A Complex Network Approach to Distributional Semantic Models

A number of studies on network analysis have focused on language networks based on free word association, which reflects human lexical knowledge, and have demonstrated the small-world and scale-free properties in the word association network. Nevertheless, there have been very few attempts at applying network analysis to distributional semantic models, despite the fact that these models have been studied extensively as computational or cognitive models of human lexical knowledge. In this paper, we analyze three network properties, namely, small-world, scale-free, and hierarchical properties, of semantic networks created by distributional semantic models. We demonstrate that the created networks generally exhibit the same properties as word association networks. In particular, we show that the distribution of the number of connections in these networks follows the truncated power law, which is also observed in an association network. This indicates that distributional semantic models can provide a plausible model of lexical knowledge. Additionally, the observed differences in the network properties of various implementations of distributional semantic models are consistently explained or predicted by considering the intrinsic semantic features of a word-context matrix and the functions of matrix weighting and smoothing. Furthermore, to simulate a semantic network with the observed network properties, we propose a new growing network model based on the model of Steyvers and Tenenbaum. The idea underlying the proposed model is that both preferential and random attachments are required to reflect different types of semantic relations in network growth process. We demonstrate that this model provides a better explanation of network behaviors generated by distributional semantic models.     

Semantic Factors Predict the Rate of Lexical Replacement of Content Words

The rate of lexical replacement estimates the diachronic stability of word forms on the basis of how frequently a proto-language word is replaced or retained in its daughter languages. Lexical replacement rate has been shown to be highly related to word class and word frequency. In this paper, we argue that content words and function words behave differently with respect to lexical replacement rate, and we show that semantic factors predict the lexical replacement rate of content words. For the 167 content items in the Swadesh list, data was gathered on the features of lexical replacement rate, word class, frequency, age of acquisition, synonyms, arousal, imageability and average mutual information, either from published databases or gathered from corpora and lexica. A linear regression model shows that, in addition to frequency, synonyms, senses and imageability are significantly related to the lexical replacement rate of content words–in particular the number of synonyms that a word has. The model shows no differences in lexical replacement rate between word classes, and outperforms a model with word class and word frequency predictors only.     

Verbal cues modulate hedonic perception of odors in 5-year-old children as well as in adults

The judgment of pleasantness/unpleasantness is the prominent reaction to the olfactory world. In human adults, the hedonic valence of odor perception is affected by various factors, among which is an individual's lexical knowledge about smells. The present study examined whether such top-down effects of lexical knowledge on hedonic judgment of olfactory input are similar in children (5-6 years) and adults (20-25 years). In both groups, the lexical knowledge was found to influence the perception of the least emotional (or most neutral) odors: the pleasantness of the smells of banana and mint was enhanced when participants were given the corresponding odor label before olfactory sensation. These results lend support to the notion that, during childhood, smells are not only encoded perceptually but that verbal encoding also steers contextual effects that may be prominent factors in the early memorization and categorization of odors.     

From a Bodily-based Format of Knowledge to Symbols. The Evolution of Human Language

Although ontogeny cannot recapitulate phylogeny, a two-level model of the acquisition of language will be here proposed and its implication for the evolution of the faculty of language will be discussed. It is here proposed that the identification of the cognitive requirements of language during ontogeny could help us in the task of identifying the phylogenetic achievements that concurred, at some point, to the acquisition of language during phylogeny. In this model speaking will be considered as a complex ability that arises in two different steps. The first step of competence widely relies on a bodily-based format of knowledge. The second step relies on more abstract meta-representations and implies high-level socio-cognitive skills. It is hypothesized that in order to reach the second level of language competence, symbolic communication and interaction with a cultural community are needed. Hence, the origins of species-specific human complex language and cognition are in both the brain and culture. Moreover, in this model, data from the embodied language research will be discussed in the light of a usage-based account of language.     

