cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
A novel microbial system to screen GPCR crosstalk during cancer proliferation
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: This seed project will engineer a novel yeast platform to characterize interactions between human G-protein coupled receptors (GPCRs) from the adenosine family, which play an integral role in the proliferation of cancer. Four cell surface adenosine GPCRs (A1R, A2aR, A2bR, and A3R) mediate cellular responses to extracellular adenosine analogs, imparting a protective function to tissues where adenosine is in excess. Tumor cells are well recognized to exist in sub-locations of excess adenosine, and certain cancerous cells (e.g. prostate cancers) are known to upregulate production and cell surface localization of the A2bR. Though treatment with an A2aR-specific antagonist has been shown to block proliferation of prostate cancers, the mechanism of this action has not yet been determined. We hypothesize that crosstalk occurs between the human adenosine A2aR and A2bR receptors in tumor cells, which alters receptor signaling and cAMP production. Specifically, we will directly test the hypothesis that addition of an A2bR selective antagonist leads to transinhibition of A2aR’s associated signal cascade. This hypothesis will directly test speculation from recent preclinical observations. Since GPCRs have been shown in recent years to exist almost exclusively as dimers in mammalian membranes, it is possible that A2bR-associated ligand binding activates neighboring signaling pathways when A2bR is dimerized with another adenosine receptor. To characterize the prevalence of adenosine receptor crosstalk, human receptors will be expressed in the yeast S. cerevisiae, which has analogous G-protein coupling signaling machinery to human cells. Through genetic engineering of the yeast endogenous signaling machinery, a "sensor" strain will be created that couples adenosine ligand binding to production of green fluorescent protein (GFP); this couples ligand activation and signaling with a fluorescent output amenable to high throughput screening. Sub-aims to be achieved over the one-year seed project include (1) sub-clone and express the human A2aR and A2bR in yeast, (2) genetically engineer the yeast G-protein signaling pathway to link agonist binding and signal transduction to a fluorescent reporter, and (3) screen AR agonists and antagonists for their ability to trigger neighboring G-protein signaling cascades in an A2aR-A2bR co-expression strain. This seed project will lay the foundation for follow-up studies that will measure association of A2b-A2a dimers in membrane platforms, and will be further extended to decouple crosst
Andiorrhinus (Amazonidrilus) bolivianus Zicsi 1995
Creators: name: Csuzdi, Csaba
name: Szederjesi, Tímea
name: Sherlock, Emma
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Animalia
Annelida
Clitellata
Haplotaxida
Glossoscolecidae
Andiorrhinus
Andiorrhinus bolivianus

description: Andiorrhinus (Amazonidrilus) bolivianus Zicsi, 1995
Andiorrhinus (Amazonidrilus) bolivianus Zicsi, 1995b Rev. suisse Zool. 102: 588.
description: Published as part of Csuzdi, Csaba, Szederjesi, Tímea & Sherlock, Emma, 2018, Annotated checklist of earthworm species described by András Zicsi (Clitellata: Megadrili), pp. 11-42 in Zootaxa 4496 (1) on page 30, DOI: 10.11646/zootaxa.4496.1.4, http://zenodo.org/record/1447011
Gerres cinereus
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
Perciformes
Gerreidae
Gerres
Gerres cinereus

