cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Inhibiting Mutation to Prevent and Treat 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: A major challenge in fighting breast cancer is that all individual cancers are different; however, all forms of cancer, including breast cancer, begin and progress the same way, with the mutation of our DNA. Some of these mutations are inherited, as in the case of mutations in the BRCA1 and BRCA2 genes. However, even in these cases, additional mutations must be acquired for the cell to become cancerous. Mutations also underlie metastasis, as well as drug resistance. Remarkably, mutation is not a passive process, and specific biochemical pathways are responsible for introducing mutations to the genome in response to DNA damage. The single known pathway of induced mutation has been studied intensively by many different research groups. However, we recently identified a novel biochemical pathway of DNA damage-induced mutation in yeast, a simple model organism that responds to DNA damage in much the same way as human cells. This appears to be the major pathway of induced mutation in yeast and involves the enzyme ribonucleotide reductase, which supplies the building blocks of DNA (dNTPs), and a polymerase enzyme that normally copies DNA without errors. We demonstrated that yeast treated with the ribonucleotide reductase inhibitor and cancer chemotherapeutic drug, hydroxyurea, were less likely than untreated cells to make mutations following exposure to the DNA damaging agent, UV light.

 Our project is designed to extend these observations in yeast to human cells in the context of mutation pathways leading to breast cancer. We will examine cultured human breast cells for DNA-damage dependent changes in the expression and activity of ribonucleotide reductase. Our work in yeast indicates that the anti-mutation effect of inhibiting ribonucleotide reductase is mediated specifically through a regulatory subunit of the enzyme. We will use gene silencing to “knockdown” expression of the two regulatory subunits of human ribonucleotide reductase and examine the role of each individually on DNA-damaged induced mutation.

 From the perspective of breast cancer biology and medicine, these mutation concepts represent a radically new view of disease development, progression, and most importantly, prevention and treatment. The CBCRP-funded research represents our next step toward developing an entirely new approach to preventing and treating breast cancer, not by treating the phenotype of the cell, but by preventing the acquisition of the mutations that are necessary and sufficient for disease progression.
Glossodrilus kaszabi Zicsi 1988
Creators: name: Csuzdi, Csaba
name: Szederjesi, Tímea
name: Sherlock, Emma
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Animalia
Annelida
Clitellata
Haplotaxida
Glossoscolecidae
Glossodrilus
Glossodrilus kaszabi

description: Glossodrilus kaszabi Zicsi, 1988
Glossodrilus kaszabi Zicsi, 1988a Acta Zool. Hung. 34 (2–3): 314.
Glossodrilus kaszabi: Zicsi 1995a Opusc. Zool. (Budapest) 27–28: 97.
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 20, DOI: 10.11646/zootaxa.4496.1.4, http://zenodo.org/record/1447011
Amphilophus supercilius Geiger, McCrary & Stauffer 2010
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
Cichlidae
Amphilophus
Amphilophus supercilius

