cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Control of leukemia cell metabolism by the PI3K/AKT pathway
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: Cancer cells displayed altered metabolic regulation compared to normal cells, and targeting cancer cell metabolism is emerging as a promising therapeutic strategy. The goal of this project is to define the mechanisms by which phosphoinositide 3-kinase (PI3K) controls leukemia cell metabolism. Essentially all tumors carry mutations that cause increased PI3K signaling. PI3K and its downstream effectors, including AKT and mTOR, are considered key molecular players in metabolic control. However, much of the evidence for control of metabolic switches by PI3K comes from experiments using non-selective inhibitors or overexpression, mainly in established cell lines. To develop effective therapies targeting this pathway, it is essential to understand the interplay between PI3K and its downstream effectors in the metabolism of primary cancer cells. We have developed a novel genetic system that is an ideal tool with which to define the functions of PI3K and its downstream targets in a primary leukemia cell model. The general approach is to transform mouse bone marrow cells with a retrovirus encoding the human oncogene BCR-ABL. Pre-B cell leukemia lines emerge that grow for weeks in vitro and cause leukemia upon transplantation into mice. We have created pre-B cell lines in which the class IA PI3K regulatory subunits are deleted by gene targeting. The PI3K-deficient cells are smaller, divide slowly, and show greatly reduced leukemogenicity in vivo. Although the gene-targeted cells display a complete absence of detectable PI3K and AKT activation, mTOR function is unexpectedly retained. Residual PI3K-independent mTOR signaling provides a possible mechanism for maintaining metabolic homeostasis and survival in these cells. Using this unique genetic system together with complementation studies we will carry out the following specific objective: (1) To define the roles of PI3K, AKT and mTOR in leukemia cell metabolism. We will assess nutrient transporter expression, glucose uptake, glycolytic rate, autophagy, and phosphorylation of key signaling intermediates, comparing wild-type to PI3K-deficient cells and to cells treated with inhibitors of AKT or mTOR. We will conduct reciprocal experiments to assess how switching on AKT or increasing mTOR function affects metabolic phenotypes in PI3K-deficient cells. The experiments in this proposal will move our laboratory in a new direction, and set the stage for broader investigations of PI3K-dependent metabolism and leukemogenesis in vitro and in vivo.
Report of the Union County Mosquito Extermination Commission, 1954
Creators: name: No Name Supplied
Publisher: name: No Publisher Supplied
Year: 1954

description: A yearly series of reports from the Union County Mosquito Extermination Commission. The reports cover finances, inspections, drainage, oiling, and salt marsh, inland, and educational work regarding the extermination and control of mosquitoes in the different towns and districts of Union County, New Jersey.
Bathygobius andrei
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
Gobiidae
Bathygobius
Bathygobius andrei

description: Bathygobius andrei (Sauvage 1880). Estuarine Frillfin; Mapo de Estero, Gobio de Estero
Vouchers: (other collections) UF 106958 (1). Distribution: Eastern Pacific Ocean; from northern Mexico to northern Peru; 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 (2010), population trend stable. Literature: Villa (1982: 227, as Bathygobius sp. —misidentification; detailed description, including illustrations and an identification key, and information on distribution and ecology), Robertson & Allen (2015: 1991; detailed description, including illustrations, and information on distribution, with a map, and ecology) and Angulo (2021: 36; 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 36, DOI: 10.11646/zootaxa.5376.1.1, http://zenodo.org/record/10208788
Estrogen promotes angiogenesis: Impact for breast 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: The estrogen receptor (ER) alpha is the single most important therapeutic target in the post-surgical treatment of the majority of human breast cancers. Approximately 70% of human breast cancers are ER# positive, and inhibition of ER with Faslodex or the SERMS Tamoxifen and raloxifene, or inhibition of estrogen synthesis with aromatase inhibitors, constitute the current treatment approaches of choice in these women. While there are data suggesting that estrogen may promote angiogenesis in addition to tumor cell growth, the data are far from clear. In this study we will test directly, using both in vitro and in vivo models whether estrogen promotes angiogenesis, and we will determine whether this is a direct effect on endothelial cells or an indirect effect of estrogen inducing tumor cell expression of pro-angiogenic factors. These studies may point the way to new approaches targeted on slowing the growth of breast tumors.
THE PROBLEM OF DEVELOPING LOGICAL THINKING IN FUTURE TEACHERS BASED ON INTERDISCIPLINARY COOPERATION AND ITS ANALYSIS
Creators: name: Solijonov, Jasurbek
Publisher: name: Zenodo
Year: 2025

