluated, we present a general approach that can be expanded to include other types of distractions, impairments, and environmental conditions.     

Using body size to predict perceptual range

We examined the relationship between body size and perceptual range (the distance at which an animal can perceive landscape elements) for a group of forest-dwelling rodents. We used previously published data on orientation ability at various distances for three sciurid species (gray squirrel, fox squirrel and chipmunk) and one murid species (white-footed mouse) to build a predictive model. We found a significant positive relationship between perceptual range and body mass. Although this model was built using a 15.5 m high horizon, we used this relation to predict the perceptual range of root voles (3.9–4.3 m) orienting towards a 0.5 m high horizon which was consistent with other empirical work suggesting a value of something less than 5 m. This model illustrates a relationship between perceptual range and body size and can be used to develop starting points for future investigations of perceptual range for similar organisms.     

Phylogeny and species traits predict bird detectability

Avian acoustic communication has resulted from evolutionary pressures and ecological constraints. We therefore expect that auditory detectability in birds might be predictable by species traits and phylogenetic relatedness. We evaluated the relationship between phylogeny, species traits, and field‐based estimates of the two processes that determine species detectability (singing rate and detection distance) for 141 bird species breeding in boreal North America. We used phylogenetic mixed models and cross‐validation to compare the relative merits of using trait data only, phylogeny only, or the combination of both to predict detectability. We found a strong phylogenetic signal in both singing rates and detection distances; however the strength of phylogenetic effects was less than expected under Brownian motion evolution. The evolution of behavioural traits that determine singing rates was found to be more labile, leaving more room for species to evolve independently, whereas detection distance was mostly determined by anatomy (i.e. body size) and thus the laws of physics. Our findings can help in disentangling how complex ecological and evolutionary mechanisms have shaped different aspects of detectability in boreal birds. Such information can greatly inform single‐ and multi‐species models but more work is required to better understand how to best correct possible biases in phylogenetic diversity and other community metrics.