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Data from: Time-dependent decline of body-specific attention to the paretic limb in chronic stroke patients
Objective: To examine whether reduced body-specific attention to paretic limb is found in chronic stroke patients in the time-dependent manner. Methods: Twenty-one patients with chronic hemiparesis (10 left and 11 right hemiparesis) after subcortical stroke and 18 age-matched healthy controls were recruited in this study. Standard neuropsychological examinations showed no clear evidence of spatial neglect in all patients. In order to quantitatively measure the spatial attention to paretic hand, a visual detection task for detecting a target appearing on the surface of either a paretic or dummy hand was used. This task can measure the body facilitation effect, which makes faster detection of a target on the body compared with one far from the body. Results: In stroke patients, there was no difference in the reaction time for visual target between on the paretic and the dummy hands, while the healthy participants showed faster detection for the visual target on the real hand than that on dummy one. The Index of the body facilitation effect, subtracting the reaction time for the target-on-paretic hand from that for the target-on-dummy one, was correlated with the duration since onset and with finger function test on the Stroke Impairment Assessment Set. Conclusions: The reduction of the body facilitation effect in paretic limb suggests the decline of body-specific attention to the paretic one in patients with chronic hemiparesis. This decline of the body-specific attention, leading to neglect for paretic limb, will be one of the most serious problems for rehabilitation based on use-dependent plasticity.
Data from: The crouching of the shrew: mechanical consequences of limb posture in small mammals
An important trend in the early evolution of mammals was the shift from a sprawling stance, whereby the legs are held in a more abducted position, to a parasagittal one, in which the legs extend more downward. After that transition, many mammals shifted from a crouching stance to a more upright one. It is hypothesized that one consequence of these transitions was a decrease in the total mechanical power required for locomotion, because side-to-side accelerations of the body have become smaller, and thus less costly with changes in limb orientation. To test this hypothesis we compared the kinetics of locomotion in two mammals of body size close to those of early mammals (< 40 g), both with parasagittally oriented limbs: a crouching shrew (Blarina brevicauda; 5 animals, 17 trials) and a more upright vole (Microtus pennsylvanicus; 4 animals, 22 trials). As predicted, voles used less mechanical power per unit body mass to perform steady locomotion than shrews did (P = 0.03). However, while lateral forces were indeed smaller in voles (15.6 ± 2.0% body weight) than in shrews (26.4 ± 10.9%; P = 0.046), the power used to move the body from side-to-side was negligible, making up less than 5% of total power in both shrews and voles. The most power consumed for both species was that used to accelerate the body in the direction of travel, and this was much larger for shrews than for voles (P = 0.01). We conclude that side-to-side accelerations are negligible for small mammals–whether crouching or more upright–compared to their sprawling ancestors, and that a more upright posture further decreases the cost of locomotion compared to crouching by helping to maintain the body's momentum in the direction of travel.
Data from: Data set incongruence and correlated character evolution: an example of functional convergence in the hind-limbs of stifftail diving ducks
The unwitting inclusion of convergent characters in phylogenetic estimates poses a serious problem for efforts to recover phylogeny. Convergence is not inscrutable, however, particularly when one group of characters tracks phylogeny and another set tracks adaptive history. In such cases, convergent characters may be correlated with one or a few functional anatomical units and readily identifiable using comparative methods. Stifftail ducks (Oxyurinae) offer one such opportunity to study correlated character evolution and function in the context of phylogenetic reconstruction. Morphological analyses place stifftail ducks as part of a large clade of diving ducks that includes the sea ducks (Mergini), Hymenolaimus, Merganetta, and Tachyeres, and possibly the pochards (Aythyini). Molecular analyses, on the other hand, place stifftails far from other diving ducks and suggest, moreover, that stifftails are polyphyletic. Mitochondrial cytochrome b gene sequences of eight stifftail species traditionally supposed to form a clade were compared with each other and with sequences from 50 other anseriform and galliform species. Stifftail ducks are not the sister group of sea ducks, but lie outside the typical ducks (Anatinae). Of the four traditional stifftail genera, monophyly of Oxyura and its sister group relationship with Nomonyx are strongly supported. Heteronetta probably is the sister group of that clade, but support is weak. Biziura is not a true stifftail. Within Oxyura, Old World species (O. australis, O. leucocephala, O. maccoa) appear to form a clade, with New World species (O. jamaicensis, O. vittata) branching basally. Incongruence between molecules and morphology is interpreted to be the result of adaptive specialization and functional convergence in the hind limbs of Biziura and true stifftails. When morphological characters are divided into classes, only hind-limb characters are significantly in conflict with the molecular tree. Null models of synonomous and nonsynonomous substitution based on patterns of codon-degeneracy and chemical dissimilarity, likewise, indicate that the nucleotide and amino acid changes postulated by the molecular tree are more plausible than those postulated by the morphological tree. These findings teach general lessons about the utility of highly adaptive characters (in particular those related to foraging ecology) and underscore the problems that convergence can pose for attempts to recover phylogeny. They also demonstrate how the concept of natural data partitions and simple models of evolution (e.g., parsimony, likelihood, neutrality) can be used to test the accuracy of independent phylogenetic estimates and provide arguments in favor of one tree topology over another.
