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1.
In humans, auditory perception reaches maturity over a broad age range, extending through adolescence. Despite this slow maturation, children are considered to be outstanding learners, suggesting that immature perceptual skills might actually be advantageous to improvement on an acoustic task as a result of training (perceptual learning). Previous non‐human studies have not employed an identical task when comparing perceptual performance of young and mature subjects, making it difficult to assess learning. Here, we used an identical procedure on juvenile and adult gerbils to examine the perception of amplitude modulation (AM), a stimulus feature that is an important component of most natural sounds. On average, Adult animals could detect smaller fluctuations in amplitude (i.e., smaller modulation depths) than Juveniles, indicating immature perceptual skills in Juveniles. However, the population variance was much greater for Juveniles, a few animals displaying adult‐like AM detection. To determine whether immature perceptual skills facilitated learning, we compared naïve performance on the AM detection task with the amount of improvement following additional training. The amount of improvement in Adults correlated with naïve performance: those with the poorest naïve performance improved the most. In contrast, the naïve performance of Juveniles did not predict the amount of learning. Those Juveniles with immature AM detection thresholds did not display greater learning than Adults. Furthermore, for several of the Juveniles with adult‐like thresholds, AM detection deteriorated with repeated testing. Thus, immature perceptual skills in young animals were not associated with greater learning. © 2010 Wiley Periodicals, Inc. Develop Neurobiol 70: 636–648, 2010  相似文献   

2.
Recent studies have shown that plant allelochemicals can have profound effects on the performance of associated species, such that plants with a history of co-existence with “chemical neighbour” plants perform better in their presence compared to naïve plants. This has cast new light on the complexity of plant–plant interactions and plant communities and has led to debates on whether plant communities are more co-evolved than traditionally thought. In order to determine whether plants may indeed evolve in response to other plants’ allelochemicals it is crucial to determine the presence of genetic variation for performance under the influence of specific allelochemicals and show that natural selection indeed operates on this variation. We studied the effect of the monoterpene carvacrol—a dominant compound in the essential oil of Thymus pulegioides—on three associated plant species originating from sites where thyme is either present or absent. We found the presence of genetic variation in both naïve and experienced populations for performance under the influence of the allelochemical but the response varied among naïve and experienced plant. Plants from experienced populations performed better than naïve plants on carvacrol soil and contained significantly more seed families with an adaptive response to carvacrol than naïve populations. This suggests that the presence of T. pulegioides can act as a selective agent on associated species, by favouring genotypes which perform best in the presence of its allelochemicals. The response to the thyme allelochemical varied from negative to neutral to positive among the species. The different responses within a species suggest that plant–plant interactions can evolve; this has implications for community dynamics and stability.  相似文献   

3.
《IRBM》2022,43(6):678-686
ObjectivesFeature selection in data sets is an important task allowing to alleviate various machine learning and data mining issues. The main objectives of a feature selection method consist on building simpler and more understandable classifier models in order to improve the data mining and processing performances. Therefore, a comparative evaluation of the Chi-square method, recursive feature elimination method, and tree-based method (using Random Forest) used on the three common machine learning methods (K-Nearest Neighbor, naïve Bayesian classifier and decision tree classifier) are performed to select the most relevant primitives from a large set of attributes. Furthermore, determining the most suitable couple (i.e., feature selection method-machine learning method) that provides the best performance is performed.Materials and methodsIn this paper, an overview of the most common feature selection techniques is first provided: the Chi-Square method, the Recursive Feature Elimination method (RFE) and the tree-based method (using Random Forest). A comparative evaluation of the improvement (brought by such feature selection methods) to the three common machine learning methods (K- Nearest Neighbor, naïve Bayesian classifier and decision tree classifier) are performed. For evaluation purposes, the following measures: micro-F1, accuracy and root mean square error are used on the stroke disease data set.ResultsThe obtained results show that the proposed approach (i.e., Tree Based Method using Random Forest, TBM-RF, decision tree classifier, DTC) provides accuracy higher than 85%, F1-score higher than 88%, thus, better than the KNN and NB using the Chi-Square, RFE and TBM-RF methods.ConclusionThis study shows that the couple - Tree Based Method using Random Forest (TBM-RF) decision tree classifier successfully and efficiently contributes to find the most relevant features and to predict and classify patient suffering of stroke disease.”  相似文献   

