cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Newspaper Clippings, January 1957
Creators: name: No Name Supplied
Publisher: name: No Publisher Supplied
Year: 1957

description: The newspaper clippings of 1957 document U.S. and U.N. policy towards Hungarian refugees.  The clippings also focus on the growing tension in Hungary between its government and its citizens. The reproduced documents represent one folder from the Hungarian Refugee Relief Files, an archival series included in the Tracy S. Voorhees Papers, a manuscript collection owned by Special Collections and University Archives, Rutgers University Libraries. For background information concerning Voorhees and the entire contents of the Hungarian Refugee Relief Files, consult (http://hi.rutgers.edu/resources/resourcesrefugees#pres-committe-relief).
Changing the Focus of Physical Education in NJ High Schools to Help Decrease the Growing Obesity Epidemic
Creators: name: Bostrom, Emily
name: Lewis Jr., Wayne
name: Lapidus, Ryan
name: So, Paul
name: Hanhrahan, Tom
name: Fagan, Julie M.
Publisher: name: No Publisher Supplied
Year: 2010

description: Changing gym requirements in NJ to allow students to participate in activities they are passionate about, to improve adolescent health
Rutgers Helps Haiti Earthquake
Creators: name: Eisen, Lauren
name: Gobbo, Dana
name: Plote, Devin
name: Powell, Jonathan
name: Fagan, Julie M.
Publisher: name: No Publisher Supplied
Year: 2010

description: From Classipedia, Fagan's team helps Haiti with medical supplies
description: Led by Dr. Julie Fagan, the Rutgers Ethics in Science Team has pulled together over 60 boxes to be sent out by Royal Caribbean to help aid Haiti in their desperate time of need.  This team is comprised of several dedicated students who have donated their time to organizing much needed medical supplies that will help the medical units in Haiti with their treatment for the survivors. These packages included needles, sutures, tubes, thousands of gloves, face masks, and beanie babies for the orphanage.
Geodynamical Simulations of Mantle Plume Melting - Jiang, et. al. 2024
Creators: name: Jiang, Shihao
Publisher: name: Zenodo
Year: 2024
Subjects: subject: Geophysics
subject: FOS: Earth and related environmental sciences

description: This release accompanies the initial submission of "Investigating the Lid Effect on the Generation of Ocean Island Basalts: 2. Geodynamical Simulations" to Geochemistry, Geophysics, Geosystems. It includes updated source files for 3-D plume simulations with varying initial conditions, geodynamical simulation files for the reference case ΔT500LT56, sample output files (h5part and pvtu files for the first few timesteps), and calculated geochemistry and lithospheric thickness over time for each case.
Human Antibody Targeted Minicell Drug Delivery Platform
Creators: name: University Of California Office Of The President
Publisher: name: University of California Office of the President
publisherIdentifier: https://ror.org/00dmfq477
publisherIdentifierScheme: ROR
Year: 2024

description: Key to developing an effective anti-cancer therapy is the creation of a robust, versatile and generally applicable platform that allows targeted delivery of therapeutics to disease sites with high specificity and in adequate concentrations. This Discovery Seed Funding proposal aims to develop such a platform based on novel human antibody-targeted biologically derived nanosized particles called minicells. Minicells are formed when normal bacterial cell divisions are disrupted by mutations. They are sterile and non-toxic. Minicells have been shown to possess the therapeutically desirable property of being able to unidirectionally take up a broad spectrum of molecules in very large quantities (millions per minicell). The key challenge now for therapeutic application of minicells is how to impart them with a targeting specificity and intracellular delivery function. We have previously screened a collection containing more than 500 million human monoclonal antibody fragments and identified a panel of novel human antibodies that bind specifically to prostate tumor cells and furthermore translocate efficiently following binding to the inside of tumor cells. We hypothesize that by combining our panel of novel tumor-targeting antibodies with minicells, we will be able to develop a generally applicable platform that allows tumor-targeted intracellular delivery of a broad spectrum of therapeutics. We propose to genetically modify minicells to display our internalizing human monoclonal antibody fragments on their surface, imparting minicells with the critical tumor targeting and intracellular delivery function required for cancer therapeutic development.
Negaprion acutidens
Creators: name: White, William T.
name: Ko'Ou, Alfred
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Chondrichthyes
Carcharhiniformes
Carcharhinidae
Negaprion
Negaprion acutidens

description: Negaprion acutidens (Rüppell, 1837)
Sicklefin Lemon Shark
Carcharias acutidens Rüppell, 1837: 65, pl. 18 (fig. 3). Lectotype: SMF 2825 (stuffed); lectotype designation by Klausewitz (1960). Type locality: Jeddah, Saudi Arabia, Red Sea.
Local synonymy: Negaprion acutidens— Filewood, 1973: 3 (PNG); Compagno, 1984: 518 (New Guinea); Kailola, 1987: 18 (Binaturi River mouth to Trobriand Islands); White et al., 2018: 170, figs (PNG).
PNG voucher material: (1 spec.) KFRS E.314, Tuma Island, Trobriand Islands, 25 Jul. 1967. Remarks: First recorded from PNG by Filewood (1973). Recorded from coastal fisheries catches in Western and Milne Bay Provinces during recent surveys.
description: Published as part of White, William T. & Ko'Ou, Alfred, 2018, An annotated checklist of the chondrichthyans of Papua New Guinea, pp. 1-82 in Zootaxa 4411 (1) on page 39, DOI: 10.11646/zootaxa.4411.1, http://zenodo.org/record/1221878
Opposition to Animals for Education
Creators: name: Esquillo, Jefferey
name: Khoo, Natalie
name: Fagan, Julie M.
Publisher: name: No Publisher Supplied
Year: 2010

