Short- and long-term changes in joint co-contraction associated with motor learning as revealed from surface EMG.

In the field of motor control, two hypotheses have been controversial: whether the brain acquires internal models that generate accurate motor commands, or whether the brain avoids this by using the viscoelasticity of musculoskeletal system. Recent observations on relatively low stiffness during trained movements support the existence of internal models. However, no study has revealed the decrease in viscoelasticity associated with learning that would imply improvement of internal models as well as synergy between the two hypothetical mechanisms. Previously observed decreases in electromyogram (EMG) might have other explanations, such as trajectory modifications that reduce joint torques. To circumvent such complications, we required strict trajectory control and examined only successful trials having identical trajectory and torque profiles. Subjects were asked to perform a hand movement in unison with a target moving along a specified and unusual trajectory, with shoulder and elbow in the horizontal plane at the shoulder level. To evaluate joint viscoelasticity during the learning of this movement, we proposed an index of muscle co-contraction around the joint (IMCJ). The IMCJ was defined as the summation of the absolute values of antagonistic muscle torques around the joint and computed from the linear relation between surface EMG and joint torque. The IMCJ during isometric contraction, as well as during movements, was confirmed to correlate well with joint stiffness estimated using the conventional method, i.e., applying mechanical perturbations. Accordingly, the IMCJ during the learning of the movement was computed for each joint of each trial using estimated EMG-torque relationship. At the same time, the performance error for each trial was specified as the root mean square of the distance between the target and hand at each time step over the entire trajectory. The time-series data of IMCJ and performance error were decomposed into long-term components that showed decreases in IMCJ in accordance with learning with little change in the trajectory and short-term interactions between the IMCJ and performance error. A cross-correlation analysis and impulse responses both suggested that higher IMCJs follow poor performances, and lower IMCJs follow good performances within a few successive trials. Our results support the hypothesis that viscoelasticity contributes more when internal models are inaccurate, while internal models contribute more after the completion of learning. It is demonstrated that the CNS regulates viscoelasticity on a short- and long-term basis depending on performance error and finally acquires smooth and accurate movements while maintaining stability during the entire learning process.

Recombination Yet Inefficient Selection along the Drosophila melanogaster Subgroup's Fourth Chromosome

A central goal of evolutionary genetics is an understanding of the forces responsible for the observed variation, both within and between species. Theoretical and empirical work have demonstrated that genetic recombination contributes to this variation by breaking down linkage between nucleotide sites, thus allowing them to behave independently and for selective forces to act efficiently on them. The Drosophila fourth chromosome, which is believed to experience no-or very low-rates of recombination has been an important model for investigating these effects. Despite previous efforts, central questions regarding the extent of recombination and the predominant modes of selection acting on it remain open. In order to more comprehensively test hypotheses regarding recombination and its potential influence on selection along the fourth chromosome, we have resequenced regions from most of its genes from Drosophila melanogaster, D. simulans, and D. yakuba. These data, along with available outgroup sequence, demonstrate that recombination is low but significantly greater than zero for the three species. Despite there being recombination, there is strong evidence that its frequency is low enough to have rendered selection relatively inefficient. The signatures of relaxed constraint can be detected at both the level of polymorphism and divergence.

Characterization of the sleep architecture in two species of fruit bat

Bats (Chiroptera) are the second-most abundant mammalian order in the world, occupying a diverse range of habitats and exhibiting many different life history traits. In order to contribute to this highly underrepresented group we describe the sleep architecture of two species of frugivorous bat, the greater short-nosed fruit bat (Cynopterus sphinx) and the lesser dawn fruit bat (Eonycteris spelaea). Electroencephalogram (EEG) and electromyogram (EMG) data were recorded from multiple individuals (>= 5) by telemetry over a 72-h period in a laboratory setting with light/dark cycles equivalent to those found in the wild. Our results show that over a 24-h period both species spent more time asleep than awake (mean 15 h), less than previous reported for Chiroptera (20 h). C sphinx spent significantly more of its non-rapid eye movement sleep (NREM) and rapid eye movement sleep (REM) quotas during the light phase, while E. spelaea divided its sleep-wake architecture equally between both light and dark phases. Comparing the sleep patterns of the two species found that C. sphinx had significantly fewer NREM and REM episodes than E. spelaea but each episode lasted for a significantly longer period of time. Potential hypotheses to explain the differences in the sleep architecture of C. sphinx with E. spelaea, including risk of predation and social interaction are discussed. (C) 2010 Published by Elsevier B.V.