4.
Predation is a pervasive selective agent shaping a prey's behaviour, morphology and life history. To survive, prey animals have to respond adaptively to predation threats and this can be achieved through learned predator recognition. Cultural transmission of predator recognition is likely a widespread means of learning in social animals, including mammals, birds and fishes. However, no studies have investigated the cultural transmission of predator recognition in amphibians. In our study, we examined whether naïve woodfrog (Rana sylvatica) tadpoles can acquire the recognition of the odour of a predatory tiger salamander (Ambystoma tigrinum) from experienced conspecifics. After conditioning some tutors to recognize salamander odour, we paired naïve observer tadpoles with either a salamander‐naïve or salamander‐experienced tutor and exposed the pairs to either salamander odour or a water control. Observers were subsequently tested alone for a response to salamander odour. We found that when given salamander odour, observer tadpoles that were paired with a salamander‐experienced tutor successfully learned to recognize the salamander odour as a threat, whereas the observers paired with salamander‐naïve tutors did not. Likewise, tadpoles exposed to the water control did not learn to recognize the salamander regardless of whether they were paired with a naïve or experienced tutor. This is the first study demonstrating cultural transmission of predator recognition in an amphibian species.  相似文献   

5.
Predation shortly after release is the main source of mortality among hatchery‐reared fish used to restore or enhance endangered salmonid populations. We found, that hatchery‐reared salmonid young originating from endangered stocks have weak innate responses to their natural fish predators. The ability to avoid predation in fish can be improved through social learning from experienced to naïve individuals. Huge benefits would be achieved, if social learning processes could be successfully applied on a large scale to enhance viability of hatchery fish prior to release into the wild. By using model predators together with chemical cues from real predators we tested if social learning could be used to train hatchery‐reared salmonid young to avoid fish predators. As there are clear differences in social behaviour among the salmonid species, we first examined whether these differences affect the probability and efficiency of learning anti‐predator skills from trained demonstrators. We compared anti‐predator responses of observers (fish trained by using experienced fish as demonstrators) with those of control fish, which had been ‘trained’ by untrained naïve conspecifics. We also examined how the efficiency of social learning depends on the ratio of experienced to naïve fish involved in social transmission trials. The results of these experiments will give guidelines how social learning could be utilized in developing hatchery scale training protocols.  相似文献   

6.
Naïve pluripotent stem cells (PSCs) display a distinctive phenotype when compared to their “primed” counterparts, including, but not limited to, increased potency to differentiate and more robust mitochondrial respiration. The cultivation and maintenance of naïve PSCs have been notoriously challenging, requiring the use of complex cytokine cocktails. NME7AB is a newly discovered embryonic stem cell growth factor that is expressed exclusively in the first few days of human blastocyst development. It has been previously reported that growing primed induced PSCs (iPSCs) in bFGF-depleted medium with NME7AB as the only added growth factor facilitates the regression of these cells to their naïve state. Here, we confirm this regression by demonstrating the reactivation of mitochondrial function in the induced naïve-like PSCs and increased ATP production in these cells, as compared to that in primed iPSCs.  相似文献   

7.
Assessment and preservation of biodiversity has been a central theme of conservation biology since the discipline's inception. However, when diversity estimates are based purely on measures of presence–absence, or even abundance, they do not directly assess in what way focal habitats support the life history needs of individual species making up biological communities. Here, we move beyond naïve measures of occurrence and introduce the concept of “informed diversity” indices which scale estimates of avian species richness and community assemblage by two critical phases of their life cycle: breeding and molt. We tested the validity of the “informed diversity” concept using bird capture data from multiple locations in northern California and southern Oregon to examine patterns of species richness among breeding, molting, and naïve (based solely on occurrence) bird communities at the landscape and local scales using linear regression, community similarity indices, and a Detrended Correspondence Analysis (DCA). At the landscape scale, we found a striking pattern of increased species richness for breeding, molting, and naïve bird communities further inland and at higher elevations throughout the study area. At the local scale, we found that some sites with species‐rich naïve communities were in fact species‐poor when informed by breeding status, indicating that naïve richness may mask more biologically meaningful patterns of diversity. We suggest that land managers use informed diversity estimates instead of naïve measures of diversity to identify ecologically valuable wildlife habitat.  相似文献   