description: Amphilophus supercilius Geiger, McCrary & Stauffer 2010. Eyebrow Cichlid; Mojarra Cejona
Vouchers: (other collections) ZSM 38821 (1), 37347 (1), 37348 (1), 37351 (2), 38751 (2), 38752 (1), 38753 (3), 38754 (1), 38776 (2), 38778 (1) and 38780 (1). Distribution: Central America; endemic to the Lago Apoyo, Nicaragua; (Nicaragua) LN (Atlantic); 73– 73 masl; Sec, Pot. Occurrence and conservation status: Nat, End; CR B1ab(iii) (2020), population trend decreasing. Literature: Geiger et al. (2010: 161; original description).
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 50, DOI: 10.11646/zootaxa.5376.1.1, http://zenodo.org/record/10208788
Control of HIV-1 mRNP Biogenesis in T 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: HIv-1 replication and expression of viral genes in T cells is regulated at many levels, including formation of nuclear RNAs and their transfer from the nucleus to the cytoplasm. The HIV-1 Tat protein enhances syntheis of viral RNAs through its ability to recruit a host cell kinase complex called P-TEFb. In resting CD4+ T cells, virus gene expression is blocked due to the absence of many host cell transcription factors that are strongly up-regulated upon T cell activation. Productive virus replication also requires that partially-spliced and unspliced viral RNAs be shielded from nucleolytic destruction by the host cell surveillance machinery, and efficiently exported out of the nucleus. Although non-productive transcription is a major cause of viral latency, low levels of multiply-spliced Tat and Rev mRNAs can be detected in resting CD4+ T cells. Interestingly, these viral RNAs have been found to be aberrantly retained in the nucleus, suggesting that nuclear export is also blocked in resting T cells. Our lab has recently identified a new link between the formation of HIV-1 RNA and downstream events required for virus gene expression, including mRNA surveillance (i.e., degradation of improperly-formed pre-mRNAs by the host cell machinery), and nuclear export. We discovered that the a human transcription factor called Spt6 assembles a complex on the transcription complex that is important for efficient nuclear export. This complex includes a host cell protein, Iws1 (“interacts with Spt6”), that was not previously known to be required for nuclear export, and the REF/ALY protein, which has been shown to control RNA export. Disruption of this complex in cells results a significant delay in HIV-1 gene expression. Our studies also suggest that this new complex associates with the host cell nuclear exosome, which is a complex that degrades improperly formed RNAs. We propose that the Spt6:Iws1 complex loads nuclear export and mRNA degradation factors onto the transcription machinery during HIV-1 transcription elongation in a manner that depends upon Tat and T cell activation. Here we will examine the affect of Tat and P-TEFb on the assembly of the Spt6:Iws1 complex and assess whether this complex is required to load REF/ALY onto nwewly-formed HIV-1 RNAs. We will determine whether this complex controls export of early viral mRNAs in T cells, and determine how its assembly is up-regulated upon activation of T cells. We will determine whether the Spt6:Iws1 complex is responsible for directing the host cell RNA export and degradation machinery to the HIV-1 genome to direct the expression of the early viral genes. Understanding this critical new step may lead to new insights into blocking the earliest steps in HIV-1 gene expression and could also help explain why latently-infected T cells fail to express viral proteins in patients treated with HAART therapy.
Teacher leaders as professional development providers
Creators: name: Rosen, Michelle L.
Publisher: name: No Publisher Supplied
Year: 2014

description: High stakes assessments mandated by 2001 No Child Left Behind Act (NCLB) have increased the focus on student achievement causing a closer examination of the link between student achievement and teacher quality. Teacher training, through professional development, has been documented to be one of the most important factors in student achievement and may be one of the few indicators of student success that a school can control.  As a result of a shift in beliefs and practices regarding professional development, current research has pointed in the direction of encouraging schools to embrace a professional development model led and supported by teacher leaders.    This study’s purpose was to examine teacher leaders who receive their own professional development through a University Literacy Center, and what they do as professional development providers in their schools. The teacher leaders receive their own professional development from the Rutgers Center for Literacy Development. The specific research questions designed were: What do teacher leaders who receive professional development through a Literacy Center do as professional development providers once they return to their schools? What influences their activities?  What are the supports and obstacles they face in doing so?    The sample was comprised of three teacher leaders from a New Jersey District and their respective three principals. A case study was used to describe factors that influence the professional development that teacher leaders provided. Data collection sources were professional development session observations, teacher leader and principal interviews, and artifacts.  Data from the interviews, professional development session observations, and examinations of relevant documents were used in order to discover emerging patterns. Data collection and analysis occurred simultaneously, as is the preferred and effective strategy in qualitative research design.      The data indicated the following factors influencing the design and implementation of the professional development: teacher leader roles and internal resources, external resources, and relationships, along with the associated challenges. Used as a vehicle to transmit, facilitate and support ongoing teachers’ learning opportunities, teacher leaders can be necessary elements in the school’s organizational structure. Additionally, professional development organizations such as the Rutgers Center for Literacy Development can use this data to inform their offerings.
Glossodrilus lacteus Zicsi & Feijoo 1994
Creators: name: Csuzdi, Csaba
name: Szederjesi, Tímea
name: Sherlock, Emma
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Animalia
Annelida
Clitellata
Haplotaxida
Glossoscolecidae
Glossodrilus
Glossodrilus lacteus

