cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Syngnathidae Bonaparte 1831
Creators: name: Angulo, Arturo
name: Betts, Joel T.
name: González-Alemán, Néstor J.
name: Castañeda, Edgar
name: Berghe, Eric Van Den
name: Elías, Diego J.
name: Mcmahan, Caleb D.
name: Matamoros, Wilfredo A.
Publisher: name: Zenodo
Year: 2023
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Syngnathiformes
Syngnathidae

description: Family Syngnathidae Bonaparte 1831 (Fig. 3H). Pipefishes; Peces Pipa
Description: Body long, slender, extremely elongated in some taxa, encased in an armor of ring-like, bony segments; up to 30 cm in length; mouth small, without teeth, at the end of a long tubular snout; gill opening very small, restricted to the top corner of the operculum; pectoral, dorsal, anal and/or caudal fins usually present; pelvic fins absent (Robertson & Allen 2015, Nelson et al. 2016). Distribution: Marine and brackish water, some species in freshwater; Atlantic, Indian and Pacific oceans (Nelson et al. 2016). Two genera and four species in Nicaraguan freshwaters.
description: Published as part of Angulo, Arturo, Betts, Joel T., González-Alemán, Néstor J., Castañeda, Edgar, Berghe, Eric Van Den, Elías, Diego J., Mcmahan, Caleb D. & Matamoros, Wilfredo A., 2023, Continental fishes of Nicaragua: diversity, distribution and conservation status; with an annotated and illustrated checklist of species and an identification guide to families, pp. 1-89 in Zootaxa 5376 (1) on page 30, DOI: 10.11646/zootaxa.5376.1.1, http://zenodo.org/record/10208788
MOESM2 of Venovenous extracorporeal membrane oxygenation devices-related colonisations and infections
Creators: name: Thomas, Guillemette
name: Hraiech, Sami
name: Cassir, Nadim
name: Lehingue, Samuel
name: Rambaud, Romain
name: Wiramus, Sandrine
name: Guervilly, Christophe
name: Klasen, Fanny
name: MĂŠlanie Adda
name: StĂŠphanie Dizier
name: Roch, Antoine
name: Papazian, Laurent
name: Forel, Jean-Marie
Publisher: name: Figshare
Year: 2017
Subjects: subject: Space Science
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Molecular Biology
subject: Physiology
subject: 69999 Biological Sciences not elsewhere classified
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Additional file 2. Table S2. Microorganisms cultured in blood culture (at the time of ECMO removal).
Faithfulness and Prosodic Circumscription
Creators: name: McCarthy, John J.
Publisher: name: Oxford University Press
Year: 1997

