Conditioning of gray crows (Corvus cornix L.) in a "giant" eight-arm radial maze

Twelve adult hooded crows (Corvus cornix) were trained to perform a standard radial-maze task in a giant eight-arm outdoor radial maze constructed at the "Chistyi les" Biological Station (Tver oblast) for comparative investigations of spatial memory in birds and mammals. The maze consists of a central part of 250 cm diameter, and has arms of 650 cm length, 170 cm height and 80 cm width. The examined hooded crows showed good task performance. Errors (repeated visits to empty arms) were few in number and were predominantly connected with the tendency to avoid arms close to an observer.     

Autonomous choice in the learning process of a turtle Chinemys reevesii

We studied animal's learning of spatial discrimination in an experimental environment. Turtles, Chinemys reevesii, were employed for the study. We focused on two independent aspects: (1) turtle's success rate in the task, which is the most common criterion to estimate the ability of the animals, and (2) the statistical properties of the time interval of the task, which is independent on the spatial criterion. For a statistical analysis, we employed the scheme of power law distributions which was recently used to estimate animal behaviors in relation to the idea of the fractal. We addressed the basic problem of whether these two criteria, or any other criteria for this matter, could or could not exclude an observer who studies the animal behavior. To demonstrate inseparability of an observer and the object, we conducted three different learning experiments: (1) complete spatial discrimination, (2) incomplete spatial discrimination, (3) another, different, complete discrimination, in this order. The incomplete one was taken to mean incomplete only for an observer. Our experiments reveal that the same result (success rate) was perceived differently by the animal if the attitude of the observer to the experiments differed. This observation comes to suggest that the notion of autonomous choice on the part of an animal is contingent upon the inseparability between an observer and the object.     

The need for the correct choice of free ligand concentration in determining parameters of benzodiazepine binding

In the studies of 3H-diazepam binding to the rat brain membranes it has been shown that insufficiently high concentrations of free ligand might lead to incorrect determination of Bmax. Thus, free ligand concentration in the range of 0.5 to 16 nM (the most often used ones) and low receptor-protein concentrations (0.08 to 0.12 mg/sample) were far from being saturating and therefore could not be applied for the analysis in Scatchard coordinates. In this case Bmax value would be considerably below the true Bmax value. It has been concluded that for the determination of Bmax of 3H-benzodiazepine binding the range of concentrations used should be at least 0.25 to 64 nM.     

An improved machine learning protocol for the identification of correct Sequest search results

Background  

Mass spectrometry has become a standard method by which the proteomic profile of cell or tissue samples is characterized. To fully take advantage of tandem mass spectrometry (MS/MS) techniques in large scale protein characterization studies robust and consistent data analysis procedures are crucial. In this work we present a machine learning based protocol for the identification of correct peptide-spectrum matches from Sequest database search results, improving on previously published protocols.     

First total synthesis of WLIP: on the importance of correct protecting group choice

Cyclic lipodepsipeptides (CLPs) are a group of metabolites produced by Pseudomonas bacteria, involved in various biological functions and displaying a wide range of properties, including antibacterial and antifungal activities. The white line‐inducing principle (WLIP) is a member of the viscosin group featuring a Glu2 amino acid. Recently, a total synthesis of pseudodesmin A – the Gln2 counterpart of WLIP – was described, and we here expand this route to Glu2 containing CLPs. We report the first total synthesis of WLIP and at the same time establish that the Gln2 to Glu2 substitution has an adverse impact on the crude purity and overall yield. A comparative study of different CLP analogues reveals the importance of the nature of the Glx2 protecting group in determining these outcomes. Replacement of the conventional tBu protecting group by the larger benzyl group for the Glu residue in our synthesis strategy indeed resulted in an improved conversion. Next to achieving the first WLIP total synthesis, we thus show the importance of a careful choice of protecting groups for the success of this type of solid‐phase synthesis approaches towards CLPs. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd.     

