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Concept: Kinematics


It is generally accepted that crew rowing requires perfect synchronization between the movements of the rowers. However, a long-standing and somewhat counterintuitive idea is that out-of-phase crew rowing might have benefits over in-phase (i.e., synchronous) rowing. In synchronous rowing, 5 to 6% of the power produced by the rower(s) is lost to velocity fluctuations of the shell within each rowing cycle. Theoretically, a possible way for crews to increase average boat velocity is to reduce these fluctuations by rowing in antiphase coordination, a strategy in which rowers perfectly alternate their movements. On the other hand, the framework of coordination dynamics explicates that antiphase coordination is less stable than in-phase coordination, which may impede performance gains. Therefore, we compared antiphase to in-phase crew rowing performance in an ergometer experiment. Nine pairs of rowers performed a two-minute maximum effort in-phase and antiphase trial at 36 strokes min(-1) on two coupled free-floating ergometers that allowed for power losses to velocity fluctuations. Rower and ergometer kinetics and kinematics were measured during the trials. All nine pairs easily acquired antiphase rowing during the warm-up, while one pair’s coordination briefly switched to in-phase during the maximum effort trial. Although antiphase interpersonal coordination was indeed less accurate and more variable, power production was not negatively affected. Importantly, in antiphase rowing the decreased power loss to velocity fluctuations resulted in more useful power being transferred to the ergometer flywheels. These results imply that antiphase rowing may indeed improve performance, even without any experience with antiphase technique. Furthermore, it demonstrates that although perfectly synchronous coordination may be the most stable, it is not necessarily equated with the most efficient or optimal performance.

Concepts: Kinetic energy, Kinematics, Power, Rowing, Indoor rower, College rowing, History of rowing


Sequence alignment is a long standing problem in bioinformatics. The Basic Local Alignment Search Tool (BLAST) is one of the most popular and fundamental alignment tools. The explosive growth of biological sequences calls for speedup of sequence alignment tools such as BLAST. To this end, we develop high speed BLASTN (HS-BLASTN), a parallel and fast nucleotide database search tool that accelerates MegaBLAST-the default module of NCBI-BLASTN. HS-BLASTN builds a new lookup table using the FMD-index of the database and employs an accurate and effective seeding method to find short stretches of identities (called seeds) between the query and the database. HS-BLASTN produces the same alignment results as MegaBLAST and its computational speed is much faster than MegaBLAST. Specifically, our experiments conducted on a 12-core server show that HS-BLASTN can be 22 times faster than MegaBLAST and exhibits better parallel performance than MegaBLAST. HS-BLASTN is written in C++ and the related source code is available at under the GPLv3 license.

Concepts: DNA, Bioinformatics, Computational phylogenetics, Computer program, Kinematics, Source code, Sequence alignment, BLAST


Although the cheetah is recognised as the fastest land animal, little is known about other aspects of its notable athleticism, particularly when hunting in the wild. Here we describe and use a new tracking collar of our own design, containing a combination of Global Positioning System (GPS) and inertial measurement units, to capture the locomotor dynamics and outcome of 367 predominantly hunting runs of five wild cheetahs in Botswana. A remarkable top speed of 25.9 m s(-1) (58 m.p.h. or 93 km h(-1)) was recorded, but most cheetah hunts involved only moderate speeds. We recorded some of the highest measured values for lateral and forward acceleration, deceleration and body-mass-specific power for any terrestrial mammal. To our knowledge, this is the first detailed locomotor information on the hunting dynamics of a large cursorial predator in its natural habitat.