description: Gerres cinereus (Walbaum 1792). Atlantic Yellowfin Mojarra; Mojarra Trompetera, Comearena, Palmito
Vouchers: LSUMZ 15367 (4). Distribution: Western Atlantic Ocean; from Bermuda, Bahamas and Florida, USA, to Rio de Janeiro, Brazil; entering estuaries and littoral lagoons and ascending river courses; (Nicaragua) WK (Atlantic); 0–6 masl; Per, Dia, Amp. Occurrence and conservation status: Nat; LC (2015), population trend unknown. Literature: Robertson & Van Tassell (2019: 4455; detailed description, including illustrations, and information on distribution, with a map, and ecology) and Angulo (2021: 65; 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 73, DOI: 10.11646/zootaxa.5376.1.1, http://zenodo.org/record/10208788
A novel role of histone methyltransferase subunits in cytokinesis
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: Defective cytokinesis and either mutations or misregulation of histone H3 lysine 4 methyltransferase (H3K4MT) both contribute to cancer formation, though there is currently no known links between the two. As one of the most characterized chromatin modifying machineries, H3K4MTs methylate histone H3 at Lys4, an evolutionarily conserved epigenetic marker of active transcription. However, almost nothing is known about these complexes in the cytoplasm. The overall objective of this proposal is to characterize an unexpected regulatory role that we discovered of cytoplasmic H3K4MT subunits in cytokinesis. Based on our preliminary study, we hypothesize that a midbody-localized H3K4MT methyltransferase complex promotes abscission during cytokinesis. We propose two independent aims to test our hypothesis. Aim1: To test whether midbody-localized H3K4MT regulatory subunits promote abscission. We will use an inducible protein interaction system to specifically sequester cytoplasmic H3K4MT regulatory subunits to mitochondria, and examine how this sequestration affects abscission. We will map the midbody-targeting domains of regulatory subunits and test if such domains exert a dominant negative effect on the midbody localization of the full-length subunits. We will also assess how interfering with subunit localization affects abscission. These experiments will establish whether H3K4MT regulatory subunits facilitate abscission from the midbody, another cytoplasmic site, or the nucleus. Aim2: To test whether H3K4MT regulatory subunits function in the context of a methyltransferase complex to promote abscission. We will examine whether a catalytic subunit and its enzymatic activity are involved in abscission. We will also investigate whether the assembly of regulatory and catalytic subunits at the midbody is required for abscission. Together, these experiments will determine whether H3K4MT regulatory subunits form a complex with a catalytic subunit to promote abscission. If this proves true, these studies will also provide insight into whether this complex functions as a methyltransferase and whether it acts at the midbody. Alternatively, our study may reveal an equally intriguing non-conventional function of regulatory subunits independent of the known catalytic subunits.
Cerebellar Granule pattern (Crochet pattern)
Creators: name: Adams, Eleanor
Publisher: name: The Francis Crick Institute
Year: 2024
Subjects: classificationCode: Research Support
subject: Research Support

description: The pattern for one of the neurone models in the "Hello Brain!" public exhibition at the Francis Crick Institute in 2024. The Crick commissioned the creation of this model and the writing of this pattern.
Gerres simillimus Regan 1907
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
Perciformes
Gerreidae
Gerres
Gerres simillimus

description: Gerres simillimus Regan 1907. Pacific Yellowfin Mojarra; Palmito Blanco, Palmito Rayado, Mojarra, Comearena
Vouchers: Not available. Distribution: Eastern Pacific Ocean; from southern Baja California, Mexico, to northern Peru, including the Galapagos islands; entering estuaries and littoral lagoons and ascending river courses; (Nicaragua) PN and Ni (Pacific); 0–5 masl; Per, Dia, Amp. Occurrence and conservation status: Nat; LC (2007), population trend unknown. Literature: Robertson &Allen (2015: 1340; detailed description, including illustrations, and information on distribution, with a map, and ecology) and Angulo (2021: 65; 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 73, DOI: 10.11646/zootaxa.5376.1.1, http://zenodo.org/record/10208788
Engineered tissue matrices to interrogate prostate cancer migration and tumor formation
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 preferential metastasis of breast and prostate cancer to the skeleton demonstrates that the bone microenvironment promotes migration and secondary tumor growth, yet it remains unknown what in the skeleton (specifically, the organic matrix) enables preferential metastasis of these types of cancers. Data show that active remodeling of the skeleton is a critical determinant of PCa metastasis to bone, indicating that a matrix-bound factor(s) which is released during remodeling promotes metastasis and/or secondary tumor formation. Further efforts are required to identify why there is preferential metastasis and tumor-forming capacity of PCa cells within the skeleton. In this application, we propose a focused, unbiased approach to identifying the components of the organic matrix and matrix-bound factors upon PCa cell migration, osteomimicry, and tumor formation. We have previously demonstrated that tissue-derived demineralized matrices (tDM) can robustly influence the osteogenic commitment of stem cells, and that altering growth factor binding through enzymatic treatment can attenuate or enhance differentiation. We hypothesize that tDM drives PCa cell migration, osteomimicry and tumor formation; further, we propose that altering tDM through enzymatic treatment will attenuate these processes. When we find a process (e.g., migration, osteomimicry, in vivo tumor formation) attenuated on enzyme-treated tDM compared to nativWe will test this hypothesis with in vitro and in vivo models that combine the fields of molecular and cellular biology with tissue engineering that leverages the individual strengths of the PI and his collaborator with the expertise at the UC Davis Center for Molecular and Genomic Imaging and services provided by the UC Davis Core Facility. The overall hypothesis will be tested under the two Specific Aims: Specific Aim 1. Interrogate the influence of native versus enzyme-treated tDM upon PCa cell migration and osteomimicry; identify differential protein presentation in native versus enzyme-treated tDM. Specific Aim 2. Interrogate the influence of native versus enzyme-treated tDM upon PCa metabolism and tumor formation in vivo in a murine heterotopic model.
Aptodrilus baloghi
Creators: name: Csuzdi, Csaba
name: Szederjesi, Tímea
name: Sherlock, Emma
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Animalia
Annelida
Clitellata
Haplotaxida
Glossoscolecidae
Aptodrilus
Aptodrilus baloghi