Comparison of the choice effect and the distance effect in a number-comparison task by FMRI

Behavioral and neurophysiological studies of numerical comparisons have shown a "distance effect," whereby smaller numerical distances between two digits are associated with longer response times and higher activity in the parietal region. In this experiment, we introduced a two-choice condition (between either the smaller/lower or the larger/higher of two digits) and examined its effect on brain activity by fMRI. We observed longer response times and greater activity with the choice of smaller numbers ("choice effect") in several brain regions including the right temporo-parietal region, (pre)cuneus, superior temporal sulcus, precentral gyrus, superior frontal gyrus, bilateral insula, and anterior cingulate cortex. These regions correspond to areas that have been suggested to play a role in attentional shift and response conflict. However, brain activity associated with the distance effect disappeared even though the behavioral distance effect remained. Despite the absence of the distance effect on brain activity, several areas changed activity in relation to response time, including regions that were reported to change activity in both a distance effect and a reaction-time-related manner. The result suggested that the level of task load may change the activity of regions that are responsible for magnitude detection.     

Minimal cross-trial generalization in learning the representation of an odor-guided choice task

There is no single way to represent a task. Indeed, despite experiencing the same task events and contingencies, different subjects may form distinct task representations. As experimenters, we often assume that subjects represent the task as we envision it. However, such a representation cannot be taken for granted, especially in animal experiments where we cannot deliver explicit instruction regarding the structure of the task. Here, we tested how rats represent an odor-guided choice task in which two odor cues indicated which of two responses would lead to reward, whereas a third odor indicated free choice among the two responses. A parsimonious task representation would allow animals to learn from the forced trials what is the better option to choose in the free-choice trials. However, animals may not necessarily generalize across odors in this way. We fit reinforcement-learning models that use different task representations to trial-by-trial choice behavior of individual rats performing this task, and quantified the degree to which each animal used the more parsimonious representation, generalizing across trial types. Model comparison revealed that most rats did not acquire this representation despite extensive experience. Our results demonstrate the importance of formally testing possible task representations that can afford the observed behavior, rather than assuming that animals’ task representations abide by the generative task structure that governs the experimental design.     

The effect of competition on choice by pigeons: foraging rate,resource availability and learning

The effect of competition on food choice by pigeons was examined in a within-subject laboratory study. Pigeons foraged on maize (the more preferred item) and wheat (the less preferred item) in two conditions: alone and with a competitor. Over the course of the experiment an effect of competition on individual choice developed: the pigeons came to choose less maize before the first grain of wheat was taken, and to show a higher proportion of choices of wheat. The effect of competition was entirely due to resource availability: no effect of the competitor per se was found once the number of grains of maize and wheat available for any one choice was taken into account. Choice behaviour changed over time because the birds learned to forage faster in competition, which in turn led to faster depletion rates.     

Effect of a learning trial on self-selected resistance training load

Previous research has shown that individuals self-select loads for resistance training that falls below the accepted threshold for overload and do not lift to volitional fatigue. The purpose of this study was to determine the effects of a resistance training learning trial on self-selected resistance training load. A control group (5 women, 3 men) and a learning group of (4 women, 4 men) novice lifters were recruited. The control group (CG) received an orientation to selected strength machines (seated bench, leg extension, back row, biceps curl, triceps extension, shoulder press). On a subsequent training day, CG self-selected a training load, while blinded to the actual loads. The learning group (LG) received an initial orientation and also was tested for estimated 1 repetition maximum (1RM) for the seated bench press. On a subsequent day, the LG completed 2 sets of the seated bench press at 75% of estimated 1RM and were encouraged to lift until failure. On a third day, LG subjects completed a self-selected trial identical to that of the CG. Both groups were assessed for estimated 1RM for each exercise on a separate day following all trials. Comparisons between CG and LG were made using independent-means t tests and adjusted using Bonferroni's equation (p < 0.01). While subjects selected a bench press load that was 21% greater for LG (63.4 +/- 6.4% 1RM) compared to the CG (50.3 +/- 12.0%), there was no statistical significance. There were no significant differences in self-selected load for any of the other exercises. There were also no significant differences for number of repetitions or rate of perceived exertion between groups. We conclude that a learning trial of the bench press exercise to increase self-selected workload is not enough to change load self-selection.     