description: Morphological processes are often sensitive to the prosodic structure of their inputs. Phenomena like these have been analyzed under the rubric of operational Prosodic Circumscription by McCarthy & Prince 1990.This article re-examines certain of the principal cases supporting positive prosodic circumscription, arguing that they can be better explained as effects of prosodic faithfulness within Optimality Theory using Correspondence. Two main types of circumscription-as-faithfulness are discussed: (i) Circumscriptional effects emerging from faithfulness to the edges or heads of prosodic constituents (Yidiny, Rotuman, Cupeno, Berber). (ii) Circumscriptional effects emerging from faithfulness to moras and mora-segment associations (Arabic broken plural).Circumscription-as-faithfulness complements the results obtained in re-analyzing infixation within OT (Prince & Smolensky 1991, 1993; McCarthy & Prince 1993ab) and it supports the explanatory goals of the theory of Prosodic Morphology.
Hyperpolarized 13C MR molecular markers of renal tumor aggressiveness
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 incidence of renal tumors, both malignant renal cell carcinomas (RCCs) and benign renal tumors, has been rising steadily in the last 20 years. Management of renal tumors is heavily reliant on imaging, which has significant limitations. Conventional imaging cannot reliably differentiate benign renal tumors from RCCs, or indolent from localized but potentially aggressive RCCs. This has led to many unnecessary surgical resections of benign renal tumors and likely overtreatment of indolent RCCs with associated surgical complications and loss of renal functions. On the other hand, 20-40% of patients undergoing nephrectomies for clinically localized RCCs develop metastases. These findings highlight the urgent unmet clinical need for a noninvasive means to characterize renal tumor aggressiveness in order to appropriately guide treatment. Hyperpolarized (HP) 13C MR is a new molecular imaging technique that provides an unprecedented gain in sensitivity (>10,000-fold increase over conventional MR) for detecting 13C-labeled bio-molecules, and allows rapid and noninvasive monitoring of dynamic metabolic processes. The goal of this study is to test the hypothesis that HP 13C molecular imaging substrates that probe changes in key glycolytic enzymes (HP 13C-pyruvate and 13C-fructose) and pH (13C-bicarbonate) can stratify renal tumor aggressiveness. To test the hypothesis, we propose to study the real-time metabolism of human renal tumors by applying HP 13C MR to patient-derived renal tumor tissues orthotopically implanted under the renal capsule of athymic mice. Such model permits the discovery of HP 13C biomarkers prior to actual patient studies. The proposed work is innovative and significant because it seeks to interrogate for the first time dynamic pathway-specific metabolic processes for noninvasive identification of renal tumor aggressiveness. The clinically translatable biomarkers identified may ultimately lead to a paradigm shift in the current renal tumor management by distinguishing patients who will most likely benefit from aggressive treatment from those for whom treatment is not needed or should be deferred.
A plastic antibody for capture and inhibition of angiogenesis-related growth factors for cancer 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: We have previously demonstrated that non-toxic synthetic polymer nanoparticles (NPs) with designed low nanomolar affinity for a venomous peptide toxin are capable of neutralizing the toxin in vitro and in vivo. These synthetic NPs are now of significant interest as “plastic antibodies” for both therapeutic and diagnostic applications. We propose to explore their use as a synthetic antibody for capturing angiogenesis-related growth factors. Angiogenesis is the cancer cells mechanism to acquire the nutrition and oxygen needed for tumor growth. It is achieved by secretion of growth factors that include vascular endothelial growth factor (VEGF). Inhibition of VEGF’s function is an attractive strategy for cancer therapy. Our synthetic polymer NPs are designed to sequester VEGF-A by binding to its heparin-binding domain. In preliminary studies several NPs that incorporate novel heparin mimic monomers have been prepared. These NPs are being evaluated for their affinity against angiogenesis-related growth factors. Our preliminary efforts have resulted in promising NP leads that show a strong affinity to VEGF-A. In recent years therapeutic antibodies have made significant contributions to medicine. However, these treatments can be very costly and impose a burden on patients and the health care system. The plastic antibody that we are developing is inexpensive to produce. The NPs are abiotic and do not therefore involve animals or live cells for their production. We anticipate that success of this research could be the first step to produce low cost alternatives for cancer therapy. At the very least it will provide important information regarding abiotic alternatives to antibody therapies. Initially, we will focus on the synthesis of small libraries of polymer NPs and the development of screens for NP-VEGF-A binding. Multiple screening protocols, quartz crystal microbalance (QCM) and surface plasmon resonance imaging (SPRi), are being developed to quantify the binding, capacity and affinity against VEGF-A and related growth factors. An iterative process will be used to optimize the NP composition to generate several leading candidates. Following the QCM binding study of NPs against VEGF-A, we will evaluate whether the NPs inhibit the binding of VEGF-A to the VEGF receptor and heparin. For in vitro assays, we will use human umbilical vein endothelial cell (HUVEC) as an angiogenic vessel cell model and colon NL 26 cells as a cancer cell model. Follow on studies will demonstrate whether the NPs can inhibit VEGF-depen
Scorpiops jendeki Kovarik 2000
Creators: name: Tang, Victoria
Publisher: name: Zenodo
Year: 2025
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Arachnida
Scorpiones
Scorpiopidae
Scorpiops
Scorpiops jendeki

description: (7) Scorpiops jendeki Kovařík, 2000
TYPE LOCALITY AND TYPE DEPOSITORY. China, Yunnan Province, Nujiang Lisu Autonomous Prefecture, Lushui City, Gaoligongshan National Nature Reserve; FKCP.
CHINESE EQUIVALENT. DZ氏ẍx.
DISTRIBUTION (●). Yunnan: Baoshan City (Longling County; Longyang District; Tengchong City); Dehong (Lianghe and Longchuan (Wangzishu Township) counties), Dali, and Nujiang (Fugong and Gongshan counties; Lushui City) prefectures.
description: Published as part of Tang, Victoria, 2025, A review of scorpiofauna of China: nomenclatural notes and updated faunistic catalogue (Arachnida: Scorpiones), pp. 1-24 in Euscorpius 404 on page 17, DOI: 10.5281/zenodo.14660932
Developing novel bioluminescent tools for cancer imaging
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: Background: Several immune cell types, including T cells and macrophages, are known to infiltrate cancer tissue, but how these cells function en masse to promote or quell tumor growth remains unknown. The ability to monitor the dynamic interplay between immune cells and tumor tissue in a single animal model would not only provide insight into how immune cells influence malignancy, but also how these processes might be exploited for therapeutic gain. The goal of this proposal is to develop a novel class of bioluminescent tools to probe immune function in cancer progression. Bioluminescence imaging employs enzymes (luciferases) that produce light with small molecule substrates (luciferins). Several luciferase-luciferin pairs exist in nature, and many have been adapted for tracking cellular location noninvasively in whole animals. Unfortunately, the optimal luciferases for in vivo imaging utilize the same substrate, and therefore cannot be used to distinguish multiple cell populations in a single subject. Thus, bioluminescence imaging to date has been largely restricted to monitoring one cell type at a time. Objective and Methods: We aim to generate several orthogonal luciferase-luciferin pairs that can be used concurrently to track multiple cell populations in mouse models. Our approach involves re-engineering the luciferase enzyme-substrate interface, creating mutants that accept distinct, chemically modified versions of luciferin. When these mutants and analogs are combined, light emission will occur only when complementary enzyme-substrate partners interact. In the proposed work, we will synthesize a novel class of sterically modified luciferins. These compounds will be screened against libraries of luciferase mutants to identify light-emitting pairs. Significance: Our work will ultimately provide a collection of bioluminescent probes suitable for tracking collections of cell types in vivo, analogous to the palette of fluorescent proteins available for multi-component imaging in vitro. Such probes will be useful for monitoring diverse collections of immune cells in animal tumor models. The ability to visualize immunity “in action”—from tumor initiation through therapeutic intervention—will provide novel insights into how immune cells influence different stages of malignancy; this, in turn, could profoundly impact how cancers are diagnosed, staged, and eventually treated.
FootForm Decomposed: Using primitive constraints in OT
Creators: name: Eisner, Jason
Publisher: name: Department of Linguistics and Philosophy, Massachusetts Institute of Technology
Year: 1997