description: Aptodrilus baloghi (Zicsi & Csuzdi, 1988)
Thamnodrilus baloghi Zicsi & Csuzdi, 1988 Opusc. Zool. (Budapest) 23: 212.
Aptodrilus baloghi: Zicsi 1997c Opusc. Zool. (Budapest) 29–30: 163.
description: Published as part of Csuzdi, Csaba, Szederjesi, Tímea & Sherlock, Emma, 2018, Annotated checklist of earthworm species described by András Zicsi (Clitellata: Megadrili), pp. 11-42 in Zootaxa 4496 (1) on page 30, DOI: 10.11646/zootaxa.4496.1.4, http://zenodo.org/record/1447011
Erythrocyte-derived optical nano-probes for near infrared fluorescence imaging of tumors
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: Detection of small tumor nodules (< 1 cm) remains as a great challenge in clinical imaging oncology. The ability to identify and remove such tumors is clinically significant, and has potentially tremendous impact on preventing tumor recurrence, treatment success, and ultimately the survival of patients suffering from a wide variety of cancers. This proposal is related to the use of a new type of optical nano-vesicles, derived from erythrocyte ghosts doped with indocyanine green (ICG), an FDA-approved near infrared (NIR) chromophore, for fluorescence imaging of small tumor nodules. We refer to these nano-vesicles as near infrared erythrocyte-mimicking transducers (NETs). Two specific aims ares proposed: (1) maximize the fluorescence emission of NETs by optimizing the concentration of ICG utilized during fabrication process; and (2) demonstrate the efficacy of in-vivo tumor imaging using NETs optimized with maximal fluorescence emission. Under specific aim 1, we will vary the ICG concentration in the range of 0.1 mM – 10 mM, and determine the optimum concentration that maximizes emission by quantifying the relative fluorescence quantum yield as our metric of evaluation. Under specific aim 2, we will evaluate the effectiveness of NETs in imaging tumor xenografts in mice. We will use four groups of mice, with each group representing the time point (1, 2, 4, and 6 weeks after tumor implantation) at which the animals in that group will be euthanized post-tumor implantation. Tumor implantation will be done by intraperitoneal injection of SKOV3 ovarian cancer cells. For each time point, we will have corresponding animals receiving either buffer solution (negative control), free ICG (positive control), or NETs. We will perform NIR imaging on whole body, open-abdomen, and and extracted tumors and organs. We will quantify the relative content of ICG in tumors and harvested organs, and determine if NETs accumulate at greater levels within tumor xenografts, and provide greater imaging sensitivity and specificity than free ICG. This proposal presents a highly innovative technology in tumor imaging, and the first step in investigating the potential of these materials for future clinical translation during intraoperative procedures to aid identification of small tumor nodules. Successful demonstration of imaging tumor nodules with NETs, optimized for maximal fluorescence emission, under this proposal, has broad implications for the potential utility of these constructs in imaging peritoneal carcinomatosis resulting fr
Diapterus auratus Ranzani 1842
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
Perciformes
Gerreidae
Diapterus
Diapterus auratus

description: Diapterus auratus Ranzani 1842. Irish Mojarra, Irish Pompano; Patao Común, Mojarra Guacha, Mojarra, Comearena, Palmito
Vouchers: Not available. Distribution: Western Atlantic Ocean; from southern Florida, USA, to southern Brazil; entering estuaries and littoral lagoons and ascending river courses; (Nicaragua) KP, Es and BF (Atlantic); 0–4 masl; Per, Dia, Amp. Occurrence and conservation status: Nat; LC (2015), population trend unknown. Literature: Villa (1982: 177, as Diapterus evermanni Meek & Hildebrand 1925 and Diapterus olisthostomus (Goode & Bean 1882) — synonyms; detailed description, including illustrations and an identification key, and information on distribution and ecology), Robertson & Van Tassell (2019: 3701; detailed description, including illustrations, and information on distribution, with a map, and ecology) and Angulo (2021: 63; 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 74, DOI: 10.11646/zootaxa.5376.1.1, http://zenodo.org/record/10208788
Additional file 5: Table S4. of Genomic characterisation of clinical and environmental Pseudomonas putida group strains and determination of their role in the transfer of antimicrobial resistance genes to Pseudomonas aeruginosa
Creators: name: Peter, Silke
name: Oberhettinger, Philipp
name: Schuele, Leonard
name: Dinkelacker, Ariane
name: Vogel, Wichard
name: DĂśrfel, Daniela
name: Bezdan, Daniela
name: Ossowski, Stephan
name: Marschal, Matthias
name: Liese, Jan
name: Willmann, Matthias
Publisher: name: Figshare
Year: 2017
Subjects: subject: Space Science
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology
subject: Computational Biology

