Search

BackgroundIn recent years large bibliographic databases have made much of the published literature of biology available for searches. However, the capabilities of the search engines integrated into these databases for text-based bibliographic searches are limited. To enable searches that deliver the results expected by comparative anatomists, an underlying logical structure known as an ontology is required.Development and testing of the ontologyHere we present the Mammalian Feeding Muscle Ontology (MFMO), a multi-species ontology focused on anatomical structures that participate in feeding and other oral/pharyngeal behaviors. A unique feature of the MFMO is that a simple, computable, definition of each muscle, which includes its attachments and innervation, is true across mammals. This construction mirrors the logical foundation of comparative anatomy and permits searches using language familiar to biologists. Further, it provides a template for muscles that will be useful in extending any anatomy ontology. The MFMO is developed to support the Feeding Experiments End-User Database Project (FEED, https://feedexp.org/), a publicly-available, online repository for physiological data collected from in vivo studies of feeding (e.g., mastication, biting, swallowing) in mammals. Currently the MFMO is integrated into FEED and also into two literature-specific implementations of Textpresso, a text-mining system that facilitates powerful searches of a corpus of scientific publications. We evaluate the MFMO by asking questions that test the ability of the ontology to return appropriate answers (competency questions). We compare the results of queries of the MFMO to results from similar searches in PubMed and Google Scholar.Results and significanceOur tests demonstrate that the MFMO is competent to answer queries formed in the common language of comparative anatomy, but PubMed and Google Scholar are not. Overall, our results show that by incorporating anatomical ontologies into searches, an expanded and anatomically comprehensive set of results can be obtained. The broader scientific and publishing communities should consider taking up the challenge of semantically enabled search capabilities.

Author(s): Bhart-Anjan S. Bhullar [sup.1] [sup.2] , Armita R. Manafzadeh [sup.3] , Juri A. Miyamae [sup.1] [sup.2] , Eva A. Hoffman [sup.4] , Elizabeth L. Brainerd [sup.3] , Catherine Musinsky [...]

Over the past two centuries, mammalian chewing and related anatomical features have been among the most discussed of all vertebrate evolutionary innovations.sup.1-3. Chief among these features are two characters: the dentary-only mandible, and the tribosphenic molar with its triangulated upper cusps and lower talonid basin.sup.3-5. The flexible mandibular joint and the unfused symphysis of ancestral mammals--in combination with transformations of the adductor musculature and palate--are thought to have permitted greater mobility of each lower jaw, or hemimandible.sup.6,7. Following the appearance of precise dental occlusion near the origin of the mammalian crown.sup.8,9, therians evolved a tribosphenic molar with a craggy topography that is presumed to have been used to catch, cut and crush food. Here we describe the ancestral tribosphenic therian chewing stroke, as conserved in the short-tailed opossum Monodelphis domestica: it is a simple symmetrical sequence of lower tooth-row eversion and inversion during jaw opening and closing, respectively, enacted by hemimandibular long-axis rotation. This sequence is coupled with an eversion-inversion rotational grinding stroke. We infer that the ancestral therian chewing stroke relied heavily on long-axis rotation, including symmetrical eversion and inversion (inherited from the first mammaliaforms) as well as a mortar-and-pestle rotational grinding stroke that was inherited from stem therians along with the tribosphenic molar. The yaw-dominated masticatory cycle of primates, ungulates and other bunodont therians is derived; it is necessitated by a secondarily fused jaw symphysis, and permitted by the reduction of high, interlocking cusps.sup.10-12. The development of an efficient masticatory system--culminating in the tribosphenic apparatus--allowed early mammals to begin the process of digestion by shearing and crushing food into small boli instead of swallowing larger pieces in the reptilian manner, which necessitates a long, slow and wholly chemical breakdown. The vast diversity of mammalian teeth has emerged from the basic tribosphenic groundplan.sup.13. The ancestral tribosphenic therian chewing stroke is conserved in Monodelphis domestica, and couples tooth-row eversion and inversion in jaw opening and closing, respectively, with a rotational grinding stroke., Author(s): Bhart-Anjan S. Bhullar [sup.1] [sup.2] , Armita R. Manafzadeh [sup.3] , Juri A. Miyamae [sup.1] [sup.2] , Eva A. Hoffman [sup.4] [sup.5] , Elizabeth L. Brainerd [sup.3] , Catherine [...]