description: The article studies the theoretical and methodological foundations of developing logical thinking in future teachers, the methodology for developing logical thinking in future teachers based on interdisciplinary cooperation, the effectiveness of developing logical thinking in future teachers based on interdisciplinary cooperation. Also, The essence and theoretical foundations of the concept of logical thinking are analyzed.
CI Compass FAIR Topical Working Group
Creators: name: Brower, Donald
name: Murillo, Angela
Publisher: name: Zenodo
Year: 2024

description: The CI Compass FAIR Topical Working Group (TWG) combines community building with improving data management and FAIR data for US National Science Foundation Major Facilities. In this sense it is a quasi-Research Colloboration Network. This presentation is an overview of the FAIR TWG given at a FAIROS RCN monthly PI meeting.
A newly discovered PI4P signaling pathway as a novel cancer therapy target
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: There is an urgent need for new cancer treatment strategies. We have discovered a novel signaling pathway downstream of the phosphoinositide PI4P that is required for normal Golgi trafficking. During the course of study of this pathway we made the unexpected discovery that manipulations of it that impair Golgi trafficking also reduce cell proliferation and viability. Our preliminary results suggest a novel mechanism based on the reduced delivery of growth factor receptors to the plasma membrane, thus impairing growth factor signaling. We have been developing powerful tools to manipulate the PI4P pathway and here we propose to use these tools to investigate the suitability of this pathway as a target for novel cancer treatment strategies. We are developing, and propose to refine, methods to inducibly and acutely deplete cells of PI4P, or to deplete them of a novel PI4P binding protein that we have discovered. Each results in rapid impairment of Golgi function. We will use these tools to study the effects on growth factor receptor trafficking and growth factor signaling in matched untransformed versus cancerous cell lines. The proposed experiments will provide the groundwork to advance our already encouraging preliminary results that suggest that this pathway has promise as a novel target for cancer treatment.
Eodrilus irregularis Zicsi 1993
Creators: name: Csuzdi, Csaba
name: Szederjesi, Tímea
name: Sherlock, Emma
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Animalia
Annelida
Clitellata
Opisthopora
Acanthodrilidae
Eodrilus
Eodrilus irregularis

description: Eodrilus irregularis Zicsi, 1993
Eodrilus irregularis Zicsi, 1993b Mitt. Hamb. Zool. Mus. Inst. 90: 171.
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 13, DOI: 10.11646/zootaxa.4496.1.4, http://zenodo.org/record/1447011
Genome-wide assessment of DNA methylation in pancreatic adenocarcinoma
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: Pancreatic ductal adenocarcinoma is a highly aggressive and lethal cancer due to its typically advanced stage at initial diagnosis, poor response to chemotherapy and propensity to recur and metastasize. Accumulating data support the concept that cancer stem or progenitor cells may be critical determinants of chemoresistance, metastasis and disease recurrence in a wide range of malignancies, including pancreatic cancer. The growth and survival of cancer progenitor cells depend on the genetic or epigenetic disruption of signaling pathways, which alters the balance between undifferentiated progenitor cells and differentiated committed cells. Epigenetic alterations, including changes in DNA methylation and post-translational histone modifications, may be the earliest initiating events in the neoplastic progression of a cancer progenitor cell. The variability and plasticity of epigenetic alterations also provide viable explanations for the heterogeneity of cell populations in tumors and their differing capacities for progression and metastasis. Nearly all studies describing DNA methylation in pancreatic adenocarcinoma have relied on the analysis of candidate genes with proposed or known roles in cancer progression. Still lacking in pancreatic cancer are studies that (1) systematically characterize tumor-associated DNA methylation changes across the entire genome in a non-biased manner and (2) address these changes in cancer progenitor cells. Such an approach has the potential to discover novel genes with causal roles in pancreatic cancer and provide a more complete explanation for the molecular events that drive pancreatic tumorigenesis. For this grant, I propose to utilize the unbiased approach of methyl-CpG island recovery assay in combination with comprehensive CpG island DNA microarrays to identify the global range of gene-associated changes in DNA methylation in pancreatic cancer. Furthermore, I will identify these changes in cancer progenitor cells, the putative cell population responsible for the self-renewal, metastatic and chemoresistant properties of pancreatic cancer. The aims of this proposal are: 1) To identify global changes in DNA methylation in human pancreatic cancer progenitor cells. 2) To establish whether the global DNA methylation profile of human pancreatic cancer progenitor cells differs from that of the bulk differentiated tumor. 3) To link tumor-specific changes in DNA methylation with alterations in gene expression.
Role of p65Nrf1 transcription factor in tumor suppression
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: Recently, we have obtained novel evidence that the Nrf1 transcription factor involved in regulating antioxidant enzymes may play a role in hepatocellular carcinoma. Hepatocytespecific inactivation of Nrf1 results in oxidative stress and liver cancer. The Nrf1 gene encodes 2 proteins with opposing functions. In addition to full-length 120-kD Nrf1, a shorter 65-kD isoform (p65Nrf1) is also expressed through translation from an internal start codon in the Nrf1 transcript. While p120Nrf1 activates gene expression, p65Nrf1 appears to be a negative regulator of gene expression. Preliminary data indicate that fibroblasts derived from Nrf1-/- embryos show increased growth that can be reversed by reexpression of the 65kD isoform of Nrf1 (p65Nrf1). In view of these results, we speculate that tumorigenesis in Nrf1 liver knockouts are not likely attributed to oxidative stress alone. Our central hypothesis is that the p65 isoform of Nrf1 plays a role as a negative regulator of cell proliferation. Thus the loss of p65Nrf1 function leads to enhanced cell growth that could potentially work in an additive or synergistic manner with oxidative stress to promote cancer development in the Nrf1 liver knockouts. To test this hypothesis, we will: examine whether inactivation of Nrf1 in mouse embryonic fibroblasts alters cell growth characteristics and susceptibility to neoplastic transformation by oncogenes; ii) examine if re-introduction of p65Nrf1 restores normal cell growth, and iii) examine if expression of p65Nrf1 in hepatocytes through a transgene blunts neoplastic growth in Nrf1 liver knockouts. The proposed studies should test if Nrf1 also plays a role in cell growth control through expression of p65 isoform. This finding would be significant, as it implies that Nrf1 not only protects against tumor initiation by regulating oxidative stress response, but also against tumor promotion by regulating cell growth.
Calliptaminae Jacobson 1905
Creators: name: Sultana, Riffat
name: Song, Hojun
Publisher: name: Zenodo
Year: 2024
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Orthoptera
Acrididae