description: Replacing animals used for education with technological dissection as an alternative
description: For years, animals have been used as a creative way to educate students on the different bodily functions of different types of species. On Rutgers campus, several science courses make it mandatory for students to engage in animal dissection as a means of increasing their knowledge about animal’s bodies and systems. Not only does this activity involve the harming of a dead animal’s body, but the way in which they do so will be graded based on performance. If students feel that this type of learning is unnecessary, it is possible that their grade can be harmed. We propose a technological means of dissecting on computer as an alternative method if students are against animal harm.
Reducing ACL Injuries by Implementing the PEP Program
Creators: name: Anzivino, Jenifer
name: DeMaio, Gina
name: Fagan, Julie M.
Publisher: name: No Publisher Supplied
Year: 2010

description: Educating coaches and players about the benefits of PEP program to reduce ACL Injuries
description: ACL injuries are the most common injury that women’s soccer players now face. In order to fix this routine that is now so evident in the women’s game, steps must be taken to ensure that players are doing the appropriate ACL prevention. By introducing the PEP program to women’s soccer players, the likelihood of suffering from an ACL injury is decreased. After talking with Dr. Arent (Exercise Physiologist) we also found that the time of day a team trains can indirectly affect susceptibility to injury through factors such as nutrition and sleeping habits.
The Wings of Nature : Immense Riches of the Bird World
Creators: name: Garg, Rishabh
Publisher: name: figshare
Year: 2025
Subjects: classificationCode: 310401
subject: Animal systematics and taxonomy

description: The world's bird population is incredibly diverse, both in terms of species and numbers, making birds the most successful terrestrial vertebrates. With 8,498 species spread across 23 orders in Class Aves, birds are found in a stunning variety of colors, bills, and feathers. Colombia, Peru, Brazil, and Indonesia are home to the greatest number of bird species. Among the most beautiful birds in the world are the birds of paradise, known for their vibrant plumage and long tails. The golden pheasant, a rare species native to China’s western forests, and the critically endangered blue-eyed ground dove, with only about 16 individuals remaining in the wild, are also notable examples of rare bird species.
Voice and Video Over Wireless Ad Hoc and Mesh Networks
Creators: name: University Of California Office Of The President
Publisher: name: University of California Office of the President
publisherIdentifier: https://ror.org/00dmfq477
publisherIdentifierScheme: ROR
Year: 2024

description: We are becoming more and more dependent on wireless devices such as cell phones, other handheld devices, and laptops for our day-to-day communications. Indeed, we now expect the communications to consist not only of voice calls or browsing web pages, but we also expect our communications to include streaming video from social, news, and entertainment web sites, downloading audio files, sharing digital images, and even two-way video communications. These connections are called Peer-to-Peer (P2P) communications. Evolving out of these examples of peer-to-peer communications are wireless peer-to-peer networks such as wireless ad hoc networks and wireless mesh networks. In wireless ad hoc networks, wireless devices not only are participants in a connection, but they also share their resources, such as disk storage, bandwidth, and processing power, with other users and often serve as network routers to create multiple interconnections between several to many wireless devices. Such wireless networks are becoming more prevalent in social and business interactions and are critical in emergency response situations, civilian tactical applications, and military environments. In these and other applications, the reliable transport of voice traffic, and some forms of video traffic (video streaming as well as two-way video communications, such as videoconferencing), are required in addition to transmitting data. While methods to support data communications such as web browsing and downloading files are well-understood, the level of support and video quality achievable by such networks for video communications has not been established. This research investigates the transmission of voice and video over multi-hop, multiple path wireless networks, such as wireless ad hoc and mesh networks, to establish the performance delivered to the end users and to determine the capacity in terms of the number of supported voice, video, and data flows with a chosen quality. This work captures the interaction among unique network structures, network protocols, voice and video applications supported by the network, the wireless channel, and perceptual indicators of delivered quality in order to design efficient, effective, high capacity wireless networks. It is expected that this research will directly impact future protocols and standards for wireless mesh and ad hoc networks. Since such networks are becoming more prevalent in social and business interactions and are critical in emergency response situations, civilian tactical applications, homeland security, and military environments, the proposed project directly accelerates innovation in California, helps grow the skilled workforce in California due to participation of students in the research, and increases the competitiveness of California companies by advancing new technologies that will lead to new products and services.
Drosophila calloptera Schiner 1868
Creators: name: Tidon, Rosana
name: Almeida, Jonathan Mendes De
Publisher: name: Zenodo
Year: 2016
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Diptera
Drosophilidae
Drosophila
Drosophila calloptera

