A formal theory for spatial representation and reasoning in biomedical ontologies

Objective: The objective of this paper is to demonstrate how a formal spatial theory can be used as an important tool for disambiguating the spatial information embodied in biomedical ontologies and for enhancing their automatic reasoning capabilities. Method and Materials: This paper presents a formal theory of parthood and location relations among individuals, called Basic Inclusion Theory (BIT). Since biomedical ontologies are comprised of assertions about classes of individuals (rather than assertions about individuals), we define parthood and location relations among classes in the extended theory BIT+Cl (Basic Inclusion Theory for Classes). We then demonstrate the usefulness of this formal theory for making the logical structure of spatial information more precise in two ontologies concerned with human anatomy: the Foundational Model of Anatomy (FMA) and GALEN. Results: We find that in both the FMA and GALEN, class-level spatial relations with different logical properties are not always explicitly distinguished. As a result, the spatial information included in these biomedical ontologies is often ambiguous and the possibilities for implementing consistent automatic reasoning within or across ontologies are limited. Conclusion: Precise formal characterizations of all spatial relations assumed by a biomedical ontology are necessary to ensure that the information embodied in the ontology can be fully and coherently utilized in a computational environment. This paper can be seen as an important beginning step toward achieving this goal, but much more work is along these lines is required

The Application of Electrokinetics to Improve Sludge Dewatering

The waste, or sludge, from a mill contains a significant amount of water. It is desirable to remove as much water as possible before the sludge goes to a landfill. In the past electrokinetics have been used to separate solids and liquids in the mining and clay industries. The objective of this thesis project was to determine if the application of electrokinetics can increase the drainage rate of sludge by transmitting an electric current through the sludge. On a larger scope, this application may be used in addition to another process for increased efficiency. The experiment contained sludge placed between two charged metal screens. The drainage was measured and compared to a control run with no voltage applied to the screens. The results demonstrated that applying en electric field to sludge increased the drainage rate. The increased drainage was due to electro-osmotic forces, which forced the water out of the electrode carrying water molecules with them. The pH of the filtrate was tested and found to change either acidic or basic, depending on the arrangement of the electrodes, which indicated chemical reactions were occurring. In conclusion, the application of electrokinetics increases sludge dewatering. I recommend further investigation into the possibilities of applying this concept to another pressing or filtering process which would result in a more efficient process. The drastic change in pH opened other areas for study, as electrokinetics can be used to remove or direct chemical contaminants

Endurants and Perdurants in Directly Depicting Ontologies

We propose an ontological theory that is powerful enough to describe both complex spatio-temporal processes and the enduring entities that participate therein. For this purpose we introduce the notion a directly depicting ontology. Directly depicting ontologies are based on relatively simple languages and fall into two major categories: ontologies of type SPAN and ontologies of type SNAP. These represent two complementary perspectives on reality and employ distinct though compatible systems of categories. A SNAP (snapshot) ontology comprehends enduring entities such as organisms, geographic features, or qualities as they exist at some given moment of time. A SPAN ontology comprehends perduring entities such as processes and their parts and aggregates as they unfold themselves through some temporal interval. We give an axiomatic account of the theory of directly depicting ontologies and of the core parts of the metaontological fragment within which they are embedded

¿DÓNDE DUERMEN LAS AVES? OBSERVACIONES DE AVES DESCANSANDO EN EL SOTOBOSQUE DE LAS TIERRAS BAJAS DE COSTA RICA

El uso del hábitat nocturno de las aves diurnas es poco conocido. Este estudio presenta observaciones de los sitios de descanso y comportamiento nocturnal de 18 especies de aves en el sotobosque de las tierras bajas de Costa Rica. Realizamos muestreos nocturnos en hábitats riparios y no-riparios en potreros, bosques secundarios y bosques maduros. Observamos un mayor número de aves posadas en hábitats riparios (67) que en hábitats no riparios (3). El sotobosque ripario es utilizado por un grupo diverso de especies de aves como dormidero. Nuestras observaciones resaltan la importancia de corredores riparios, especialmente en hábitats alterados por el ser humano como los potreros

Description of the Tadpoles of \u3cem\u3eGastrophryne pictiventris\u3c/em\u3e and \u3cem\u3eNelsonophryne aterrima\u3c/em\u3e (Anura: Microhylidae), with a Review of Morphological Variation in Free-Swimming Microhylid Larvae

The tadpoles of Gastrophryne pictiventris and Nelsonophryne aterrima are described based on material collected in Costa Rica and Panama, respectively. The tadpole of G. pictiventris resembles those of the other species of Gastrophryne. The tadpole of N. aterrima differs from other New World microhylid tadpoles in location of the vent tube (medial), the spiracular opening (ventral to the gut), and eyes (dorsolateral). The unique configuration of mouthparts in N. aterrima is described. Morphological variation in microhylid tadpoles is reviewed and six larval characters are analyzed cladistically for IO New World microhylid genera

The logic of systems of granular partitions

The theory of granular partitions is designed to capture in a formal framework important aspects of the selective character of common-sense views of reality. It comprehends not merely the ways in which we can view reality by conceiving its objects as gathered together not merely into sets, but also into wholes of various kinds, partitioned into parts at various levels of granularity. We here represent granular partitions as triples consisting of a rooted tree structure as first component, a domain satisfying the axioms of Extensional Mereology as second component, and a mapping (called ’projection’) of the first into the second as a third component. We define ordering relations among granular partitions the resulting structures are called partition frames. We then introduce an axiomatic theory which sentences are interpreted in partition frame