description: Glossodrilus lacteus Zicsi & Feijoo, 1994
Glossodrilus lacteus Zicsi & Feijoo, 1994 Mitt. Hamb. Zool. Mus. Inst. 89 (2): 56.
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 20, DOI: 10.11646/zootaxa.4496.1.4, http://zenodo.org/record/1447011
Additional file 1: of Circulating brain-enriched microRNAs as novel biomarkers for detection and differentiation of neurodegenerative diseases
Creators: name: Sheinerman, Kira
name: Toledo, Jon
name: Tsivinsky, Vladimir
name: Irwin, David
name: Grossman, Murray
name: Weintraub, Daniel
name: Hurtig, Howard
name: Chen-Plotkin, Alice
name: Wolk, David
name: McCluskey, Leo
name: Elman, Lauren
name: Trojanowski, John
name: Umansky, Samuil
Publisher: name: Figshare
Year: 2017
Subjects: subject: Biochemistry
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Neuroscience
subject: Sociology
subject: FOS: Sociology
subject: Developmental Biology

description: Age and sex distribution in AD, FTD, PD, and ALS groups and control. (PDF 171 kb)
Additional file 3: Figure S2. of Developing and validating of Ramathibodi Appendicitis Score (RAMA-AS) for diagnosis of appendicitis in suspected appendicitis patients
Creators: name: Chumpon Wilasrusmee
name: Boonying Siribumrungwong
name: Samart Phuwapraisirisan
name: Napaphat Poprom
name: Patarawan Woratanarat
name: Panuwat Lertsithichai
name: Attia, John
name: Ammarin Thakkinstian
Publisher: name: Figshare
Year: 2017
Subjects: subject: Medicine
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences

description: Receiver operating characteristic (ROC) curves of RAMA-AS for diagnosis of appendicitis. (PDF 153Â kb)
Amphilophus tolteca Recknagel, Kusche, Elmer & Meyer 2013
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
Cichlidae
Amphilophus
Amphilophus tolteca

description: Amphilophus tolteca Recknagel, Kusche, Elmer & Meyer 2013. Asososca Cichlid; Mojarra de Asososca
Vouchers: (other collections) AMCK 13965 (1), 13966 (1), 13968 (1), 13969 (1), 13970 (1), 13972 (1), 13978 (1), 14041 (1), 14058 (1), 14059 (1), 14061 (1), 14063 (1), 14066 (1), 14067 (1), 14069 (1), 14070 (1), 14071 (1), 14072 (1), 14073 (1), 14074 (1), 14075 (1), 14076 (1), 14077 (1), 14078 (1),14079 (1), 14082 (1), 14083 (1), 14084 (1), 14085 (1), 14089 (1), 14094 (1), 14104 (1), 14108 (1), BMNH 2012.9.2.1 (1) and 2012.9.2.2-4 (1). Distribution: Central America; endemic to the Lago de Asososca, Nicaragua; (Nicaragua) LN (Atlantic); 57– 57 masl; Sec, Pot. Occurrence and conservation status: Nat, End; VU D2 (2020), population trend stable. Literature: Recknagel et al. (2013: 212; original description).
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 50, DOI: 10.11646/zootaxa.5376.1.1, http://zenodo.org/record/10208788
Geogenia ambita Plisko 1998, comb. n.
Creators: name: Jadwiga Danuta Plisko
Publisher: name: Zenodo
Year: 2006
Subjects: Biodiversity
Taxonomy
Animalia
Annelida
Clitellata
Haplotaxida
Microchaetidae
Geogenia
Geogenia ambita

