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1.  Spatial Memory During Progressive Disorientation 
Human spatial representations of object locations in a room-sized environment were probed for evidence that the object locations were encoded relative not just to the observer (egocentrically) but also to each other (allocentrically). Participants learned the locations of 4 objects and then were blindfolded and either (a) underwent a succession of 70° and 200° whole-body rotations or (b) were fully disoriented and then underwent a similar sequence of 70° and 200° rotations. After each rotation, participants pointed to the objects without vision. Analyses of the pointing errors suggest that as participants lost orientation, represented object directions generally “drifted” off of their true directions as an ensemble, not in random, unrelated directions. This is interpreted as evidence that object-to-object (allocentric) relationships play a large part in the human spatial updating system. However, there was also some evidence that represented object directions occasionally drifted off of their true directions independently of one another, suggesting a lack of allocentric influence. Implications regarding the interplay of egocentric and allocentric information are considered.
PMCID: PMC2883724  PMID: 18444759
spatial representation; egocentric–allocentric frames of reference; spatial updating
2.  Use of Self-to-object and Object-to-object Spatial Relations in Locomotion 
Eight experiments examined the use of representations of self-to-object or object-to-object spatial relations during locomotion. Participants learned geometrically regular or irregular layouts of objects while standing at the edge or in the middle, and then pointed to objects while blindfolded in three conditions: before turning (baseline), after rotating 240 degrees (updating), and after disorientation (disorientation). The internal consistency of pointing in the disorientation condition was equivalent to that in the updating condition when participants learned the regular layout. The internal consistency of pointing was disrupted by disorientation when participants learned the irregular layout. However when participants who learned the regular layout were instructed to use self-to-object spatial relations, the effect of disorientation on pointing consistency appeared. When participants who learned the irregular layout at the periphery of the layout were instructed to use object-to-object spatial relations, the effect of disorientation disappeared. These results suggest that people represent both self-to-object and object-to-object spatial relations, and primarily use object-to-object spatial representation in a regular layout and self-to-object spatial representation in an irregular layout.
PMCID: PMC2774707  PMID: 19686010
self-to-object spatial relations; object-to-object spatial relations; spatial updating; disorientation
3.  Retrieving Enduring Spatial Representations after Disorientation 
Cognition  2012;124(2):143-155.
Four experiments tested whether there are enduring spatial representations of objects’ locations in memory. Previous studies have shown that under certain conditions the internal consistency of pointing to objects using memory is disrupted by disorientation. This disorientation effect has been attributed to an absence of or to imprecise enduring spatial representations of objects’ locations. Experiment 1 replicated the standard disorientation effect. Participants learned locations of objects in an irregular layout and then pointed to objects after physically turning to face an object and after disorientation. The expected disorientation was observed. In Experiment 2, after disorientation, participants were asked to imagine they were facing the original learning direction and then physically turned to adopt the test orientation. In Experiment 3, after disorientation, participants turned to adopt the test orientation and then were informed of the original viewing direction by the experimenter. A disorientation effect was not observed in Experiment 2 or 3. In Experiment 4, after disorientation, participants turned to face the test orientation but were not told the original learning orientation. As in Experiment 1, a disorientation effect was observed. These results suggest that there are enduring spatial representations of objects’ locations specified in terms of a spatial reference direction parallel to the learning view, and that the disorientation effect is caused by uncertainty in recovering the spatial reference direction relative to the testing orientation following disorientation.
PMCID: PMC3395066  PMID: 22682765
4.  Egocentric Representation Acquired from Offline Map Learning 
PLoS ONE  2013;8(3):e60194.
It is widely accepted that people establish allocentric spatial representation after learning a map. However, it is unknown whether people can directly acquire egocentric representation after map learning. In two experiments, the participants learned a distal environment through a map and then performed the egocentric pointing tasks in that environment under three conditions: with the heading aligned with the learning perspective (baseline), after 240° rotation from the baseline (updating), and after disorientation (disorientation). Disorientation disrupted the internal consistency of pointing among objects when the participants learned the sequentially displayed map, on which only one object name was displayed at a time while the location of “self” remained on the screen all the time. However, disorientation did not affect the internal consistency of pointing among objects when the participants learned the simultaneously displayed map. These results suggest that the egocentric representation can be acquired from a sequentially presented map.