Data from: Modulation of the cutaneous silent period in the upper-limb with whole-body instability
The silent period induced by cutaneous electrical stimulation of the digits has been shown to be task-dependent, at least in the grasping muscles of the hand. However, it is unknown if the cutaneous silent period is adaptable throughout muscles of the entire upper limb, in particular when the task requirements are substantially altered. The purpose of the present study was to examine the characteristics of the cutaneous silent period in several upper limb muscles when introducing increased whole-body instability. The cutaneous silent period was evoked in 10 healthy individuals with electrical stimulation of digit II of the right hand when the subjects were seated, standing, or standing on a wobble board while maintaining a background elbow extension contraction with the triceps brachii of ~5% of maximal voluntary contraction (MVC) strength. The first excitatory response (E1), first inhibitory response (CSP), and second excitatory response (E2) were quantified as the percent change from baseline and by their individual durations. The results showed that the level of CSP suppression was lessened (47.7 ± 7.7% to 33.8 ± 13.2% of baseline, p = 0.019) and the duration of the CSP inhibition decreased (p = 0.021) in the triceps brachii when comparing the seated and wobble board tasks. For the wobble board task the amount of cutaneous afferent inhibition of EMG activity in the triceps brachii decreased; which is proposed to be due to differential weighting of cutaneous feedback relative to the corticospinal drive, most likely due to presynaptic inhibition, to meet the demands of the unstable task.
Data from: Using the Mus musculus hybrid zone to assess covariation and genetic architecture of limb bone lengths
Two subspecies of the house mouse, Mus musculus domesticus and Mus musculus musculus, meet in a narrow contact zone across Europe. Mice in the hybrid zone are highly admixed, representing the full range of mixed ancestry from the two subspecies. Given the distinct morphologies of these subspecies, these natural hybrids can be used for genome-wide association mapping at sufficiently high resolution to directly infer candidate genes. We focus here on limb bone length differences, which is of special interest for understanding the evolution of developmentally correlated traits. We used 172 first-generation descendants of wild-caught mice from the hybrid zone to measure the length of stylopod (humerus / femur), zeugopod (ulna / tibia) and autopod (metacarpal / metatarsal) elements in skeletal CT scans. We find phenotypic covariation between limb elements in the hybrids similar to patterns previously described in M. m. domesticus inbred strains, suggesting that the hybrid genotypes do not influence the covariation pattern in a major way. Mapping was performed using 143,592 SNPs and identified several genomic regions associated with length differences in each bone. Each candidate region explains only a small proportion of phenotypic variance, suggesting that bone length is highly polygenic. None of the candidate regions includes the canonical genes known to control embryonic limb development. Instead, we are able to identify candidate genes with known roles in osteoblast differentiation and bone structure determination, as well as recently evolved genes of, as yet, unknown function.
Data from: One foot out the door: limb function during swimming in terrestrial versus aquatic turtles
Specialization for a new habitat often entails a cost to performance in the ancestral habitat. Although aquatic lifestyles are ancestral among extant cryptodiran turtles, multiple lineages, including tortoises (Testudinidae) and emydid box turtles (genus Terrapene), independently specialized for terrestrial habitats. To what extent is swimming function retained in such lineages despite terrestrial specialization? Because tortoises diverged from other turtles over 50 Ma, but box turtles did so only 5 Ma, we hypothesized that swimming kinematics for box turtles would more closely resemble those of aquatic relatives than those of tortoises. To test this prediction, we compared high-speed video of swimming Russian tortoises (Testudo horsfieldii), box turtles (Terrapene carolina) and two semi-aquatic emydid species: sliders (Trachemys scripta) and painted turtles (Chrysemys picta). We identified different kinematic patterns between limbs. In the forelimb, box turtle strokes most resemble those of tortoises; for the hindlimb, box turtles are more similar to semi-aquatic species. Such patterns indicate functional convergence of the forelimb of terrestrial species, whereas the box turtle hindlimb exhibits greater retention of ancestral swimming motions.
