CM 55

QTL IciMapping is integrated software for linkage map construction and QTL detection. QEI mapping has been implemented in version 4.0 of the software as the MET functionality [37 ]. In this study, unlinked and linked QTL models were both considered to evaluate the efficiency of QEI mapping. The genome consisted of six chromosomes, each of 150 cM in length with 16 evenly distributed markers. Two environments were considered with equal heritability in the broad sense in both models. In the unlinked QTL model, five QTL were located on five chromosomes, and the broad sense heritability was 0.5 for both environments. QTL additive effects in the two environments were given in Table 3, representing three QEI levels, i.e., strong interaction (Q2), environment-specific interaction (Q3 and Q4) and no interaction (Q1 and Q5).
Eight QTL effect scenarios were considered for two linked QTL (Table 4), i.e., Q1 and Q2, located at 25 and 55 cM on chromosome 1. These scenarios represented different QEI levels and linkage phases (coupling or repulsion phases). For example, Q1 and Q2 had strong QEI, and they were linked in the coupling phase in model L3, and in the repulsion phase in model L7. Three levels of heritability were considered, i.e., H² = 0.1, H² = 0.5 and H² = 0.8.
One thousand DH populations, each of a size of 200, were generated for unlinked model (S3 File) and for each effect scenario of the two linked QTL under each heritability level (S4–S6 Files). The LOD threshold was set at 3.11 by empirical formula to ensure the genome-wide Type-I error rate (α_g) to be less than 0.05. The scanning step was set at 1 cM. The two probabilities for entering and removing variables in stepwise regression were set at 0.001 and 0.002.
Detection power and FDR were used to evaluate the efficiency of QEI mapping. Each predefined QTL was assigned to a support interval of 10 cM centered at the predefined location. Power of each QTL was calculated as the percentage of the simulation runs having significant peaks higher than the LOD threshold in its support interval. QTL identified but out of this interval were treated as false positives. FDR was calculated as the ratio of the number of false positives to the total number of significant discovery [26 ,38 (link)]. For each genetic model, estimated positions and effects were calculated as the average values of all detected QTL.

The WAZM is a transformation of the elevated zero maze (EZM) to an integrated wet and dry context. This novel apparatus is constructed from an annular platform (90 cm diameter; 10 cm width), made out of black plywood, joined to a plastic tank (70 cm diameter, 55 cm deep) elevating it 55 cm above the ground. The annular platform has two opposite, enclosed quadrants (with walls 35 cm height) and two open quadrants (with borders 5 mm height). The plastic tank that holds this platform is filled up with water (22 ± 2°C, 50 cm deep), arising to 10 cm below the platform level. Thus, the annular platform and the plastic tank comprise one unified arena (Figure 1). For the tests, rats were first habituated to the room for 4 min and then were placed into one of the open quadrants facing a closed part of the apparatus. Rats were allowed to explore the arena for a 5 mins session. During this time rats behavior was tracked, recorded and analyzed by the Etho-Vision system (Noldus Information Technology, Wageningen, Netherlands). Behavioral measures that were analyzed include the time spent in the open quadrants, distance traveled in the open quadrants, distance traveled in the closed quadrants and total freezing behavior.

During their first and second visits infants were administered a face preference task very similar to that reported by [28] . Looking behaviour was recorded with a Tobii eye tracker. The Tobii system has an infrared light source and a camera mounted below a 17 in. flat-screen monitor to record corneal reflection data. The Tobii system measures the gaze direction of each eye separately and from these measurements evaluates where on the screen the individual is looking. During the eye tracker tasks the child is seated on his/her caregivers lap, at 50–55 centimeters from the Tobii screen. The height and distance of the screen are adjusted for each child to obtain good tracking of the eyes. First a five-point calibration sequence is run, with recording only started when at least four points are marked as properly calibrated for each eye. Gaze data were recorded at 50 Hz.
In the present task, 14 different arrays, each with five stimuli, were presented (see Fig. 1 for an example). Each array contained a colour image of one of fourteen different faces with direct gaze used as the target. Different exemplars from each of the following categories: mobile phones, birds, and cars were also included in the array. Another stimulus was a visual ‘noise’ image, generated from the same face presented within the array, by randomizing the phase spectra of the faces whilst keeping the amplitude and colour spectra constant [33] (link). The slides were counterbalanced for gender, ethnicity, and vertical and horizontal location of the face within the array. To verify that faces were similar to other categories in terms of visual saliency, saliency ranks were calculated for each area of interest on all 14 slides using the Saliency Toolbox 2.2 [63] (link).2 Categories had very similar average saliency ranks. When placed at a distance of 55 cm from the child the five individual images on the slide had an eccentricity of 9.3° and covered an approximate area of 5.2° × 7.3°.
Before each slide a small animation was presented in the center of the screen to ensure that the children's gaze was directed to the centre. Each slide presentation lasted 15 s. To assist in maintaining the children's attention, the visual presentation was accompanied by music. If the child stopped looking at the slide one of the experimenters prompted the infant to look at the screen again, without naming or referring to any of the stimuli. When the infant looked away for more than 5 s, the experimenter terminated presentation of the given slide. Rectangular AOIs were defined around each object image and the center of the screen using Tobii Studio software. Gaze data were extracted for each AOI: centre, face, noise, car, bird, phone, and total (the entire slide).