PMCID: PMC3610764  PMID: 23555922
5.  Transient and enduring spatial representations under disorientation and self-rotation 
Current theories of environmental cognition typically differentiate between an online, transient, and dynamic system of spatial representation and an offline and enduring system of memory representation. Here we present additional evidence for such two-system theories in the context of the disorientation paradigm introduced by Wang and Spelke (2000). Several experiments replicate the finding that disorientation results in a decrease in the precision of people’s estimates of relative directions. In contrast to the typical interpretation of this effect as indicating the primacy of a transient spatial system, our results are generally more consistent with an interpretation of it as indicating a switch from a relatively precise online representation to a relatively coarse enduring one. Further experiments examine the relative precision of transient and enduring representations, and show that switching between them does not require disorientation, but can also be produced by self-rotations as small as 135°.
PMCID: PMC1501085  PMID: 16822154
Spatial representation; spatial memory; egocentric updating; spatial updating; cognitive maps
6.  Misperception of exocentric directions in auditory space 
Acta psychologica  2008;129(1):72-82.
Previous studies have demonstrated large errors (over 30°) in visually perceived exocentric directions (the direction between two objects that are both displaced from the observer’s location; e.g., Philbeck et al., in press). Here, we investigated whether a similar pattern occurs in auditory space. Blindfolded participants either attempted to aim a pointer at auditory targets (an exocentric task) or gave a verbal estimate of the egocentric target azimuth. Targets were located at 20° to 160° azimuth in the right hemispace. For comparison, we also collected pointing and verbal judgments for visual targets. We found that exocentric pointing responses exhibited sizeable undershooting errors, for both auditory and visual targets, that tended to become more strongly negative as azimuth increased (up to −19° for visual targets at 160°). Verbal estimates of the auditory and visual target azimuths, however, showed a dramatically different pattern, with relatively small overestimations of azimuths in the rear hemispace. At least some of the differences between verbal and pointing responses appear to be due to the frames of reference underlying the responses; when participants used the pointer to reproduce the egocentric target azimuth rather than the exocentric target direction relative to the pointer, the pattern of pointing errors more closely resembled that seen in verbal reports. These results show that there are similar distortions in perceiving exocentric directions in visual and auditory space.
PMCID: PMC2614239  PMID: 18555205
manual pointing; auditory space perception; perception / action; perceived direction; spatial cognition
7.  Geometric cues influence head direction cells only weakly in non-disoriented rats 
The influential hypothesis that environmental geometry is critical for spatial orientation has been extensively tested behaviorally, and yet findings have been conflicting. Head direction (HD) cells, the neural correlate of the “sense of direction”, offer a window into the processes underlying directional orientation, and may help clarify the issue. In the present study, HD cells were recorded as rats foraged in enclosures of varying geometry, with or without simultaneous manipulation of landmarks and self-motion cues (path integration). All geometric enclosures had single-order rotational symmetry and thus completely polarized the environment. They also had unique features, such as corners, which could, in principle, act like landmarks. Despite these strongly polarizing geometric cues, HD cells in non-disoriented rats never rotated with these shapes. By contrast, when a cue card (white or grey) was added to one wall, HD cells readily rotated with the enclosure. When path integration was disrupted by disorienting the rat, HD cells now did rotate with the enclosure even without the landmark. Collectively these findings indicate that geometry exerts little or no influence on heading computations in non-disoriented rats, but it can do so in disoriented rats. We suggest that geometric processing is only a weak influence, providing a backup system for heading calculations and being recruited only under conditions of disorientation.
PMCID: PMC3242014  PMID: 22049411
geometry; head direction cells; navigation; orientation; path integration; landmarks
8.  Multiple Motor Learning Strategies in Visuomotor Rotation 
PLoS ONE  2010;5(2):e9399.