8.
There is a growing amount of empirical evidence that premating reproductive isolation of two closely related species can be reinforced by natural selection arising from avoidance of maladaptive hybridization. However, as an alternative for this popular reinforcement theory, it has been suggested that learning to prefer conspecifics or to discriminate heterospecifics could cause a similar pattern of reinforced premating isolation, but this possibility is much less studied. Here, we report results of a field experiment in which we examined (i) whether allopatric Calopteryx virgo damselfly males that have not encountered heterospecific females of the congener C. splendens initially show discrimination, and (ii) whether C. virgo males learn to discriminate heterospecifics or learn to associate with conspecifics during repeated experimental presentation of females. Our experiment revealed that there was a statistically nonsignificant tendency for C. virgo males to show initial discrimination against heterospecific females but because we did not use sexually naïve individuals in our experiment, we were not able to separate the effect of innate or associative learning. More importantly, however, our study revealed that species discrimination might be further strengthened by learning, especially so that C. virgo males increase their association with conspecific females during repeated presentation trials. The role of learning to discriminate C. splendens females was less clear. We conclude that learning might play a role in species recognition also when individuals are not naïve but have already encountered potential conspecific mates.  相似文献   

9.
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11.
Proteome-wide identification of protein-protein interactions is a formidable task which has yet to be sufficiently addressed by experimental methodologies. Many computational methods have been developed to predict proteome-wide interaction networks, but few leverage both the sensitivity of structural information and the wide availability of sequence data. We present PEPPI, a pipeline which integrates structural similarity, sequence similarity, functional association data, and machine learning-based classification through a naïve Bayesian classifier model to accurately predict protein-protein interactions at a proteomic scale. Through benchmarking against a set of 798 ground truth interactions and an equal number of non-interactions, we have found that PEPPI attains 4.5% higher AUROC than the best of other state-of-the-art methods. As a proteomic-scale application, PEPPI was applied to model the interactions which occur between SARS-CoV-2 and human host cells during coronavirus infection, where 403 high-confidence interactions were identified with predictions covering 73% of a gold standard dataset from PSICQUIC and demonstrating significant complementarity with the most recent high-throughput experiments. PEPPI is available both as a webserver and in a standalone version and should be a powerful and generally applicable tool for computational screening of protein-protein interactions.  相似文献   

12.
A short G1 phase is a characteristic feature of mouse embryonic stem cells (ESCs). To determine if there is a causal relationship between G1 phase restriction and pluripotency, we made use of the Fluorescence Ubiquitination Cell Cycle Indicator (FUCCI) reporter system to FACS-sort ESCs in the different cell cycle phases. Hence, the G1 phase cells appeared to be more susceptible to differentiation, particularly when ESCs self-renewed in the naïve state of pluripotency. Transitions from ground to naïve, then from naïve to primed states of pluripotency were associated with increased durations of the G1 phase, and cyclin E-mediated alteration of the G1/S transition altered the balance between self-renewal and differentiation. LIF withdrawal resulted in a lengthening of the G1 phase in naïve ESCs, which occurred prior to the appearance of early lineage-specific markers, and could be reversed upon LIF supplementation. We concluded that the short G1 phase observed in murine ESCs was a determinant of naïve pluripotency and was partially under the control of LIF signaling.  相似文献   

13.
Naïve and primed pluripotent stem cells recapitulate the peri- and post-implantation development, respectively. Thus, investigation of distinct traits between each pluripotent stem cell type would shed light on early embryonic processes. Herein, by screening a fluorescent probe library, we found that intracellular glycogen led to specific reactivity to CDg4, a glycogen fluorescence sensor, in both human and mouse naïve embryonic stem cells (ESCs). The requirement of constant inhibition of Gsk3β as well as high oxidative phosphorylation (OxPHOS) in naïve compared to primed ESCs was closely associated to high level of intracellular glycogen in naïve ESCs. Both capacity of OxPHOS and stored glycogen, rescued naïve ESCs by transient inhibition of glycolysis, which selectively eliminated primed ESCs. Additionally, naïve ESCs with active OxPHOS were enriched from a mixture with primed ESCs by high reactivity to ATP-Red1, a mitochondrial ATP fluorescence probe. These results indicate the active OxPHOS and high intracellular glycogen as a novel “biomarker” delineating metabolic remodeling during the transition of naïve pluripotency.  相似文献   

