An official website of the United States government
Abstract Proleptic (or prothetic) objects (Majaliwa remembered about Samson that he’s sick) present a particular puzzle because they appear to instantiate an unconstrained cross-clausal dependency between the proleptic object (Samson) and a correlate (he). The current analytical approach to prolepsis is relies on a syntactic mechanism of treating the embedded clause as a predicate, derived by merging a null operator which unselectively binds the correlate. This approach faces a number of known empirical challenges. Moreover, this work does not meaningfully engage with any of the recent semantic innovations in our understanding of embedded clauses (Kratzer 2006. Decomposing attitude verbs. Available at:http://semanticsarchive.net/Archive/DcwY2JkM/attitude-verbs2006.pdf). I offer an alternative to the CP-predicate approach, adopting three (semi-)independently motivated ideas concerning (i) the syntax of cross-clausal dependencies in Lohninger et al. (2022. From prolepsis to hyperraising.Philosophies7(32)), (ii) the semantics of embedded clauses in Kratzer (2006. Decomposing attitude verbs. Available at:http://semanticsarchive.net/Archive/DcwY2JkM/attitude-verbs2006.pdf)/Moulton (2009. Not moving clauses: Connectivity in clausal arguments.Syntax16(3). 250–291), and (iii) the semantics ofaboutin Rawlins (2013. About about.Proceedings of SALT23. 336–357)/Onea and Mardale (2020. From topic to object, grammaticalization differential object marking in Romanian.Canadian Journal of Linguistics/Revue Canadienne de Linguistique65(3). 350–392). I argue that proleptic objects are complex-NPs, roughly,the thing about Samson. The somewhat particular properties of prolepsis are natural consequences of these combined ideas. I further present empirical evidence from Japanese that the complex-NP analysis is on the right track. This analysis deepens our understanding of prolepsis by including both semantic and syntactic factors.
more »
« less
Developing and applying computational resources for biochemistry education
Abstract Biochemistry is about structure and function, but it is also about data and this is where computers come in. From my time as a graduate student and post doc, whenever I encountered data I thought, “I can work this up by hand, but I think a computer could do a better job.” Since that time, I have been working at the interface of biochemistry and computers, by attracting talented students and collaborating with colleagues with complementary skills. This has resulted in several exciting projects: a simulation of 2D electrophoresis and tandem mass spectrometry, the human visualization project, and two different programs that enable biochemists to search protein structures for enzyme active sites: ProMOL (promol.org) and Moltimate (moltimate.appspot.com). The human side of software development for education involved finding the right students and colleagues, communicating effectively across disciplines, building and managing effective teams and the importance of serendipity throughout the process.
more »
« less
- Award ID(s):
- 1709170
- PAR ID:
- 10455704
- Publisher / Repository:
- Wiley Blackwell (John Wiley & Sons)
- Date Published:
- Journal Name:
- Biochemistry and Molecular Biology Education
- Volume:
- 48
- Issue:
- 6
- ISSN:
- 1470-8175
- Page Range / eLocation ID:
- p. 579-584
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
Abstract The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), funded by the US National Science Foundation, National Institutes of Health, and Department of Energy, has served structural biologists and Protein Data Bank (PDB) data consumers worldwide since 1999. RCSB PDB, a founding member of the Worldwide Protein Data Bank (wwPDB) partnership, is the US data center for the global PDB archive housing biomolecular structure data. RCSB PDB is also responsible for the security of PDB data, as the wwPDB‐designated Archive Keeper. Annually, RCSB PDB serves tens of thousands of three‐dimensional (3D) macromolecular structure data depositors (using macromolecular crystallography, nuclear magnetic resonance spectroscopy, electron microscopy, and micro‐electron diffraction) from all inhabited continents. RCSB PDB makes PDB data available from its research‐focusedRCSB.orgweb portal at no charge and without usage restrictions to millions of PDB data consumers working in every nation and territory worldwide. In addition, RCSB PDB operates an outreach and educationPDB101.RCSB.orgweb portal that was used by more than 800,000 educators, students, and members of the public during calendar year 2020. This invited Tools Issue contribution describes (i) how the archive is growing and evolving as new experimental methods generate ever larger and more complex biomolecular structures; (ii) the importance of data standards and data remediation in effective management of the archive and facile integration with more than 50 external data resources; and (iii) new tools and features for 3D structure analysis and visualization made available during the past yearviatheRCSB.orgweb portal.more » « less
-
Abstract In-situ visual observations of marine organisms is crucial to developing behavioural understandings and their relations to their surrounding ecosystem. Typically, these observations are collected via divers, tags, and remotely-operated or human-piloted vehicles. Recently, however, autonomous underwater vehicles equipped with cameras and embedded computers with GPU capabilities are being developed for a variety of applications, and in particular, can be used to supplement these existing data collection mechanisms where human operation or tags are more difficult. Existing approaches have focused on using fully-supervised tracking methods, but labelled data for many underwater species are severely lacking. Semi-supervised trackers may offer alternative tracking solutions because they require less data than fully-supervised counterparts. However, because there are not existing realistic underwater tracking datasets, the performance of semi-supervised tracking algorithms in the marine domain is not well understood. To better evaluate their performance and utility, in this paper we provide (1) a novel dataset specific to marine animals located athttp://warp.whoi.edu/vmat/, (2) an evaluation of state-of-the-art semi-supervised algorithms in the context of underwater animal tracking, and (3) an evaluation of real-world performance through demonstrations using a semi-supervised algorithm on-board an autonomous underwater vehicle to track marine animals in the wild.more » « less
-
A Gram-stain-negative, rod-shaped bacterial strain, designatedVibrio floridensisIRLE0018 (=NRRL B-65642=NCTC 14661), was isolated from a cyanobacterial bloom along the Indian River Lagoon (IRL), a large and highly biodiverse estuary in eastern Florida (USA). The results of phylogenetic, biochemical, and phenotypic analyses indicate that this isolate is distinct from species of the genusVibriowith validly published names and is the closest relative to the emergent human pathogen,Vibrio vulnificus. Here, we present the complete genome sequence ofV. floridensisstrain IRLE0018 (4 535 135 bp). On the basis of the established average nucleotide identity (ANI) values for the determination of different species (ANI <95 %), strain IRLE0018, with an ANI of approximately 92 % compared with its closest relative,V. vulnificus, represents a novel species within the genusVibrio. To our knowledge, this represents the first time this species has been described. The results of genomic analyses ofV. floridensisIRLE0018 indicate the presence of antibiotic resistance genes and several known virulence factors, however, its pathogenicity profile (e.g. survival in serum, phagocytosis avoidance) reveals limited virulence potential of this species in contrast toV. vulnificus.more » « less
-
Abstract Journal editors have a large amount of power to advance open science in their respective fields by incentivising and mandating open policies and practices at their journals. The Data PASS Journal Editors Discussion Interface (JEDI, an online community for social science journal editors:www.dpjedi.org) has collated several resources on embedding open science in journal editing (www.dpjedi.org/resources). However, it can be overwhelming as an editor new to open science practices to know where to start. For this reason, we created a guide for journal editors on how to get started with open science. The guide outlines steps that editors can take to implement open policies and practices within their journal, and goes through the what, why, how, and worries of each policy and practice. This manuscript introduces and summarizes the guide (full guide:https://doi.org/10.31219/osf.io/hstcx).more » « less
