Classical Taxonomies Research Articles

Surfing the OCEAN: The machine learning psycholexical approach 2.0 to detect personality traits in texts.

We aimed to develop a machine learning model to infer OCEAN traits from text. The psycholexical approach allows retrieving information about personality traits from human language. However, it has rarely been applied because of methodological and practical issues that current computational advancements could overcome. Classical taxonomies and a large Yelp corpus were leveraged to learn an embedding for each personality trait. These embeddings were used to train a feedforward neural network for predicting trait values. Their generalization performances have been evaluated through two external validation studies involving experts (N = 11) and laypeople (N = 100) in a discrimination task about the best markers of each trait and polarity. Intrinsic validation of the model yielded excellent results, with R2 values greater than 0.78. The validation studies showed a high proportion of matches between participants' choices and model predictions, confirming its efficacy in identifying new terms related to the OCEAN traits. The best performance was observed for agreeableness and extraversion, especially for their positive polarities. The model was less efficient in identifying the negative polarity of openness and conscientiousness. This innovative methodology can be considered a "psycholexical approach 2.0," contributing to research in personality and its practical applications in many fields.

El "blockbuster" como género analógico

Las películas blockbuster son definidas, habitualmente, por su éxito económico. Sin embargo, nosotros, en la medida en que hemos crecido y participado en la sociedad occidental contemporánea, somos capaces de distinguir qué película es (o puede llegar a ser) un blockbuster sin necesidad de saber la cantidad de dólares que ha hecho ni la cantidad de espectadores que la han visto. Podemos decir, así, que resulta imposible colocar la taquilla en el centro de la definición del blockbuster. En el presente artículo, intentaremos profundizar en las especificidades de este género y repensar dos conceptos que han sido empleados para investigar la cultura de masas desde las perspectivas de las teorías de la recepción: las nociones kitsch (Eco) y trash (Fernández Porta). Nuestro objetivo será esbozar la particular manera en que la lógica del blockbuster se ha cristalizado en un género analógico que va más allá de –y no casa exactamente con– las taxonomías clásicas aceptadas por la teoría fílmica.

Advanced Microbial Taxonomy Combined with Genome-Based-Approaches Reveals that Vibrio astriarenae sp. nov., an Agarolytic Marine Bacterium, Forms a New Clade in Vibrionaceae.

Advances in genomic microbial taxonomy have opened the way to create a more universal and transparent concept of species but is still in a transitional stage towards becoming a defining robust criteria for describing new microbial species with minimum features obtained using both genome and classical polyphasic taxonomies. Here we performed advanced microbial taxonomies combined with both genome-based and classical approaches for new agarolytic vibrio isolates to describe not only a novel Vibrio species but also a member of a new Vibrio clade. Two novel vibrio strains (Vibrio astriarenae sp. nov. C7T and C20) showing agarolytic, halophilic and fermentative metabolic activity were isolated from a seawater sample collected in a coral reef in Okinawa. Intraspecific similarities of the isolates were identical in both sequences on the 16S rRNA and pyrH genes, but the closest relatives on the molecular phylogenetic trees on the basis of 16S rRNA and pyrH gene sequences were V. hangzhouensis JCM 15146T (97.8% similarity) and V. agarivorans CECT 5085T (97.3% similarity), respectively. Further multilocus sequence analysis (MLSA) on the basis of 8 protein coding genes (ftsZ, gapA, gyrB, mreB, pyrH, recA, rpoA, and topA) obtained by the genome sequences clearly showed the V. astriarenae strain C7T and C20 formed a distinct new clade protruded next to V. agarivorans CECT 5085T. The singleton V. agarivorans has never been included in previous MLSA of Vibrionaceae due to the lack of some gene sequences. Now the gene sequences are completed and analysis of 100 taxa in total provided a clear picture describing the association of V. agarivorans into pre-existing concatenated network tree and concluded its relationship to our vibrio strains. Experimental DNA-DNA hybridization (DDH) data showed that the strains C7T and C20 were conspecific but were separated from all of the other Vibrio species related on the basis of both 16S rRNA and pyrH gene phylogenies (e.g., V. agarivorans CECT 5085T, V. hangzhouensis JCM 15146T V. maritimus LMG 25439T, and V. variabilis LMG 25438T). In silico DDH data also supported the genomic relationship. The strains C7T also had less than 95% average amino acid identity (AAI) and average nucleotide identity (ANI) towards V. maritimus C210, V. variabilis C206, and V. mediterranei AK1T, V. brasiliensis LMG 20546T, V. orientalis ATCC 33934T, and V. sinaloensis DSM 21326. The name Vibrio astriarenae sp. nov. is proposed with C7 as the type strains. Both V. agarivorans CECT 5058T and V. astriarenae C7T are members of the newest clade of Vibrionaceae named Agarivorans.