Concepts: Kinematics, Units of measurement, Hunting, Global Positioning System, Cheetah, Dimensional analysis, Global navigation satellite system, Speed of light


How extinct, non-avian theropod dinosaurs moved is a subject of considerable interest and controversy. A better understanding of non-avian theropod locomotion can be achieved by better understanding terrestrial locomotor biomechanics in their modern descendants, birds. Despite much research on the subject, avian terrestrial locomotion remains little explored in regards to how kinematic and kinetic factors vary together with speed and body size. Here, terrestrial locomotion was investigated in twelve species of ground-dwelling bird, spanning a 1,780-fold range in body mass, across almost their entire speed range. Particular attention was devoted to the ground reaction force (GRF), the force that the feet exert upon the ground. Comparable data for the only other extant obligate, striding biped, humans, were also collected and studied. In birds, all kinematic and kinetic parameters examined changed continuously with increasing speed, while in humans all but one of those same parameters changed abruptly at the walk-run transition. This result supports previous studies that show birds to have a highly continuous locomotor repertoire compared to humans, where discrete ‘walking’ and ‘running’ gaits are not easily distinguished based on kinematic patterns alone. The influences of speed and body size on kinematic and kinetic factors in birds are developed into a set of predictive relationships that may be applied to extinct, non-avian theropods. The resulting predictive model is able to explain 79-93% of the observed variation in kinematics and 69-83% of the observed variation in GRFs, and also performs well in extrapolation tests. However, this study also found that the location of the whole-body centre of mass may exert an important influence on the nature of the GRF, and hence some caution is warranted, in lieu of further investigation.

Concepts: Bird, Classical mechanics, Kinematics, Reaction, Locomotion, Animal locomotion, Dinosaur, Theropoda


Forest ecosystems have been exposed to climate change for more than 100 years, whereas the consequences on forest growth remain elusive. Based on the oldest existing experimental forest plots in Central Europe, we show that, currently, the dominant tree species Norway spruce and European beech exhibit significantly faster tree growth (+32 to 77%), stand volume growth (+10 to 30%) and standing stock accumulation (+6 to 7%) than in 1960. Stands still follow similar general allometric rules, but proceed more rapidly through usual trajectories. As forest stands develop faster, tree numbers are currently 17-20% lower than in past same-aged stands. Self-thinning lines remain constant, while growth rates increase indicating the stock of resources have not changed, while growth velocity and turnover have altered. Statistical analyses of the experimental plots, and application of an ecophysiological model, suggest that mainly the rise in temperature and extended growing seasons contribute to increased growth acceleration, particularly on fertile sites.

Concepts: Statistics, Europe, Germany, Acceleration, Velocity, Kinematics, Central Europe, Beech


Aging is the greatest risk factor for neurodegeneration, but the connection between the two processes remains opaque. This is in part for want of a rigorous way to define physiological age, as opposed to chronological age. Here we develop a comprehensive metric for physiological age inDrosophila,based on genome-wide expression profiling. We applied this metric to a model of adult-onset neurodegeneration, increased or decreased expression of the activating subunit of the Cdk5 protein kinase, encoded by the geneCdk5α, the ortholog of mammalian p35.Cdk5α-mediated degeneration was associated with a 27-150% acceleration of the intrinsic rate of aging, depending on the tissue and genetic manipulation. Gene ontology analysis and direct experimental tests revealed that affected, age-associated processes included numerous core phenotypes of neurodegeneration, including enhanced oxidative stress and impaired proteostasis. Taken together, our results suggest thatCdk5α-mediated neurodegeneration results from accelerated aging, in combination with cell-autonomous neuronal insults. These data fundamentally recast our picture of the relationship between neurodegeneration and its most prominent risk factor, natural aging.

Concepts: DNA, Gene, Signal transduction, Classical mechanics, Acceleration, Kinematics, Euclidean vector, Rate


Granular dynamics govern earthquakes, avalanches, and landslides and are of fundamental importance in a variety of industries ranging from energy to pharmaceuticals to agriculture. Nonetheless, our understanding of the underlying physics is poor because we lack spatially and temporally resolved experimental measurements of internal grain motion. We introduce a magnetic resonance imaging methodology that provides internal granular velocity measurements that are four orders of magnitude faster compared to previous work. The technique is based on a concerted interplay of scan acceleration and materials engineering. Real-time probing of granular dynamics is explored in single- and two-phase systems, providing fresh insight into bubble dynamics and the propagation of shock waves upon impact of an intruder. We anticipate that the methodology outlined here will enable advances in understanding the propagation of seismic activity, the jamming transition, or the rheology and dynamics of dense suspensions.