description: Hayes (1995) gives a typology of the world's metrical stress systems, which is marked by several striking asymmetries (parametric gaps). Most work on metrical stress within Optimality Theory (OT) has adopted this typology without explaining the gaps. Moreover, the OT versions use uncomfortably non-local constraints (Align, FootForm, FtBin).This paper presents a rather different and in some ways more explanatory typology of stress, couched in the restrictive framework of primitive Optimality Theory (OTP), which allows only primitive, radically local constraints. For example, Generalized Alignment is not allowed. The paper presents a single, coherent system of rerankable constraints that yields the basic facts about iambic and trochaic foot form, iambic lengthening, quantity sensitivity, unbounded feet, simple word-initial and word-final stress, directionality of footing, syllable (and foot) extrametricality, degenerate feet, and word-level stress.The metrical part of the account rests on the following intuitions:(a) iambs are special because syllable structure allows them to lengthen their strong ends;(b) directionality of footing is really the result of local lapse avoidance;(c) any lapses are forced by a (localist) generalization of right extrametricality;(d) degenerate feet are absolutely banned, but primary stress does not require a foot in all languages. An interesting prediction of (b) and (c) is that left-to-right trochees should be incompatible with extrametricality. This prediction is robustly confirmed in Hayes.
Novel function of Nkx2.5 during hematopoiesis
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: Leukemia/lymphoma accounts for 50% of the malignant neoplasm during childhood. One of the major chromosomal translocations in acute and chronic lymphoblastic leukemia cells, t(5;14), causes ectopic upregulation of a pivotal cardiac transcription factor, Nkx2.5, implicating the involvement of Nkx2.5 during leukemogenesis. While the role of Nkx2.5 in the cardiomyocytes has been analyzed intensively, its function in hematopoiesis is still unclear. Given that the molecular pathways regulating oncogenesis often recapitulate aberrations of processes governing embryogenesis, understanding the function of Nkx2.5 during normal hematopoiesis will lead to the development of novel therapeutic approaches to leukemia. Surprisingly, Nkx2.5 is not expressed in any of the normal circulating blood cells in the postnatal tissues. The question is when, where and how Nkx2.5 exerts its hemogenic function. Our preliminary studies demonstrate that Nkx2.5 is expressed in a subset of endocardium and yolk sac endothelium during embryogenesis, and that Nkx2.5-positive endocardial cells display hemogenic activity ex vivo. Molecular regulation of Nkx2.5 has been characterized in cardiac lineage and leukemic cell lines; Nkx2.5 upstream regulators (BMP/Smad and Pu.1), binding partner GATAs and downstream factors (MEF2c and Lyl1). Interestingly, these genes are all expressed in endocardium. These preliminary data and previous findings lead to the hypothesis that the Nkx2.5 is required for the normal and pathological hematopoiesis during the embryogenesis and leukemogenesis. Using genetically modified mouse lines, leukemic cell lines and patient samples, we specifically propose: (1) To examine the hemogenic potential of Nkx2.5-positive endocardium and yolk sac endothelium Our preliminary data suggest that Nkx2.5-positive subset of endocardial and yolk sac endothelial cells give rise to the circulating erythroid and myeloid during embryogenesis. We will rigorously characterize the cell fate of Nkx2.5-derived blood population using genetically modified mice. (2) To examine the role of Nkx2.5 as a hematopoietic regulator. Our preliminary microarray analysis suggest Cbfa2/Runx1/AML1 is direct target of Nkx2.5. We will test this using mouse lines, cell lines and patient samples. Successful completion of this project will uncover novel function of the endocardium as a de novo hematopoiesis, and novel Nkx2.5-dependent molecular pathway of hematopoiesis. Aim 1 will potentially change the long-held dogma that AGM is the first major site of
Language Change and SA-OT: The case of sentential negation
Creators: name: Lopopolo, Alessandro
name: Bíró, Tamás
Publisher: name: No Publisher Supplied
Year: 2011