description: Calliptaminae Jacobson, 1905
Genus Acorypha Krauss, 1877
16. Acorypha glaucopsis (Walker, 1870)
Genus Calliptamus Serville, 1831
17. Calliptamus balucha balucha Uvarov, 1938 18. Calliptamus balucha brachypterus (Dirsh, 1957) 19. Calliptamus barbarus barbarus (Costa, 1836) 20. Calliptamus italicus (Linnaeus, 1758) 21. Calliptamus tenuicercis Tarbinsky, 1930
Genus Sphodromerus Stål, 1873
22. Sphodromerus luteipes rubripes Uvarov, 1943 23. Sphodromerus undulatus pedestris Uvarov, 1943 24. Sphodromerus undulatus salinus Uvarov, 1943 25. Sphodromerus undulatus undulatus (Kirby, 1914) 26. Sphodromerus undulatus afghanus Bey-Bienko, 1949 27. Sphodromerus indus Soomro and Wagan 2005
description: Published as part of Sultana, Riffat & Song, Hojun, 2024, Annotated catalogue of Pakistani Acrididae (Orthoptera: Caelifera: Acridoidea), pp. 1-47 in Zootaxa 5486 (1) on page 5, DOI: 10.11646/zootaxa.5486.1.1, http://zenodo.org/record/13209743
Eodrilus loksai Zicsi 1993
Creators: name: Csuzdi, Csaba
name: Szederjesi, Tímea
name: Sherlock, Emma
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Animalia
Annelida
Clitellata
Opisthopora
Acanthodrilidae
Eodrilus
Eodrilus loksai

description: Eodrilus loksai Zicsi, 1993
Eodrilus loksai Zicsi, 1993c Rev. suisse Zool. 100 (3): 633.
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 13, DOI: 10.11646/zootaxa.4496.1.4, http://zenodo.org/record/1447011
Bathygobius mystacium Ginsburg 1947
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
Gobiidae
Bathygobius
Bathygobius mystacium

description: Bathygobius mystacium Ginsburg 1947. Island Frillfin, Island Frillfin Goby; Gobio Bandeado
Vouchers: Not available. Distribution: Western Atlantic Ocean; from southern Florida, USA, to Colombia and the lesser antilles; entering estuaries and littoral lagoons and ascending river courses; (Nicaragua) KP, Es and BF (Atlantic); 0–5 masl; Per, Dia, Amp. Occurrence and conservation status: Nat; LC (2015), population trend unknown. Literature: Villa (1982: 227; detailed description, including illustrations and an identification key, and information on distribution and ecology) and Robertson & Van Tassell (2019: 4105; detailed description, including illustrations, and information on distribution, with a map, and ecology).
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 36, DOI: 10.11646/zootaxa.5376.1.1, http://zenodo.org/record/10208788
Additional file 1: of Depletion of somatic mutations in splicing-associated sequences in cancer genomes
Creators: name: Hurst, Laurence
name: Batada, Nizar
Publisher: name: Figshare
Year: 2017
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Evolutionary Biology
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

