VPMCD: variable interaction modeling approach for class discrimination in biological systems

Data classification algorithms applied for class prediction in computational biology literature are data specific and have shown varying degrees of performance. Different classes cannot be distinguished solely based on interclass distances or decision boundaries. We propose that inter-relations among the features be exploited for separating observations into specific classes. A new variable predictive model based class discrimination (VPMCD) method is described here. Three well established and proven data sets of varying statistical and biological significance are utilized as benchmark. The performance of the new method is compared with advanced classification algorithms. The new method performs better during different tests and shows higher stability and robustness. The VPMCD is observed to be a potentially strong classification approach and can be effectively extended to other data mining applications involving biological systems.     

Receiver bias for exaggerated signals in honeybees and its implications for the evolution of floral displays

Mechanistic models of animal signals posit the occurrence of biases on the part of receivers that could be potentially exploited by signallers. Such biases are most obvious when animals are confronted with exaggerated versions of signals they normally encounter. Signalling systems operating in plant-pollinator interactions are among the most highly coevolved, with plants using a variety of floral signals to attract pollinators. A number of observations suggest that pollinators preferentially visit larger floral displays although the benefit of this to either the plant or the pollinator is not always clear. We use a standard dual-choice experimental protocol to show that honeybees display a receiver bias for exaggerated size and colour contrast--two important components of floral signals--even when such signals do not indicate quality. We discuss the implications of this receiver bias for the evolution of floral displays and its possible exploitation by invading alien plants.     

Individuality,kin similarity and experimental playback of contact calls in cooperatively breeding riflemen

Riflemen/tītipounamu (Acanthisitta chloris) are kin-based cooperatively breeding birds, which appear able to recognise their relatives. Here, we investigate the potential for vocalisations to act as recognition cues in riflemen. We identified an appropriate contact call and recorded it at the nest from 19 adult riflemen. Measurements of call characteristics were individually repeatable. In addition, call similarity was significantly correlated with relatedness among all birds and among males. Thus, in principle, these contact calls contain sufficient information for individual recognition of familiar kin, and some assessment of relatedness between unfamiliar birds. To test whether riflemen responded differently to calls of kin, we broadcast calls of relatives and non-relatives as separate treatments in a playback experiment. Focal birds rarely responded aggressively or affiliatively, and their tendency to do so was unrelated to treatment. We conclude that zip calls are suitable kin recognition cues, but whether they are used as such remains unknown.     

Giant clams discriminate threats along a risk gradient and display varying habituation rates to different stimuli

It is often beneficial for animals to discriminate between different threats and to habituate to repeated exposures of benign stimuli. While much is known about risk perception in vertebrates and some invertebrates, risk perception in marine invertebrates is less extensively studied. One method to study risk perception is to habituate animals to a series of exposures to one stimulus, and then present a novel stimulus to test if it transfers habituation. Transfer of habituation is seen as a continued decrease in response while lack of transfer is seen either by having a similar or greater magnitude response. We asked whether giant clams (Tridacna maxima) discriminate between biologically relevant types of threats along a risk gradient. Giant clams retract their mantle and close their shell upon detecting a threat. While closed, they neither feed nor photosynthesize, and prior work has shown that the cost of being closed increases as the duration of their response increases. We recorded a clam's latency to emerge after simulated threats chosen to represent a risk gradient: exposure to a small shading event, a medium shading event, a large shading event (chosen to simulate fish swimming above them), tapping on their shell and touching their mantle (chosen to simulate different degrees of direct attack). Although these stimuli are initially perceived as threatening, we expected clams to habituate to them because they are ultimately non‐damaging and it would be costly for clams to remain closed for extended periods of time when there is no threat present. Clams had different initial latencies to emerge and different habituation rates to these treatments, and they did not transfer habituation to higher risk stimuli and to some lower risk stimuli. These results suggest that clams discriminated between these stimuli along a risk gradient and the lack of habituation transfer shows that the new stimulus was perceived as a potential threat. This study demonstrates that sessile bivalves can discern between levels of predatory threat. These photosynthetic clams may benefit from being able to categorize predator cues for efficient energy allocation.     

Effect of laterality discrimination on joint position sense and cervical range of motion in patients with chronic neck pain: a randomized single-blind clinical trial

Purpose: The main objective of the present study was to evaluate the effects of laterality discrimination training on neck joint position sense and cervical range of motion (ROM) in patients with chronic non-specific neck pain (NSCNP).

Materials and methods: Forty-eight patients with NSCNP were randomly assigned to the neck group (NG) that observed neck images or the foot group (FG) that observed foot images. Response time, response accuracy, cervical ROM, and joint position error (JPE) were the main variables. The secondary outcome measures included psychosocial variables.