description: Simulated Annealing for Optimality Theory (SA-OT) updates Optimality Theory by adding a model of performance to a theory of linguistic competence. Our aim is to show that SA-OT can contribute to language change simulations. Performance "errors" are considered to be one of the causes of variation and change. We have chosen to model the evolution of sentential negation (SN). The descriptive background adopts Jespersen's Cycle, according to which the evolution of sentential negation follows three main stages (1. pre-verbal, 2. discontinuous, and 3. post-verbal). Therefore, we advance a novel model for SN, based on SA-OT. It reproduces the three pure and the two observed mixed stages, whereas it correctly predicts the lack of an intermediate stage between 3 and 1. The success of the approach corroborates the computational, performance-based approach to the data. Finally, we employ the iterated learning paradigm to reproduce historical changes in a "simulated corpus study". This enterprise turns out to be more difficult than one would naively believe.
Mostly Predictable: Cyclicity and the Distribution of Schwa in Itelmen
Creators: name: Bobaljik, Jonathan David
Publisher: name: Department of Linguistics, California State University
Year: 1997

description: The Itelmen language shows many instances of regular schwa/zero alternations. Even though the language permits quite extensive consonant clusters, I argue in this paper that the alternating schwas (and perhaps all instances of schwa) are epenthetic; schwa is inserted to break up a disfavoured consonant cluster. The rule which inserts schwa must apply cyclically in the verbal system, but non-cyclically in the nominal system. Apparent examples of cyclic rule application are problematic for non-derivational, constraint-based approaches to phonology, such as many versions of Optimality Theory (OT). Thus, much recent work has been devoted to reanlayzing purported examples of cyclicity from an O.T. perspective. While it may be possible to devise an account of the Itelmen data in terms of parallel constraint evaluation, current O.T. approaches are insufficient; in particular, the best candidate for an explanation of the Noun/Verb differences (Base Identity) makes exactly the wrong predictions for Itelmen.
Sympathy theory and German truncations
Creators: name: Ito, Junko
name: Mester, Armin
Publisher: name: University of Maryland
Year: 1997

description: Phonological opacity, in the proposal of McCarthy 199&, arises through constraints on a new type of correspondence relation holding within the candidate set that Gen produces for a given input, i.e., a relation between co-candidates. A candidate may win because it is in sympathy with a particular failed co-candidate, one that is optimal with respect to a specific lower-ranking constraint. This paper presents independent evidence for Sympathy by arguing that, enriched with the new notion, Optimality Theory can explain a certain type of prosodic-morphological formations requiring access to virtual forms accessible neither in the input in the output. The empirical focus throughout is a productive pattern of truncation in contemporary German deriving hypocoristics and other kinds of shortenings. In a broader vein, it is suggested that with the inclusion of Sympathy, the power of Output-Output constraints can be drastically reduced, leading to a simpler overall theory.
Scorpiops kovariki Tang, Ouyang, Liu & Stahlavsky 2024
Creators: name: Tang, Victoria
Publisher: name: Zenodo
Year: 2025
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Arachnida
Scorpiones
Scorpiopidae
Scorpiops
Scorpiops kovariki

description: (9) Scorpiops kovariki Tang, Ouyang, Liu & Šťáhlavský, 2024
TYPE LOCALITY AND TYPE DEPOSITORY. China, Tibet Autonomous Region, Nyingchi City, Zayü County; VT.
CHINESE EQUIVALENT. ṅ氏ẍx.
DISTRIBUTION (●). Xizang: Nyingchi City (Zayü County).
description: Published as part of Tang, Victoria, 2025, A review of scorpiofauna of China: nomenclatural notes and updated faunistic catalogue (Arachnida: Scorpiones), pp. 1-24 in Euscorpius 404 on page 17, DOI: 10.5281/zenodo.14660932
Microphis lineatus
Creators: name: Angulo, Arturo
name: Betts, Joel T.
name: González-Alemán, Néstor J.
name: Castañeda, Edgar
name: Berghe, Eric Van Den
name: Elías, Diego J.
name: Mcmahan, Caleb D.
name: Matamoros, Wilfredo A.
Publisher: name: Zenodo
Year: 2023
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Squamata
Syngnathiformes
Syngnathidae
Microphis
Microphis lineatus