description: calloptera Schiner, 1868: 239. Type locality: Brazil, Pará, Santarém, Fazenda Taperinha. ST F (NMW). NT Distr.: Mexico to Colombia (Cundinamarca (Fusagasugá), Magdalena (Sierra Nevada de Santa Marta)), Peru and Brazil, Puerto Rico, Cuba. Refs.: Hunter & Navarro, 1969: 1102; Hoenigsberg, 1995a: 87, 1995b: 177.
Paramycodrosophila tephritoptera Hendel, 1936: 95. Type locality: Brazil, Pará, Santarém, Fazenda Taperinha. ST F (NMW). Comb. & syn. Burla & Pavan, 1953: 300.
description: Published as part of Tidon, Rosana & Almeida, Jonathan Mendes De, 2016, FAMILY DROSOPHILIDAE, pp. 719-751 in Zootaxa 4122 (1) on page 725, DOI: 10.11646/zootaxa.4122.1.63, http://zenodo.org/record/263272
Prionace Cantor 1849
Creators: name: White, William T.
name: Ko'Ou, Alfred
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Chondrichthyes
Carcharhiniformes
Carcharhinidae
Prionace

description: Genus Prionace Cantor, 1849
Blue Shark
Prionace Cantor, 1849: 1381. Type species: Squalus glaucus Linnaeus, 1758, designated by the ICZN (on official list, Opinion 723.3d, 1965, name no. 1660).
description: Published as part of White, William T. & Ko'Ou, Alfred, 2018, An annotated checklist of the chondrichthyans of Papua New Guinea, pp. 1-82 in Zootaxa 4411 (1) on page 39, DOI: 10.11646/zootaxa.4411.1, http://zenodo.org/record/1221878
Bridging the Gap Between Students and Pesticide Applications at Rutgers
Creators: name: Cicalese, Kelly Ann
name: Deppa, Jeffrey
name: Fagan, Julie M.
Publisher: name: No Publisher Supplied
Year: 2010

description: Pesticide applications on Rutgers grounds pose minimal risks to students. Yet, it is vital for students to be aware of when they are being applied.
description: After noticing the white flags that are scattered around campus during fall and spring, both my partner and I became curious of their purpose. Following the questioning of employees associated with ground operations at Rutgers, we discovered that these flags indicate locations of pesticide application. Furthermore, we were pleased to discover that these pesticides pose minimal risk to students; however, it is nearly impossible for pesticides to pose absolutely no risks. Therefore, it is important that students are aware and take preventative methods when pesticides are being applied to avoid even the minimal risk. Such awareness can be achieved through better communication to students about such applications.
Drosophila canalinea Patterson & Mainland 1944
Creators: name: Tidon, Rosana
name: Almeida, Jonathan Mendes De
Publisher: name: Zenodo
Year: 2016
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Diptera
Drosophilidae
Drosophila
Drosophila canalinea

description: canalinea Patterson & Mainland, 1944: 50. Type locality: Mexico, Veracruz, San Juan. T A (USMN). NT Distr.: Mexico to Brazil, Antilles. Colombia (Bogota, D.C, Valle del Cauca (Palmira)). Refs.: Wheeler, 1957: 90; Hunter, 1964: 39.
description: Published as part of Tidon, Rosana & Almeida, Jonathan Mendes De, 2016, FAMILY DROSOPHILIDAE, pp. 719-751 in Zootaxa 4122 (1) on page 725, DOI: 10.11646/zootaxa.4122.1.63, http://zenodo.org/record/263272
Eliminating Steroid Use in Adolescents and High School Students
Creators: name: Hering, Steve
name: Gard, Steve
name: Mendez, Mark
name: Parris, Matthew
name: Fagan, Julie M.
Publisher: name: No Publisher Supplied
Year: 2010

description: In hope to raise awareness about the negative impact on steroids
description: The use of steroids has been controversial in professional sports for several years, but now, the issue has grown to include a rising number of student athletes who are actively using performance enhancing drugs. The known effects have been found through recent research and has proven to be overwhelmingly negative. Our project is to get the word out to student athletes about the negative side effects that steroids have on youth. By speaking to youth athletic organizations about these negative aspects, we hope to show them healthy alternatives to using performance enhancing drugs.
Reducing Food Waste in Colleges by Reducing Tray Size or Removing Trays
Creators: name: Wu, BinXi
name: Kuo, James
name: Fagan, Julie M.
Publisher: name: No Publisher Supplied
Year: 2010

description: By removing trays, college dining halls can reduce about 30% food waste as well as the water needed to clean them.
description: Using trays in buffet style college dining hall encourages students to take more food than they can consume. Therefore, removing trays or reducing tray size could potentially reduce the amount of food waste generated by the student. In our service project, we wrote to the school newspaper and spoke to Dining Hall managers, in attempt to inform the student of this option and change the administrator’s mind to remove or to reduce tray size. In addition, we plan to spread this information to other publications, so more people, specifically students, know about it.
Newspaper Clippings, November 1956
Creators: name: No Name Supplied
Publisher: name: No Publisher Supplied
Year: 1956

description: These newspaper clippings from 1956 relate to the appointment of Tracy S. Voorhees as head of the American Refugee and Rehabilitation Program for Hungary. The reproduced documents represent one folder from the Hungarian Refugee Relief Files, an archival series included in the Tracy S. Voorhees Papers, a manuscript collection owned by Special Collections and University Archives, Rutgers University Libraries. For background information concerning Voorhees and the entire contents of the Hungarian Refugee Relief Files, consult (http://hi.rutgers.edu/resources/resourcesrefugees#pres-committe-relief).
Drosophila carablanca Hunter 1979
Creators: name: Tidon, Rosana
name: Almeida, Jonathan Mendes De
Publisher: name: Zenodo
Year: 2016
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Diptera
Drosophilidae
Drosophila
Drosophila carablanca