Singing Behavior and Singing Functions of Black-Crested Gibbons (Nomascus concolor jingdongensis) at Mt. Wuliang, Central Yunnan, China

We used data on loud duetted and solo songs collected from one habituated polygynous group of black-crested gibbons (Nomascus concolor jingdongensis) on Mt. Wuliang, Yunnan, to test several hypotheses about the functions of these songs. The major function

Phylogeny and zoogeography of the cyprinid genus Epalzeorhynchos Bleeker (Cyprinidae : Ostariophysi)

A total of 62 variable osteological and external characters was found among the five currently recognized species of Epalzeorhynchos. When the genera Crossocheilus and Paracrossocheilus are combined as the outgroup, only 30 of these characters can be polarized. This includes six autapomorphies. The remaining 24 polarized characters form a data matrix which yields a single, 26-step tree with a Consistency Index (CI) of 1 and a Retention Index (RI) of 1, The analysis was also performed on a combined dataset in which the 32 unpolarized characters (characters for which the combined outgroup was dimorphic) were added and coded as missing data (i.e., "?"), Analyzing this data matrix with all multistate characters ordered generates the same single most-parsimonious tree with a length of 63 steps, a CI of 0.98 and a RI of 0.97, When either Crossocheilus or Paracrossocheilus is used as the sole outgroup, the same single most-parsimonious tree is produced although the numbers of informative characters and some of the polarities differ. Evidence is presented to support the following hypotheses: (1) E, kalopterus + E, frenatus + E. bicolor + E. munensis form a monophyletic group; (2) E. frenatus + E, bicolor + E, munensis form a monophyletic group with E, kalopterus as its sister group; this speciation event is congruent with the predictions of vicariant speciation mode I; and (3) E. bicolor and E. munensis are sister groups, again congruent with vicariant speciation mode I, Evidence presented here also supports the zoogeographical hypothesis that the faunas of the Indochinese region and the Greater Sundas are more closely related to each other than either of them is to the lower Salween basin fauna and that the lower Mekong, Chao Phraya, and Mac Khlong basin faunas are more closely related to each other than any of them is to the Greater Sundas, In addition, the monophyly of Epalzeorhynchos is also preliminarily discussed by including either Paracrossocheilus or Crossocheilus in the ingroup. It is demonstrated that E. bicornis clusters with Paracrossocheilus when Paracrossocheilus is included in the ingroup. It seems likely that the taxonomic position of E. bicornis will be resolved as more fishes of the Crossocheilus group are included in future studies.

KARYOTYPE EVOLUTION OF SHREW MOLES (SORICOMORPHA: TALPIDAE)

The Chinese long-tailed mole (Scaptonyx fusicaudus) closely resembles American (Neurotrichus gibbsii) and Japanese (Dymecodon pilirostris and Urotrichus talpoides) shrew moles in size, appearance, and ecological habits, yet it has traditionally been classified either together with (viz subfamily Urotrichinae) or separately (tribe Scaptonychini) from the latter genera (tribe Urotrichini sensu lato). We explored the merit of these competing hypotheses by comparing the differentially stained karyotypes of S.fusicaudus and N. gibbsii with those previously reported for both Japanese taxa. With few exceptions, diploid chromosome number (2n = 34), fundamental autosomal number (FNa = 64), relative size, and G-banding pattern of S. fusicaudus were indistinguishable from those of D. pilirostris and U. talpoides. In fact, only chromosome 15 differed significantly between these species, being acrocentric in D. pilirostris, subtelocentric in U. talpoides, and metacentric in S. fusicaudus. This striking similarity is difficult to envisage except in light of a shared common ancestry, and is indicative of an exceptionally low rate of chromosomal evolution among these genera. Conversely, the karyotype of N. gibbsii deviates markedly in diploid chromosome and fundamental autosomal number (2n = 38 and FNa = 72, respectively), morphology, and G-banding pattern from those of Scaptonyx and the Japanese shrew moles. These differences cannot be explained by simple chromosomal rearrangements, and Suggest that rapid chromosomal reorganization Occurred ill the karyotype evolution of this species, possibly due to founder or bottleneck events.

The biology, ecology, population parameters and the fishery of the Nile tilapia, Oreochromis niloticus (L)

Oreochromis niloticus (the Nile tilapia) and three other ti1apine species: Oreochromis leucostictus, Tilapia zi11ii and T. rendallii were introduced into Lakes Victoria, Kyoga and Nabugabo in 1950s and 1960s. The source and foci of the stockings are given by Welcomme (1966) but the origin of the stocked species was Lake Albert. The Nile tilapia was introduced as a management measure to relieve fishing pressure on the endemic tiapiines and, since it grows to a bigger size, to encourage a return to the use of larger mesh gill nets. Ti1apia zillii was introduced to fill a vacant ,niche of macrophytes which could not be utilised' by the other tilapiines. Tilapia rendallii, and possibly T. leucosticutus could been introduced into these lakes accidently as a consquence of one of the species being tried out for aquaculture. The Nile perch and Nile tilapia have since fully established themselves and presently dominate the commercial fisheries of Lakes Victoria and Kyoga. The original fisheries based on the endemic tilapiines O. escu1entus and o. variabilis have collapsed. It is hypothesized that the ecological and limnological changes that are observed in Lakes Victoria and Kyoga are due to a truncation of the original food webs of the two lakes. Under the changed conditions, O. niloticus to be either playing a stabilizing role or fuelling nutrient turnover in the lakes. Other testable hypotheses point to the possible role of predation by the Nile perch, change in regional climate and hydrology in the lake basins.

