A corpus of full-text journal articles is a robust evaluation tool for revealing differences in performance of biomedical natural language processing tools

ABSTRACT: BACKGROUND: We introduce the linguistic annotation of a corpus of 97 full-text biomedical publications, known as the Colorado Richly Annotated Full Text (CRAFT) corpus. We further assess the performance of existing tools for performing sentence splitting, tokenization, syntactic parsing, and named entity recognition on this corpus. RESULTS: Many biomedical natural language processing systems demonstrated large differences between their previously published results and their performance on the CRAFT corpus when tested with the publicly available models or rule sets. Trainable systems differed widely with respect to their ability to build high-performing models based on this data. CONCLUSIONS: The finding that some systems were able to train high-performing models based on this corpus is additional evidence, beyond high inter-annotator agreement, that the quality of the CRAFT corpus is high. The overall poor performance of various systems indicates that considerable work needs to be done to enable natural language processing systems to work well when the input is full-text journal articles. The CRAFT corpus provides avaluable resource to the biomedical natural language processing community for evaluation and training of new models for biomedical full text publications.     

Degenerative and regenerative processes in the olfactory system of homing pigeons.

Experimental resection of the olfactory nerve in the homing pigeon induces a total degeneration of the nerve and olfactory epithelium. The orthograde degenerative process starts before the retrograde one. Ten days after resection, new neurons begin to differentiate from the basal cells. The axon forms earlier than the distal dendritic process, and the speed of growth increases slowly. The regenerated axons only reach the bulb in the 5th month. Two months after resection the olfactory epithelium is similar to that of the intact control side. The ultrastructural features of the mucosa and olfactory axons are similar to those of normal ones.     

[S2], [S3], and [N3] coordination modes of hydrotris(thioxotriazolyl)borato. Zinc, nickel, cobalt, and bismuth complexes

The ligand hydrotris(1,4-dihydro-3-methyl-4-phenyl-5-thioxo-1,2,4-triazolyl)borato (Tr^Ph,Me) was synthetized as natrium salt and the complexes [Zn(Tr^Ph,Me)₂] · 7.5H₂O · 1.5CH₃CN (2a), [Zn(Tr^Ph,Me)₂] · 8DMF (2b), [Co(Tr^Ph,Me)₂] · 8DMF (3a), [Ni(Tr^Ph,Me)₂] · H₂O · 6DMSO (4a), [Bi(Tr^Ph,Me)₂]NO₃ (5), have been isolated and structurally characterized by X-ray diffraction. In the zinc derivatives the ligand adopts different denticity and coordination modes, η² and [S₂] for 2a and η³ and [N₃] for 2b, depending on the crystallization solvent, giving rise to tetrahedral and octahedral geometry, respectively. In the octahedral cobalt and nickel complexes the ligand is η³ and [N₃] coordinated whereas in the bismuth complex the η³ and [S₃] coordination is exhibited.     

Transcriptomic Analysis of Single Isolated Myofibers Identifies miR-27a-3p and miR-142-3p as Regulators of Metabolism in Skeletal Muscle

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A new species of Cucullanus (Nematoda: Cucullanidae) parasitizing Conger orbignianus (Pisces: Congridae) from Argentinean waters

In total, 17 specimens of Conger orbignianus Valenciennes, 1847 from waters off Mar del Plata, Argentina (38 degrees 08'S, 57 degrees 32'W) were examined for parasitic nematodes. A new nematode species, Cucullanus pedroi n. sp., is described (prevalence 76.5%, x intensity +/- SD = 3.8 +/- 2.7). The new species closely resembles some species parasitizing other anguilliform fishes; however, it can be distinguished from most of its congeners by the distribution pattern of caudal papillae (particularly fourth and eight pairs) and phasmids. Those congeners with similar pattern of papillae differ from the new species by the length of the spicules and gubernaculum and by the position of the excretory pore and deirids.     

Pauciconfibula patagonensis sp. nov. (Monogenea: Microcotylidae) parasitizing the horsefish, Congiopodus peruvianus (Pisces: Congiopodidae), from the Patagonian Shelf, Argentina

Pauciconfibula patagonensis sp. nov. (Monogenea: Microcotylidae), parasite of gill filaments of the horsefish, Congiopodus peruvianus (Congiopodidae) collected in the Patagonian Shelf, Argentina, is described and illustrated. The new species is characterized by having intestinal caeca not confluent and entering into the haptor, vitelline follicles extending from the genital pore to near the posterior portion of haptor, two parallel rows each comprised of 16-20 microcotylid clamps in the haptor, 25-43 testes and a fusiform egg with one very long tangled polar filament. P. patagonensis is the only member of the genus known to parasitize a scorpaeniform host and represents the first record of a representative of this genus in the southern Atlantic Ocean.     

Seasonal changes in serum metabolites in free-ranging alpine marmots (<Emphasis Type="Italic">Marmota marmota</Emphasis>)

Circannual changes in serum parameters and body mass were studied in free-ranging Marmota marmota that had been shot in Switzerland (Grisons) for management reasons in May, July, and September of 1995, 1996, and 1997; and in April 1996. Markers of lipid (triglycerides, cholesterol), protein (total protein, urea-nitrogen) and mineral (calcium, inorganic phosphate) metabolism were evaluated in 111 haemolysis-free serum samples; the effects of sex, age, reproductive status, season and year were tested. Mean body mass was higher in adult males than in adult females in July and September, and serum cholesterol concentrations were lower in adult males in May. Pregnant females had lower concentrations of total protein than non-pregnant females, and triglyceride concentrations were negatively correlated with the number of uterine ampullae. Inorganic phosphate decreased and total protein increased with age. In adults, triglycerides, cholesterol and urea-nitrogen increased mainly from May to July and decreased between September and May. Total protein, calcium and phosphate did not change throughout the year. This suggests that, during the active season, ingested lipids and amino acids were utilised for metabolic needs or lipid storage, while in winter, lipids were catabolised and protein was spared. Quantitative differences between years, observed for triglycerides and total protein during the active season, were probably due to different climatic conditions in each year.