description: Microphis lineatus (Kaup 1856). Opossum Pipefish; Pez Pipa Culebra
Vouchers: LSUMZ 15310 (1), 15321 (2), 15337 (14), 15356 (3) and 15375 (1); other collections: IBUNAM 13846 (1) and UF 233188 (1). Distribution: Western Atlantic Ocean; from New Jersey, USA, to southern Brazil; entering estuaries and littoral lagoons and ascending river courses; (Nicaragua) Co, UI, WK, Pr, GM, KP, Es, BF, IM and To (Atlantic); 0–10 masl; Per, Dia, Amp. Occurrence and conservation status: Nat; LC (2019), population trend unknown. Literature: Villa (1982: 152; detailed description, including illustrations and an identification key, and information on distribution and ecology), van den Berghe (2015: 47, as Oostethus brachyurus (Bleeker 1854) — misidentification; listed, including an illustration and information on distribution and ecology), Robertson & Van Tassell (2019: 972; detailed description, including illustrations, and information on distribution, with a map, and ecology) and Angulo (2021: 32; listed, including information on distribution).
description: Published as part of Angulo, Arturo, Betts, Joel T., González-Alemán, Néstor J., Castañeda, Edgar, Berghe, Eric Van Den, Elías, Diego J., Mcmahan, Caleb D. & Matamoros, Wilfredo A., 2023, Continental fishes of Nicaragua: diversity, distribution and conservation status; with an annotated and illustrated checklist of species and an identification guide to families, pp. 1-89 in Zootaxa 5376 (1) on page 31, DOI: 10.11646/zootaxa.5376.1.1, http://zenodo.org/record/10208788
Emergent templates: the unusual case of Tiene
Creators: name: Hyman, Larry M.
name: Inkelas, Sharon
Publisher: name: University of Maryland
Year: 1997

description: Tiene is unusual among Bantu languages in imposing prosodic restrictions on derivational verb morphology. The Tiene verb stem fits the Bantu mold: a CV(C) root combines with zero or more -VC derivational suffixes and an obligatory final vowel. However, Tiene requires derived stems to be either CVVCV or CVCVCV, where C2 and C3 agree in nasality, C2 is coronal, and C3 is grave. The latter constraints drive infixation when the root ends in a grave consonant and the suffix is coronal. An Optimality Theory analysis is provided which derives the two templates, furthering McCarthy and Prince's (1994) program of prosodic morphology in Optimality Theory. The data have an interesting added theoretical implication. As Tiene shows, segmental (rather than prosodic) conditions can force infixation, bringing up the question of how Optimality Theory is to capture the well-known generalization that infixes are never more than one prosodic (rather than segmental) constituent away from a word edge.
Contextual metrical invisibility
Creators: name: Hagstrom, Paul
Publisher: name: Department of Linguistics and Philosophy, Massachusetts Institute of Technology
Year: 1997

description: In some languages, certain vowels are invisible to syllable-sensitive processes, but only in certain contexts. This paper argues that metrically invisible vowels are undominated by a syllable node in prosodic structure. Considering mainly Mohawk and Passamaquoddy, the behavior of these "weak vowels" is derived from pressure to avoid using weak vowels as syllable nuclei, countered by pressure to realize underlying segments in well-formed syllables. Because not only epenthetic vowels can be weak vowels, their unsuitability as syllable nuclei is derived representationally, through amount of underlying prosodic structure. Existing analyses of the data are critiqued, and the theoretical implications and potential extensions are discussed.
Parsing in OT
Creators: name: Hammond, Michael
Publisher: name: No Publisher Supplied
Year: 1997

description: Optimality Theory (Prince & Smolensky, 1993; McCarthy & Prince, 1993) maintains that phonological generalizations can be treated by a two-step process. First, all possible pronunciations for some string are generated by the GEN operation. Then, the best of these different pronunciations is chosen by a set of ranked and violable constraints. This is the dominant theory of phonology today. This theory poses a serious problem for theories of phonological performance; the model cannot be implemented in real time because the candidate set is infinite. Even if we eliminate a number of options in generating candidates, we are still left with an extremely large number of candidate pronunciations to sift through in finite time.In this paper, I propose to implement syllabification in OT as a parser. I propose several innovations that result in a finite and small candidate set. The candidate set problem is handled with several moves: i) MAX and DEP violations are not hypothesized by the parser, ii) candidates are encoded locally, and iii) EVAL is applied constraint by constraint. The parser I propose is implemented in Prolog. It has a number of desirable consequences. First, it runs and thus provides an existence proof that syllabification can be implemented in OT. There are a number of other desirable consequences as well. First, constraints are implemented as finite-state transducers. Second, the parser makes several interesting claims about the phonological properties of so-called nonrecoverable insertions and deletions. Third, the implementation suggests some particular reformulations of some of the benchmark constraints in the OT arsenal, e.g. *COMPLEX, PARSE, ONSET, and NOCODA. Finally, the implementation is compared with various other proposals in the literature, e.g. Ellison (1994), Hammond (1995), Tesar (1995), and Eisner (199&).
Site specific role of progesterone anti-tumor actions in endometrial cancer
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: Endometrial cancer is a hormonally regulated tumor arising from epithelial cells lining the uterine cavity. The standard treatment is removal of the uterus followed by combinations of radiation and chemotherapy. Administration of progesterone is an alternative, well tolerated therapeutic option in primary treatment and an alternative to chemotherapy in recurrent disease with response rates as high as 50%. Currently there is no reliable method for determining whether a patient will respond to progesterone treatment. In tumors that do demonstrate a response to progesterone therapy, the anti-tumor mechanism and site of action for progesterone remain unknown. As a result hormonal therapy is under utilized in treating this hormonally driven malignancy. We hypothesize that progesterone attacks tumors by binding to the progesterone receptor (PR) in stromal cells residing in the tumor microenvironment and decreasing the secretion of paracrine factors that are permissive for growth of uterine epithelia. To test this hypothesis, we will utilize an in vivo endometrial cancer model resulting from loss of PTEN in uterine epithelia, established and published by our group. Our previous work demonstrated that tumors resulting from the loss of epithelial PTEN are sensitive to progesterone therapy (unpublished data). In this proposal we will determine if progesterone exerts its effect via PR and whether the anti-tumor effects of progesterone are mediated through tumor stroma (i.e., an extrinsic, paracrine effect) or epithelia (i.e., an intrinsic effect). Our specific aims are: (1) Determine if progesterone anti tumor effects in endometrial tumors are mediated through the stromal progesterone receptor. Established PTEN endometrial tumors will be treated with progesterone therapy in vivo concomitant with the deletion of PR in tumor stroma using an inducible Cre-loxP recombination system. Following eight weeks of treatment with progesterone, the response of tumors to this treatment will be analyzed. (2) Ascertain the role of epithelial PR in mediating response to progesterone therapy in endometrial tumors. Using an inducible Cre-loxP recombination system, PR will be deleted in the epithelium of PTEN deficient endometrial tumors and the response of these tumors to progesterone therapy will be assessed in vivo. If epithelial specific PR negative tumors are responsive to progesterone, this would indicate that progesterone response is mediated through stromal cells. The findings from this study will add in
Unbounded Stress and Factorial Typology
Creators: name: Bakovic, Eric
Publisher: name: Blackwell Publishing
Year: 1998