When exposed to a continuous directional discrepancy between movements of a visible hand cursor and the actual hand (visuomotor rotation), subjects adapt their reaching movements so that the cursor is brought to the target. Abrupt removal of the discrepancy after training induces reaching error in the direction opposite to the original discrepancy, which is called an aftereffect. Previous studies have shown that training with gradually increasing visuomotor rotation results in a larger aftereffect than with a suddenly increasing one. Although the aftereffect difference implies a difference in the learning process, it is still unclear whether the learned visuomotor transformations are qualitatively different between the training conditions.
Methodology/Principal Findings
We examined the qualitative changes in the visuomotor transformation after the learning of the sudden and gradual visuomotor rotations. The learning of the sudden rotation led to a significant increase of the reaction time for arm movement initiation and then the reaching error decreased, indicating that the learning is associated with an increase of computational load in motor preparation (planning). In contrast, the learning of the gradual rotation did not change the reaction time but resulted in an increase of the gain of feedback control, suggesting that the online adjustment of the reaching contributes to the learning of the gradual rotation. When the online cursor feedback was eliminated during the learning of the gradual rotation, the reaction time increased, indicating that additional computations are involved in the learning of the gradual rotation.
The results suggest that the change in the motor planning and online feedback adjustment of the movement are involved in the learning of the visuomotor rotation. The contributions of those computations to the learning are flexibly modulated according to the visual environment. Such multiple learning strategies would be required for reaching adaptation within a short training period.
PMCID: PMC2827554  PMID: 20195373
9.  Sex-specific asymmetries in communication sound perception are not related to hand preference in an early primate 
BMC Biology  2008;6:3.
Left hemispheric dominance of language processing and handedness, previously thought to be unique to humans, is currently under debate. To gain an insight into the origin of lateralization in primates, we have studied gray mouse lemurs, suggested to represent the most ancestral primate condition. We explored potential functional asymmetries on the behavioral level by applying a combined handedness and auditory perception task. For testing handedness, we used a forced food-grasping task. For testing auditory perception, we adapted the head turn paradigm, originally established for exploring hemispheric specializations in conspecific sound processing in Old World monkeys, and exposed 38 subjects to control sounds and conspecific communication sounds of positive and negative emotional valence.
The tested mouse lemur population did not show an asymmetry in hand preference or in orientation towards conspecific communication sounds. However, males, but not females, exhibited a significant right ear-left hemisphere bias when exposed to conspecific communication sounds of negative emotional valence. Orientation asymmetries were not related to hand preference.
Our results provide the first evidence for sex-specific asymmetries for conspecific communication sound perception in non-human primates. Furthermore, they suggest that hemispheric dominance for communication sound processing evolved before handedness and independently from each other.
PMCID: PMC2266901  PMID: 18199316
10.  Orientation and disorientation in aviation 
On the ground, the essential requirement to remain orientated is a largely unconscious activity. In flight, orientation requires a conscious effort by the pilot particularly when the visual environment becomes degraded and a deceptive force environment becomes the frame of reference. Furthermore, an unusual force environment can determine the apparent location of objects within a limited visual scene, sometimes with disastrous consequences. This review outlines the sources of pilot disorientation that arise from the visual and force environment of flight and their interaction. It challenges the value of the traditional illusion-based approach to the subject both to aircrew and to surveys of disorientation. Also, it questions the emphasis on the shortcomings of vestibular function as the physiological basis for disorientation. While military accidents from all causes have shown a decline, there has been no corresponding reduction in accidents involving disorientation, 85% of which are the results of unrecognised disorientation. This finding has implications for the way in which pilots are taught about disorientation in the interest of enhanced flight safety. It argues for a greater use of conventional fixed base simulators to create disorientating scenarios rather than complex motion devices to create unusual sensations.
