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Diachronic semantics: changes of meaning of words over time and the consequences for keeping classification systems up to date
<p>Meanings of words in a natural language are changing over time under the influences of different factors. Words adapt to new meanings, lose old meanings, rearrange current meanings and change some parts of previous meanings, etc. The language as a living organism needs to be able to accept and adapt to those changes. Like natural languages, artificial languages such as classification systems or subject indexing systems have to adjust to those changes too. Linguist F. de Saussure defines language as a 'system of signs'. If we transfer this definition into the artificial language such as a classification system (e.g., Universal Decimal Classification (UDC)) and define it also as a 'system of signs' which has a vocabulary, a grammar and a syntax, we could draw parallels between phenomena which occur in natural and in artificial languages. The young linguistic discipline which deals with changes in meanings over time is called diachronic semantics and this paper explores how its mechanisms can be used to analyze the changes that occur in classification systems over time. Diachronic semantics uses various mechanisms to describe adapting and changing meanings of words. These mechanisms include: metaphor, metonymy, specialization, generalization, analogy and splitting. This paper also aims to explain the borrowing and adjusting of the theory from the field of linguistics into the field of information sciences.</p>
Table e-1 and e-references for: Neurogenic dysphagia: a systematic review and proposal of a classification system
<p><b>Objective:</b> Introduction of a phenotypic classification of dysphagia with differential diagnostic implications and its validation in different disease groups using videos of flexible endoscopic evaluation of swallowing (FEES).</p> <p><b>Methods: </b>A systematic literature review was performed to summarize disease-typical FEES-findings.<b> </b>In an interdisciplinary team, a FEES-based classification of neurogenic dysphagia was developed which distinguishes different dysphagia phenotypes. The classification was validated using 1012 randomly selected FEES videos of patients with various neurological disorders. Chi-square tests were applied to investigate the relationship between the disease groups and each dysphagia phenotype.</p> <p><b>Results: </b>Seven dysphagia phenotypes were defined and all phenotypes were significantly associated with specific neurological disease groups: (1) "Premature bolus spillage" and (2) "delayed swallowing reflex" occurred mainly in stroke patients, (3) "predominance of residue in the valleculae" was most common in Parkinson's disease, (4) "predominance of residue in the piriform sinus" occurred only in myositis, motoneuron disease and brainstem stroke patients, (5) "pharyngolaryngeal movement disorder" was found in atypical Parkinsonian syndromes and stroke patients, (6) "fatigable swallowing weakness" was common in patients with myasthenia gravis, and (7) "complex disorder" with a heterogeneous dysphagia pattern was the leading mechanism in amyotrophic later sclerosis. The interrater reliability showed a strong agreement (kappa = 0.84).</p> <p><b>Conclusion: </b>Neurogenic dysphagia is not a mere symptom, but a multi-etiological syndrome with different phenotypic patterns depending on the underlying disease. Dysphagia phenotypes can facilitate differential diagnosis in patients with dysphagia of unclear etiology.</p>
Figure 5 from: Trajano E, Carvalho MR (2017) Towards a biologically meaningful classification of subterranean organisms: a critical analysis of the Schiner-Racovitza system from a historical perspective, difficulties of its application and implications for conservation. Subterranean Biology 22: 1-26. https://doi.org/10.3897/subtbiol.22.9759
Figure 5 - Highly troglomorphic catfish, genus Rhamdiopsis (Siluriformes: Heptapteridae), a relict from Campo Formoso karst area, northeastern Brazil (Photo: Dante Fenolio).
Figure 2 from: Trajano E, Carvalho MR (2017) Towards a biologically meaningful classification of subterranean organisms: a critical analysis of the Schiner-Racovitza system from a historical perspective, difficulties of its application and implications for conservation. Subterranean Biology 22: 1-26. https://doi.org/10.3897/subtbiol.22.9759
Figure 2 - Interrelationships between evolutionary (historical) and ecological (present-day) factors, defining the conditions of trogloxenes versus troglophiles versus troglobites for subterranean organisms.
Figure 1 from: Trajano E, Carvalho MR (2017) Towards a biologically meaningful classification of subterranean organisms: a critical analysis of the Schiner-Racovitza system from a historical perspective, difficulties of its application and implications for conservation. Subterranean Biology 22: 1-26. https://doi.org/10.3897/subtbiol.22.9759
Figure 1 - Trichomycterus itacarambiensis (Siluriformes: Trichomycteridae), troglobitic catfish from eastern Brazil, showing intrapopulation variation in pigmentation and eye development (Photos: Dante Fenolio). A pigmented individual, with reduced eyes and pigmentation B albino (DOPA (–) individual, with very reduced eyes, not visible externally.