MULTIVARIATE COMPARISON OF THE FORELIMB BETWEEN STUMP-TAILED AND RHESUS MACAQUES

Rhesus macaques and stump-tailed macaques are sympatric in western Yunnan (China), coexisting or occupying habitats that show little difference. This paper tests hypotheses based on theoretical expectation from the differing biomechanical demands of terrestrial and arboreal quadrupedalism in stump-tailed macaques and rhesus macaques, respectively. Individuals of these two macaque taxa were markedly separated by the first two principal components and discriminant analyses based on 18 variables of the upper limb. The rhesus macaques appear to be more adapted for arboreal quadruped habits because of elongation of the clavicle and forearm, a larger humeral head and greater midshaft sagittal diameters of the radius and ulna.

Combining information sources for confidence estimation with CRF models

Obtaining accurate confidence measures for automatic speech recognition (ASR) transcriptions is an important task which stands to benefit from the use of multiple information sources. This paper investigates the application of conditional random field (CRF) models as a principled technique for combining multiple features from such sources. A novel method for combining suitably defined features is presented, allowing for confidence annotation using lattice-based features of hypotheses other than the lattice 1-best. The resulting framework is applied to different stages of a state-of-the-art large vocabulary speech recognition pipeline, and consistent improvements are shown over a sophisticated baseline system. Copyright © 2011 ISCA.

Use of contexts in language model interpolation and adaptation

Language models (LMs) are often constructed by building multiple individual component models that are combined using context independent interpolation weights. By tuning these weights, using either perplexity or discriminative approaches, it is possible to adapt LMs to a particular task. This paper investigates the use of context dependent weighting in both interpolation and test-time adaptation of language models. Depending on the previous word contexts, a discrete history weighting function is used to adjust the contribution from each component model. As this dramatically increases the number of parameters to estimate, robust weight estimation schemes are required. Several approaches are described in this paper. The first approach is based on MAP estimation where interpolation weights of lower order contexts are used as smoothing priors. The second approach uses training data to ensure robust estimation of LM interpolation weights. This can also serve as a smoothing prior for MAP adaptation. A normalized perplexity metric is proposed to handle the bias of the standard perplexity criterion to corpus size. A range of schemes to combine weight information obtained from training data and test data hypotheses are also proposed to improve robustness during context dependent LM adaptation. In addition, a minimum Bayes' risk (MBR) based discriminative training scheme is also proposed. An efficient weighted finite state transducer (WFST) decoding algorithm for context dependent interpolation is also presented. The proposed technique was evaluated using a state-of-the-art Mandarin Chinese broadcast speech transcription task. Character error rate (CER) reductions up to 7.3 relative were obtained as well as consistent perplexity improvements. © 2012 Elsevier Ltd. All rights reserved.

N-best error simulation for training spoken dialogue systems

A recent trend in spoken dialogue research is the use of reinforcement learning to train dialogue systems in a simulated environment. Past researchers have shown that the types of errors that are simulated can have a significant effect on simulated dialogue performance. Since modern systems typically receive an N-best list of possible user utterances, it is important to be able to simulate a full N-best list of hypotheses. This paper presents a new method for simulating such errors based on logistic regression, as well as a new method for simulating the structure of N-best lists of semantics and their probabilities, based on the Dirichlet distribution. Off-line evaluations show that the new Dirichlet model results in a much closer match to the receiver operating characteristics (ROC) of the live data. Experiments also show that the logistic model gives confusions that are closer to the type of confusions observed in live situations. The hope is that these new error models will be able to improve the resulting performance of trained dialogue systems. © 2012 IEEE.

Discriminative spoken language understanding using word confusion networks

Current commercial dialogue systems typically use hand-crafted grammars for Spoken Language Understanding (SLU) operating on the top one or two hypotheses output by the speech recogniser. These systems are expensive to develop and they suffer from significant degradation in performance when faced with recognition errors. This paper presents a robust method for SLU based on features extracted from the full posterior distribution of recognition hypotheses encoded in the form of word confusion networks. Following [1], the system uses SVM classifiers operating on n-gram features, trained on unaligned input/output pairs. Performance is evaluated on both an off-line corpus and on-line in a live user trial. It is shown that a statistical discriminative approach to SLU operating on the full posterior ASR output distribution can substantially improve performance both in terms of accuracy and overall dialogue reward. Furthermore, additional gains can be obtained by incorporating features from the previous system output. © 2012 IEEE.