Small worlds and semantic network growth in typical and late talkers

Network analysis has demonstrated that systems ranging from social networks to electric power grids often involve a small world structure-with local clustering but global ac cess. Critically, small world structure has also been shown to characterize adult human semantic networks. Moreover, the connectivity pattern of these mature networks is consistent with lexical growth processes in which children add new words to their vocabulary based on the structure of the language-learning environment. However, thus far, there is no direct evidence that a child's individual semantic network structure is associated with their early language learning. Here we show that, while typically developing children's early networks show small world structure as early as 15 months and with as few as 55 words, children with language delay (late talkers) have this structure to a smaller degree. This implicates a maladaptive bias in word acquisition for late talkers, potentially indicating a preference for "oddball" words. The findings provide the first evidence of a link between small-world connectivity and lexical development in individual children.     

The pig: a model for human infectious diseases

An animal model to study human infectious diseases should accurately reproduce the various aspects of disease. Domestic pigs (Sus scrofa domesticus) are closely related to humans in terms of anatomy, genetics and physiology, and represent an excellent animal model to study various microbial infectious diseases. Indeed, experiments in pigs are much more likely to be predictive of therapeutic treatments in humans than experiments in rodents. In this review, we highlight the numerous advantages of the pig model for infectious disease research and vaccine development and document a few examples of human microbial infectious diseases for which the use of pigs as animal models has contributed to the acquisition of new knowledge to improve both animal and human health.     

A complementary systems account of word learning: neural and behavioural evidence

In this paper we present a novel theory of the cognitive and neural processes by which adults learn new spoken words. This proposal builds on neurocomputational accounts of lexical processing and spoken word recognition and complementary learning systems (CLS) models of memory. We review evidence from behavioural studies of word learning that, consistent with the CLS account, show two stages of lexical acquisition: rapid initial familiarization followed by slow lexical consolidation. These stages map broadly onto two systems involved in different aspects of word learning: (i) rapid, initial acquisition supported by medial temporal and hippocampal learning, (ii) slower neocortical learning achieved by offline consolidation of previously acquired information. We review behavioural and neuroscientific evidence consistent with this account, including a meta-analysis of PET and functional Magnetic Resonance Imaging (fMRI) studies that contrast responses to spoken words and pseudowords. From this meta-analysis we derive predictions for the location and direction of cortical response changes following familiarization with pseudowords. This allows us to assess evidence for learning-induced changes that convert pseudoword responses into real word responses. Results provide unique support for the CLS account since hippocampal responses change during initial learning, whereas cortical responses to pseudowords only become word-like if overnight consolidation follows initial learning.     

Q-ball imaging of macaque white matter architecture

Diffusion-weighted magnetic resonance imaging holds substantial promise as a technique for non-invasive imaging of white matter (WM) axonal projections. For diffusion imaging to be capable of providing new insight into the connectional neuroanatomy of the human brain, it will be necessary to histologically validate the technique against established tracer methods such as horseradish peroxidase and biocytin histochemistry. The macaque monkey provides an ideal model for histological validation of the diffusion imaging method due to the phylogenetic proximity between humans and macaques, the gyrencephalic structure of the macaque cortex, the large body of knowledge on the neuroanatomic connectivity of the macaque brain and the ability to use comparable magnetic resonance acquisition protocols in both species. Recently, it has been shown that high angular resolution diffusion imaging (HARDI) can resolve multiple axon orientations within an individual imaging voxel in human WM. This capability promises to boost the accuracy of tract reconstructions from diffusion imaging. If the macaque is to serve as a model for histological validation of the diffusion tractography method, it will be necessary to show that HARDI can also resolve intravoxel architecture in macaque WM. The present study therefore sought to test whether the technique can resolve intravoxel structure in macaque WM. Using a HARDI method called q-ball imaging (QBI) it was possible to resolve composite intravoxel architecture in a number of anatomic regions. QBI resolved intravoxel structure in, for example, the dorsolateral convexity, the pontine decussation, the pulvinar and temporal subcortical WM. The paper concludes by reviewing remaining challenges for the diffusion tractography project.     