Figure 4 from: Trajano E, Carvalho MR (2017) Towards a biologically meaningful classification of subterranean organisms: a critical analysis of the Schiner-Racovitza system from a historical perspective, difficulties of its application and implications for conservation. Subterranean Biology 22: 1-26. https://doi.org/10.3897/subtbiol.22.9759
Figure 4 - Ctenus fasciatus (Arachnida: Araneae), a common troglophile in caves from southeastern Brazil (Photo: Renata Nunes).
Figure 3 from: Trajano E, Carvalho MR (2017) Towards a biologically meaningful classification of subterranean organisms: a critical analysis of the Schiner-Racovitza system from a historical perspective, difficulties of its application and implications for conservation. Subterranean Biology 22: 1-26. https://doi.org/10.3897/subtbiol.22.9759
Figure 3 - Acutisoma spelaeum (Arachnida: Opilioes), an obligatory trogloxene from caves in southeastern Brazil: female taking care of eggs (Photo: Renata Nunes).
FIG. 36 in A new subfamily classification of the highly diversified Dorippidae H. Milne Edwards, 1837 (Crustacea, Decapoda, Brachyura, Dorippoidea), using morphological, molecular and palaeotonlogical data, with special emphasis on its unique female reproductive system
FIG. 36. — Schematic reconstructions of some female reproductive systems in Brachyura: A, in a podotreme crab, with spermatheca as cuticular invagination derived from a split between plates of intersegmental phragma 7/8, independent of the rest of reproductive system (gonopore on P3 coxa), and with external fertilisation; B, in Dorippe sinica (Dorippinae n. stat.), with glandular and cuticle chambers independent of seminal receptacle (not connected to ovary) and extension of vulva where fertilisation can take place (from Hayer et al. 2016a: fig. 8A). In Paradorippinae n. subfam. (not shown, but see Fig. 35D), without seminal receptacle, the fertilisation occurs externally in vulva opening (according to Vehof et al. 2018b: fig. 3; Vehof 2020); C, in Ethusa mascarone (Ethusidae), with glandular and cuticle chambers largely independent of the seminal receptacle (according to Hayer et al. 2016b: fig. 8); D, in a generalised eubrachyuran (one of several patterns), with seminal receptacle directly connected to ovary via oviduct, with vulvar opening on sternite 6 and with internal fertilisation. Abbreviations: as, spermathecal aperture; cc, cuticule chamber; cx3, coxa of P3 with coxal gonopore; gc, glandular chamber; m, musculature; od, oviduct; ov, ovary; P3, third pereiopod; sp, spermatheca; sr, seminal receptacle; vg, vagina; v, vulva.
FIG. 24. — Paradorippinae n in A new subfamily classification of the highly diversified Dorippidae H. Milne Edwards, 1837 (Crustacea, Decapoda, Brachyura, Dorippoidea), using morphological, molecular and palaeotonlogical data, with special emphasis on its unique female reproductive system
FIG. 24. — Paradorippinae n. subfam. Paradorippe granulata (De Haan, 1841): habitus: A, ♂ 23.6 × 27.3 mm, NE Taiwan, I-Lan county, ZRC 2001.0014; B, ovigerous ♀ 23. 2 × 25.7 mm, Japan, off Hota, ZRC 1999.0082.
FIG. 26. — Paradorippinae n in A new subfamily classification of the highly diversified Dorippidae H. Milne Edwards, 1837 (Crustacea, Decapoda, Brachyura, Dorippoidea), using morphological, molecular and palaeotonlogical data, with special emphasis on its unique female reproductive system
FIG. 26. — Paradorippinae n. subfam. Paradorippe granulata (De Haan, 1841): A-C, ovigerous ♀ 23.2 × 25.7 mm, Japan, off Hota, ZRC 1999.0082. D, ♀ 22.7 × 24, 7 mm, China, Tuandao, off Quingdao, MNHN-IU-2016-10753. A, anterior ventral view; B, C, thoracic sternum and pleon; D, vulvae.
FIG. 22. — Medorippinae n in A new subfamily classification of the highly diversified Dorippidae H. Milne Edwards, 1837 (Crustacea, Decapoda, Brachyura, Dorippoidea), using morphological, molecular and palaeotonlogical data, with special emphasis on its unique female reproductive system
FIG. 22. — Medorippinae n. subfam. Medorippe lanata (Linnaeus, 1767): A, ♂ 18.5 × 23.2 mm, Dahomey Coasts, ZRC 2009.0411: habitus; B, ovigerous ♀ 21.2 × 27.7 mm, Israel, ZRC 1999.0632: habitus; C-E, ♂ 18.5 × 23.2 mm, same data as A: C, anterior ventral view; D, thoracic sternum, press-button and G1; E, G1 and G2. F, ♂ 23.2 × 28.9 mm, no data, ZRC 2009.0412 (ex MNHN): thoracic sternum with pleon.