CT visualization of the mandible and dentition of Hadrocodium wui, a stem mammaliaform from the Lower Jurassic Lower Lufeng Formation of Yunnan, China has revealed new features not accessible by previous microscopic study of the fossil. Its mandible shows a postdentary trough with an overhanging medial ridge and a short Meckel's sulcus. An incomplete part of the ectotympanic and possibly a remnant of Meckel's element are preserved in the postdentary trough. Thus, Hadrocodium is similar to other mammaliaforms in retaining a mandibular middle ear, contrary to our earlier interpretation. The mandible exhibits a large postcanine diastema from shedding of anterior premolars without replacement, an age-dependent feature better developed in older adults. Another adult feature is the alignment of the ultimate molar to the coronoid process. This is consistent with age-dependent changes in other mammaliaforms where the last molars of the toothrow shift from medial of the coronoid process in the juvenile, to a position in front of the coronoid process in the adult. The mandible has a short mobile symphysis. The dentition consists of I5, C1 (two-rooted), P3 (including P1 position) and M2 (M2 with confluent roots), and i4, c1 (partially two-rooted), p3, and m2 (m2 with partially confluent roots). The two-rooted upper canines are more derived than other Early Jurassic mammaliaforms from the same fauna, although similar to docodontans. Hadrocodium is unique in that the lower m2 cusp a occludes in the embrasure between upper M1-M2, but the posterior part of m2 shows between-cusp occlusion with upper M2 main cusp A. M2 is half the size of the lower m2, and occludes only with the distal half of m2. The upper postcanines show a steep gradient of posteriorly decreasing tooth size, more so than other mammaliaforms. The CT examination corroborates that there are no unerupted teeth in the upper or lower jaws, and the holotype of H. wui is dentally and osteologically mature and capable of independent feeding. [ABSTRACT FROM AUTHOR]

Background: In recent years large bibliographic databases have made much of the published literature of biology available for searches. However, the capabilities of the search engines integrated into these databases for text-based bibliographic searches are limited. To enable searches that deliver the results expected by comparative anatomists, an underlying logical structure known as an ontology is required. Development and Testing of the Ontology Here we present the Mammalian Feeding Muscle Ontology (MFMO), a multi-species ontology focused on anatomical structures that participate in feeding and other oral/pharyngeal behaviors. A unique feature of the MFMO is that a simple, computable, definition of each muscle, which includes its attachments and innervation, is true across mammals. This construction mirrors the logical foundation of comparative anatomy and permits searches using language familiar to biologists. Further, it provides a template for muscles that will be useful in extending any anatomy ontology. The MFMO is developed to support the Feeding Experiments End-User Database Project (FEED, https://feedexp.org/), a publicly-available, online repository for physiological data collected from in vivo studies of feeding (e.g., mastication, biting, swallowing) in mammals. Currently the MFMO is integrated into FEED and also into two literature-specific implementations of Textpresso, a text-mining system that facilitates powerful searches of a corpus of scientific publications. We evaluate the MFMO by asking questions that test the ability of the ontology to return appropriate answers (competency questions). We compare the results of queries of the MFMO to results from similar searches in PubMed and Google Scholar. Results and Significance Our tests demonstrate that the MFMO is competent to answer queries formed in the common language of comparative anatomy, but PubMed and Google Scholar are not. Overall, our results show that by incorporating anatomical ontologies into searches, an expanded and anatomically comprehensive set of results can be obtained. The broader scientific and publishing communities should consider taking up the challenge of semantically enabled search capabilities.

The masticatory motor patterns of three tammar wallabies and two red kangaroos were determined by analyzing the pattern of electromyographic (EMG) activity of the jaw adductors and correlating it with lower jaw movements, as recorded by digital video and videoradiography. Transverse jaw movements were limited by the width of the upper incisal arcade. Molars engaged in food breakdown during two distinct occlusal phases characterized by abrupt changes in the direction of working-side hemimandible movement. Separate orthal (Phase I) and transverse (Phase II) trajectories were observed. The working-side lower jaw initially was drawn laterally by the balancing-side medial pterygoid and then orthally by overlapping activity in the balancing- and working-side temporalis and the balancing-side superficial masseter and medial pterygoid. Transverse movement occurred principally via the working-side medial pterygoid and superficial masseter. This pattern contrasted to that of placental herbivores, which are known to break down food when they move the working-side lower jaw transversely along a relatively longer linear path without changing direction during the power stroke. The placental trajectory results from overlapping activity in the working- and balancing-side adductor muscles, suggesting that macropods and placental herbivores have modified the primitive masticatory motor pattern in different ways., Anthropology