Bacterial classification using genomic fingerprints obtained by virtual hybridization

In silico genomic fingerprints were produced by virtual hybridization of 191 fully sequenced bacterial genomes using a set of 15,264 13-mer probes specially designed to produce universal whole genome fingerprints. A novel approach for constructing phylogenetic trees, based on comparative analysis of genomic fingerprints, was developed. The resultant bacterial phylogenetic tree had strong similarities to those produced from the alignment of conserved sequences. Notably, the trees derived from the alignment of other conserved COG genes divided the Bacillus and Corynebacterium genera into the same subgroups produced by the novel bacterial tree. A number of discrepancies between both techniques were observed for the grouping of some Lactobacillus species. However, a detailed analysis of the alignment of these genomes using other bioinformatics tools revealed that the grouping of these organisms in the novel tree was more satisfactory than the groupings from previous classifications, which used only a few conserved genes. All these data suggest that the bacterial taxonomy produced by genomic fingerprints is satisfactory, but sometimes different from classical taxonomies. Discrepancies probably arise because the fingerprinting technique analyzes genomic sequences and reveals more information than previously used approaches.

Mapping the Semantic Space for the Subjective Experience of Emotional Responses to Odors

Two studies were conducted to examine the nature of the verbal labels that describe emotional effects elicited by odors. In Study 1, a list of terms selected for their relevance to describe affective feelings induced by odors was assessed while participants were exposed to a set of odorant samples. The data were submitted to a series of exploratory factor analyses to 1) reduce the set of variables to a smaller set of summary scales and 2) get a preliminary sense of the differentiation of affective feelings elicited by odors. The goal of Study 2 was to replicate the findings of Study 1 with a larger sample of odorant samples and participants and to validate the preliminary model obtained in Study 1 by using confirmatory factor analysis. Overall, the findings point to a structure of affective responses to odors that differs from the classical taxonomies of emotion such as posited by discrete or bidimensional emotion theories. These findings suggest that the subjective affective experiences or feelings induced by odors are structured around a small group of dimensions that reflect the role of olfaction in well-being, social interaction, danger prevention, arousal or relaxation sensations, and conscious recollection of emotional memories.