description: carablanca Hunter, 1979: 376. Type locality: Colombia, near Bogotá. HT M (CAS). NT Distr.: Colombia (Bogota, D:C). Refs.: Vilela & Bächli, 1990: 85; Hunter, 1992: 197.
description: Published as part of Tidon, Rosana & Almeida, Jonathan Mendes De, 2016, FAMILY DROSOPHILIDAE, pp. 719-751 in Zootaxa 4122 (1) on page 725, DOI: 10.11646/zootaxa.4122.1.63, http://zenodo.org/record/263272
Newspaper Clippings, May 1957
Creators: name: Petrella, Joe
Publisher: name: No Publisher Supplied
Year: 1957

description: The Newspaper clippings of May 1957 focus on the disbanding of the Presidential Committee for Hungarian refugee relief.The reproduced documents represent one folder from the Hungarian Refugee Relief Files, an archival series included in the Tracy S. Voorhees Papers, a manuscript collection owned by Special Collections and University Archives, Rutgers University Libraries. For background information concerning Voorhees and the entire contents of the Hungarian Refugee Relief Files, consult (http://hi.rutgers.edu/resources/resourcesrefugees#pres-committe-relief).
English stress preservation and Stratal Optimality Theory
Creators: name: Collie, Sarah
Publisher: name: No Publisher Supplied
Year: 2007

description: Since Chomsky & Halle (1968), English stress preservation has been important in generative discussions of morphophonological interaction. This thesis carries out empirical investigations into English stress preservation, and uses their results to argue for a particular version of Optimality Theory: Stratal Optimality Theory ('Stratal OT') (Kiparsky, 1998a, 2000, 2003a; Bermudez-Otero, 1999, 2003, in preparation). In particular, the version of Stratal OT proposed in Bermudez-Otero (in preparation) and Bermudez-Otero & McMahon (2006) is supported.The empirical investigations focus upon the type of preservation where preserved stress is subordinated in the preserving word ('weak preservation'). Evidence for the existence of weak preservation is presented. However, it is also shown that weak preservation is not consistently successful, but that it is, rather, probabilistically dependent upon word frequency. This result is expected in light of work like Hay (2003), where it is proposed that word frequency affects the strength of relationships between words: stress preservation is an indicator of such a relationship.Stratal OT can handle the existence of English stress preservation: by incorporating the cyclic interaction between morphological and phonological modules proposed in Lexical Phonology and Morphology ('LPM'), Stratal OT has the intrinsic serialism which is necessary to predict a phenomenon like English stress preservation. It is shown that the same cannot be said for those of models of OT which attempt to handle preservation while avoiding such serialism, notably, Benua (1997).Bermudez-Otero's (in preparation) proposal of 'fake cyclicity' for the first stratum in Stratal OT can capture weak preservation's probabilistic dependence upon word frequency. Fake cyclicity rejects the cycle which has previously been proposed to handle weak stress preservation, in LPM and elsewhere; instead, fake cyclicity proposes that weak preservation is a result of blocking among stored lexical entries. Blocking is independently established as a psycholinguistic phenomenon that is probabilistically dependent upon word frequency; in contrast, the cycle is not a probabilistic mechanism, and so can only handle instances of stress preservation failure by stipulation.
Solar Autonomous Boat for Oceanographic Data Gathering
Creators: name: University Of California Office Of The President
Publisher: name: University of California Office of the President
publisherIdentifier: https://ror.org/00dmfq477
publisherIdentifierScheme: ROR
Year: 2024

description: The collection of a wide variety of ocean data is a fundamental prerequisite for progress in the ocean and marine sciences. However, despite the fact that most of the Earth's surface is covered by water, our understanding of ocean processes and properties is far from complete. This is due in part to limitations on our ability to make periodic, systematic, high quality measurements of ocean properties at the appropriate temporal and spatial scales at reasonable cost. To address these limitations and augment current methods, we propose to develop an autonomous ocean data gathering platform. While satellites, gliders, and ocean buoys (both fixed and drifting) all provide good sensor platforms, each has its drawbacks. Satellites are constrained to remote sensing from orbit and can thus only measure large-scale phenomena, while buoys are tethered to the ocean floor and can only measure proximate effects. Drift---or Lagrangian---buoys are limited by power and size, and gliders even more so. Surveys performed by large research vessels add a great deal to our collective understanding of ocean processes and phenomena; however, these trips require large investments in both expertise and capital. Additionally, these vessels are a scarce resource, limiting operational flexibility, availability, and imposing large cost constraints on research budgets. Within this spectrum of technologies, there lacks a low-cost method for augmenting the large vessel capabilities in an automated fashion. We propose to develop and deploy a multipurpose oceanographic data-gathering system comprised of a real-time, unmanned, autonomous surface oceangoing solar-electric vessel. This vessel will increase the quantity, resolution and efficiency of oceanographic measurements while significantly decreasing operational costs. As a sensor platform for oceanographic research, the proposed vessel will be a powerful, flexible tool in extending our understanding of littoral and open water and the intricate balance of the ocean ecosystem. The benefits to coastal oceanographic research are especially applicable to California, with its enormous and productive coastline. Examples of research projects currently underway at UC Santa Cruz in the Ocean Sciences department include upwelling biology, algal bloom phenomena and computer modeling of the California coastal ecosystem. Each of these research projects would benefit greatly by a data gathering platform such as the one proposed. Effective stewardship of California's resource-rich coastal environments depends on access to accurate and timely information. The broad impact of the ocean's state on the human condition, coupled with the particular sensitivity of coastal waters to climate change, have triggered a recent surge of interest and funding for nationwide and global coastal monitoring programs.
Prionace glauca
Creators: name: White, William T.
name: Ko'Ou, Alfred
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Chondrichthyes
Carcharhiniformes
Carcharhinidae
Prionace
Prionace glauca