PMCID: PMC3710190  PMID: 23849216
Spatial disorientation; Somatogravic; Oculogravic; Vestibular system; Aircraft accidents
11.  Dynamic modulation of cerebellar excitability for abrupt, but not gradual visuomotor adaptation 
The cerebellum is critically important for error driven adaptive motor learning, as evidenced by the fact that cerebellar patients do not adapt well to sudden predictable perturbations. However, recent work has shown that cerebellar patients adapt much better if the perturbation is gradually introduced. Here we explore physiological mechanisms that underlie this distinction between abrupt and gradual motor adaptation in humans. We used Transcranial Magnetic Stimulation (TMS) to evaluate whether neural mechanisms within the cerebellum contribute to either process during a visuomotor reach adaptation. When a visuomotor rotation was introduced abruptly, cerebellar excitability changed early in learning, and approached baseline levels near the end of the adaptation block. However, we observed no modulation of cerebellar excitability when we presented the visuomotor rotation gradually during learning. Similarly, we did not observe cerebellar modulation during trial-by-trial adaptation to random visuomotor displacements or during reaches without perturbations. This suggests that the cerebellum is most active during the early-phases of adaptation when large perturbations are successfully compensated.
PMCID: PMC3435878  PMID: 22915105
Motor Learning; M1; Error; Reaching; Stimulation
12.  Ageing of the postural vertical 
Age  2009;32(1):51-60.
A postural vertical (PV) tilted backward has been put forward as a reason explaining the backward disequilibrium often observed in elderly fallers. This raises the question of a possible ageing process of the PV involving a backward tilt of verticality perception increasing with age. We have explored this hypothesis by measuring PV in pitch using the wheel paradigm in 87 healthy subjects aged from 20 to 97 years. The possibility that this physiological ageing accelerated in the second part of life was also analysed. Two indices were calculated: the mean orientation (PV-orient) and the dispersion (PV-uncert). The correlation between age and PV-orient was r = −0.2 (p < 0.05). Added to the fact that PV was twice as shifted backward in the 38 seniors over 50 years (−1.15° ± 1.40°) as in the 49 young adults under 50 years (−0.45° ± 0.97°; t = 2.75, p < 0.01), this indicates the existence of a physiological ageing process on the direction perceived as vertical by the whole body, with a slight backward shift of PV throughout the life span. The correlation between age and PV-uncert was r = 0.35 (p < 0.001) in all subjects and r = 0.59 (p < 0.001) in seniors. This indicates that subjects get less and less accurate in their perception of the postural vertical with age, especially very old subjects who show great uncertainty in determining with their body the direction of the vertical. Taken together, these findings indicate that the internal model of verticality is less robust in elderly people. This may play a part in their postural decline.
PMCID: PMC2829644  PMID: 19711197
Verticality; Postural control; Subjective vertical; Postural vertical; Ageing
13.  Vestibular prosthesis tested in rhesus monkeys 
We are studying the effectiveness of a semicircular canal prosthesis to improve postural control, perception of spatial orientation, and the VOR in rhesus monkeys with bilateral vestibular hypofunction. Balance is examined by measuring spontaneous sway of the body during quiet stance and postural responses evoked by head turns and rotation of the support surface; perception is measured with a task derived from the subjective visual vertical (SVV) test during static and dynamic rotation in the roll plane; and the angular VOR is measured during rotation about the roll, pitch, and yaw axes. After the normal responses are characterized, bilateral vestibular loss is induced with intratympanic gentamicin, and then multisite stimulating electrodes are chronically implanted into the ampullae of all three canals in one ear. The postural, perceptual, and VOR responses are then characterized in the ablated state, and then bilateral, chronic electrical stimulation is applied to the ampullary nerves using a prosthesis that senses angular head velocity in three-dimensions and uses this information to modulate the rate of current pulses provided by the implanted electrodes. We are currently characterizing two normal monkeys with these paradigms, and vestibular ablation and electrode implantation are planned for the near future. In one prior rhesus monkey tested with this approach, we found that a one-dimensional (posterior canal) prosthesis improved balance during head turns, perceived head orientation during roll tilts, and the VOR in the plane of the instrumented canal. We therefore predict that the more complete information provided by a three-dimensional prosthesis that modulates activity in bilaterally-paired canals will exceed the benefits provided by the one-dimensional, unilateral approach used in our preliminary studies.
PMCID: PMC3594774  PMID: 22254795
14.  Chronic Alcohol Drinking Alters Neuronal Dendritic Spines in the Brain Reward Center Nucleus Accumbens 
Brain research  2007;1134(1):148-161.