Modeling Coevolution between Language and Memory Capacity during Language Origin

Memory is essential to many cognitive tasks including language. Apart from empirical studies of memory effects on language acquisition and use, there lack sufficient evolutionary explorations on whether a high level of memory capacity is prerequisite for language and whether language origin could influence memory capacity. In line with evolutionary theories that natural selection refined language-related cognitive abilities, we advocated a coevolution scenario between language and memory capacity, which incorporated the genetic transmission of individual memory capacity, cultural transmission of idiolects, and natural and cultural selections on individual reproduction and language teaching. To illustrate the coevolution dynamics, we adopted a multi-agent computational model simulating the emergence of lexical items and simple syntax through iterated communications. Simulations showed that: along with the origin of a communal language, an initially-low memory capacity for acquired linguistic knowledge was boosted; and such coherent increase in linguistic understandability and memory capacities reflected a language-memory coevolution; and such coevolution stopped till memory capacities became sufficient for language communications. Statistical analyses revealed that the coevolution was realized mainly by natural selection based on individual communicative success in cultural transmissions. This work elaborated the biology-culture parallelism of language evolution, demonstrated the driving force of culturally-constituted factors for natural selection of individual cognitive abilities, and suggested that the degree difference in language-related cognitive abilities between humans and nonhuman animals could result from a coevolution with language.     

Terminology-driven mining of biomedical literature

MOTIVATION: With an overwhelming amount of textual information in molecular biology and biomedicine, there is a need for effective literature mining techniques that can help biologists to gather and make use of the knowledge encoded in text documents. Although the knowledge is organized around sets of domain-specific terms, few literature mining systems incorporate deep and dynamic terminology processing. RESULTS: In this paper, we present an overview of an integrated framework for terminology-driven mining from biomedical literature. The framework integrates the following components: automatic term recognition, term variation handling, acronym acquisition, automatic discovery of term similarities and term clustering. The term variant recognition is incorporated into terminology recognition process by taking into account orthographical, morphological, syntactic, lexico-semantic and pragmatic term variations. In particular, we address acronyms as a common way of introducing term variants in biomedical papers. Term clustering is based on the automatic discovery of term similarities. We use a hybrid similarity measure, where terms are compared by using both internal and external evidence. The measure combines lexical, syntactical and contextual similarity. Experiments on terminology recognition and clustering performed on a corpus of MEDLINE abstracts recorded the precision of 98 and 71% respectively. AVAILABILITY: software for the terminology management is available upon request.     

Interpolated Compressed Sensing for 2D Multiple Slice Fast MR Imaging

Sparse MRI has been introduced to reduce the acquisition time and raw data size by undersampling the k-space data. However, the image quality, particularly the contrast to noise ratio (CNR), decreases with the undersampling rate. In this work, we proposed an interpolated Compressed Sensing (iCS) method to further enhance the imaging speed or reduce data size without significant sacrifice of image quality and CNR for multi-slice two-dimensional sparse MR imaging in humans. This method utilizes the k-space data of the neighboring slice in the multi-slice acquisition. The missing k-space data of a highly undersampled slice are estimated by using the raw data of its neighboring slice multiplied by a weighting function generated from low resolution full k-space reference images. In-vivo MR imaging in human feet has been used to investigate the feasibility and the performance of the proposed iCS method. The results show that by using the proposed iCS reconstruction method, the average image error can be reduced and the average CNR can be improved, compared with the conventional sparse MRI reconstruction at the same undersampling rate.     