description: Supplementary Figures S1â  S8. (PDF 1831 kb)
Catantopinae Brunner von Wattenwyl 1893
Creators: name: Sultana, Riffat
name: Song, Hojun
Publisher: name: Zenodo
Year: 2024
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Orthoptera
Acrididae

description: Catantopinae Brunner von Wattenwyl, 1893
Tribe Catantopini Brunner von Wattenwyl, 1893
Subtribe Catantopina Brunner von Wattenwyl, 1893
Genus Catantops Schaum, 1853
28. Catantops erubescens (Walker, 1870)
Genus Diabolocatantops Jago, 1984
29. Diabolocatantops innotabilis (Walker, 1870)
Tribe Paraconophymatini Otte, 1995
Genus Paraconophyma Uvarov, 1921
30. Paraconophyma kashmirica Mistshenko, 1950 31. Paraconophyma scabra (Walker, 1870) 32. Paraconophyma minuta Bey-Bienko, 1949
Genus Xenocatantops Dirsh, 1953
33. Xenocatantops dirshi dammeren sis Willemse, 1968 34. Xenocatantops humile (Serville, 1838)
description: Published as part of Sultana, Riffat & Song, Hojun, 2024, Annotated catalogue of Pakistani Acrididae (Orthoptera: Caelifera: Acridoidea), pp. 1-47 in Zootaxa 5486 (1) on pages 5-6, DOI: 10.11646/zootaxa.5486.1.1, http://zenodo.org/record/13209743
Epigenetic regulation of SOCS1 in glioblastoma multiforme
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: Glioblastoma Multiforme (GBM) is a highly malignant, incurable brain cancer. Current treatments prove ineffective due to the development of resistance to anti-cancer therapies, in particular ionizing radiation (IR). Our laboratory has identified defects in the expression of a family of molecules called Suppressors of Cytokine Signaling (SOCS) in GBM that regulate the radiation response and are likely to play an important role in the development of cancer and the acquisition of radioresistance. Our goal is to determine the mechanism by which SOCS genes are aberrantly regulated in GBM and how defects in SOCS gene expression contribute to GBM pathogenesis. We have shown that the expression of SOCS1, a potential tumor suppressor, is repressed epigenetically by CpG island methylation in GBM. In Specific Aim 1, we will map the aberrantly methylated CpG dinucleotides in the SOCS1 promoter of GBM cell lines and using genomic bisulfite sequencing (GBS). In Specific Aim 2, we will analyze the loading of transcription factors, HDACs and DNMTs onto the SOCS1 promoter in GBM cells to determine the mechanism of SOCS1 gene silencing. In Specific Aim 3, we will analyze the biological significance of SOCS1 gene repression in GBM by measuring radiation responses and activation of signaling pathways in GBM cells treated with DNA methyltransferase (DNMT) inhibitors, and in cells ectopically expressing SOCS1. Our research focuses on the identification and characterization of novel molecular lesions in GBM that induce tumor cell transformation and cause resistance to anticancer therapies. The SOCS family of proteins represents novel biomarkers of radiation-resistant GBM, and therefore may be useful in the development of new targeted therapies that regulate SOCS expression, enhance GBM cell death in response to radiation therapy, and improve long-term survival of GBM patients.
MOESM1 of Population structure and genomic inbreeding in nine Swiss dairy cattle populations
Creators: name: Signer-Hasler, Heidi
name: Burren, Alexander
name: Neuditschko, Markus
name: Frischknecht, Mirjam
name: Garrick, Dorian
name: Stricker, Christian
name: Gredler, Birgit
name: Bapst, Beat
name: Flury, Christine
Publisher: name: Figshare
Year: 2017
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Biotechnology
subject: Evolutionary Biology
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Additional file 1: Table S1. Number of genotyped bulls per population with their minimum and maximum birth year, as well as number of breeding animals per population, responsible breeding organization and breed-specific characteristics such as major use, breeding goal and proportion of artificial insemination.
Induction of anti-tumor immunity by specific innate immune receptors
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 innate immune system links recognition of microbial infection to induction of the adaptive immune response. In particular, innate signals can polarize T helper (Th) cells toward specific cellular fates. These Th cell subsets include Th1 cells, Th2 cells, and Th17 cells. Each of these subsets orchestrates a qualitatively distinct adaptive immune response, including production of different antibody isotypes and recruitment of different cell types during inflammation. A promising avenue of cancer therapy is to direct the power of the adaptive immune system against tumor cells.1-4 Our objective is to determine the innate immune signals needed to elicit different Th cell subsets. This information will then be used to evaluate which T-cell subsets are most effective in anti-cancer immunity. Aim I. Analyze the induction of T cell subsets in response to combinations of Toll-like receptor (TLR) and NOD-like receptor (NLR) ligands in vivo. Our understanding of which innate immune signals lead to the differentiation of particular Th cell subsets is poor. We will perform mouse immunization experiments using different combinations of TLR and NLR ligands to determine what T-cell subsets are generated in each case. Aim II. Identify specific gene programs activated in response to combinations of TLR and NLR ligands. There is currently very little data to show how TLR and NLR pathways synergize to activate novel transcriptional responses. These combinations of pathways may be fundamental in directing the adaptive immune response toward a particular fate. We will analyze the transcription response to combinations of TLR and NLR ligands using whole genome microarrays. Aim III. Assess the ability for mice to reject tumors following the administration of tumor antigens in the presence of different TLR and NLR ligand combinations as adjuvant. We will test the ability of tumor-specific Th cell subsets to reject tumors in vivo using the well-characterized B16 melanoma tumor model. Ovalbumin (OVA) immunized mice will be challenged with B16 tumor cells expressing OVA (B16-OVA) and monitored for the development of tumors. Also, mice with established B16-OVA tumors will be immunized with OVA in the presence of TLR and NLR ligands to determine whether a tumor-specific adaptive response can prevent tumor growth.
MOESM2 of Population structure and genomic inbreeding in nine Swiss dairy cattle populations
Creators: name: Signer-Hasler, Heidi
name: Burren, Alexander
name: Neuditschko, Markus
name: Frischknecht, Mirjam
name: Garrick, Dorian
name: Stricker, Christian
name: Gredler, Birgit
name: Bapst, Beat
name: Flury, Christine
Publisher: name: Figshare
Year: 2017
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified

description: Additional file 2: Table S2. Number of SNPs per chromosome, range covered by SNPs per chromosome and in total.
Bathygobius ramosus Ginsburg 1947
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
Gobiidae
Bathygobius
Bathygobius ramosus

description: Bathygobius ramosus Ginsburg 1947. Panamic Frillfin; Mapo de Pozo, Mapo Panámico
Vouchers: Not available. Distribution: Eastern Pacific Ocean; from Bahía Magdalena and the Gulf of California, Mexico, to northern Peru, including the Revillagigedo and Cocos islands; entering estuaries and littoral lagoons and ascending river courses; (Nicaragua) PN (Pacific); 0–5 masl; Per, Dia, Amp. Occurrence and conservation status: Nat; LC (2010), population trend stable. Literature: Robertson & Allen (2015: 1994; detailed description, including illustrations, and information on distribution, with a map, and ecology) and Angulo (2021: 37; 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 36, DOI: 10.11646/zootaxa.5376.1.1, http://zenodo.org/record/10208788
Coptacrinae Brunner von Wattenwyl 1893
Creators: name: Sultana, Riffat
name: Song, Hojun
Publisher: name: Zenodo
Year: 2024
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Orthoptera
Acrididae

description: Coptacrinae Brunner von Wattenwyl, 1893
Genus Apalacris Walker, 1870 35. Apalacris varicornis Walker, 1870
description: Published as part of Sultana, Riffat & Song, Hojun, 2024, Annotated catalogue of Pakistani Acrididae (Orthoptera: Caelifera: Acridoidea), pp. 1-47 in Zootaxa 5486 (1) on page 6, DOI: 10.11646/zootaxa.5486.1.1, http://zenodo.org/record/13209743
Parachilota hogsbacki Zicsi 1998
Creators: name: Csuzdi, Csaba
name: Szederjesi, Tímea
name: Sherlock, Emma
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Animalia
Annelida
Clitellata
Opisthopora
Acanthodrilidae
Parachilota
Parachilota hogsbacki

description: Parachilota hogsbacki Zicsi, 1998
Parachilota hogsbacki Zicsi, 1998a Mitt. Hamb. Zool. Mus. Inst. 95: 67.
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 13, DOI: 10.11646/zootaxa.4496.1.4, http://zenodo.org/record/1447011
FDG-PET/CT and molecular markers for early prediction of efficacy in advanced NSCLC patients treated with the EGFR-TKI erlotinib
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: NSCLC is expected to cause over 160,000 deaths in the USA in 2007. Erlotinib is a targeted therapy that has been shown to be effective in a sub-population of patients with advanced lung cancer. A combination of advanced imaging, molecular, genomic and clinical markers may allow early determination of this sub-population, which will avoid unneccessary toxicities for patients unlikely to benefit. Objectives: To estimate the capability of FDG-PET/CT (with and without patial volume correction) for the early prediction of efficacy with erlotinib therapy in advanced non-small cell lung cancer (NSCLC) patients, and to explore whether molecular, genomic and clinical markers can be combined with radiologic markers to improve prediction of outcome. Methods: We will perform FDG-PET/CT imaging at baseline, at one week after therapy start and at one month after therapy start for 30 patients initiating Erlotinib therapy for advanced NSCLC. Target lesions selected at baseline will have volumes estimated using a semi-automatic iterative watershed approach validated at UC Davis. Standard Uptake Values for the target lesions will be computed from the PET data with and with the application of partial volume corrections derived from the volumentric measurements. Measurement changes will be correlated with outcomes determined by progression-free survival (determined using standard radiological criteria), and the degrees of correlation compared. Molecular and genomic markers of Epidermal Growth Factor Receptor status will also be measured as these are known to be correlated with outcome – they will be combined with the imaging biomarkers in a prortional hazards model.
Parachilota karkloofi Zicsi 1998
Creators: name: Csuzdi, Csaba
name: Szederjesi, Tímea
name: Sherlock, Emma
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Animalia
Annelida
Clitellata
Opisthopora
Acanthodrilidae
Parachilota
Parachilota karkloofi