description: In this paper I demonstrate how a small set of constraints independently motivated for the analysis of bounded stress systems within Optimality Theory (OT; Prince & Smolensky 1993) is sufficient to account for the gross characteristics of strikingly different unbounded stress systems (see also Tesar 1998). This sufficiency is an important factorial typological consequence of the ranking of violable universal constraints, the cornerstone assumption of OT, a fact that serves as the primary motivating force behind this line of investigation. The constraints involved in the analysis and the logic of their interactions with one another turn out to reveal some important properties of constraint (in)activity through ranking in OT, a topic to which I devote particular attention.
The architecture of the English lexicon
Creators: name: Alcántara, Jonathan B.
Publisher: name: No Publisher Supplied
Year: 1998

description: This study provides an analysis of stress assignment and vowel alternation in the Latinate vocabulary of English, using the mechanisms of Optimality Theory to express the entire phonology, including lexical information, through the medium of the constraint hierarchy.Generative solutions depend crucially upon the underlying lexical forms which feed the grammar. A computational study of the English lexicon has been undertaken, identifying the distribution of stress, syllable weight and vowel length throughout the English lexicon. Forms have been classified on morphological and prosodic grounds, and comparative pattern frequencies have been calculated. This reveals a series of majority and minority patterns, each with significant distributions, rather than a large set of regular forms with a residue of exceptions. The majority patterns are enforced by prosodic constraints, while the minority stress patterns can also be accounted for, without recourse to unstructured exception marking, by proposing additional structure for their underlying forms. Such structure is restricted to constituents already found in the grammar. The distribution of vowel quantity in the data suggests that long vowels seen in alternating forms should be understood as resulting from a morphologically conditioned vowel lengthening. Reassessing these forms as underlyingly short accounts for both vowel alternation and certain otherwise inexplicable stress retractions. Previously exceptional forms, which failed to "shorten", are hence understandable as underlyingly long. Stress in morphologically complex forms is treated via subcategorization constraints, and all stress and vowel alternation patterns are accounted for with a single constraint hierarchy. To account for the now small residue of exceptional forms, such as suppletive stems or irregular allomorphs, a new conception of the lexicon within OT is proposed. Morpheme selection is understood to be governed by lexical selection constraints. While "regular" forms result from the interaction of generally applicable constraints, exceptions are enforced by high-ranking specific constraints, which take complex structures as arguments. The contrast between general and specific constraints can be used to explain competing trends within the lexicon, such as type vs. token frequency. This proposal moves the entire grammar into the realm of the constraint hierarchy, and allows for a principled evaluation metric.
Additional file 4: of Globular domain structure and function of restriction-like-endonuclease LINEs: similarities to eukaryotic splicing factor Prp8
Creators: name: M. Mahbub
name: Saiful Chowdhury
name: Christensen, Shawn
Publisher: name: Figshare
Year: 2017
Subjects: subject: Biochemistry
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Evolutionary Biology
subject: Developmental Biology

description: Glu C mapping data (internal peptides). (PDF 541Â kb)
Polyphlebium Copel. (Copeland 1938
Creators: name: Ahamada H. Saïd
name: Sabine Hennequin
name: Germinal Rouhan
name: Jean-Yves Dubuisson
Publisher: name: Zenodo
Year: 2017
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Polypodiopsida
Hymenophyllales
Hymenophyllaceae
Polyphlebium