description: Overview of the closest related type strains based on the average nucleotide identity (ANI). (DOCX 16Â kb)
Single molecule detection of miRNA on dynamic nanoarrays
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: Progress toward understanding the complex roles of miRNAs in cancers as well as the development of related diagnostic and therapeutic techniques critically depends on the ability to accurately and reliably profile the expression of miRNAs. The expression levels of miRNAs may vary by four orders of magnitude and even small variations in expression levels may be biologically significant. Leading approaches to high-throughput miRNA profiling require multiple time-consuming and bias-prone steps of enzymatic and chemical modification to amplify and label the targets. A promising alternative is to use nanoarrays, of which the small sizes may dramatically increase the target capture efficiency and detection sensitivity. The goal of the proposed research is to evaluate the potential of single molecule atomic force microscopy detection and novel nanoarrays in ultra-sensitive, label- and amplification-free determination of miRNAs. Our hypothesis is that miRNAs can be reliably and efficiently captured by nanoarrays with dynamic surface interactions and a uniform spatial distribution of capture probes. Aim 1: Produce a nanoarray with probes targeting different miRNAs. Nanografting will be used to produce spots in which the probe molecules are randomly distributed. The surface will be passivated with chemical functionalities that have switchable interactions with nucleic acid molecules. Aim 2: Probe and detect miRNA hybridization on nanoarrays. The switchable surface interactions can ensure both facile hybridization with minimal nonspecific adsorption and single molecule AFM quantification. The probe density and surface interactions will be varied to investigate and optimize the target capture. Moreover, multiplexed detection of four miRNA targets will be demonstrated. The proposed nanoarrays may allow the ultrasensitive detection of miRNAs without any labeling or amplification and in only a few hours. The proposed research will demonstrate the potential of nanoarrays in significantly advancing the state of the art of miRNA profiling. Moreover, by imaging the capture probe surface at the single molecule level, the study will provide fundamental knowledge of the hybridization process at the nanoscale, which is important for optimizing a broad range of surface-based hybridization assays.
Targeting the telomere with small molecule anticancer compounds
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: A hallmark of all cancer cells is uncontrolled cell growth. The ability of a cancer cell to bypass critical cell growth checkpoints is invariably linked to the stable maintenance of telomeres, specialized chromatin structures that cap the ends of linear chromosomes. Stable telomere length maintenance confers a high degree of proliferative capacity to cancer cells by avoiding the permanent cell growth arrest triggered by a critically short telomere. The myriad links between telomeres, cellular growth potential, and cancer have motivated intensive research aimed at identifying small molecules that interfere with telomere maintenance in cancer cells. Although the strategy of disrupting telomere homeostasis to kill cancer cells holds great promise, there remain large gaps in our understanding of how known telomere DNA binding compounds impact telomere structure. Furthermore, there exist a relatively small number of drug candidates that target the telomere, thus motivating discovery efforts to identify novel telomere targeting compounds. The primary objectives of this proposal are to analyze the mode of action of several known telomere binding drugs, as well as to identify and characterize novel telomere DNA binding anticancer compounds. Aim 1: Determine the impact of known telomere DNA binding compounds on telomere DNA structure. Our approach will employ novel single-molecule biophysical techniques established in our laboratory which offer the unique opportunity to precisely analyze the interaction between telomere DNA and small molecules in real-time, using extremely small quantities of sample material. Initially, experiments will focus on selected porphyrin compounds and the glycosidic soy isoflavones (daidzin and genistin) which have each been reported to bind and alter the structure of telomere DNA. Aim 2: Establish a cell-imaging based screen to identify novel telomere DNA binding compounds.Among the most potent telomere binding drugs discovered to date is the natural product telomestatin, which has been shown to induce cell death in several cancer cell types. We propose to capitalize on the unique marine natural product libraries collected by Prof. Roger Linnington at UCSC, as well as the UCSC small molecule scree ning center run by Prof. Scott Lokey, to establish a high throughput screen for novel telomere DNA binding drugs. The screen will use automated fluorescence microscopy to directly detect the ability of potential telomere DNA binding compounds to displace the essential telomere b
Linking chromatin modification and remodeling in cellular growth control and stress response
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: Chromatin modification and remodeling is linked to diverse cancers and to normal function of key oncogenes such as Myc and p53 and many other cancer-associated genes. This proposal builds on our discovery of critical connections between two activities that we find act antagonistically during normal growth: lysine acetylation and ISWI-mediated chromatin remodeling. Both enzyme classes are broadly conserved with human homologs that are directly tied to specific cancers as well as regulated processes that are disrupted in cancer, such as apoptosis and repair of DNA damage. The proposed studies will deepen basic mechanistic understanding of chromatin function and growth control and may establish novel targets for genetic or pharmacological intervention for cancers. The objectives and methods for this project are focused to answer three questions: 1) What is the molecular basis for the ISWI2-mediated suppression of gcn5 sas3 lethality? We found that deletion of ISW2 suppresses conditional lethality of the gcn5 sas3 mutant. Isw2 exists in two biochemically distinct complexes whose specific functions are not fully understood. We will dissect the complexes and test newly defined functional domains of Isw2 for their roles in suppression. 2) What is the nucleosomal landscape under conditions of sickness and suppression? We will test the hypothesis that nucleosome spacing and stability around the nucleosome-free regions (NFR) of target genes are critical in the modification-remodeling dynamic. We will use chromatin immunoprecipitation (ChIP) and high resolution ChIP-exo mapping to address our hypotheses and build molecular models for the acetyltransferase-remodeling interplay. 3) What is the role of Gcn5/Sas3 and ISWI remodelers in response to environmental stressors associated with cancer? The acetyltransferases and many remodelers regulate stress response genes associated with many cancers. In new and unpublished results, we have discovered a significant interaction of the genes under study in response to heavy metal stress and toxicity, a significant class of environmental carcinogens. We will evaluate gene expression dynamics and examine specific chromatin modifications with the long-term goal of establishing small molecule screens to modulate these effects.
Mechanisms of cancer cell transmigration during tumor metastasis
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: The ability of cancer cells to metastasize to distant sites contributes to over 90% of cancer-related death. Preventing the migration of cancer cells to new sites would have a tremendous impact on reducing metastasis and improving clinical outcomes in cancer patients. In order to develop effective therapeutics to limit metastasis, it is critical to have a clear understanding of the mechanisms used by cancer cells to exit the bloodstream and enter new tissues. Currently, however, these processes are poorly understood. We have taken an innovative, multidisciplinary approach to develop a fluidic system that functions like an artificial blood vessel. Using this system we can visualize cells interacting with and transmigrating across blood vessel endothelium. We will use this system to compare the adhesion and migration of metastatic vs noninvasive cancer cells across human brain endothelium to identify mechanisms used by these cells to establish sites of metastasis. Objective and Methods: The metastatic breast cancer lines MDA-MB-231 and MDA-MB-435 will be compared to the MCF-7 cell line, which is weakly invasive. The cells will be fluorescently labeled and flowed through the fluidic device containing primary human brain microvascular endothelium. The number of adhesion events, the velocity, and the pathlength of each type of cell will be compared. We will then investigate the molecules involved in adhesion, focusing on E-selectin on the endothelium and its ligands on the cancer cells. In the second aim, we will analyze the transendothelial migration of the adherent cancer cells and specifically examine their route of transmigration (paracellular or transcellular). Significance: The proposed research is expected to provide a molecular understanding of how human breast cancer cells interact with brain endothelium. We will utilize a novel dynamic imaging approach to compare the adhesion and transmigration of metastatic and noninvasive breast cancer lines across human brain microvascular endothelial cells. This contribution is significant because these interactions are critical for cancer cells to leave the bloodstream and enter tissues where they establish metastatic disease. We anticipate that this research will reveal novel insights about cancer cell pathogenesis and facilitate the development of therapeutics to limit metastasis and cancer-related disease and death.
Aptodrilus botari
Creators: name: Csuzdi, Csaba
name: Szederjesi, Tímea
name: Sherlock, Emma
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Animalia
Annelida
Clitellata
Haplotaxida
Glossoscolecidae
Aptodrilus
Aptodrilus botari