description: Prionace glauca (Linnaeus, 1758)
Blue Shark
Squalus glaucus Linnaeus, 1758: 235. No types known. Type locality: northeastern Atlantic (localities include England and Italy).
Local synonymy: Prionace glauca— Filewood, 1973: 3 (PNG); Kailola, 1987: 18 (PNG); White et al., 2018: 172, figs (PNG).
PNG voucher material: None.
Remarks: First recorded from PNG by Filewood (1973). Common in bycatch of pelagic fisheries in PNG; verified by photographs, with accompanying muscle and vertebral samples, from fisheries observers during recent surveys. Found to be occasionally misidentified as longfin mako Isurus paucus.
description: Published as part of White, William T. & Ko'Ou, Alfred, 2018, An annotated checklist of the chondrichthyans of Papua New Guinea, pp. 1-82 in Zootaxa 4411 (1) on pages 39-40, DOI: 10.11646/zootaxa.4411.1, http://zenodo.org/record/1221878
The Phonology and Phonetics of Consonant-Tone Interaction
Creators: name: Tang, Katrina Elizabeth
Publisher: name: No Publisher Supplied
Year: 2008

description: While it has long been known that consonants and tones interact with one another, the question of how they interact has received relatively little attention in the literature.  I approach this question first from the perspective of a cross-linguistic survey of consonant-tone interaction.  The results show that, while the more commonly studied interaction between voicing and low tone is the most frequent type of consonant-tone interaction, consonant-tone interaction also includes a much larger variety of consonants than is often assumed (e.g. Bradshaw, 1999; Bao, 1999; Odden, 2002; Yip, 1995). It also includes a wider variety of tone types than have been assumed by earlier phonological models. This survey, along with the phonetic connection between the realization of laryngeal features and the production of F0, becomes the basis for the theoretical approach taken in the dissertation.  I discuss the concept of a tone span and argue that this provides an environment in which a suprasegmental feature and a segmental feature can interact without being merged into a single feature; because many consonants are able to interact with tone, I argue that a merged feature approach cannot account for the full range of data.  Within a tone span, phonetically based constraints require compatible laryngeal features to co-occur or prohibit incompatible from co-occurring.  I further explore these ideas by providing a detailed account of the phonology of two typologically distinct languages, Bade and Kam.  Finally, I examine the F0 patterns in Bade to see how the phonology is reflected in the phonetics.  The results show that voiced obstruents, with a low tone affinity, lower F0, and voiceless obstruents, with a high tone affinity, raise F0.  Sonorants have an intermediate effect on F0 and are neutral with regard to consonant-tone interaction. Implosives are also neutral with regard to consonant-tone interaction, but they show similarities to both voiced and voiceless consonants in their effect on F0.  The tone span, marked with the phonological boundaries hypothesized for Bade, is also shown to be a phonetically distinct unit for F0 measurement.
EXPLORE ANTI-HIV ACTIVITY OF APOBECS FOR NOVEL AIDS THERAPY
Creators: name: University Of California Office Of The President
Publisher: name: University of California Office of the President
publisherIdentifier: https://ror.org/00dmfq477
publisherIdentifierScheme: ROR
Year: 2024

description: APOBEC3G (A3G) is a human protein that is a promising candidate for future anti-HIV therapeutics. A3G is a powerful DNA mutating enzyme that has the capability of blocking an HIV-1 infection. When A3G is encapsidated into HIV-1 virions, A3G disrupts viral replication and incorporation of viral DNA into human genome. However, the HIV-1 virus produces a protein called viral infectivity factor (Vif) that induces the degradation of A3G by a cellular complex called the proteasome and prevents A3G encapsidation into the HIV-1 virions. A3G inhibition of HIV-1 infection in the absence of Vif has been well documented by numerous laboratories. Therefore, blocking the interactions between A3G and Vif that induce the cellular depletion of A3G would likely restore the body¡¯s natural defense against an HIV-1 infection. The Chen laboratory has solved the only atomic structures available for A3G and a similarly related protein, APOBEC2. The A3G atomic structure is akin to a photograph revealing structural information that can be used to design a drug with the perfect fit to bind A3G and prevent interactions with Vif. This drug design approach is called structure-based drug design. To facilitate progress with developing novel anti-HIV-1 drugs, we plan to solve more atomic structures for A3G and HIV-1 Vif. We will use these structures to enhance our understanding of how A3G inhibits HIV-1 replication by binding viral RNA and DNA. Additionally, these structures will allow us to visualize the atomic details that promote Vif binding to A3G, which results in A3G degradation. With such information, we can begin to use computers to analyze the atomic structures and determine which types of drugs can disrupt Vif/A3G interactions. Our laboratory has the advantage of our success in obtaining large quantities of highly purified A3G and Vif proteins. We will use these reagents to develop assays that monitor the interactions of A3G and Vif, and screen computer designed inhibitors of A3G/Vif interactions. To achieve these goals, we are taking an innovative approach in combining the state of the art technology in X-ray protein crystallography with computational biology, molecular biology, biophysics, and functional biochemistry, an approach that has been successfully applied by this group of scientists to achieve the preliminary results described in the proposal as well as in recent publications.
Drosophila cardini Sturtevant 1916
Creators: name: Tidon, Rosana
name: Almeida, Jonathan Mendes De
Publisher: name: Zenodo
Year: 2016
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Diptera
Drosophilidae
Drosophila
Drosophila cardini