A confidence-based approach for improving keyword hypothesis scores

The task in keyword spotting (KWS) is to hypothesise times at which any of a set of key terms occurs in audio. An important aspect of such systems are the scores assigned to these hypotheses, the accuracy of which have a significant impact on performance. Estimating these scores may be formulated as a confidence estimation problem, where a measure of confidence is assigned to each key term hypothesis. In this work, a set of discriminative features is defined, and combined using a conditional random field (CRF) model for improved confidence estimation. An extension to this model to directly address the problem of score normalisation across key terms is also introduced. The implicit score normalisation which results from applying this approach to separate systems in a hybrid configuration yields further benefits. Results are presented which show notable improvements in KWS performance using the techniques presented in this work. © 2013 IEEE.

How neurons migrate: a dynamic in-silico model of neuronal migration in the developing cortex.

BACKGROUND: Neuronal migration, the process by which neurons migrate from their place of origin to their final position in the brain, is a central process for normal brain development and function. Advances in experimental techniques have revealed much about many of the molecular components involved in this process. Notwithstanding these advances, how the molecular machinery works together to govern the migration process has yet to be fully understood. Here we present a computational model of neuronal migration, in which four key molecular entities, Lis1, DCX, Reelin and GABA, form a molecular program that mediates the migration process. RESULTS: The model simulated the dynamic migration process, consistent with in-vivo observations of morphological, cellular and population-level phenomena. Specifically, the model reproduced migration phases, cellular dynamics and population distributions that concur with experimental observations in normal neuronal development. We tested the model under reduced activity of Lis1 and DCX and found an aberrant development similar to observations in Lis1 and DCX silencing expression experiments. Analysis of the model gave rise to unforeseen insights that could guide future experimental study. Specifically: (1) the model revealed the possibility that under conditions of Lis1 reduced expression, neurons experience an oscillatory neuron-glial association prior to the multipolar stage; and (2) we hypothesized that observed morphology variations in rats and mice may be explained by a single difference in the way that Lis1 and DCX stimulate bipolar motility. From this we make the following predictions: (1) under reduced Lis1 and enhanced DCX expression, we predict a reduced bipolar migration in rats, and (2) under enhanced DCX expression in mice we predict a normal or a higher bipolar migration. CONCLUSIONS: We present here a system-wide computational model of neuronal migration that integrates theory and data within a precise, testable framework. Our model accounts for a range of observable behaviors and affords a computational framework to study aspects of neuronal migration as a complex process that is driven by a relatively simple molecular program. Analysis of the model generated new hypotheses and yet unobserved phenomena that may guide future experimental studies. This paper thus reports a first step toward a comprehensive in-silico model of neuronal migration.

Bead-probe complex capture a couple of SINE and LINE family from genomes of two closely related species of East Asian cyprinid directly using magnetic separation

Background: Short and long interspersed elements (SINEs and LINEs, respectively), two types of retroposons, are active in shaping the architecture of genomes and powerful tools for studies of phylogeny and population biology. Here we developed special protocol to apply biotin-streptavidin bead system into isolation of interspersed repeated sequences rapidly and efficiently, in which SINEs and LINEs were captured directly from digested genomic DNA by hybridization to bead-probe complex in solution instead of traditional strategy including genomic library construction and screening. Results: A new couple of SINEs and LINEs that shared an almost identical 3'tail was isolated and characterized in silver carp and bighead carp of two closely related species. These SINEs (34 members), designated HAmo SINE family, were little divergent in sequence and flanked by obvious TSD indicated that HAmo SINE was very young family. The copy numbers of this family was estimated to 2 x 10(5) and 1.7 x 10(5) per haploid genome by Real-Time qPCR, respectively. The LINEs, identified as the homologs of LINE2 in other fishes, had a conserved primary sequence and secondary structures of the 3'tail region that was almost identical to that of HAmo SINE. These evidences suggest that HAmo SINEs are active and amplified recently utilizing the enzymatic machinery for retroposition of HAmoL2 through the recognition of higher-order structures of the conserved 42-tail region. We analyzed the possible structures of HAmo SINE that lead to successful amplification in genome and then deduced that HAmo SINE, SmaI SINE and FokI SINE that were similar in sequence each other, were probably generated independently and created by LINE family within the same lineage of a LINE phylogeny in the genomes of different hosts. Conclusion: The presented results show the advantage of the novel method for retroposons isolation and a pair of young SINE family and its partner LINE family in two carp fishes, which strengthened the hypotheses containing the slippage model for initiation of reverse transcription, retropositional parasitism of SINEs on LINEs, the formation of the stem loop structure in 3'tail region of some SINEs and LINEs and the mechanism of template switching in generating new SINE family.