Disease-mediated inbreeding depression in a large,open population of cooperative crows

Disease-mediated inbreeding depression is a potential cost of living in groups with kin, but its general magnitude in wild populations is unclear. We examined the relationships between inbreeding, survival and disease for 312 offspring, produced by 35 parental pairs, in a large, open population of cooperatively breeding American crows (Corvus brachyrhynchos). Genetic analyses of parentage, parental relatedness coefficients and pedigree information suggested that 23 per cent of parental dyads were first- or second-order kin. Heterozygosity–heterozygosity correlations suggested that a microsatellite-based index of individual heterozygosity predicted individual genome-wide heterozygosity in this population. After excluding birds that died traumatically, survival probability was lower for relatively inbred birds during the 2–50 months after banding: the hazard rate for the most inbred birds was 170 per cent higher than that for the least inbred birds across the range of inbreeding index values. Birds that died with disease symptoms had higher inbreeding indices than birds with other fates. Our results suggest that avoidance of close inbreeding and the absence of inbreeding depression in large, open populations should not be assumed in taxa with kin-based social systems, and that microsatellite-based indices of individual heterozygosity can be an appropriate tool for examining the inbreeding depression in populations where incest and close inbreeding occur.     

SeqCor: correct the effect of guide RNA sequences in clustered regularly interspaced short palindromic repeats/Cas9 screening by machine learning algorithm

Clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9-based screening using various guide RNA (gRNA) libraries has been executed to identify functional components for a wide range of phenotypes with regard to numerous cell types and organisms. Using data from public CRISPR/Cas9-based screening experiments, we found that the sequences of gRNAs in the library influence CRISPR/Cas9-based screening. As building a standard strategy for correcting results of all gRNA libraries is impractical, we developed SeqCor, an open-source programming bundle that enables researchers to address the result bias potentially triggered by the composition of gRNA sequences via the organization of gRNA in the library used in CRISPR/Cas9-based screening. Furthermore, SeqCor completely computerizes the extraction of sequence features that may influence single-guide RNA knockout efficiency using a machine learning approach. Taken together, we have developed a software program bundle that ought to be beneficial to the CRISPR/Cas9-based screening platform.     

Counterfactual choice and learning in a neural network centered on human lateral frontopolar cortex

Decision making and learning in a real-world context require organisms to track not only the choices they make and the outcomes that follow but also other untaken, or counterfactual, choices and their outcomes. Although the neural system responsible for tracking the value of choices actually taken is increasingly well understood, whether a neural system tracks counterfactual information is currently unclear. Using a three-alternative decision-making task, a Bayesian reinforcement-learning algorithm, and fMRI, we investigated the coding of counterfactual choices and prediction errors in the human brain. Rather than representing evidence favoring multiple counterfactual choices, lateral frontal polar cortex (lFPC), dorsomedial frontal cortex (DMFC), and posteromedial cortex (PMC) encode the reward-based evidence favoring the best counterfactual option at future decisions. In addition to encoding counterfactual reward expectations, the network carries a signal for learning about counterfactual options when feedback is available-a counterfactual prediction error. Unlike other brain regions that have been associated with the processing of counterfactual outcomes, counterfactual prediction errors within the identified network cannot be related to regret theory. Furthermore, individual variation in counterfactual choice-related activity and prediction error-related activity, respectively, predicts variation in the propensity to switch to profitable choices in the future and the ability to learn from hypothetical feedback. Taken together, these data provide both neural and behavioral evidence to support the existence of a previously unidentified neural system responsible for tracking both counterfactual choice options and their outcomes.     