Alcohol is known to affect glutamate transmission. However, how chronic alcohol affects the synaptic structure mediating glutamate transmission is unknown. Repeated alcohol exposure in a subject with familial alcoholic history often leads to alcohol addiction. The current study adopts alcohol-preferring rats, which are known to develop high drinking. Two-photon microscopy analysis indicates that chronic alcohol of 14 weeks either, under continuous alcohol (C-Alc) or with repeated deprivation (RD-Alc), causes dysmorphology–– thickened, beaded, and disoriented dendrites that are reminiscent of reactive astrocytes –– in a subpopulation of medium spiny neurons. The density of dendritic spines was found differentially lower in the nucleus accumbens of RD-Alc and C-Alc groups as compared with those of Water groups. Large-sized spines and multiple-headed spines were increased in the RD-Alc group. The NMDA receptor subunit NR1 proteins, as analyzed with western blot, were upregulated in C-Alc, but not in RD-Alc. The upregulated NMDA receptor subunits of NR1 however, are predominantly a splice variant isoform with truncated exon 21, which is required for membrane-bound trafficking or anchoring into a spine synaptic site. These maladaptations may contribute to the transformation of spines. The changes, in density and head-size of spines and the corresponding NMDA receptors, demonstrated an alteration of microcircuitry for glutamate reception. The current study demonstrates for the first time that chronic alcohol exposure causes structural alteration of dendrites and their spines in the key reward brain region in animals that have a genetic background leading to alcohol addiction.
PMCID: PMC1857312  PMID: 17198693
Glutamate; NMDA; Extended amygdala; repeated deprivation; medium spiny neurons; Two-photon laser microscopy; postsynaptic; GABA; addiction; genetics; P rats
15.  Flexible Cognitive Strategies during Motor Learning 
PLoS Computational Biology  2011;7(3):e1001096.
Visuomotor rotation tasks have proven to be a powerful tool to study adaptation of the motor system. While adaptation in such tasks is seemingly automatic and incremental, participants may gain knowledge of the perturbation and invoke a compensatory strategy. When provided with an explicit strategy to counteract a rotation, participants are initially very accurate, even without on-line feedback. Surprisingly, with further testing, the angle of their reaching movements drifts in the direction of the strategy, producing an increase in endpoint errors. This drift is attributed to the gradual adaptation of an internal model that operates independently from the strategy, even at the cost of task accuracy. Here we identify constraints that influence this process, allowing us to explore models of the interaction between strategic and implicit changes during visuomotor adaptation. When the adaptation phase was extended, participants eventually modified their strategy to offset the rise in endpoint errors. Moreover, when we removed visual markers that provided external landmarks to support a strategy, the degree of drift was sharply attenuated. These effects are accounted for by a setpoint state-space model in which a strategy is flexibly adjusted to offset performance errors arising from the implicit adaptation of an internal model. More generally, these results suggest that strategic processes may operate in many studies of visuomotor adaptation, with participants arriving at a synergy between a strategic plan and the effects of sensorimotor adaptation.
Author Summary
Motor learning has been modeled as an implicit process in which an error, signaling the difference between the predicted and actual outcome is used to modify a model of the actor-environment interaction. This process is assumed to operate automatically and implicitly. However, people can employ cognitive strategies to improve performance. It has recently been shown that when implicit and explicit processes are put in opposition, the operation of motor learning mechanisms will offset the advantages conferred by a strategy and eventually, performance deteriorates. We present a computational model of the interplay of these processes. A key insight of the model is that implicit and explicit learning mechanisms operate on different error signals. Consistent with previous models of sensorimotor adaptation, implicit learning is driven by an error reflecting the difference between the predicted and actual feedback for that movement. In contrast, explicit learning is driven by an error based on the difference between the feedback and target location of the movement, a signal that directly reflects task performance. Empirically, we demonstrate constraints on these two error signals. Taken together, the modeling and empirical results suggest that the benefits of a cognitive strategy may lie hidden in many motor learning tasks.