description: cardini Sturtevant, 1916: 336. Type locality: Cuba, Ciudad de la Habana, Habana. HT M (MCZ). NT NE AU Distr.: Texas, Forida, Mexico to Colombia (Bogota, D:C, Antioquia (Medellin), Cundinamarca (Fusagasugá), Magdalena (Sierra Nevada de Santa Marta)), Argentina, Antilles; Hawaii. Refs.: Hunter, 1964: 39; Hunter, 1966: 417; Hunter & Navarro, 1969: 1102; Hoenigsberg, 1995a: 87, 1995b: 177.
description: Published as part of Tidon, Rosana & Almeida, Jonathan Mendes De, 2016, FAMILY DROSOPHILIDAE, pp. 719-751 in Zootaxa 4122 (1) on page 725, DOI: 10.11646/zootaxa.4122.1.63, http://zenodo.org/record/263272
Rhizoprionodon Whitley 1929
Creators: name: White, William T.
name: Ko'Ou, Alfred
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Chondrichthyes
Carcharhiniformes
Carcharhinidae
Rhizoprionodon

description: Genus Rhizoprionodon Whitley, 1929
Sharpnose Sharks
Rhizoprionodon Whitley, 1929: 354; a replacement name for Rhizoprion Ogilby, 1915, preoccupied by Rhizoprion Jourdan, 1861 in mammals. Type species: Carcharias (Scoliodon) crenidens Klunzinger, 1880, by original designation, a junior synonym of Carcharias acutus Rüppell, 1837.
description: Published as part of White, William T. & Ko'Ou, Alfred, 2018, An annotated checklist of the chondrichthyans of Papua New Guinea, pp. 1-82 in Zootaxa 4411 (1) on page 40, DOI: 10.11646/zootaxa.4411.1, http://zenodo.org/record/1221878
Design and discovery of HIV-1 IN inhibitors with novel mechanism of action
Creators: name: University Of California Office Of The President
Publisher: name: University of California Office of the President
publisherIdentifier: https://ror.org/00dmfq477
publisherIdentifierScheme: ROR
Year: 2024

description: AIDS is one of the world’s most serious health problems. In 2006, one million people were infected with HIV in the U.S. with a 56% mortality rate according to a UNAIDS report on the global AIDS epidemic. The emergence of drug-resistant viral strains and exponential HIV infections taking place worldwide echoes an urgency to develop new HIV-1 inhibitors with novel mechanisms of action to incorporate into HAART drug regimes. The long term goal of this study is to identify novel lead molecules as potential clinical candidates for the prevention of HIV-1 replication. Successful retroviral replication and HIV infection requires the aid of cellular transcriptional co-activator LEDGF/p75 through the formation of integrase-LEDGF/p75 protein-protein complex. Thus, designing compounds to disrupt IN-LEDGF/p75 complexes serves as a novel inhibition strategy different from current antiviral therapies. Herein I propose to utilize computer generated models developed from integrase-LEDGF/p75 complexes to identify new potent inhibitors from a commercial database of five million compounds. I further propose that biological testing, synergy studies with known HAART inhibitors, and physiological absorption simulations will allow me to build accurate predictive models to inhibit HIV-1 integrase in vivo. Inhibitors identified with positive physiological and synergistic effects serve as a focusing tool for the rational design of new lead candidates. In collaboration with a renown viral laboratory (Debyser group), we will test the lead molecules against HIV virally infected cells and drug-resistant cell lines and validate the proposed models.
Noniterativity is an Emergent Property of Grammar
Creators: name: Kaplan, Aaron F.
Publisher: name: No Publisher Supplied
Year: 2008

description: Many rule-based theories of phonology include an iterativity parameter so that rules can either be stipulated to apply as many times as possible or restricted to a single application. Optimality Theory cannot replicate this simple device: Constraints that produce iterativity (Agree, Align, Spread, Parse ...) do not produce noniterativity with a simple parameter switch. Furthermore, OT's architecture prevents the generation of true noniterativity: In order to determine whether or not a feature has spread just once, for example, the markedness constraint that imposes noniterativity must know the input configuration. But markedness constraints are not allowed to access the input. OT, then, is more restrictive than rule-based phonology on this point and predicts that truly noniterative phenomena -- processes defined in part by a noniterativity requirement -- should not exist.This dissertation evaluates whether OT is too restrictive in this prediction by examining five seemingly noniterative phenomena in detail: vowel harmony in Lango, umlaut in Chamorro, tone spread in Chichewa, tone shift in Kikuyu, and postlexical spreading in various languages. The noniterative nature of these phenomena is argued to be a byproduct of a confluence of factors that are not concerned with noniterativity specifically. For example, in Lango and Chamorro, spreading from affixes to the root is noniterative not because a parameter stipulates this kind of spreading, but because a constraint motivates spreading to the root. Once the root (which is adjacent to the affix) is reached, further spreading is unmotivated. Other factors that can lead to noniterativity are identified. The conclusion is that no noniterative phenomenon requires an analysis that explicitly calls for noniterativity, and thus rule-based phonology is wrong to adopt an iterativity parameter. The implication of this result is that phonological grammars are, as OT asserts, concerned with representations and not the processes that give rise to these representations. The absence of true noniterativity lends support for OT in an area that at first glance presents a strong challenge to the theory.
Formal and Cognitive Restrictions on Vowel Harmony
Creators: name: Finley, Sara
Publisher: name: No Publisher Supplied
Year: 2008