Data from: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice
Evolutionary studies are often limited by missing data that are critical to understanding the history of selection. Selection experiments, which reproduce rapid evolution under controlled conditions, are excellent tools to study how genomes evolve under selection. Here we present a genomic dissection of the Longshanks selection experiment, in which mice were selectively bred over 20 generations for longer tibiae relative to body mass, resulting in 13% longer tibiae in two replicates. We synthesized evolutionary theory, genome sequences and molecular genetics to understand the selection response and found that it involved both polygenic adaptation and discrete loci of major effect, with the strongest loci tending to be selected in parallel between replicates. We show that selection may favor de-repression of bone growth through inactivating two limb enhancers of an inhibitor, Nkx3-2. Our integrative genomic analyses thus show that it is possible to connect individual base-pair changes to the overall selection response.
Data from: Fatiguing effects of indirect vibration stimulation in upper limb muscles- post and during isometric contractions superimposed on upper limb vibration
Whole body vibration and upper limb vibration (ULV), continues to gain popularity as exercise intervention for rehabilitation and sports applications. However, the fatiguing effects of indirect vibration stimulation are not yet fully understood. We investigated the effects of ULV stimulation superimposed on fatiguing isometric contractions using a purpose developed upper limb stimulation device. Thirteen healthy volunteers were exposed to both ULV superimposed to fatiguing isometric contractions (V) and isometric contractions alone- Control (C). Both Vibration (V) and Control (C) exercises were performed at 80% of the maximum voluntary contractions. The stimulation used was 30 Hz frequency of 0.4 mm amplitude. Surface-electromyographic (EMG) activity of the Biceps Brachii, Triceps Brachii, and Flexor Carpi Radialis were measured. EMG amplitude (EMGrms) and mean frequency (MEF) were computed to quantify muscle activity and fatigue levels. All muscles displayed significantly higher reduction in MEFs and corresponding significant increase in EMGrms with the V than the Control, during fatiguing contractions (P < 0.05). Post vibration, all muscles showed higher levels of MEFs after recovery compared to the control. Our results show that near maximal isometric fatiguing contractions superimposed on vibration stimulation lead to a higher rate of fatigue development compared to the isometric contraction alone in the upper limb muscles. Results also show higher manifestation of mechanical fatigue post treatment with vibration compared to the control. Vibration superimposed on isometric contraction not only seems to alter the neuromuscular function during fatiguing efforts by inducing higher neuromuscular load but also post vibration treatment.
Data from: A three-dimensional analysis of the morphological evolution and locomotor behaviour of the carnivoran hind limb
Background: The shape of the appendicular bones in mammals usually reflects adaptations towards different locomotor abilities. However, other aspects such as body size and phylogeny also play an important role in shaping bone design. We used 3D landmark-based geometric morphometrics to analyse the shape of the hind limb bones (i.e., femur, tibia, and pelvic girdle bones) of living and extinct terrestrial carnivorans (Mammalia, Carnivora) to quantitatively investigate the influence of body size, phylogeny, and locomotor behaviour in shaping the morphology of these bones. We also investigated the main patterns of morphological variation within a phylogenetic context. Results: Size and phylogeny strongly influence the shape of the hind limb bones. In contrast, adaptations towards different modes of locomotion seem to have little influence. Principal Components Analysis and the study of phylomorphospaces suggest that the main source of variation in bone shape is a gradient of slenderness-robustness. Conclusion: The shape of the hind limb bones is strongly influenced by body size and phylogeny, but not to a similar degree by locomotor behaviour. The slender-robust "morphological bipolarity" found in bone shape variability is probably related to a trade-off between maintaining energetic efficiency and withstanding resistance to stresses. The balance involved in this trade-off impedes the evolution of high phenotypic variability. In fact, both morphological extremes (slender/robust) are adaptive in different selective contexts and lead to a convergence in shape among taxa with extremely different ecologies but with similar biomechanical demands. Strikingly, this "one-to-many mapping" pattern of evolution between morphology and ecology in hind limb bones is in complete contrast to the "many-to-one mapping" pattern found in the evolution of carnivoran skull shape. The results suggest that there are more constraints in the evolution of the shape of the appendicular skeleton than in that of skull shape because of the strong biomechanical constraints imposed by terrestrial locomotion.
Data from: Thrifty phenotype vs cold adaptation: trade-offs in upper limb proportions of Himalayan populations of Nepal
The multi-stress environment of high altitude has been associated with growth deficits in humans, particularly in zeugopod elements (forearm, lower leg). This is consistent with the thrifty phenotype hypothesis, which has been observed in Andeans, but has yet to be tested in other high altitude populations. In Himalayan populations, other factors, such as cold stress, may shape limb proportions. The current study investigated whether relative upper limb proportions of Himalayan adults (n=254) differ between highland and lowland populations, and whether cold adaptation or a thrifty phenotype mechanism may be acting here. Height, weight, humerus length, ulna length, hand length, and hand width were measured using standard methods. Relative to height, total upper limb and ulna lengths were significantly shorter in highlanders compared to lowlanders in both sexes, whilst hand and humerus length were not. Hand width did not significantly differ between populations. These results support the thrifty phenotype hypothesis, as hand and humerus proportions are conserved at the expense of the ulna. The reduction in relative ulna length could be attributed to cold adaptation, but the lack of difference between populations in both hand length and width indicate that cold adaptation is not shaping hands proportions in this case.