description: Aptodrilus botari (Zicsi & Csuzdi, 1988)
Thamnodrilus botari Zicsi & Csuzdi, 1988 Opusc. Zool. (Budapest) 23: 214.
Aptodrilus botari: Zicsi 1997c Opusc. Zool. (Budapest) 29–30: 158.
description: Published as part of Csuzdi, Csaba, Szederjesi, Tímea & Sherlock, Emma, 2018, Annotated checklist of earthworm species described by András Zicsi (Clitellata: Megadrili), pp. 11-42 in Zootaxa 4496 (1) on page 30, DOI: 10.11646/zootaxa.4496.1.4, http://zenodo.org/record/1447011
Determinants of response and resistance in pediatric low-grade gliomas
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: Gliomas represent the most common solid tumors of childhood, with pediatric gliomas among the most recalcitrant. Pediatric low-grade gliomas (PLGGs) represent a perfect platform on which to initiate personalized approaches to treatment. We are initiating a hypothesis-driven clinical trial of the mTOR inhibitor everolimus for PLGG and tissue will be acquired from every enrolled child. We have documented PI3K/mTOR activation in approximately half of PLGGs, and such pathway activation has been shown in vitro and in animal models to predict response to mTOR inhibition. But does PI3K/mTOR activation predict response to mTOR inhibition in patients, and in PLGGs in particular? We request support from the CRCC for molecular studies to test the hypothesis that PI3K/mTOR activation will predict response to mTOR inhibition in the clinical trial. In addition, since acquired resistance to targeted agents is a rule, we propose parallel laboratory-based studies that explore mechanisms of resistance to inhibitors of mTOR, to inform the next generation of combination studies for PLGGs. Our overall goals are to define molecular features of PLGGs that predict responses to mTOR inhibitors, and to identify mechanisms of resistance that can be overcome by rational therapeutic combinations. Specific Aims: 1. In the context of a multi-institutional Phase II study, to identify, through molecular profiling of tumors, those children most likely to benefit from mTOR inhibition. First, tumors will be classified as PI3K/AKT/mTOR activated or non-activated based on immunohistochemistry (IHC) for p-S6 ribosomal protein (Ser240/244). Then, to evaluate whether everolimus is active only in PLGGs with PI3K/AKT/mTOR activation, we will employ an adaptive Simon two-stage design for Phase II studies of targeted therapies. We will also analyze key molecular features including activation of the PI3K, mTOR and MAPK pathways, aberrations in PTEN and p53, PDGFRA amplification, CDKN2A loss, and activating mutations in BRAF. 2. In the context of preclinical strategies to prevent emergence of resistance, to test combination therapy using everolimus and MAPK pathway inhibitors in BRAF activated PLGG. We will investigate viability, flow cytometry, and clonogenicity assays, to ask whether BRAF activation (the most common aberration in PLGGs) confers resistance to everolimus, comparing effects of BRAFV600E and KIAA1549:BRAF.
Haemulidae Gill 1885
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
Perciformes
Haemulidae