Auyantepui herpetofauna

147 p. : ill. (some col.), map ; 26 cm.Includes bibliographical references (p. 138-147).Auyantepui is an immense sandstone table mountain in the Venezuelan Guayana. This mesa did not appear on aviation maps and was unknown to the literate world prior to the late 1930s. It was explored from the air by Jimmy Angel, a bush pilot and colorful soldier of fortune for whom the world's highest waterfall is named (Angel Falls at the northern end of Auyantepui). About the same time, in 1937, Captain Félix Cardona Puig and Gustavo Heny discovered an access crack in the sandstone, allowing ascent onto the southern end of the mesa. The first scientific exploration followed immediately--the 1937-1938 Phelps Venezuelan Expedition of the American Museum of Natural History made the first zoological and general botanical collections. Today, no tepui other than the "Lost World" of Cerro Roraima is better known to the general public. The summit of Auyantepui has a known fauna of 24 species of amphibians and reptiles, including species added by the Robert G. Goelet American Museum-TERRAMAR Expedition in 1994. This expedition collected 16 species during a month of fieldwork in the dry season (February), in five camps at elevations of 1700-2100 m above sea level. All species known from the summit of Auyantepui are treated in this bulletin; illustrations where possible include tadpoles, bioacoustic spectrograms, and hemipenes. Four new species are described--two frogs (Hypsiboas angelicus, n. sp., Eleutherodactylus auricarens, n. sp.), a lizard (Arthrosaura montigena, n. sp.), and a snake (Atractus guerreroi, n. sp.). Arthrosaura montigena possesses a hemipenial character not previously described--an orifice (orificium) of unknown function, situated in the lobular crotch between the two lobes. Attention is called to a probably undescribed snake (Liophis "miliaris" sensu lato) from the nearby Gran Sabana. The herpetofauna of the Auyán summit comprises 12 families, 20 genera, and 24 species. This is compared with the known herpetofauna of the Chimantá massif, lying less than 50 km south-southeast of Auyantepui. Despite the proximity and similar dimensions, the summits of Auyantepui and Chimantá have in common only 11% of the combined number of species (4 of 36), 44% of the genera (11 of 25), and 62% of the families represented (8 of 13), showing that neighboring tepuis may have herpetofaunas very different from one another. Nonetheless, the adjacent mountains that constitute the more fragmented Chimantá massif are relatively close to one another and seem to have a unified herpetofauna

Yutajé-Corocoro massif.

85 p. : ill. (some col.) ; 26 cm.Includes bibliographical references (p. 82-85).The Yutajé-Corocoro massif is a highly eroded sandstone table mountain, with internal drainage mainly to the central valley of the Río Corocoro, a stream in the headwater drainage of the Río Manapiare--some 100 km east of the middle Río Orinoco, at the northern edge of the State of Amazonas in southern Venezuela. The rocky soil supports a mosaic of diverse scrubland and forest, with small tepui meadows at the higher elevations. The herpetofauna is depauperate, as is typical of the Venezuelan tepuis. Eight species of amphibians and reptiles were collected during a 7-day period in the dry season (February). This sample includes two new frogs (Hyalinobatrachium eccentricum, n. sp., Centrolenidae; Colostethus undulatus, n. sp., Dendrobatidae) and a new genus and species of lizards (Adercosaurus vixadnexus, n. gen. & sp., Teiidae), all of which were found in humid montane mossy forest at 1700-1750 m elevation. Another new lizard (Tropidurus panstictus, n. sp., Tropiduridae) was discovered at lower elevations (180-1220 m), especially in dry scrub. The fauna also includes a widespread lowland frog (Pseudopaludicola llanera Lynch), two tepui frogs (Eleutherodactylus cantitans Myers and Donnelly; E. yaviensis Myers and Donnelly), a tepui lizard (Prionodactylus goeleti (Myers and Donnelly), new combination), a snake (Liophis?) that escaped capture, and another snake (Thamnodynastes corocoroensis Gorzula and Ayarzagüena) obtained by S. Gorzula in 1987. The two Eleutherodactylus and the Prionodactylus also occur on neighboring Cerro Yaví (the type locality), although one of the frogs (E. yaviensis) and the lizard show evidence of differentiation. Based on the original description, the snake Thamnodynastes corocoroensis appears to be distinct from a related species on Cerro Yaví. Two of the new species exhibit characters that are novel or not previously noted. The dendrobatid frog Colostethus undulatus, n. sp. has a glandular supracarpal pad atop the wrist, being best developed in males. This species, which also has the parasphenoid bone curiously concealed, seems to be unusual among tepui Colostethus in lacking the recently described median lingual process. The centrolenid frog Hyalinobatrachium eccentricum, n. sp. has a peculiar bicolored iris, with a dark median sector that conceals the pupil and which apparently dilates with the pupil. This character is retained in preservative and differentiates H. eccentricum from H. crurifasciatum Donnelly and Myers. Both species share a previously overlooked bubblelike structure in the web between the third and fourth fingers, herein termed bulla (possibly parasite induced?)