FIGURE 3 in A new genus and species of eyelid-less and limb reduced gymnophthalmid lizard from northeastern Brazil (Squamata, Gymnophthalmidae)
FIGURE 3. Living specimen of Scriptosaura catimbau from Parque Nacional do Catimbau.
FIGURE 1 in A new species of fringe-limb frog, genus Ecnomiohyla (Anura: Hylidae), from the Atlantic slope of Costa Rica, Central America
FIGURE 1. Ecnomiohyla sukia new species. Hand (left) and foot (right). Uncataloged paratype.
FIGURE 4 in A remarkable new species of Callulina (Amphibia: Anura: Brevicipitidae) with massive, boldly coloured limb glands
FIGURE 4. Views of the habitat at the type locality of Callulina meteora sp. nov.
FIGURE 3 in A remarkable new species of Callulina (Amphibia: Anura: Brevicipitidae) with massive, boldly coloured limb glands
FIGURE 3. Sonograms of Callulina species.
Which lower-limb joints compensate for destabilising energy introduced by unilateral treadmill belt accelerations delivered during walking in humans?
<p>Dataset including kinematics, kinetics, and mechanical powers during human walking with unilateral treadmill perturbations delivered in early or late stance.</p>
Data_of_Temporal_dynamics_of_the_sensorimotor_convergence_underlying_voluntary_limb_movement
<p>Software and dataset used in a manuscript.</p>
Figure 5 from: Perez J, Barquez R, Diaz M (2017) Morphology of the limbs in the semi-fossorial desert rodent species of Tympanoctomys (Octodontidae, Rodentia). ZooKeys 710: 77-96. https://doi.org/10.3897/zookeys.710.14033
Figure 5 - Right femur, anterior, posterior, and distal views. A Tympanoctomys aureus B Tympanoctomys barrerae C Tympanoctomys kirchnerorum D Tympanoctomys loschalchalerosorum. fh, femoral head; gt, greater trochanter; if, intercondylar fossa; lc, lateral condyle; lt, lesser trochanter; mc, medial condyle; pg, patellar groove; tt, third trochanter. Scale bars 5 mm for all views except distal view where the scale bars are 1 mm.
Figure 4 from: Perez J, Barquez R, Diaz M (2017) Morphology of the limbs in the semi-fossorial desert rodent species of Tympanoctomys (Octodontidae, Rodentia). ZooKeys 710: 77-96. https://doi.org/10.3897/zookeys.710.14033
Figure 4 - Right ulna, proximal portion in cranial and distal views of radio and ulna. A Tympanoctomys aureus B Tympanoctomys barrerae C Tympanoctomys kirchnerorum D Tympanoctomys loschalchalerosorum. lcp, lateral coronoid process; mcp, medial coronoid process; ol, olecranon; r, radio distal surface; rn, radial notch; ul, ulnar distal surface; ulptc, ulnar lateral proximal trochlear crest; umptc, ulnar medial proximal trochlear crest. Scale bars 1 mm.
Figure 3 from: Perez J, Barquez R, Diaz M (2017) Morphology of the limbs in the semi-fossorial desert rodent species of Tympanoctomys (Octodontidae, Rodentia). ZooKeys 710: 77-96. https://doi.org/10.3897/zookeys.710.14033
Figure 3 - Cranial and proximal views of the proximal portion of the right radio. A Tympanoctomys aureus B Tympanoctomys barrerae C Tympanoctomys kirchnerorum D Tympanoctomys loschalchalerosorum. cf, central fossa; h, head; n, notch. Scale bars 1mm.
Figure 1 from: Perez J, Barquez R, Diaz M (2017) Morphology of the limbs in the semi-fossorial desert rodent species of Tympanoctomys (Octodontidae, Rodentia). ZooKeys 710: 77-96. https://doi.org/10.3897/zookeys.710.14033
Figure 1 - Measurements of the long bones. apdh, anteroposterior diameter of the humerus; deh, diameter of the epicondyles; dlh, deltoid length of the humerus; fl, functional femur length; hl, functional humerus length; ful, functional ulna length; ol, length of the olecranon process; tdf, transverse diameter of the femur.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.