description: Family Haemulidae Gill 1885 (Fig. 5B). Grunts, Porkfishes, Salemas; Roncadores, Burros, Salemas, Tenientes, Corocoros, Roncos, Viejas, Corcovados
Description: Body oblong, compressed; up to 75 cm in length; mouth relatively small, usually with thick lips; teeth on jaws usually cardiform, generally absent on vomer; a pair of conspicuous pores plus (in almost all genera) a central groove under the chin; scales rough, over entire body and head, except in the front of the snout, lips and chin; dorsal fin continuous, with 9–14 spines and 11–26 soft rays; anal fin with three spines and 6–18 soft rays; caudal fin concave to forked (Robertson & Allen 2015, Nelson et al. 2016). Distribution: Marine (many in brackish water, rarely in freshwaters); Atlantic, Indian and Pacific oceans (Nelson et al. 2016). Four genera and six 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 74, DOI: 10.11646/zootaxa.5376.1.1, http://zenodo.org/record/10208788
title: AUTONOMOUS SHUTTLE CAR DOCKING TO A CONTINUOUS MINER USING RGB-DEPTH IMAGERY
Creators: name: Rose, Sky
Publisher: name: University of Kentucky Libraries
Year: 2024
Subjects: classificationCode: 2.7
subject: FOS: Environmental engineering

description: A great deal of research is currently being conducted in automating mining equipment to improve worker health and safety and increase mine productivity. Significant progress has been made in some applications, e.g., autonomous haul trucks for surface mining. However, little progress has been made in autonomous face haulage in underground room-and pillar coal mines. Accordingly, this thesis addresses automating the operation of a shuttle car, focusing on positioning the shuttle car under the continuous miner coal-discharge conveyor during cutting and loading operations. The approach uses a stereo depth camera as the sensor, and machine-learning algorithms are used to identify various objects in the mine environment, such as the continuous miner coal-discharge conveyor, continuous miner body, roof, ribs, etc. An occupancy map is generated, a path to the continuous miner discharge conveyor is planned, and a controller is used to execute the path. The approach is developed and tested on a 1/6th-scale mock mine and in a simulated mine laboratory using full-scale equipment and manual controls.
description: 2024 Sky Rose
Aptodrilus chilesensis Zicsi 1997
Creators: name: Csuzdi, Csaba
name: Szederjesi, Tímea
name: Sherlock, Emma
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Animalia
Annelida
Clitellata
Haplotaxida
Glossoscolecidae
Aptodrilus
Aptodrilus chilesensis