The experiment was conducted on a ThinkPad (ThinkBook Plus 17) laptop running Windows 10. Visual stimuli were created using MATLAB R2016a (MathWorks, Natick, MA) and Psychtoolbox 3.0 software. Stimuli were presented on a 17-inch monitor with a resolution of 3,072 × 1,440 pixels and a refresh rate of 120 Hz. Individual participants were seated ~ 55 cm in front of the monitor of the laptop and were tested individually in a quiet room. The entire experiment consisted of 30 trials in two blocks separated by a 3-min rest period (total, ~ 12 min). Before the start of the formal session, the participants completed six practice trials to ensure that they were familiar with the procedure. At the beginning of each test block, the instruction “press the left mouse button to start the task” was presented on the screen. In each trial, a white fixation symbol (+) was displayed in the center of a gray background (visual field, 37.98 × 21.0°) for 2,000 ms, followed by the presentation of 10 white-field circles (0.65 diameter) for 1,000 ms. Four filled circles were highlighted blue and flickered three times for a total of 3 s to mark them as the targets. Thereafter, the target circles returned to white so that no cue remained to discriminate them from the untracked items (distractors). Next, the 10 filled circles moved in random directions at a constant speed of 10°/s, with the movement of each circle affected only by collisions (The dots changed their directions randomly when they reached the edge of the screen border. There were no extra constraints in the dots’ trajectories hence there was the possibility that they crossing each other for an instant). After 8 s, the filled circles stopped moving. The participants were instructed to identify the targets by pressing a mouse button (Figure 1). Their responses also triggered the start of the next trial. The tracking accuracy recorded with all other study data in MATLAB R2016a (The Math Works).

DFRC was performed according to the original protocol (13 (link), 58 , 73 ). MWLs (30-mg scale) and DHPs (20-mg scale) were examined, and two replicates (n = 2) were used. The degradation products were analyzed by GC-MS (Shimadzu GC-2010 with mass spectrometer: GCMS-QP2010 Plus) fitted with a fused silica high-temperature capillary column [Phenomenex Zebron ZB-5HT Inferno Column, 15 m, 0.25 mm inside diameter (ID), 0.25-μm film thickness (d_f)]. An aliquot of the product solution (1 μl) was injected at a split ratio of 20:1. Helium was used as the carrier gas at a linear velocity of 55 cm/s. The oven was heated from 100°C and held for 1 min, then ramped at 10°C/min to 300°C, and held for 15 min at that temperature. The injector was set at 250°C, and the transfer line was kept at 300°C. The acetylated DFRC standard compounds were prepared and identified on the basis of their mass spectra and relative retention times and quantified using acetylated 1,1-bis-(4-hydroxyphenyl)ethane (BPO), 1,1-bis-(4-acetoxyphenyl)ethane (BPA), as an internal standard. The ratios for the components were calculated using the peak areas for each batch and used the response factors.

Zebrafish were released into an arena with one half of the tank surrounded by white corrugated plastic and the other half black corrugated plastic. Preference for either zone was calculated by cumulative time spent in each zone. Decreased time spent in the black zone was considered indicative of decreased anxiety. When the fish were released into the arena, the net was placed facing the long axis of the testing arena at the line dividing the black and white zones, to avoid biasing the fish to either side of the arena. The light/dark arena was 9.4 cm wide by 55 cm long and 9.5 cm deep and was filled to a water depth of 5 cm. The arena walls were surrounded by white and black corrugated plastic placed against the clear Plexiglas walls. White non-reflective corrugated plastic was attached to the bottom of the arena to provide contrast between the fish and the background (Fig. 1B). Each day, the arena was rotated 180 degrees after half of the fish had been tested to eliminate bias resulting from external visual stimuli due to the orientation of the arena. The light/dark test consisted of 5-min trials. Behaviours examined for analysis were duration of time spent in defined zones (light and dark half of the tank), average velocity, and time spent immobile.