14.
Protein–protein interactions (PPIs) play crucial roles in a number of biological processes. Recently, protein interaction networks (PINs) for several model organisms and humans have been generated, but few large-scale researches for mice have ever been made neither experimentally nor computationally. In the work, we undertook an effort to map a mouse PIN, in which protein interactions are hidden in enormous amount of biomedical literatures. Following a co-occurrence-based text-mining approach, a probabilistic model—naïve Bayesian was used to filter false-positive interactions by integrating heterogeneous kinds of evidence from genomic and proteomic datasets. A support vector machine algorithm was further used to choose protein pairs with physical interactions. By comparing with the currently available PPI datasets from several model organisms and humans, it showed that the derived mouse PINs have similar topological properties at the global level, but a high local divergence. The mouse protein interaction dataset is stored in the Mouse protein–protein interaction DataBase (MppDB) that is useful source of information for system-level understanding of gene function and biological processes in mammals. Access to the MppDB database is public available at http://bio.scu.edu.cn/mppi.  相似文献   

15.
Bolstad ES  Anderson AC 《Proteins》2008,73(3):566-580
Accurate ranking during in silico lead optimization is critical to drive the generation of new ligands with higher affinity, yet it is especially difficult because of the subtle changes between analogs. In order to assess the role of the structure of the receptor in delivering accurate lead ranking results, we docked a set of forty related inhibitors to structures of one species of dihydrofolate reductase (DHFR) derived from crystallographic, NMR solution data, and homology models. In this study, the crystal structures yielded the superior results: the compounds were placed in the active site in the conserved orientation and the docking scores for 80% percent of the compounds clustered into the same bins as the measured affinity. Single receptor structures derived from NMR data or homology models did not serve as accurate docking receptors. To our knowledge, these are the first experiments that assess ranking of homologous lead compounds using a variety of receptor structures. We then extended the study to investigate whether ensembles, either computationally or experimentally derived, of all of the single starting structures aid, hinder or have no effect on the performance of the starting template. Impressively, when ensembles of receptor structures derived from NMR data or homology models were employed, docking accuracy improved to a level equal to that of the high resolution crystal structures. The same experiments using a second species of DHFR and set of ligands confirm the results. A comparison of the structures of the individual ensemble members to the starting structures shows that the effect of the ensembles can be ascribed to protein flexibility in addition to absorption of computational error.  相似文献   

16.
This article presents the classification of blood characteristics by a C4.5 decision tree, a naïve Bayes classifier and a multilayer perceptron for thalassaemia screening. The aim is to classify eighteen classes of thalassaemia abnormality, which have a high prevalence in Thailand, and one control class by inspecting data characterised by a complete blood count (CBC) and haemoglobin typing. Two indices namely a haemoglobin concentration (HB) and a mean corpuscular volume (MCV) are the chosen CBC attributes. On the other hand, known types of haemoglobin from six ranges of retention time identified via high performance liquid chromatography (HPLC) are the chosen haemoglobin typing attributes. The stratified 10-fold cross-validation results indicate that the best classification performance with average accuracy of 93.23% (standard deviation = 1.67%) and 92.60% (standard deviation = 1.75%) is achieved when the naïve Bayes classifier and the multilayer perceptron are respectively applied to samples which have been pre-processed by attribute discretisation. The results also suggest that the HB attribute is redundant. Moreover, the achieved classification performance is significantly higher than that obtained using only haemoglobin typing attributes as classifier inputs. Subsequently, the naïve Bayes classifier and the multilayer perceptron are applied to an additional data set in a clinical trial which respectively results in accuracy of 99.39% and 99.71%. These results suggest that a combination of CBC and haemoglobin typing analysis with a naïve Bayes classifier or a multilayer perceptron is highly suitable for automatic thalassaemia screening.  相似文献   

17.
《MABS-AUSTIN》2013,5(6):673-685
Advances in recombinant antibody technology and protein engineering have provided the opportunity to reduce antibodies to their smallest binding domain components and have concomitantly driven the requirement for devising strategies to increase serum half-life to optimise drug exposure, thereby increasing therapeutic efficacy. In this study, we adopted an immunization route to raise picomolar affinity shark immunoglobulin new antigen receptors (IgNARs) to target human serum albumin (HSA). From our model shark species, Squalus acanthias, a phage display library encompassing the variable binding domain of IgNAR (VNAR) was constructed, screened against target, and positive clones were characterized for affinity and specificity. N-terminal and C-terminal molecular fusions of our lead hit in complex with a naïve VNAR domain were expressed, purified and exhibited the retention of high affinity binding to HSA, but also cross-selectivity to mouse, rat and monkey serum albumin both in vitro and in vivo. Furthermore, the naïve VNAR had enhanced pharmacokinetic (PK) characteristics in both N- and C-terminal orientations and when tested as a three domain construct with naïve VNAR flanking the HSA binding domain at both the N and C termini. Molecules derived from this platform technology also demonstrated the potential for clinical utility by being available via the subcutaneous route of delivery. This study thus demonstrates the first in vivo functional efficacy of a VNAR binding domain with the ability to enhance PK properties and support delivery of multifunctional therapies.  相似文献   