description: Aptodrilus chilesensis Zicsi, 1997
Aptodrilus chilesensis Zicsi, 1997c Opusc. Zool. (Budapest) 29–30: 166.
description: Published as part of Csuzdi, Csaba, Szederjesi, Tímea & Sherlock, Emma, 2018, Annotated checklist of earthworm species described by András Zicsi (Clitellata: Megadrili), pp. 11-42 in Zootaxa 4496 (1) on page 30, DOI: 10.11646/zootaxa.4496.1.4, http://zenodo.org/record/1447011
Aphodiini Leach 1815
Creators: name: Ziani, Stefano
Publisher: name: Zenodo
Year: 2024
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Scarabaeidae

description: Tribe Aphodiini Leach, 1815
Genus Gaindaphodius Král and Mencl, 2024
description: Published as part of Ziani, Stefano, 2024, A new species of Gaindaphodius Král and Mencl from Nepal (Coleoptera: Scarabaeidae: Aphodiinae), pp. 1-7 in Insecta Mundi 2024 (64) on page 1, DOI: 10.5281/zenodo.14662280
The City of Newark sustainability action plan
Creators: name: No Name Supplied
Publisher: name: No Publisher Supplied
Year: 2013

description: The Sustainability Action Plan offers a vision of a community plan to make Newark a healthy, vibrant, and sustainable city. The document incorporates input of residents and organizational leaders who attended meetings and participated in Sustainability Office activities.  This Sustainability Action Plan lays out strategies for making Newark’s environment a positive force in the life of the city. It articulates a policy framework of four policy goals: (1) improved public health; 2) cost savings; 3) enhanced quality of life; and 4) expanded green economic opportunity for Newarkers. It also identifies several priority action items regarding air quality; energy; recycling and materials management; stormwater management and community greening; greenhouse gas emissions; and healthy food access.
Uroplectes ebogo Euscorpius & No., 2024, sp. n.
Creators: name: Euscorpius
name: No.
Publisher: name: Zenodo
Year: 2024
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Arachnida
Scorpiones
Buthidae
Uroplectes
Uroplectes ebogo

description: Uroplectes ebogo sp. n.
(Figs. 1–37, Table 1)
description: Published as part of Euscorpius & No., 2024, Uroplectes ebogo sp n (Scorpiones: Buthidae) from Cameroon, pp. 1-13 in Euscorpius 397 on page 2, DOI: 10.5281/zenodo.14660523
Conodon nobilis
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
Perciformes
Haemulidae
Conodon
Conodon nobilis

description: Conodon nobilis (Linnaeus 1758). Barred Grunt; Ronco Canario
Vouchers: Not available. Distribution: Western Atlantic Ocean; from Eastern Florida, USA, to Argentina; entering estuaries and littoral lagoons and ascending river courses; (Nicaragua) Pr and BF (Atlantic); 0–5 masl; Per, Dia, Amp. Occurrence and conservation status: Nat; LC (2015), population trend unknown. Literature: Fowler (1923: 29; listed, including information on distribution), van den Berghe (2015: 44, as Pomadasys bayanus Jordan & Evermann 1898—misidentification; listed, including an illustration and information on distribution and ecology), Robertson & Van Tassell (2019: 3714; detailed description, including illustrations, and information on distribution, with a map, and ecology) and Angulo (2021: 65; 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 74, DOI: 10.11646/zootaxa.5376.1.1, http://zenodo.org/record/10208788
Aptodrilus griseus Zicsi 1997
Creators: name: Csuzdi, Csaba
name: Szederjesi, Tímea
name: Sherlock, Emma
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Animalia
Annelida
Clitellata
Haplotaxida
Glossoscolecidae
Aptodrilus
Aptodrilus griseus

description: Aptodrilus griseus Zicsi, 1997
Aptodrilus griseus Zicsi, 1997c Opusc. Zool. (Budapest) 29–30: 162.
description: Published as part of Csuzdi, Csaba, Szederjesi, Tímea & Sherlock, Emma, 2018, Annotated checklist of earthworm species described by András Zicsi (Clitellata: Megadrili), pp. 11-42 in Zootaxa 4496 (1) on page 30, DOI: 10.11646/zootaxa.4496.1.4, http://zenodo.org/record/1447011
Finnish Environment Institute's (Syke) action plan for the responsible assessment of research and researchers 2025-2028
Creators: name: Finnish Environment Institute
Publisher: name: Zenodo
Year: 2025
Subjects: research assessment
action plan
Finnish Environment Institute
CoARA