PMCID: PMC3048379  PMID: 21390266
16.  Chunking in Spatial Memory 
In order to gain insight into the nature of human spatial representations, the current study examined how those representations are affected by blind rotation. Evidence was sought on the possibility that whereas certain environmental aspects may be updated independently of one another, other aspects may be grouped (or chunked) together and updated as a unit. Participants learned the locations of an array of objects around them in a room, then were blindfolded and underwent a succession of passive, whole-body rotations. After each rotation, participants pointed to remembered target locations. Targets were located more precisely relative to each other if they were (a) separated by smaller angular distances, (b) contained within the same regularly configured arrangement, or (c) corresponded to parts of a common object. A hypothesis is presented describing the roles played by egocentric and allocentric information within the spatial updating system. Results are interpreted in terms of an existing neural systems model, elaborating the model’s conceptualization of how parietal (egocentric) and medial temporal (allocentric) representations interact.
PMCID: PMC2892259  PMID: 20438258
spatial memory; spatial updating; egocentric; allocentric; chunking
17.  Multilevel control of run orientation in Drosophila larval chemotaxis 
Chemotaxis is a powerful paradigm to study how orientation behavior is driven by sensory stimulation. Drosophila larvae navigate odor gradients by controlling the duration of their runs and the direction of their turns. Straight runs and wide-amplitude turns represent two extremes of a behavioral continuum. Here we establish that, on average, runs curl toward the direction of higher odor concentrations. We find that the orientation and strength of the local odor gradient perpendicular to the direction of motion modulates the orientation of individual runs in a gradual manner. We discuss how this error-correction mechanism, called weathervaning, contributes to larval chemotaxis. We use larvae with a genetically modified olfactory system to demonstrate that unilateral function restricted to a single olfactory sensory neuron (OSN) is sufficient to direct weathervaning. Our finding that bilateral sensing is not necessary to control weathervaning highlights the role of temporal sampling. A correlational analysis between sensory inputs and behavioral outputs suggests that weathervaning results from low-amplitude head casts implemented without interruption of the run. In addition, we report the involvement of a sensorimotor memory arising from previous reorientation events. Together, our results indicate that larval chemotaxis combines concurrent orientation strategies that involve complex computations on different timescales.
PMCID: PMC3923145  PMID: 24592220
active sensing; chemotaxis; Drosophila larva; sensorimotor integration; stereo-olfaction; weathervaning
18.  Perceptual-Attentional and Motor-Intentional Bias in Near and Far Space 
Brain and cognition  2008;68(1):9-14.
Spatial bias demonstrated in tasks such as line-bisection may stem from perceptual-attentional (PA) “where” and motor-intentional (MI) “aiming” influences. We tested normal participants’ line bisection performance in the presence of an asymmetric visual distracter with a video apparatus designed to dissociate PA from MI bias. An experimenter stood as a distractor to the left or right of a video monitor positioned in either near or far space, where participants viewed lines and a laser point they directed under 1) natural and 2) mirror-reversed conditions. Each trial started with the pointer positioned at either the top left or top right corner of the screen, and alternated thereafter. Data analysis indicated that participants made primarily PA leftward errors in near space, but not in far space. Furthermore, PA, but not MI, bias increased bilaterally in the direction of distraction. In contrast, MI, but not PA, bias was shifted bilaterally in the direction of startside. Results support the conclusion that a primarily PA left sided bias in near space is consistent with right hemisphere spatial attentional dominance. A bottom-up visual distractor specifically affected PA “where” spatial bias while top-down motor cuing influenced MI “aiming” bias.
PMCID: PMC2586818  PMID: 18381226
line bisection; pseudoneglect; attention; perception; motor bias
19.  What is the Safest Sprint Starting Position for American Football Players? 
The main objective of this study was to perform a biomechanical analysis of three different sprint start patterns to determine the safest position in term of neck injury and Sport-Related Concussion (SRC). The second objective was to collect data on the learning process effect between football players and non-players. Three different sprint initial positions adopted by football players were studied (i.e., 4-, 3- and 2-point positions). Twenty five young healthy males, including 12 football players, participated to this study. A stereophotogrammetric system (i.e., Vicon) was used to record motion patterns and body segments positions. Various measurements related to head and trunk orientation, and player field-of-view were obtained (e.g., head height, trunk bending, time to reach upright position, head speed (vertical direction) and body speed (horizontal direction)). Learning process was found to have no influence on studied parameters. Head redress is also delayed when adopting a 4-point position leading to a reduce field-of-view during the start and increasing therefore the probability of collision. Concerning the three different positions, the 4-point position seems to be the more dangerous because leading to higher kinetic energy than the 2- and 3-point start positions. This study proposes a first biomechanical approach to understand risk/benefit balance for athletes for those three different start positions. Results suggested that the 4-point position is the most risky for football players.