You know what it is: learning words through listening to hip-hop

Music listeners have difficulty correctly understanding and remembering song lyrics. However, results from the present study support the hypothesis that young adults can learn African-American English (AAE) vocabulary from listening to hip-hop music. Non-African-American participants first gave free-response definitions to AAE vocabulary items, after which they answered demographic questions as well as questions addressing their social networks, their musical preferences, and their knowledge of popular culture. Results from the survey show a positive association between the number of hip-hop artists listened to and AAE comprehension vocabulary scores. Additionally, participants were more likely to know an AAE vocabulary item if the hip-hop artists they listen to use the word in their song lyrics. Together, these results suggest that young adults can acquire vocabulary through exposure to hip-hop music, a finding relevant for research on vocabulary acquisition, the construction of adolescent and adult identities, and the adoption of lexical innovations.     

The acquisition of Sesotho nominal agreement

The acquisition of Bantu noun class prefixes has long been an issue of theoretical interest, due in part to the large number of gender classes. In contrast, the acquisition of Bantu nominal agreement has received little attention. Given findings from other languages, one might expect the phonologically transparent system of Bantu agreement to be mastered early and easily. However, the recent discovery that Sotho languages permit null prefixes under certain grammatical conditions raises the possibility that learning nominal agreement might be more challenging than originally thought. The goal of this study was therefore to assess Sesotho-speaking 2–3-year-olds’ acquisition of nominal agreement as a function of full versus reduced noun class prefixes. Although the children exhibited early phonological underspecification, they otherwise represented nominal agreement with little problem, whether the noun class prefix was produced or not. The implications for learnability, and the development of lexical representations more generally, are discussed.     

Top-down modulations from dorsal stream in lexical recognition: an effective connectivity FMRI study

Both the ventral and dorsal visual streams in the human brain are known to be involved in reading. However, the interaction of these two pathways and their responses to different cognitive demands remains unclear. In this study, activation of neural pathways during Chinese character reading was acquired by using a functional magnetic resonance imaging (fMRI) technique. Visual-spatial analysis (mediated by the dorsal pathway) was disassociated from lexical recognition (mediated by the ventral pathway) via a spatial-based lexical decision task and effective connectivity analysis. Connectivity results revealed that, during spatial processing, the left superior parietal lobule (SPL) positively modulated the left fusiform gyrus (FG), while during lexical processing, the left SPL received positive modulatory input from the left inferior frontal gyrus (IFG) and sent negative modulatory output to the left FG. These findings suggest that the dorsal stream is highly involved in lexical recognition and acts as a top-down modulator for lexical processing.     

Introduction and evaluation of case-based learning in the first foundational course of an undergraduate medical curriculum

Case-based learning (CBL) has been proposed as an effective method to promote student knowledge and motivation. The timing and methods for implementation have varied among schools, and data regarding the effectiveness of this pedagogy compared to other learning modalities are inconclusive. We introduced five different cases in the first course of our medical school as part of small-group CBL, and monitored student satisfaction and performance in summative evaluations. We observed that (1) students were very satisfied with the CBL sessions; (2) performance in essay examinations was significantly higher in CBL topics, compared to non-CBL topics, as evaluated at the end of the course, and three months after course conclusion; and (3) there was a trend of higher performance in multiple-choice questions about CBL topics, but this was not statistically significant. Our results indicate that CBL is an acceptable pedagogy to be incorporated from the beginning of undergraduate medical education to promote acquisition and retention of knowledge, students’ interest in foundational sciences, and integration of basic science disciplines and clinical medicine. When evaluating knowledge acquired using the CBL method, integrative essays represent a valuable tool to assess the depth of comprehension and application of information.     

A model for the incorporation of metal from the copper chaperone CCS into Cu,Zn superoxide dismutase.