Analyzing aphasia data in a multidimensional symptom space

The utility of single-case vs. group studies has been debated in neuropsychology for many years. The purpose of the present study is to illustrate an alternative approach to group studies of aphasia, in which the same symptom dimensions that are commonly used to assign patients to classical taxonomies (fluency, naming, repetition, and comprehension) are used as independent and continuous predictors in a multivariate design, without assigning patients to syndromes. One hundred twenty-six Italian-speaking patients with aphasia were first classified into seven classic aphasia categories, based on fluency, naming, auditory comprehension, and repetition scales. There were two goals: (1) compare group analyses based on aphasia types with multivariate analyses that sidestep classification and treat aphasic symptoms as continuous variables; (2) present correlation-based outlier analyses that can be used to identify individuals who occupy unusual positions in the multivariate “symptom space.” In the service of the first goal, group performance on an external validation measure (the Token Test) was assessed in three steps: analyses of variance based on aphasia type, regressions using the same cut-offs for fluency, naming, comprehension and repetition as independent but dichotomous predictors, and regressions using the same subscales as continuous predictors (with no cut-offs). More variance in Token Test performance was accounted for when symptoms were treated as continuous predictors than with the other two methods, though use of independent but dichotomous predictors accounted for more variance than aphasia taxonomies. Thus, if we by-pass classical taxonomies and treat patients as points in a multidimensional symptom space, better predictions are obtained. Outlier analyses show that group results depend on heterogeneity among patients, which can be used as a search tool to identify potentially interesting dissociations. Hence this multivariate group approach is complementary to and compatible with single-case methods.

A Molecular Perspective on the Systematics and Evolution of the GenusArvicanthis(Rodentia, Muridae): Inferences from Complete CytochromebGene Sequences

Systematics of the genusArvicanthis,the African unstriped grass rat, are somewhat controversial. Most recent taxonomic revisions list five to six species but the definition of some of these (Arvicanthis dembeensis, Arvicanthis nairobae,andArvicanthis niloticus) is uncertain. The complete mitochondrial cytochromebgene (1140 bp) was sequenced for 20 specimens from throughout the range of the genus to determine the intrageneric genetic structure, construct a molecular phylogeny, and evaluate classical taxonomies. Neighbor-joining and maximum parsimony analyses yielded identical phylogenetic trees that identify two major lineages: the first one (1) is composed of specimens usually referred toA. niloticusbut representing several distinct species, and the other (2) is a complex including “true”A. niloticusfrom Egypt and northern West Africa as well asArvicanthis abyssinicus, Arvicanthis dembeensis,andArvicanthis somalicus.An analysis on a 357-bp fragment of the cytochromebincluding published data onA. nairobaeindicates that this taxon is part of clade (1). Calibration of the number of 3rd position transversion changes with the murid fossil record suggests that clades (1) and (2) diverged approximately 5 Myr ago.Arvicanthis niloticusas currently recognized is a paraphyletic association and this name should be restricted to the Egyptian and northern West African sample. We also suggest referring toA. dembeensisasA. niloticus,as our cytochromebdata do not support its recognition as a distinct species. Clade (1) is subdivided in three lineages, geographically corresponding to southern West, Central, and East Africa. The high genetic divergence detected between the Central African lineage and the other two lineages suggests that they probably represent separate species. Clade (2) experienced rapid cladogenetic events during the late Pliocene, with theA. somalicuslineage being the first to emerge, followed by the ancestor ofA. abyssinicusandA. blicki.This period was characterized by significant climatic and environmental changes, such as the extension of open habitats, which might have provided a stimulus for speciation in this savanna-dwelling genus. Confrontation of our molecular results with chromosomal data shows a high degree of congruence between the two datasets.

New Perspectives for Media Education, Theory and Practice

The development of information technologies and new electronic media has changed the classifications of classical educational media taxonomies: new technologies change the practice, and renew the educational usage. In order to integrate these new media, media education must modify its approach, its framwork of theoretical reference and its methods. The article develops first of all the theoretical framework which acts as the conductor to the new training of instructors in the field of ‘Media and Informatics’ (Department of Psychology and Educational Science, University of Geneva, 1996–97). It is principally a question of redefining the concept of media based on Anderson's work on communication theories: a medium is above all a human activity which has been brought to completion. From this follows such concepts as texts, discussions, course, presentational systems, areas of social interaction, etc. From a methodological view point this idea implies first of all the separation of the different aspects of the mediatization process, so as to then carry out an analysis of their interactions. In the second part, the article presents first of all an operational model which allows the application of this framework to media, and then a look at some work carried out by the students working on this new programme. The article then turns to the analysis of the coherence between a theoretical model and the conditions for its application within a programme of training.