description: Geogenia ambita (Plisko, 1998), comb. n.
Microchaetus ambitus: Plisko 1998: 258; 2003: 281.
Only known from Vernon Crookes Nature Reserve, KwaZulu-Natal.
description: Published as part of Jadwiga Danuta Plisko, 2006, A systematic reassessment of the genus Microchaetus Rapp, 1849: its amended definition, reinstatement of Geogenia Kinberg, 1867, and erection of a new genus Kazimierzus (Oligochaeta: Microchaetidae), pp. 31-56 in African Invertebrates 47 (1) on page 43, DOI: 10.5281/zenodo.160162
Cellular role of the HIV-1 integration factor, LEDGF
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: An early step in the HIV-1 infection cycle involves the stable integration of the virus into the human genome. Lentiviruses such as HIV-1 are unusual in that the integration occurs primarily into the body of actively-expressed host cell genes, and indeed integration has been reported to most frequently target the most active genes. A key cellular protein that controls HIV-1 integration is LEDGF/p75, a protein present at low levels in resting cells but strongly induced in stressed (heat or oxidative stress) cells. However, it is not clear how LEDGF/p75 recognizes active genes to target viral integration. Human DNA normally wraps around histone proteins for compaction, and is then packaged into regular arrays of nucleosomes, the substructure of the chromosome. The histones can be differently marked by protein modification, and one common modification is methylation of histone H3 at Lys-36, which is almost exclusively found at actively-expressed genes. Our lab has discovered a new protein complex that travels with the transcription machinery, and is responsible for generating the histone H3-Lys36 methylation mark. Because LEDGF/p75 somehow targets HIV-1 to active genes, we reasoned that it might be part of this new complex, and we show here that it is a component of the transcription machinery. We propose to study how the HIV-1 integrase protein might recognize LEDGF/p75 within this complex, and to test whether the complex transfers LEDGF/p75 to chromosomal DNA to await viral integration. We find that LEDGF/p75 associates with the integrated viral genome, and will study its possible function in virus mRNA biosynthesis. This is a new pilot project to better define the mechanism of action of LEDGF/p75 and HIV-1 integrase in the early steps of the virus life cycle, and will identify new proteins that play key roles in this process.
Additional file 2: of Barriers to HPV self-sampling and cytology among low-income indigenous women in rural areas of a middle-income setting: a qualitative study
Creators: name: Betania Allen-Leigh
name: Uribe-Zúñiga, Patricia
name: León-Maldonado, Leith
name: Brown, Brandon
name: Lörincz, Attila
name: Salmeron, Jorge
name: Lazcano-Ponce, Eduardo
Publisher: name: Figshare
Year: 2017
Subjects: subject: Medicine
subject: Sociology
subject: FOS: Sociology
subject: Developmental Biology
subject: Cancer
subject: Science Policy
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Topics included in guides (data collection tools)-Allen-Leigh. Topics included in guides for pre- and post-testing focus and discussion groups and individual interviews, study on HPV and cytology among rural, indigenous women in Mexico. (DOCX 96 kb)
Geogenia benhami Rosa 1891, comb. n.
Creators: name: Jadwiga Danuta Plisko
Publisher: name: Zenodo
Year: 2006
Subjects: Biodiversity
Taxonomy
Animalia
Annelida
Clitellata
Haplotaxida
Microchaetidae
Geogenia
Geogenia benhami

description: Geogenia benhami (Rosa, 1891), comb. n.
Microchaeta Benhami: Rosa 1891: 382.
Microchaeta benhami: Beddard 1895: 673.
Microchaetus benhami: Michaelsen 1891: 382; 1900: 451; 1913 a: 538; 1913 b: 61; 1918: 316; Pickford 1975: 2; Reynolds & Cook 1976: 77; Plisko 1992: 339; 1993 b: 235; 1995 b: 46.
This species is known from numerous sites, all in Stellenbosch district, Western Cape. Described from an unknown locality by Rosa (1891), reported by Michaelsen (1913 a, b) and Pickford (1975) from garden soil in Stellenbosch. Two recently collected adult specimens (NMSA/Olig.03925), and verbal information from Frana Fourie (University of Stellenbosch), confirm a large population of this species near a local dam in Papegaaiberg close to Stellenbosch. It is noteworthy that benhami is morphologically close to mkuzi (Plisko 1992), which occurs in natural sites in northern KwaZulu-Natal (Plisko 1992, 1998, 2003).
description: Published as part of Jadwiga Danuta Plisko, 2006, A systematic reassessment of the genus Microchaetus Rapp, 1849: its amended definition, reinstatement of Geogenia Kinberg, 1867, and erection of a new genus Kazimierzus (Oligochaeta: Microchaetidae), pp. 31-56 in African Invertebrates 47 (1) on page 43, DOI: 10.5281/zenodo.160162
Glossodrilus landeszi Zicsi 1988
Creators: name: Csuzdi, Csaba
name: Szederjesi, Tímea
name: Sherlock, Emma
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Animalia
Annelida
Clitellata
Haplotaxida
Glossoscolecidae
Glossodrilus
Glossodrilus landeszi