Dynamic properties of the advertisement calls of gray tree frogs: patterns of variability and female choice

We assessed the potential for several acoustic properties ofthe advertisement calls of male gray tree frogs to affect relativemating success by relating patterns of variation in these propertiesto minimum differences required to elicit female choice. Dynamicproperties (pulse number, PN; call rate, CR; and duty cycle,DC, the ratio of call duration to call period) varied much morewithin bouts of calling than a static property (dominant frequency,DF) but nevertheless exhibited significant between male variationin three of four breeding seasons. Many multiply recorded malesconsistently produced calls with values substantially aboveor below mean values of males recorded on the same nights. Nightlyranges of variation in PN and CR were often greater than theminimum differences required to elicit female preferences inthe laboratory. In most experiments, females chose high-PN orfast-CR calls over low-PN or slow-CR alternatives, respectively,even if the preferred stimuli were farther away or 6-10 dB lowerin sound pressure level (SPL), provided that differences inPN or CR were 100%. Consistent with these results, females didnot always choose the closer of two calling males in the field.Nightly ranges of variation in DF rarely equaled the minimumdifference required to elicit SPL independent preferences. Femalespreferred a stimulus of high-PN and slow-CR over an alternativeof low-PN or fast-CR with the same acoustic on-time; in twoexperiments, females chose calls of high-PN over low-PN alternativeseven though the playback of the high-PN call was interruptedand the low-PN call was broadcast continuously. Thus, femalepreferences were not merely based on the total time of acousticstimulation. Responses of females tested twice in the same experimentsuggest that phenotypic variation in preference was limitedin our study populations.     

Performance prediction of deep learning applications training in GPU as a service systems

Cluster Computing - Data analysts predict that the GPU as a service (GPUaaS) market will grow to support 3D models, animated video processing, gaming, and deep learning model training. The main...     

Helpers at the nest compensate for reduced maternal investment in egg size in carrion crows

Life history theory predicts that mothers should trade off current and future reproductive attempts to maximize lifetime fitness. When breeding conditions are favourable, mothers may either increase investment in the eggs to improve the quality of the offspring or save resources for future reproduction as the good raising environment is likely to compensate for a 'bad start'. In cooperatively breeding birds, the presence of helpers improves breeding conditions so that mothers may vary the number, size and quality of the eggs in response to the composition of the group. Here, we show that in cooperatively breeding carrion crows Corvus corone corone, where nonbreeding males are more philopatric and more helpful at the nest than females, breeding females decreased egg size as the number of subordinate males in the group increased. However, despite the smaller investment in egg size, fledglings' weight increased in groups with more male subordinates, improving post-fledging survival and indicating that helpers fully compensated for the initial 'bad start'. These results highlight a 'hidden effect' of helpers that bears profound implications for understanding the ultimate function of helping.     

Discontinuous and incremental processes in the song learning of birds: evidence for a primer effect

Studies on the song learning in birds revealed a puzzling property of the acquisition system: Stimulus memorization becomes effective after remarkably few exposures, but nevertheless shows a relationship to the frequency of exposure to learning stimuli. This raises questions on the amount of learning that will occur during a given exposure to song. To examine this issue, we tutored handraised fledgling nightingales (Luscinia megarhynchos) with song strings, in which the serial succession of species-typical master songs was altered upon subsequent exposures. The sequencing of imitations obtained from the birds' adult singing revealed the following results: (1) A single exposure was sufficient for subjects to acquire serial information on song-type sequencing. (2) The first exposure to a master string played a key role for this accomplishment. (3) Nevertheless, the acquisition of serial information improved with increasing exposure frequency of master strings. (4) The acquisition of song patterns was not impaired by a non-regular presentation of master song-types. With respect to the particular salience of the first exposure for sequence memorization, we termed the phenomenon primer effect. The findings suggest that stimulus acquisition during perceptual song learning is mediated by a discontinuous process. Once acquired, information is then consolidated gradually, i.e. through an incremental process.