Results: Differences between groups in the cervical ROM for flexion (p?=?.043) were obtained, being NG group the one which obtained greater values. NG showed an improvement in right rotation (p?=?.018) and a decrease in flexion was found in the FG (p?=?.039). In JPE, differences between groups were obtained in the left rotation (p?=?.021) and significant changes were found in the NG for flexion, extension, and left rotation movements (p?<?.05). Moderate associations were found between left and right accuracy regarding to post-intervention flexion and right rotation (r?=?0.46, r?=?0.41; p?<?.05) in NG.

Conclusion: Improvements in cervical range of motion and joint position sense are obtained after the performance of the laterality discrimination task of images of the neck but not the feet. Visualization of images of the painful region presents moderate correlations with the accuracy and response time in the movements of flexion and right rotation.     

The effect of the diameter of cyclic peptide nanotube on its chirality discrimination

In this work, the transport behaviors of the enantiomers of lactic acid (LA) in two cyclic peptide nanotubes (CPNTs) with different diameters were studied using steered molecular dynamic (SMD) simulation to investigate the effect of the diameter of CPNT on the discrimination of the enantiomers of LA. For this purpose, two cyclic peptides with two different sizes ([Ala-_D-Ala-_L]₅ and [Ala-_D-Ala-_L]₄) were used for constructing two CPNTs so that each CPNT was composed of eight cyclic peptide units. The docking calculations were performed to obtain the appropriate position of each enantiomer at the lumen of each CPNT. The variation of the pulling force versus time, exerted on the enantiomers moving in the CPNTs was calculated using the SMD simulations with two different strategies (positional and directional).The obtained results showed that the diameter of CPNT has considerable effect on the discrimination of the LA enantiomers so that the increase of the diameter of CPNT, increased the velocity difference between two enantiomers and improved the performance of CPNT for the chirality discrimination. The SMD simulations indicated that the velocity of S-enantiomer became more than R-enantiomer and its motion became more comfortable than R-enantiomer when the diameter of CNPT increased. The RDFs of the H and O atoms of the LA enantiomers relative to the O atoms of CPNT were calculated and it was found that the increase of the diameter of CPNT creates the significant changes in the RDFs of H1, H2 and H3 atoms of the enantiomers.     

NKG2D discriminates diverse ligands through selectively mechano‐regulated ligand conformational changes

Stimulatory immune receptor NKG2D binds diverse ligands to elicit differential anti‐tumor and anti‐virus immune responses. Two conflicting degeneracy recognition models based on static crystal structures and in‐solution binding affinities have been considered for almost two decades. Whether and how NKG2D recognizes and discriminates diverse ligands still remain unclear. Using live‐cell‐based single‐molecule biomechanical assay, we characterized the in situ binding kinetics of NKG2D interacting with different ligands in the absence or presence of mechanical force. We found that mechanical force application selectively prolonged NKG2D interaction lifetimes with the ligands MICA and MICB, but not with ULBPs, and that force‐strengthened binding is much more pronounced for MICA than for other ligands. We also integrated steered molecular dynamics simulations and mutagenesis to reveal force‐induced rotational conformational changes of MICA, involving formation of additional hydrogen bonds on its binding interface with NKG2D, impeding MICA dissociation under force. We further provided a kinetic triggering model to reveal that force‐dependent affinity determines NKG2D ligand discrimination and its downstream NK cell activation. Together, our results demonstrate that NKG2D has a discrimination power to recognize different ligands, which depends on selective mechanical force‐induced ligand conformational changes.     

Genetic information improves the prediction of major adverse cardiovascular events in the GENEMACOR population

The inclusion of a genetic risk score (GRS) can modify the risk prediction of coronary artery disease (CAD), providing an advantage over the use of traditional models. The predictive value of the genetic information on the recurrence of major adverse cardiovascular events (MACE) remains controversial. A total of 33 genetic variants previously associated with CAD were genotyped in 1587 CAD patients from the GENEMACOR study. Of these, 18 variants presented an hazard ratio >1, so they were selected to construct a weighted GRS (wGRS). MACE discrimination and reclassification were evaluated by C-Statistic, Net Reclassification Index and Integrated Discrimination Improvement methodologies. After the addition of wGRS to traditional predictors, the C-index increased from 0.566 to 0.572 (p=0.0003). Subsequently, adding wGRS to traditional plus clinical risk factors, this model slightly improved from 0.620 to 0.622 but with statistical significance (p=0.004). NRI showed that 17.9% of the cohort was better reclassified when the primary model was associated with wGRS. The Kaplan-Meier estimator showed that, at 15-year follow-up, the group with a higher number of risk alleles had a significantly higher MACE occurrence (p=0.011). In CAD patients, wGRS improved MACE risk prediction, discrimination and reclassification over the conventional factors, providing better cost-effective therapeutic strategies.