Concepts: Energy, Nuclear magnetic resonance, Magnetic resonance imaging, Materials science, Kinematics, Earthquake, Earthquake engineering, Seismology


To coordinate movements with events in a dynamic environment the brain has to anticipate when those events occur. A classic example is the estimation of time to contact (TTC), that is, when an object reaches a target. It is thought thatTTCis estimated from kinematic variables. For example, a tennis player might use an estimate of distance (d) and speed (v) to estimateTTC(TTC=d/v). However, the tennis player may instead estimateTTCas twice the time it takes for the ball to move from the serve line to the net line. This latter strategy does not rely on kinematics and instead computesTTCsolely from temporal cues. Which of these two strategies do humans use to estimateTTC? Considering that both speed and time estimates are inherently uncertain and the ability of the human brain to combine different sources of information, we hypothesized that humans estimateTTCby integrating speed information with temporal cues. We evaluated this hypothesis systematically using psychophysics and Bayesian modeling. Results indicated that humans rely on both speed information and temporal cues and integrate them to optimize theirTTCestimates when both cues are present. These findings suggest that the brain’s timing mechanisms are actively engaged when interacting with dynamic stimuli.

Concepts: Neuron, Brain, Human brain, Cerebral cortex, Cerebellum, Approximation, Estimation, Kinematics


Scaffolded DNA origami has proven to be a powerful and efficient technique to fabricate functional nanomachines by programming the folding of a single-stranded DNA template strand into three-dimensional (3D) nanostructures, designed to be precisely motion-controlled. Although two-dimensional (2D) imaging of DNA nanomachines using transmission electron microscopy and atomic force microscopy suggested these nanomachines are dynamic in 3D, geometric analysis based on 2D imaging was insufficient to uncover the exact motion in 3D. Here we use the individual-particle electron tomography method and reconstruct 129 density maps from 129 individual DNA origami Bennett linkage mechanisms at ~ 6-14 nm resolution. The statistical analyses of these conformations lead to understanding the 3D structural dynamics of Bennett linkage mechanisms. Moreover, our effort provides experimental verification of a theoretical kinematics model of DNA origami, which can be used as feedback to improve the design and control of motion via optimized DNA sequences and routing.

Concepts: DNA, Electron, Gene, Nanotechnology, DNA replication, Scanning tunneling microscope, Kinematics, Dynamics


In the present study we investigated displacement, time, velocity and acceleration history of center of mass (COM) and electrical activity of knee extensors to estimate the dominance of the factors influencing the vertical velocity in squat jumps (SJs), countermovement jumps (CMJs) and drop jumps (DJs) performed with small (40°) and large (80°) range of joint motion (SROM and LROM). The maximum vertical velocity (v4) was 23.4% (CMJ) and 7.8% (DJ) greater when the jumps were performed with LROM compared with SROM (p<0.05). These differences are considerably less than it could be expected from the greater COM and knee angular displacement and duration of active state. This small difference can be attributed to the greater deceleration during eccentric phase (CMJ:32.1%, DJ:91.5%) in SROM than that in LROM. v4 was greater for SJ in LROM than for SJ in SROM indicating the significance of the longer active state and greater activation level (p<0.001). The difference in v4 was greater between SJ and CMJ in SROM (38.6%) than in LROM (9.0%), suggesting that elastic energy storage and re-use can be a dominant factor in the enhancement of vertical velocity of CMJ and DJ compared with SJ performed with SROM.

Concepts: Energy, Kinetic energy, Classical mechanics, Acceleration, Velocity, Kinematics, Newton's laws of motion, Motion