Key pointsMotion analysis and biomechanical analysis of the initial start position of the sprint could be used to increase the safety of the football players.Analysis of kinematic and trajectory of the head and the time to reach the upright position could be used to determine whether or not a player can return to play after concussion.A balance needs to be found between player’s safety (2-point start) and speed (4-point start).
PMCID: PMC3990900  PMID: 24790500
Sports; sports medicine; brain concussion; biomechanics
20.  From Modes to Movement in the Behavior of Caenorhabditis elegans 
PLoS ONE  2010;5(11):e13914.
Organisms move through the world by changing their shape, and here we explore the mapping from shape space to movements in the nematode Caenorhabditis elegans as it crawls on an agar plate. We characterize the statistics of the trajectories through the correlation functions of the orientation angular velocity, orientation angle and the mean-squared displacement, and we find that the loss of orientational memory has significant contributions from both abrupt, large amplitude turning events and the continuous dynamics between these events. Further, we discover long-time persistence of orientational memory in the intervals between abrupt turns. Building on recent work demonstrating that C. elegans movements are restricted to a low-dimensional shape space, we construct a map from the dynamics in this shape space to the trajectory of the worm along the agar. We use this connection to illustrate that changes in the continuous dynamics reveal subtle differences in movement strategy that occur among mutants defective in two classes of dopamine receptors.
PMCID: PMC2982830  PMID: 21103370
21.  Tracking pigeons in a magnetic anomaly and in magnetically “quiet” terrain 
Die Naturwissenschaften  2011;98(7):575-581.
Pigeons were released at two sites of equal distance from the loft, one within a magnetic anomaly, the other in magnetically quiet terrain, and their tracks were recorded with the help of GPS receivers. A comparison of the beginning of the tracks revealed striking differences: within the anomaly, the initial phase lasted longer, and the distance flown was longer, with the pigeons' headings considerably farther from the home direction. During the following departure phase, the birds were well homeward oriented at the magnetically quiet site, whereas they continued to be disoriented within the anomaly. Comparing the tracks in the anomaly with the underlying magnetic contours shows considerable differences between individuals, without a common pattern emerging. The differences in magnetic intensity along the pigeons' path do not differ from a random distribution of intensity differences around the release site, indicating that the magnetic contours do not directly affect the pigeons' routes. Within the anomaly, pigeons take longer until their flights are oriented, but 5 km from the release point, the birds, still within the anomaly, are also significantly oriented in the home direction. These findings support the assumption that magnetically anomalous conditions initially interfere with the pigeons' navigational processes, with birds showing rather individual responses in their attempts to overcome these problems.
Electronic supplementary material
The online version of this article (doi:10.1007/s00114-011-0802-3) contains supplementary material, which is available to authorized users.
PMCID: PMC3128737  PMID: 21691766
Magnetic anomaly; Pigeon navigation; Homing; GPS tracking; Magnetic “map” factors; Point of Decision
22.  An Electron Microscope Study of the Salamander Thyroid during Hormonal Stimulation 
Cytological changes in thyroid glands following administration of thyroid-stimulating hormone (TSH), were studied in adult salamanders, Ambystoma tigrinum, Triturus torosus, and Triturus viridescens by electron and light microscopy. Thyroids from untreated salamanders contained large follicles, faintly basophilic colloid, low follicle cells with flattened nuclei, and scant, slightly basophilic cytoplasm. After TSH administration the cell height and nuclear volume increased. Cytoplasmic basophilia was markedly increased and follicle lumina were reduced. In electron micrographs, stacks of ergastoplasmic lamellae appeared near the nucleus occasionally in contact with the nuclear membrane. In more advanced stages of stimulation, lamellar arrays were largely replaced by small disoriented vesicles and larger vacuoles containing colloid-like material. Sections of obliquely oriented ergastoplasmic membranes contained rows of extremely fine particles. Microvilli increased in size and number and Golgi structures became more extensive. Homogeneous osmiophilic droplets increased in size and abundance. Some of the smaller droplets were seen associated with the Golgi zone. Droplets similar in size and density frequently contained closely packed, whorled lamellae. Mitochondria showed no structural changes but occurred in aggregates interposed between the nucleus and highly folded portions of the basal cell membrane.