FIG. 17. — Dorippoidinae n in A new subfamily classification of the highly diversified Dorippidae H. Milne Edwards, 1837 (Crustacea, Decapoda, Brachyura, Dorippoidea), using morphological, molecular and palaeotonlogical data, with special emphasis on its unique female reproductive system
FIG. 17. — Dorippoidinae n. subfam. Dorippoides facchino (Herbst, 1785): A-C, ♂ 25.3 × 32 mm, Malaysia, Johore, Pontian, ZRC 1991.66-72: A, anterior ventral view; B, thoracic sternum with pleon; C, without pleon. D, ovigerous ♀ 21 × 25 mm, South China Sea, MNHN-IU-2018-5195 (= MNHN-B18802): vulvae.
FIG. 15. — Dorippinae H. Milne Edwards, 1837 n in A new subfamily classification of the highly diversified Dorippidae H. Milne Edwards, 1837 (Crustacea, Decapoda, Brachyura, Dorippoidea), using morphological, molecular and palaeotonlogical data, with special emphasis on its unique female reproductive system
FIG. 15. — Dorippinae H. Milne Edwards, 1837 n. stat.: A-D, J, Dorippe trilobata Manning, 1993, holotype, ♂ 20.5 × 21.1 mm, off Mitchell River, Admiralty Gulf, AM P27124: A, habitus; B, ventral surface; C, carapace; D, pleon; J, callosity. E-I: Dorippe glabra Manning, 1993, holotype, ovigerous ♀ 24.3 × 26.7 mm, Chambers Bay, Australia, AM P13363: E, habitus with detached right cheliped, right P2 and P3, left P3; F, carapace; G, ventral surface; H, pleon; I, callosity.
FIG. 38 in A new subfamily classification of the highly diversified Dorippidae H. Milne Edwards, 1837 (Crustacea, Decapoda, Brachyura, Dorippoidea), using morphological, molecular and palaeotonlogical data, with special emphasis on its unique female reproductive system
FIG. 38. — Phylogenetic tree of the concatenated dataset obtained by Bayesian Inference analysis. Numbers above branches indicate Bayesian posterior probabilities; numbers under branches indicate Maximum Likelihood bootstrap values (tree by Valentin de Mazancourt).
FIG. 3 in A new subfamily classification of the highly diversified Dorippidae H. Milne Edwards, 1837 (Crustacea, Decapoda, Brachyura, Dorippoidea), using morphological, molecular and palaeotonlogical data, with special emphasis on its unique female reproductive system
FIG. 3. — Carapace diversity in the nine dorippid genera: A, Dorippe Weber, 1795 (D. quadridens); B, Dorippoides Serène & Romimohtarto, 1969 (D. facchino); C, Medorippe Manning & Holthuis, 1981 (?M. crosnieri); D, Heikeopsis Ng, Guinot & Davie, 2008 (H. aff. japonica); E, Neodorippe Serène & Romimohtarto, 1969 (N. callida); F, Nobilum Serène & Romimohtarto, 1969 (N. histrio); G, Paradorippe Serène & Romimohtarto, 1969 (P. cathayana); H, Philippidorippe Chen, 1986 (P. philippinensis); I, Phyllodorippe Manning & Holthuis, 1981 (P. armata). A-G, I: modified from Sin et al. (2009: fig. 3); H, from Chen (1986: pl. 1, fig. 3). The strip, which is shown here only in Dorippoides facchino (Herbst, 1785) and Medorippe?crosnieri Chen, 1988, is in fact present in all species of dorippids.
EEG Classification System for Dementia
ClinicalTrials.gov study NCT02273921. IPD Sharing: Not stated. Countries: 0. Publications: 3.
A Decision Support System Based on Classification Algorithms for the Diagnosis of Periodontal Disease
ClinicalTrials.gov study NCT06071338. IPD Sharing: NO. Countries: 0. Publications: 2.
Data from: A classification system for zebrafish adipose tissues
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Data from: Census parcels cropping system classification from multitemporal remote imagery: a proposed universal methodology
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Table e-1 and e-references for: Neurogenic dysphagia: a systematic review and proposal of a classification system
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.