description: The action plan describes the Finnish Environment Institute’s (Syke) current state and key challenges in assessing research and researchers. It sets goals and actions for developing responsible research assessment at Syke for the years 2025-2028.
Advanced ESD Protection for Integrated Circuits in Nano Scal
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: Semiconductor technology is the corner stone of IT revolution. Microelectronics industry is the power train that has been driven California economy for four decades. Reliability and quality assurance is the key to the success of microelectronics products. As semiconductor technologies rapidly migrate into nano regime, electrostatic discharge (ESD) failure quickly emerges as the most devastating reliability to the industry. ESD failure occurs in every phase of integrated circuit (IC) life span, from manufacturing to applications. On-chip ESD protection is hence required to protect every IC product. Today, ESD robustness for ICs is also a major market competition factor that is gaining global attention. The proposed research aims to develop advanced on-chip ESD protection solution and modeling technique for nano scale IC technologies. Success of this research project provides enabling technology and solutions to keep the California micro-nano-electronics industry on the leading edge, which in turn, shall boost the prosperity and economy of California. This project fits well into the Electronics Manufacturing and Nanotechnology tracks of the IUCRP Program. Technology innovation and quality workforce are the main reason that California can keep its economic competitiveness in today’s turbulent hi-tech competition. While California semiconductor companies have been traditional strong in providing reliable IC products, we do not have any advantage in delivering hi-reliable IC products with emerging high ESD protection requirements. Standing on the same start line with overseas competitors, we must spend more R&D resources to enhance our leading position in quality assurance. Meanwhile, having highly qualified workforce in ESD protection designs is critical for California companies to keep pace with the global competitors. US is gradually losing valuable technical talents to our overseas competitors, including in ESD protection field. Conduction of this project serves to provide hands-on and in-depth training of undergraduate and graduate students, as well as postdoctoral researchers. Further, success of this project shall provide enabling technologies for California companies to produce new IC products with high ESD protection, hence, high quality, which, in turn, will enhance the competitiveness of our IC products, boost R&D and manufacturing capacities in California, and create new jobs in California. It contributes directly to keeping the prosperity of California. In long term, success of this project helps the PI to establish global leadership position in the research field, build up a long-lasting partnership with the industry and attract more external funding to conduct related research.
Haemulopsis leuciscus
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
Perciformes
Haemulidae
Haemulopsis
Haemulopsis leuciscus

description: Haemulopsis leuciscus (Günther 1864). Raucous Grunt; Ronco Chinilla, Ronco Ruco
Vouchers: Not available. Distribution: Eastern Pacific Ocean; from northern Baja California, Mexico, to northern Peru; entering estuaries and littoral lagoons and ascending river courses; (Nicaragua) PN and Ni (Pacific); 0–8 masl; Per, Dia, Amp. Occurrence and conservation status: Nat; LC (2010), population trend unknown. Literature: Villa (1982: 182, as Pomadasys leuciscus —synonym; detailed description, including illustrations and an identification key, and information on distribution and ecology), Robertson & Allen (2015: 1365; detailed description, including illustrations, and information on distribution, with a map, and ecology) and Angulo (2021: 65; 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 74, DOI: 10.11646/zootaxa.5376.1.1, http://zenodo.org/record/10208788
Aptodrilus lacteus Zicsi 1997
Creators: name: Csuzdi, Csaba
name: Szederjesi, Tímea
name: Sherlock, Emma
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Animalia
Annelida
Clitellata
Haplotaxida
Glossoscolecidae
Aptodrilus
Aptodrilus lacteus

description: Aptodrilus lacteus Zicsi, 1997
Aptodrilus lacteus Zicsi, 1997c Opusc. Zool. (Budapest) 29–30: 159.
description: Published as part of Csuzdi, Csaba, Szederjesi, Tímea & Sherlock, Emma, 2018, Annotated checklist of earthworm species described by András Zicsi (Clitellata: Megadrili), pp. 11-42 in Zootaxa 4496 (1) on page 30, DOI: 10.11646/zootaxa.4496.1.4, http://zenodo.org/record/1447011
Additional file 6: Figure S2. of Genomic characterisation of clinical and environmental Pseudomonas putida group strains and determination of their role in the transfer of antimicrobial resistance genes to Pseudomonas aeruginosa
Creators: name: Peter, Silke
name: Oberhettinger, Philipp
name: Schuele, Leonard
name: Dinkelacker, Ariane
name: Vogel, Wichard
name: DĂśrfel, Daniela
name: Bezdan, Daniela
name: Ossowski, Stephan
name: Marschal, Matthias
name: Liese, Jan
name: Willmann, Matthias
Publisher: name: Figshare
Year: 2017
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: 16S rRNA based maximum-likelihood tree of the P. putida group isolates and reference strains. The numbers displayed at the nodes are bootstrap values. The scale bar represents the expected number of changes per site. (PDF 456Â kb)