description: Parachilota karkloofi Zicsi, 1998
Parachilota karkloofi Zicsi, 1998a Mitt. Hamb. Zool. Mus. Inst. 95: 65.
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 13, DOI: 10.11646/zootaxa.4496.1.4, http://zenodo.org/record/1447011
Bathygobius soporator
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
Gobiidae
Bathygobius
Bathygobius soporator

description: Bathygobius soporator (Valenciennes 1837). Frillfin Goby; Mapo Aguado, Gobio Mapo
Vouchers: UCR 0363-013 (4). Distribution: Atlantic Ocean; from Florida Keys, USA, Bermuda and the Bahamas to Santa Catarina, Brazil, in the western Atlantic, and from Senegal to Angola, including the islands of the Gulf of Guinea, in the eastern Atlantic, also in the Mediterranean Sea; entering estuaries and littoral lagoons and ascending river courses; (Nicaragua) KP and Es (Atlantic); 0–5 masl; Per, Dia, Amp. Occurrence and conservation status: Nat; LC (2019), population trend unknown. Literature: Villa (1982: 227; detailed description, including illustrations and an identification key, and information on distribution and ecology), Robertson & Van Tassell (2019: 4106; detailed description, including illustrations, and information on distribution, with a map, and ecology) and Angulo (2021: 37; 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 36, DOI: 10.11646/zootaxa.5376.1.1, http://zenodo.org/record/10208788
Regulation of N-cadherin-mediated cell-cell adhesion in invasion of malignant cells
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 objective of this project is to understand the role of N-cadherin-mediated cell-cell adhesion during invasion of malignant carcinomas. The physical integrity of epithelial tissues is tightly regulated by adhesion proteins. The loss of epithelial (E)-cadherin, a calcium-dependent adhesion molecule, has been suggested as a primary reason for the weakening of cell-cell adhesion that results in the invasive phenotype required for metastasis. In many carcinomas, however, the expression of neuronal (N)-cadherin is upregulated and often coincides with the loss of E-cadherin. Surprisingly, the up-regulation of N-cadherin does not compensate for the E-cadherin loss, even though their binding strengths were found to be similar. Instead, N-cadherin expressing malignant cells are less adhesive and more motile than benign tumor cells that do not express N-cadherin. We hypothesize that N-cadherin forms more dynamic adhesion sites than E-cadherin, and that this causes the more motile and invasive phenotype observed in Ncadherin positive malignant cells. To test this hypothesis, we will generate a model epithelial tissue in a three-dimensional collagen matrix and study realistic malignant cell invasion using high-resolution confocal microscopy. To determine whether N-cadherin at the sites of cell-cell contacts is static or dynamic, we will quantify the fluorescence recovery after photobleaching (FRAP) of GFPtagged N-cadherin in 3-D culture. The rate of fluorescence recovery is a direct measure of the turnover rate of N-cadherin molecules at the sites of cell-cell contacts. Furthermore, we predict that N-cadherin-mediated cell-cell adhesion is tightly regulated by cytoskeletal linkages of N-cadherin that may be different from those of E-cadherin. Using FRAP, we will directly compare the kinetics of the actin cytoskeletal network at the sites of N- and Ecadherin- mediated cell-cell adhesion. We expect to observe more rapid turnover of actin network at the sites of N- cadherin mediated cell-cell contact, which would indicate a more dynamic type of cell-cell adhesion. Understanding the molecular regulation of N-cadherin adhesion will yield potential insights for diagnostic and therapeutic applications.
Cyrtacanthacridinae Kirby 1910
Creators: name: Sultana, Riffat
name: Song, Hojun
Publisher: name: Zenodo
Year: 2024
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Orthoptera
Acrididae