description: Genus Polyphlebium Copel. (Copeland 1938)
This genus, here newly reported for the archipelago, is mostly neotropical with almost 15 species and a few ones in Asia, Australia, Pacific islands and a single species in tropical Africa and the western Indian Ocean. All species are epiphytic or lithophytic, small to large plants characterized by long-creeping, filiform rhizomes bearing pending simply-pinnate to highly divided fronds. The marginal sori have a cylindrical base and lips are more or less developed. Small to medium-sized taxa can be easily confused with Crepidomanes species by sharing the same growth-form and often the same gross frond shape and division. But all Polyphlebium species bear roots, even if few and reduced, while Crepidomanes species are all rootless or bear root-like shoots with caulinary anatomy (Schneider 2000), which are never observed in Polyphlebium. In addition, laminae never exhibit false veins or folds imitating veins, often observed in Crepidomanes.
description: Published as part of Ahamada H. Saïd, Sabine Hennequin, Germinal Rouhan & Jean-Yves Dubuisson, 2017, Disentangling the diversity and taxonomy of Hymenophyllaceae (Hymenophyllales, Polypodiidae) in the Comoros, pp. 1-53 in European Journal of Taxonomy 313 on page 29, DOI: 10.5852/ejt.2017.313, http://zenodo.org/record/896401
Sleeping beauty transposon mutagenesis to identify genes involved in melanoma progression
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: Melanoma is noted for its rapidly increasing incidence, aggressive clinical behavior and proclivity for lethal metastasis. This worrying epidemiological and clinical picture illustrates the urgent need for an improved understanding of disease pathogenesis, especially genetic/epigenetic mechanisms contributing to malignant progression of initiated melanocytes. Mutational activation of BRAF is the earliest and most common genetic alteration in melanoma and a key driver of melanoma maintenance. However, mutated BRAF is also detected at high frequency in benign sun-induced moles (a.k.a. nevi), which rarely progress to melanoma. The best evidence suggests that BRAF mutation is an initiating event in melanoma, but progression to malignancy requires cooperating events that bypass oncogenic BRAF-induced cell cycle arrest and senescence. Consistent with this, mice with melanocyte-specific expression of oncogenic BRAF(V600E) develop multiple benign nevi, which fail to progress to malignant melanoma unless tumor suppressors are silenced. Because of the failure of BRAF(V600E)-induced benign nevi to progress to melanoma, we conducted a “Sleeping Beauty” transposon mutagenesis screen to identify genes that cooperate with BRAF(V600E) in melanoma progression. This screen has been spectacularly successful in identifying >1000 potential BRAF(V600E)-cooperating melanoma suppressors and/or oncogenes, of which approximately 300 appear directly relevant to the cognate human disease. To validate putative melanoma tumor suppressors or oncogenes identified in the Sleeping Beauty screen, we will use lentivirus-mediated gene transfer to express either cDNAs or shRNAs corresponding to candidate melanoma cooperating genes in BRAF(V600E)-initiated melanocytes in mouse skin. Candidate validation will be prioritized based on evidence that the gene(s) identified by Sleeping Beauty transposition in mouse melanomas are also altered in human melanoma. This project will lead to identification of new melanoma tumor suppressors and/or oncogenes combined with a mechanistic understanding of how they promote malignant melanoma progression. Moreover, the protein products of these genes, or the pathways in which they operate, may be tractable targets for melanoma biomarker or drug discovery.
Tetramorium pacificum Mayr
Creators: name: Bolton, B.
Publisher: name: Zenodo
Year: 1979
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hymenoptera
Formicidae
Tetramorium
Tetramorium pacificum