description: Vowel harmony, a phonological process whereby adjacent vowels share values of a phonological feature, has raised important challenges for generative phonology, particularly Optimality Theory (OT) (Prince and Smolensky, 1993/2004), a theory of linguistic typology in which output forms are computed in parallel from an infinite candidate set. The parallel nature of computations in OT, as well as the unconstrained candidate set for possible outputs poses challenges for a theory of vowel harmony, which applies in a local fashion, such that vowels share the same feature value as their nearest neighbor. Particularly, standard theories of vowel harmony in OT predict the existence of pathological vowel harmony processes that are unconstrained by locality, producing patterns that are never found in natural language. Building on the work of Turbidity Theory (Goldrick, 2001), this dissertation proposes Turbid Spreading, a theory of representations for harmony that provides a solution to the 'myopia' generalization in OT. Representations for features are both rich as well as constrained, making it possible to account for several aspects of vowel harmony (e.g., non-participating vowels and epenthetic vowels) without over-predicting. Evidence for the completeness of the predicted typology is provided using computational methods (i.e., finite-state machines). The cognitive bases for the typological restrictions on vowel harmony typology are verified in a series of 12 experiments using the artificial grammar learning paradigm in adults. In these experiments, English speakers are exposed to mini versions of vowel harmony languages, followed by a forced-choice comprehension test. This test contains novel items as well as items from the training set. In particular, several novel test items include novel representations (e.g., novel vowels), which have been specifically held out from training to test. This 'poverty of the stimulus' method (Wilson, 2006) makes it possible to test learners' bi inferences towards ambiguous stimuli. The results of these experiments suggest that learners' biases conform to the cross-linguistic typology of harmony languages. Learners are biased to learn harmony patterns that are frequently occurring and phonetically natural, but biased against rare or non-existing patterns. These findings support the hypothesis that typological restrictions are grounded in learning biases.
Structure of HIV-1 Vif and interactions with APOBEC proteins
Creators: name: University Of California Office Of The President
Publisher: name: University of California Office of the President
publisherIdentifier: https://ror.org/00dmfq477
publisherIdentifierScheme: ROR
Year: 2024

description: To establish an infection, viruses must overcome innate host defense mechanisms. The human immunodeficiency virus type-1 (HIV-1) encodes a protein called Viral infectivity factor (Vif), which neutralizes the anti-viral activity of the human APOBEC proteins, such as APOBEC3G (A3G) and APOBEC3F (A3F). In the absence of Vif, A3G and A3F are incorporated into the budding virions where they cause multiple mutations of the nascent viral DNA and prevent its replication. Vif overcomes this replication block by binding to the APOBEC proteins and targeting them for destruction by the cellular degradation machinery. Therefore, a novel approach to AIDS therapy would be to target the Vif-APOBEC interactions, while maintaining the anti-viral properties of the DNA mutating APOBEC proteins. Towards this end, we will use protein X-ray crystallography to determine the three-dimensional structure of Vif. Furthermore, using a series of biochemical assays including a deamination assay, DNA, RNA gel-shift assays and rotational anisotropy we will elucidate the effects of Vif binding on APOBEC’s anti-viral properties. Together our structural and biochemical studies will provide a detailed picture of the Vif-APOBEC interaction and will enable us to design inhibitors/drugs that will target this interaction, but protect the anti-viral properties of the APOBEC proteins. These studies will lay the groundwork for future AIDS therapeutics that will preserve the host innate immune defenses.
Drosophila cardinoides Dobzhansky & Pavan 1943
Creators: name: Tidon, Rosana
name: Almeida, Jonathan Mendes De
Publisher: name: Zenodo
Year: 2016
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Diptera
Drosophilidae
Drosophila
Drosophila cardinoides

description: cardinoides Dobzhansky & Pavan, 1943: 21. Type locality: Brazil, São Paulo, Iporanga. HT M (MZUSP). NT Distr.: Mexico to Brazil. Colombia (Cundinamarca (Fusagasugá), Magdalena (Sierra Nevada de Santa Marta), Santander (Bucaramanga, Rio Negro), Valle del Cauca (Palmira)). Refs.: Hunter, 1964: 39; Hunter & Navarro, 1969: 1102; Heed & Russel, 1971: 100; Hoenigsberg, 1995b: 177; Yoon, 1996: 41.
description: Published as part of Tidon, Rosana & Almeida, Jonathan Mendes De, 2016, FAMILY DROSOPHILIDAE, pp. 719-751 in Zootaxa 4122 (1) on page 725, DOI: 10.11646/zootaxa.4122.1.63, http://zenodo.org/record/263272
Rhizoprionodon oligolinx Springer 1964
Creators: name: White, William T.
name: Ko'Ou, Alfred
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Chondrichthyes
Carcharhiniformes
Carcharhinidae
Rhizoprionodon
Rhizoprionodon oligolinx