description: Cyrtacanthacridinae Kirby, 1910
Tribe Cyrtacanthacridini Kirby, 1910
Genus Anacridium Uvarov, 1923
36. Anacridium aegyptium (Linnaeus, 1764)
37. Anacridium rubrispinum Bey-Bienko, 1948
Genus Chondracris Uvarov, 1923
38. Chondracris rosea (De Geer, 1773)
Genus Cyrtacanthacris Walker, 1870
39. Cyrtacanthacris tatarica (Linnaeus, 1758)
Genus Pachyacris Uvarov, 1923
40. Pachyacris vinosa (Walker,1870)
Genus Patanga Uvarov,1923
41. Patanga japonica (Bolívar, 1898)
42. Patanga succincta (Johannson, 1763)
Genus Schistocerca Stål, 1873
43. Schistocerca gregaria (Forskål, 1775)
description: Published as part of Sultana, Riffat & Song, Hojun, 2024, Annotated catalogue of Pakistani Acrididae (Orthoptera: Caelifera: Acridoidea), pp. 1-47 in Zootaxa 5486 (1) on page 6, DOI: 10.11646/zootaxa.5486.1.1, http://zenodo.org/record/13209743
Functions of an actin nucleating protein that interacts with the transcriptional coactivator p300 and the tumor suppressor p53
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: Cancer cells are defined by their ability to undergo uncontrolled proliferation, leading to tumor formation, and their ability to invade tissues away from the primary tumor site, leading to metastasis. The actin cytoskeleton plays a critical role in cellular processes relevant to both tumorigenesis and metastasis, including cell division, cell shape change and cell migration. In addition to these well-known functions, a population of actin in the nucleus has also been shown to regulate gene expression by participating in processes such as chromatin remodeling and transcription. However, the molecular mechanisms that may connect these diverse functions of actin are not well understood. The goal of this project is to determine the cellular functions of a protein that may serve as a molecular link between the cytoplasmic and nuclear functions of actin. This protein, called JMY, was initially identified based on its ability to interact with the acetyltransferase enzyme and chromatin remodeling factor p300, and with the transcription factor and tumor suppressor p53. Furthermore, JMY was shown to enhance p53-dependent transcription and apoptosis. The connection with p53 highlights the relevance of JMY to the cancer problem. In addition to its interaction with p300 and p53, our preliminary results suggest that JMY is a nucleation promoting factor for the Arp2/3 complex, a central regulator of actin nucleation in the cell. This suggests that JMY may act as a molecular link between chromatin remodeling, transcription regulation, and the actin cytoskeleton. However, at this time we understand very little about the functions of JMY. The goal of the experiments described here is to characterize the basic cellular properties of JMY and to examine its roles in the cell. The specific aims are to: (1) determine where JMY is localized and what proteins it associates with in cells using a localization and affinity purification approach, and (2) silence JMY expression using RNA interference and assess the phenotypic effect on cell migration, transcription and apoptosis. Our findings will lead to a greater understanding of the connections between the actin cytoskeleton and the p300 and p53 pathways, and may also suggest novel strategies for developing therapeutics and diagnostics to treat cancer.
Parachilota minimus Zicsi & Pajor 1992
Creators: name: Csuzdi, Csaba
name: Szederjesi, Tímea
name: Sherlock, Emma
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Animalia
Annelida
Clitellata
Opisthopora
Acanthodrilidae
Parachilota
Parachilota minimus

description: Parachilota minimus Zicsi & Pajor, 1992
Parachilota minimus Zicsi & Pajor, 1992 Opusc. Zool. (Budapest) 25: 133.
Parachilota minimus: Plisko 2008 Afr. Invert. 49 (2): 32.
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 13, DOI: 10.11646/zootaxa.4496.1.4, http://zenodo.org/record/1447011
Circadian control of cancer: A molecular link
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: Cancer patients know about the biological clock. Many of our body's internal processes are cyclical and are governed by the biological clock. Only recently we have started to understand the dramatic impact that these rhythms have on cancer patients, specifically by lowering the amount of side effects from chemotherapy drugs. For example, the side effects of Adriamycin and cisplatin could be cut in half if given in the morning and evening, respectively. Therefore, an essential goal should be to identify how the cancer cell cycle is affected by circadian physiology. This not only will provide hints of when is the best time to administer cancer-killing drugs, but also pave the way to the development of new pharmaceutical and therapeutic strategies. Our proposal is based on recent findings from our laboratory that establish a direct link between the cancer cell cycle and the circadian clock. The circadian clock is molecular machinery composed of ‘clock genes’ that regulates a number of central physiological and metabolic functions in our bodies. We have recently found that the circadian regulator CLOCK is an enzyme that induces chromatin remodeling (Doi et al., 2006; Cell 125, 297-508). Strikingly, CLOCK regulates various genes whose function directly influences the cancer cell cycle. Our aim is to dissect how CLOCK influences the cell cycle and thereby cancer growth. These studies will allow the identification of unique elements within CLOCK and its interaction partners. This will ultimately lead to the development of new avenues of pharmacological intervention, by designing molecules that would target specifically the CLOCK protein and its connections to cancer cell cycle components. It should be mentioned that I have moved my laboratory from France to the University of California, Irvine, in May 2006. As a consequence I have lost all French and European funds, including personal salary, lab equipment and research running support. Likewise, postdoctoral fellows in my team (3 have followed, which has insured essential continuity) have also lost their salaries.
Eyprepocnemidinae Brunner von Wattenwyl 1893
Creators: name: Sultana, Riffat
name: Song, Hojun
Publisher: name: Zenodo
Year: 2024
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Orthoptera
Acrididae