description: Tetramorium pacificum Mayr
(Fig. 44)
Tetramorium pacificum Mayr, 1870: 972, 976. Syntype workers, female, Tonga: Tongatabu (BMNH; NM, Vienna) [examined]. [For a statement of current synonymy oi pacificum see Bolton, 1977: 102.]
Worker. TL 3.7 - 4.6, HL 0.86 - 1.10, HW 0.72 - 1.02, CI 83 - 90, SL 0.62 - 0.82, SI 79 - 87, PW 0.54 - 0.68, AL 1.04 - 1.30 (45 measured).
Mandibles usually unsculptured except for hair-pits but in some populations with feeble traces of striation. Anterior clypeal margin with a median notch or impression; median portion of clypeus with three strong longitudinal carinae. Frontal carinae long and strongly developed, usually approaching the occipital margin. Maximum diameter of eye c. 0.18 - 0.21, about 0.22 - 0.25 x HW. Propodeal spines long and acute, usually narrow and often somewhat upcurved along their length. Metapleural lobes acute and upcurved, usually broad. Petiole in profile characteristically shaped (Fig. 44), with the posterior face higher than the anterior so that the convex dorsum slopes upwards posteriorly and the posterodorsal angle is higher than the anterodorsal. Anterior face and dorsum confluent through a curve. Sculpture variable in density and intensity. On the head varying from a blanketing rugoreticulum to a system which is predominantly longitudinal but with cross-meshes present from the level of the anterior margins of the eyes; always with a reticulum posteriorly, close to the occiput. Ground-sculpture between rugae superficial but quite conspicuous. Dorsal alitrunk reticulate-rugose; often pedicel segments similarly sculptured but in some the sculpture predominantly longitudinal. First gastral tergite usually with at least traces of basal costulae; although these are often vestigial they are only rarely completely absent. Erect or suberect long hairs numerous on all dorsal surfaces of head and body. Colour a uniform dark brown, blackish brown or black.
T. pacificum ranges throughout the Oriental and Indo-Australian regions and occurs in northern Australia. It is very widespread in most or all of the island-systems of the Pacific (Wilson & Taylor, 1967; Bolton, 1977) and has been recorded from California in the U. S. A. (M. R. Smith, 1943; Creighton, 1950). The shape of the petiole in pacificum is unique amongst tetramoriines occurring in the New World and should serve to identify instantly this species.
description: Published as part of Bolton, B., 1979, The ant tribe Tetramoriini (Hymenoptera: Formicidae). The genus Tetramorium Mayr in the Malagasy region and in the New World., pp. 129-181 in Bulletin of the British Museum (Natural History) Entomology 38 on page 168
Spreading in functional phonology
Creators: name: Boersma, Paul
Publisher: name: Holland Academic Graphics
Year: 1998

description: The occurrence of and the restrictions on the temporal spreading of phonological feature values (assimilation, harmony) are the results of interactions between the functional principles of minimizing articulatory effort and minimizing perceptual confusion. This proposal is tested on the typology of opacity to nasal spreading. While the sonority approach of Gnanadesikan (1995) meets with insuperable problems with regard to the position of /h/ in the hierarchy, and the feature-geometric representational approach of Piggott (1992) needs to take recourse to ad-hoc conditions in UG in order to get the hierarchy right, the functional approach accurately predicts the attested typology.
Probabilistic radiographic atlas of molecular and interventional phenotypes in human glioblastoma
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: Objectives! The overall goal of this project is to construct voxel-wise probabilistic atlases of glioblastoma frequency of tumor occurrence for important biological and interventional phenotypes by first developing a comprehensive imaging database of pre-treatment glioblastoma MR images, then determining the most prevalent tumor locations expressed by different tumor phenotypes (probabilistic atlases) using statistical parameter mapping (SPM) techniques. We hypothesize: 1) Contrast-enhancing and T2/FLAIR hyperintense lesions will occur in a high frequency within the periventricular spaces adjacent to the subventricular zone, reflecting regions known to harbor neural stem cells; 2) gliomas with specific phenotypes will occur in a significantly high frequency within particular regions of the brain; 3) patients with tumors in particular areas of the brain respond differently to specific treatments; and 4) tumor morphometry will differ between different biological and interventional phenotypes. ! ! ! Methods! To accomplish the aforementioned objectives, we propose (Aim1) constructing a comprehensive imaging database of pre-treatment glioblastoma MR images, registering these images to stereotactic atlas space and contouring different tumor contrasts (T2/FLAIR hyperintensity, contrast-enhancement, and necrosis). (Aim2) We will then use this information to determine the most prevalent tumor locations expressed by different biological phenotypes, including age, KPS, WHO grade, MGMT promoter methylation, IDH1 mutation, EGFR VIII amplification, PTEN deletion, and molecular gene profile, as well as “interventional phenotypes”, including extent of surgical resection, RANO response to standard radiochemotherapy, PFS to standard therapy, RANO response to upfront bevacizumab, PFS in upfront bevacizumab, and OS regardless of treatment. We will use statistical parameter mapping (SPM) techniques, such as the voxel-wise Fisher’s exact test, for determining regions with a statistically significant frequency of occurrence between different phenotypes. (Aim3) Using the contoured lesions from Aim 1 and the various categories outlined in Aim 2, we will also compare morphometry, or tumor measurement characteristics such as volume, volume ratios between different contrasts, sphericity, texture, etc., between different biological and interventional phenotypes.
Phonology as Cognition
Creators: name: Hale, Mark
name: Reiss, Charles
Publisher: name: Oxford University Press
Year: 2000

description: This paper attempts to ground phonology within psychology. That is, we are interested in phonology as a branch of the study of mental representation, the psychology of mind. In order to develop this `phonology of mind' we need to understand the relationship between formal properties of grammars and the `substance' which representations represent. Current trends in phonology fail to offer a coherent conception of form and substance and are also inconsistent with basic principles of science. In addition to critiquing the phonological literature on markedness and related issues, we offer a modest result in the study of the formal properties of the phonology: we demonstrate that phonology needs to make use of quantification to characterize the structural descriptions of rule and constraints.