description: Rhizoprionodon oligolinx Springer, 1964
Grey Sharpnose Shark
Rhizoprionodon (Protozygaena) oligolinx Springer, 1964: 621, Figs 12–13, Pl. 2 (fig. c). Holotype: USNM 196799. Type locality: Bangkok market, caught in Gulf of Thailand.
Local synonymy: White et al., 2018: 176, figs (PNG).
PNG voucher material: None.
Remarks: Based on a dried jaw in the KFRS collection which appears to be conspecific with this species. Other specimens required from PNG to further validate. Also known from Australia based on a single specimen caught in the Gulf of Carpentaria (Last & Stevens, 2009).
description: Published as part of White, William T. & Ko'Ou, Alfred, 2018, An annotated checklist of the chondrichthyans of Papua New Guinea, pp. 1-82 in Zootaxa 4411 (1) on page 41, DOI: 10.11646/zootaxa.4411.1, http://zenodo.org/record/1221878
Cumulative faithfulness effects in phonology
Creators: name: Farris-Trimble, Ashley W.
Publisher: name: No Publisher Supplied
Year: 2008

description: One of the hallmarks of optimality theory (OT) is strict domination: multiple low-ranked constraint violations cannot gang up on a higher-ranked constraint.  However, such cumulative interactions have been shown to occur.  This thesis examines the subset of cumulative interactions called cumulative faithfulness effects (CFEs).  CFEs occur when a single unfaithful mapping is allowed in a word, but multiple unfaithful mappings are not.  In languages with CFEs, violations of multiple lower-ranked faithfulness constraints gang up on a single higher-ranked constraint to eliminate outputs that are unfaithful in multiple ways, while allowing singly-unfaithful outputs to survive.  The key generalization is that for languages in which multiple repair processes could be used to repair a marked element, the least unfaithful repair process is chosen.  The fact that these effects are attested in a variety of languages and language domains presents a problem for OT, which cannot account for them.  Moreover, CFEs produce transparent outputs and resemble conspiracies, two phonological phenomena for which OT is typically adept at accounting.The thesis thus has three goals.  The first is descriptive: I seek to determine under what circumstances CFEs occur.  A typology of CFEs is proposed, illustrating that there are at least three different ways in which faithfulness constraints can behave cumulatively.  The second goal is to determine in what phonological domains CFEs occur.  It is shown that CFEs are a pervasive phenomenon; examples are provided from fully-developed languages, first-language acquisition, and loanword adaptation.  Finally, the third goal is analytical: what is the best constraint-based analysis for CFEs?  Because OT cannot account for them, either some addendum to OT must be proposed, or some other constraint-based theory must be appealed to.  Harmonic grammar (HG), a constraint-based theory in which each constraint carries a weight and candidates are evaluated based on the cumulative weight of their violations, is argued to provide the best analysis of CFEs.  Multiple low-weight constraints may thus combine to overcome a single higher-weight constraint.  Moreover, HG can account not only for those cases in which multiply-unfaithful outputs are disallowed, but also for cases in which multiply-unfaithful outputs occur.
Optimal Interleaving: Serial Phonology-Morphology Interaction in a Constraint-Based Model
Creators: name: Wolf, Matthew Adam
Publisher: name: No Publisher Supplied
Year: 2008

description: This dissertation proposes a novel theory of the phonology-morphology interface called Optimal Interleaving (OI). OI is based on Optimality Theory with Candidate Chains (OT-CC), which is proposed by McCarthy (2007a) as a serial architecture for Optimality Theory (Prince & Smolensky 2004 [1993]). OI adds to OT-CC the hypothesis that morphological spell-out (Halle & Marantz 1993's 'vocabulary insertion') occurs in the phonological component of the grammar. OI thus allows phonological and morphological operations to be interleaved in a fashion similar to that assumed in the theory of Lexical Phonology (Kiparsky 1982a,b, Mohanan 1982).Chapters 2 and 3 argue that OI makes a number of correct predictions about phonologically-conditioned allomorph selection. Chiefly, OI derives the empirical generalization that allomorph selection is always opaque with respect to phonology conditioned by the competing allomorphs (Paster 2005, 2006, to appear). It does so while keeping phonologically-driven allomorphy in the phonology and governed by phonological constraints. OI therefore avoids a version of the Duplication Problem (Clayton 1976) which is faced by theories which derive the opacity generalization by attributing all allomorph selection to subcategorization in the morphology (Paster 2005, 2006, to appear; Bye 2007).Chapter 4 shows that OI, and more generally OT-CC, can be applied to non-derived environment blocking (NDEB: Kiparsky 1973a). It is shown that OI makes five correct predictions about NDEB which are not collectively predicted by any other theory of this phenomenon. OI achieves these results without having to make any special assumptions specific to NDEB. This places OT-CC at a considerable advantage as a theory of opacity relative to rule-based phonology, where NDEB requires stipulated restrictions on rule application like the Strict Cycle Condition (Kean 1974, MascarÃ³ 1976).Chapter 5 shows that OI also lends itself to the two other main types of serial phonology/morphology interactions: 'cyclic' overapplication of a process, and underapplication of a process in a morphologically-derived environment. The chapter also critiques existing theories of these effects, particularly OO-faithfulness (Benua 1997), Stratal OT (Kiparsky 2000), and the phonological application of the theory of phases (Marvin 2002).