Phylogeography of Brown Bears (Ursus arctos) of Alaska and Paraphyly within the Ursidae

Complete nucleotide sequences of the mitochondrial cytochrome b, tRNAproline, and tRNAthreoninegenes were described for 166 brown bears (Ursus arctos) from 10 geographic regions of Alaska to describe natural genetic variation, construct a molecular phylogeny, and evaluate classical taxonomies. DNA sequences of brown bears were compared to homologous sequences of the polar bear (maritimus) and of the sun bear (Helarctos malayanus), which was used as an outgroup. Parsimony and neighbor-joining methods each produced essentially identical phylogenetic trees that suggest two distinct clades of mtDNA for brown bears in Alaska: one composed only of bears that now reside on some of the islands of southeastern Alaska and the other which includes bears from all other regions of Alaska. The very close relationship of the polar bear to brown bears of the islands of southeastern Alaska as previously reported by us and the paraphyletic association of polar bears to brown bears reported by others have been reaffirmed with this much larger data set. A weak correlation is suggested between types of mtDNA and habitat preference by brown bears in Alaska. Our mtDNA data support some, but not all, of the currently designated subspecies of brown bears whose descriptions have been based essentially on morphology.

A Numerical Taxonomic Study of a Group of Selected Strongylates (Nematoda)

Moss, W. W. (Div. Entomol., U. Calif., Berkeley 94720) and Webster, W. A. 1969. A numerical taxonomic study of a group of selected strongylates (Nematoda). Syst. Zool., 18: 423-443.-A preliminary study of a group of parasitic nematodes tested the usefulness of numerical taxonomy in the recognition of overall similarities and groupings. Two approaches were followed, a 7-OTU study involving average character values, and a 27-OTU study using character values taken from individual replicates. Qualitative and quantitative characters were used, with measurements expressed as percentages of total body length. Distance and correlation coefficients were structured by graphic and cluster analysis, and the various groupings obtained in the two studies were compared. [Numerical phenetics. Experimental taxonomy. Nematoda.] Chitwood (1957) has attributed much of the taxonomic confusion prevalent in modem nematology to four major causes, these being the state of preservation of the material, its interpretation, the presentation of results and, perhaps most important, a general lack of knowledge regarding the limits of intraspecific variability. Goodey (1959) attempted to alleviate some of these difficulties when he proposed numerous criteria to be followed when reporting on new taxa, although even with these precautions the recognition of species limits remains a major problem. The biological species concept has, at present, little applicability to the field of parasitic nematology, an area in which species must be recognized almost entirely on the basis of anatomical evidence. Accordingly, the morphological species concept must still be considered a practical necessity in the recognition of nematode classifications. Classical nematological taxonomies are based on the interpretation of structure, but are frequently influenced strongly by the importance placed by the taxonomist on any given structure, character complex or character. The different systems of classification derived from such interpretations are often radically opposed to each other and frequently, indeed, represent classifications of particular structures, rather than of complete organisms (i.e., they are special, rather than natural classifications in the sense of Davis and Heywood, 1963). In practical terms, when one attempts to place a given nematode in the taxonomic hierarchy, he soon learns that there are about as many systems of classification as there are monographs on the subject. It is obvious that an attempt should be made to stabilize the classification of the parasitic Nematoda, especially since the problem of instability is being constantly compounded by the appearance of additional revisionary works. Without doubt, highly valuable information is contained in many existing nematode taxonomies. However, some of these taxonomies derive largely from interpretations of supposed phylogenetic relationships among nematodes, or among parts of nematodes. This type of taxonomic work, basically authoritarian in concept, can be more detrimental than beneficial to, the progress of an expanding science. In view of the fact that the paleontological record is virtually blank for the parasitic Nematoda, the various evolutionary or phyletic relationships that have been suggested to date for this group are entirely speculative in nature and must be recognized as such. Although some progress has been made on operational phyletic studies in other taxa