18.
The characteristics of pluripotent embryonic stem cells of human and mouse are different. The properties of human embryonic stem cells (hESCs) are similar to those of mouse epiblast stem cells (mEpiSCs), which are in a later developmental pluripotency state, the so-called “primed state” compared to mouse embryonic stem cells (mESCs) which are in a naïve state. As a result of the properties of the primed state, hESCs proliferate slowly, cannot survive as single cells, and can only be transfected with genes at low efficiency. Generating hESCs in the naïve state is necessary to overcome these problems and allow their application in regenerative medicine. Therefore, clarifying the mechanism of the transition between the naïve and primed states in pluripotent stem cells is important for the establishment of stable methods of generating naïve state hESCs. However, the signaling pathways which contribute to the transition between the naïve and primed states are still unclear. In this study, we carried out induction from mESCs to mEpiSC-like cells (mEpiSCLCs), and observed an increase in the activation of Fas signaling during the induction. The expression of Fgf5, an epiblast marker, was diminished by inhibition of Fas signaling using the caspase-8 and -3 blocking peptides, IETD and DEVD, respectively. Furthermore, during the induction, we observed increased expression of 3-O sulfated heparan sulfate (HS) structures synthesized by HS 3-O-sulfotransferase (3OST), which are recognized by the HS4C3 antibody (HS4C3-binding epitope). Knockdown of 3OST-5 reduced Fas signaling and the potential for the transition to mEpiSCLCs. This indicates that the HS4C3-binding epitope is necessary for the transition to the primed state. We propose that Fas signaling through the HS4C3-binding epitope contributes to the transition from the naïve state to the primed state.  相似文献   

19.
Signaling pathways orchestrated by PI3K/Akt, Raf/Mek/Erk and Wnt/β-catenin are known to play key roles in the self-renewal and differentiation of pluripotent stem cells. The serine/threonine protein kinase Gsk3β has roles in all three pathways, making its exact function difficult to decipher. Consequently, conflicting reports have implicated Gsk3β in promoting self-renewal, while others suggest that it performs roles in the activation of differentiation pathways. Different thresholds of Gsk3β activity also have different biological effects on pluripotent cells, making this situation even more complex. Here, we describe a further level of complexity that is most apparent when comparing “naïve” murine and “primed” human pluripotent stem cells. In naïve cells, Gsk3β activity is restrained by PI3K/Akt, but when released from inhibitory signals it antagonizes self-renewal pathways by targeting pluripotency factors such as Myc and Nanog. This situation also applies in primed cells, but, in addition, a separate pool of Gsk3β is required to suppress canonical Wnt signaling. These observations suggest that different Gsk3β-protein complexes shift the balance between naïve and primed pluripotent cells and identify fundamental differences in their cell signaling. Altogether, these findings have important implications for the mechanisms underpinning the establishment of different pluripotent cell states and for the control of self-renewal and differentiation.  相似文献   

20.
Inference of functional networks—representing the statistical associations between time series recorded from multiple sensors—has found important applications in neuroscience. However, networksexhibiting time-locked activity between physically independent elements can bias functional connectivity estimates employing passive measurements. Here, a perturbative and adaptive method of inferring network connectivity based on measurement and stimulation—so called “evoked network connectivity” is introduced. This procedure, employing a recursive Bayesian update scheme, allows principled network stimulation given a current network estimate inferred from all previous stimulations and recordings. The method decouples stimulus and detector design from network inference and can be suitably applied to a wide range of clinical and basic neuroscience related problems. The proposed method demonstrates improved accuracy compared to network inference based on passive observation of node dynamics and an increased rate of convergence relative to network estimation employing a naïve stimulation strategy.  相似文献   

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