description: Eyprepocnemidinae Brunner von Wattenwyl, 1893
Genus Cataloipus Bolívar, 1890
44. Cataloipus cognatus (Walker, 1870)
Genus Choroedocus Bolívar, 1914
45. Choroedocus illustris (Walker, 1870)
46. Choroedocus pallens Uvarov, 1933
47. Choroedocus robustus (Serville, 1838)
Tribe Eyprepocnemidini Brunner von Wattenwyl, 1893
Genus Eyprepocnemis Fieber, 1853
48. Eyprepocnemis alacris alacris (Serville, 1838)
49. Eyprepocnemis alacris impicta Uvarov, 1933
50. Eyprepocnemis rosea Uvarov, 1942
Genus Heteracris Walker, 1870
51. Heteracris adspersa (Redtenbacher, 1889)
52. Heteracris littoralis (Rambur, 1838)
53. Heteracris notabilis (Uvarov, 1942)
54. Heteracris persa (Uvarov, 1933)
Genus Tylotropidius Stål, 1873
55. Tylotropidius varicornis (Walker, 1870)
description: Published as part of Sultana, Riffat & Song, Hojun, 2024, Annotated catalogue of Pakistani Acrididae (Orthoptera: Caelifera: Acridoidea), pp. 1-47 in Zootaxa 5486 (1) on pages 6-7, DOI: 10.11646/zootaxa.5486.1.1, http://zenodo.org/record/13209743
Protein-viral RNA interactions and IRES-mediated translation in EBV-associated malignancies
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 ability of small noncoding RNAs to affect changes ingene expression has only recently been recognized and potential modes of action for these RNAs are still being elucidated. Epstein-Barr virus (EBV) encodes two small noncoding RNAs with clear pathogenic potential. Expression of these RNAs (EBERs) is sufficient to confer significant tumorigenic potential upon a nontumorigenic EBV-negative Burkitt lymphoma cell line. Despite several reports in the literature proposing EBER-dependent regulation of a number of genes, the mechanism of action of the EBERs has not been defined nor has a clear link between these genes and a mechanism of pathogenic potential been established. In this application we are pursuing the hypothesis that EBERfunction can be elucidated through identification of cellular proteins which interact directly with the EBERs. Consequently, our first specific aim is to identify components of the EBER-1 and EBER-2 ribonucleoprotein complexes. Several proteins have been identified as bindingto the EBERs, although in some instances the data is limited to in vitro studies. These previously identified EBER-binding proteins share a common function in that they have been demonstrated to be involved in internal ribosome entry site (IRES)-mediated translation in viral systems. These proteins are members of a group of proteins which has been termed the IRES-specific cellular trans-acting factors or ITAFs. The presence or absence of these factors has been shown to modulate the activity of a number of viral proteins whose translation is IRES-dependent. Given the link between the EBERs and these proteins, we are proposing to pursue the hypothesis that interaction with and potential sequestration of these cellular ITAFs by the EBERs results in modulation of IRES-mediated translation of a subset of cellular proteins, which in turn has pathogenic consequences. We will initiate our studies on the effect of EBER expression on IRES-mediated translation using viral IRES sequences which have been well defined in the literature and for which the requirement for specific ITAFs which are known EBER-binding proteins has been defined. Although this does not directly address the role of EBERs in EBV infection, it will provide evidence as towhether this is a likely mechanism of action for the EBERs. We will subsequently progress to more direct evaluation of the consequences of EBER expression on IRES-mediated translation in EBV-associated malignancies. In sum, these studiesare focused on defining the mechanism of actio
Additional file 1: of Changes of intestinal microbiota composition and diversity in very low birth weight infants related to strategies of NEC prophylaxis: protocol for an observational multicentre pilot study
Creators: name: Kurath-Koller, Stefan
name: Moissl-Eichinger, Christine
name: Gorkiewicz, Gregor
name: Kraschl, Raimund
name: Kanduth, Claudia
name: Hopfer, Barbara
name: Urlesberger, Berndt
name: Resch, Bernhard
Publisher: name: Figshare
Year: 2017
Subjects: subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Ecology
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: Science Policy
subject: Computational Biology

description: SPIRIT 2013 checklist. (DOC 120 kb)