BACKGROUND: Recent studies have identified the human copper chaperone CCS as the presumed factor responsible for copper incorporation into superoxide dismutase (SOD). A lack of knowledge of the chaperone's three-dimensional structure has prevented understanding of how the copper might be transferred. RESULTS: The three-dimensional structure of CCS was homology modelled using the periplasmic protein from the bacterial mercury-detoxification system and the structure of one subunit of the human SOD dimeric enzyme as templates. On the basis of the three-dimensional model, a mechanism for the transfer of copper from CCS to SOD is proposed that accounts for electrostatic acceptor recognition, copper storage and copper-transfer properties. CONCLUSIONS: The proposed model identifies a path for copper transfer based on the presence of different metal sites characterized by sulphur ligands. Such a model permits the development of strategies able to interfere with copper incorporation in SOD, providing a possible way to prevent or arrest degeneration in the fatal motor neuron disorder amyotrophic lateral sclerosis.     

Patterns and Processes in Cultural Evolution

Darwinian models of cultural change have been motivated, in part, by the desire to provide a framework for the unification of the biological and the human sciences. In this paper, drawing upon a distinction between the evolution of enabling mechanisms for the acquisition and dissemination of knowledge (EEM) and the evolution of epistemic theses as cultural products (EET), we propose a model of how culture emerges as a product of biological evolution on the basis of the concept of reaction norms. The goal of this model is to provide a means for conceptualizing how the biological and the cultural realms are connected, when they start to disconnect, and what the key transitions are. We then assess the viability of a Darwinian approach to cultural change. We conclude that the prospects of producing a Darwinian model of cultural change that unifies the human sciences in a way that mirrors the unification of the biological sciences in the light of Darwin’s theory are rather dim.     

The Generation of a Comprehensive Spectral Library for the Analysis of the Guinea Pig Proteome by SWATH‐MS

Advances in liquid chromatography‐mass spectrometry have facilitated the incorporation of proteomic studies to many biology experimental workflows. Data‐independent acquisition platforms, such as sequential window acquisition of all theoretical mass spectra (SWATH‐MS), offer several advantages for label‐free quantitative assessment of complex proteomes over data‐dependent acquisition (DDA) approaches. However, SWATH data interpretation requires spectral libraries as a detailed reference resource. The guinea pig (Cavia porcellus) is an excellent experimental model for translation to many aspects of human physiology and disease, yet there is limited experimental information regarding its proteome. To overcome this knowledge gap, a comprehensive spectral library of the guinea pig proteome is generated. Homogenates and tryptic digests are prepared from 16 tissues and subjected to >200 DDA runs. Analysis of >250 000 peptide‐spectrum matches resulted in a library of 73 594 peptides from 7666 proteins. Library validation is provided by i) analyzing externally derived SWATH files ( https://doi.org/10.1016/j.jprot.2018.03.023 ) and comparing peptide intensity quantifications; ii) merging of externally derived data to the base library. This furnishes the research community with a comprehensive proteomic resource that will facilitate future molecular‐phenotypic studies using (re‐engaging) the guinea pig as an experimental model of relevance to human biology. The spectral library and raw data are freely accessible in the MassIVE repository (MSV000083199).     

The ferric iron-binding protein of pathogenic Neisseria spp. functions as a periplasmic transport protein in iron acquisition from human transferrin

The ferric iron-binding protein (Fbp) expressed by pathogenic Neisseria spp. has been proposed to play a central role in the high-affinity acquisition of iron from human transferrin. The results of this investigation provide evidence that Fbp participates in this process as a functional analogue of a Gram-negative periplasmic-binding protein component, which operates as a part of a general active transport process for the receptor-mediated, high-affinity transport of iron from human transferrin. Known properties of Fbp are correlated with those of other well-characterized periplasmic-binding proteins, including structural features and the reversible binding of ligand. Predictive of a periplasmic-binding protein, which functions in the high-affinity acquisition of iron, is that Fbp is a transient participant in the process of iron acquisition from human transferrin. Evidence for this is demonstrated by results of pulse–chase experiments. Taken together, the data described here and elsewhere suggest that pathogenic Neisseria spp. use a periplasmic-binding protein-mediated active transport mechanism for the acquisition of iron from human transferrin.