Muscle Logic: New Knowledge Resource for Anatomy Enables Comprehensive Searches of the Literature on the Feeding Muscles of Mammals.

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.

Ink Under the Fingernails: Making Print in Nineteenth-Century Mexico City

This dissertation examines Mexico City’s material politics of print—the central actors engaged in making print, their activities and relationships, and the legal, business, and social dimensions of production—across the nineteenth century. Inside urban printshops, a socially diverse group of men ranging from manual laborers to educated editors collaborated to make the printed items that fueled political debates and partisan struggles in the new republic. By investigating how print was produced, regulated, and consumed, this dissertation argues that printers shaped some of the most pressing conflicts that marked Mexico’s first formative century: over freedom of expression, the role of religion in government, and the emergence of liberalism. Printers shaped debates not only because they issued texts that fueled elite politics but precisely because they operated at the nexus where new liberal guarantees like freedom of the press and intellectual property intersected with politics and patronage, the regulatory efforts of the emerging state, and the harsh realities of a post-colonial economy.

Historians of Mexico have typically approached print as a vehicle for texts written by elites, which they argue contributed to the development of a national public sphere or print culture in spite of low literacy levels. By shifting the focus to print’s production, my work instead reveals that a range of urban residents—from prominent printshop owners to government ministers to street vendors—produced, engaged, and deployed printed items in contests unfolding in the urban environment. As print increasingly functioned as a political weapon in the decades after independence, print production itself became an arena in struggles over the emerging contours of politics and state formation, even as printing technologies remained relatively unchanged over time.

This work examines previously unexplored archival documents, including official correspondence, legal cases, business transactions, and printshop labor records, to shed new light on Mexico City printers’ interactions with the emerging national government, and reveal the degree to which heated ideological debates emerged intertwined with the most basic concerns over the tangible practices of print. By delving into the rich social and cultural world of printing—described by intellectuals and workers alike in memoirs, fiction, caricatures and periodicals— it also considers how printers’ particular status straddling elite and working worlds led them to challenge boundaries drawn by elites that separated manual and intellectual labors. Finally, this study engages the full range of printed documents made in Mexico City printshops not just as texts but also as objects with particular visual and material qualities whose uses and meanings were shaped not only by emergent republicanism but also by powerful colonial legacies that generated ambivalent attitudes towards print’s transformative power.