PMCID: PMC2224857  PMID: 13852243
23.  Navigation as a source of geometric knowledge: Young children’s use of length, angle, distance, and direction in a reorientation task 
Cognition  2012;123(1):144-161.
Geometry is one of the highest achievements of our species, but its foundations are obscure. Consistent with longstanding suggestions that geometrical knowledge is rooted in processes guiding navigation, the present study examines potential sources of geometrical knowledge in the navigation processes by which young children establish their sense of orientation. Past research reveals that children reorient both by the shape of the surface layout and the shapes of distinctive landmarks, but it fails to clarify what shape properties children use. The present study explores two-year-old children's sensitivity to angle, length, distance and direction by testing disoriented children’s search in a variety of fragmented rhombic and rectangular environments. Children reoriented themselves in accord with surface distances and directions, but they failed to use surface lengths or corner angles either for directional reorientation or as local landmarks. Thus, navigating children navigate by some but not all of the abstract properties captured by formal Euclidean geometry. While navigation systems may contribute to children's developing geometric understanding, they likely are not the sole source of abstract geometric intuitions.
PMCID: PMC3306253  PMID: 22257573
24.  Probe set algorithms: is there a rational best bet? 
BMC Bioinformatics  2006;7:395.
Affymetrix microarrays have become a standard experimental platform for studies of mRNA expression profiling. Their success is due, in part, to the multiple oligonucleotide features (probes) against each transcript (probe set). This multiple testing allows for more robust background assessments and gene expression measures, and has permitted the development of many computational methods to translate image data into a single normalized "signal" for mRNA transcript abundance. There are now many probe set algorithms that have been developed, with a gradual movement away from chip-by-chip methods (MAS5), to project-based model-fitting methods (dCHIP, RMA, others). Data interpretation is often profoundly changed by choice of algorithm, with disoriented biologists questioning what the "accurate" interpretation of their experiment is. Here, we summarize the debate concerning probe set algorithms. We provide examples of how changes in mismatch weight, normalizations, and construction of expression ratios each dramatically change data interpretation. All interpretations can be considered as computationally appropriate, but with varying biological credibility. We also illustrate the performance of two new hybrid algorithms (PLIER, GC-RMA) relative to more traditional algorithms (dCHIP, MAS5, Probe Profiler PCA, RMA) using an interactive power analysis tool. PLIER appears superior to other algorithms in avoiding false positives with poorly performing probe sets. Based on our interpretation of the literature, and examples presented here, we suggest that the variability in performance of probe set algorithms is more dependent upon assumptions regarding "background", than on calculations of "signal". We argue that "background" is an enormously complex variable that can only be vaguely quantified, and thus the "best" probe set algorithm will vary from project to project.
PMCID: PMC1569879  PMID: 16942624
25.  Response mode differences in perspective taking: Differences in representation or differences in retrieval? 
Memory & cognition  2008;36(4):863-872.
Three experiments explored whether response mode differences in perspective taking result from different spatial representations or different retrieval processes. Participants learned object locations and then, while blindfolded, pointed to or verbally described object locations from perspectives aligned or misaligned with their facing direction and aligned or misaligned with the learning perspective. Pointing was facilitated from the perspective aligned with the body during testing. Similar facilitation occurred when verbally labeling, but only when conducted in the context of pointing (e.g., after pointing). Without this pointing context, or after third-person strategy instructions, the effect of body alignment was eliminated for verbal responses. Pointing was less responsive to context and strategy. Across all conditions, performance was facilitated for the learning perspective. Taken together, these experiments indicate that response mode differences are due to differences in the retrieval process, which varies with strategy, rather than differences in the organization of the underlying spatial memory.
PMCID: PMC2685252  PMID: 18604967

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