description: Glossodrilus landeszi Zicsi, 1988
Glossodrilus landeszi Zicsi, 1988a Acta Zool. Hung. 34 (2–3): 316.
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 20, DOI: 10.11646/zootaxa.4496.1.4, http://zenodo.org/record/1447011
21st century girls’ schools: for what reasons are new independent girls' schools opening in the United States?
Creators: name: Palmieri, James R.
Publisher: name: No Publisher Supplied
Year: 2014

description: For a multitude of reasons, the founding of an independent school in the modern-day United States is an extremely challenging undertaking. The list of essentials necessary to envision, prepare, open, and operate a functioning school are endless, yet school founders are driven to do so out of a commitment to and passion for a particular school environment. Independent schools benefit from four defining freedoms that make them truly independent: a) defining the school mission, b) admitting and retaining only those students who are well served by the school’s mission, c) determining qualifications for hiring teachers, and d) determining how the school will fulfill its mission through curriculum and instruction (McConaghy, 2006). The primary differentiating factor for the start-up schools used in this study was single-gender education for girls and young women – “all-girls” schools.  Interestingly, after years of decline, there is an increasing number of families seeking this type of learning environment for their daughters. Though literature on the mid-to-late 20th century decline of girls’ schools is vast, literature on the current revival and projected future of all-girls schooling is limited. To understand better how and for what reasons new independent elementary and secondary girls’ schools are opening in the United States, this study employed an exploratory qualitative analysis approach, utilizing a sample set of schools determined by their founding years (between 1995 and 2013). A thorough review and analysis of the ten youngest independent girls’ schools recognized by the National Association of Independent Schools (NAIS) – from coast to coast, provided a deep understanding of the similarities and differences of each school’s founding, and the total sample’s relevance to the current status and future of all-girls schooling. The results demonstrate, generally, school founders’ desires for: a more challenging academic environment; a greater focus on socio-emotional development; the removal of the distractions of coeducation; the promotion of gender equity and women’s leadership; a religious affiliation; and/or a combination of the above. Combining the latest research on how girls learn best, with both innovative and interdisciplinary approaches to pedagogy, technology, and social issues, these ten young independent girls’ school have resulted in high-achieving academic communities that are exciting to students, parents, and educators alike. Providing this current research on the heavily debated topic of single-sex education is essential to determining its present value and future within the United States educational market.
Allo-reactive CTL to treat breast cancer metastatic to brain
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: Women with breast cancer are living longer and experiencing an improved quality of life because powerful new therapies can control metastases in many sites including liver, lung and bone. At the same time breast cancer metastasis to the brain is being diagnosed more frequently because these systemic therapies do not prevent or control brain metastasis. For many women with advanced breast cancer, brain metastases present the greatest conceivable threat. Our interest is to explore a novel type of immunotherapy to treat brain metastasis. For this we will create cytotoxic lymphocytes (CTL) from healthy donors that are “trained” in the laboratory to recognize “Human Leukocyte Antigens” (HLA) from breast cancer cell lines. This approach is particularly useful in cancer sites where the normal cells express little or no HLA, such as gliomas.

 First, we will generate alloCTL from peripheral blood mononuclear cells (PBMC) from human donors against breast cancer cell lines with the propensity to metastasize to the brain (BCM2 BrainG2, MDA-MB-231-1883) using established stimulation protocols. The cytotoxicity of alloCTL against relevant tumor targets and irrelevant controls will be determined by standard assays. Next, the alloCTLs will be induced to proliferate in response to incubation with relevant breast cancer brain metastasis antigen targets. HLA expression on breast cancer targets will be increased with interferon or knocked down by RNA interference to establish alloCTL cytotoxicity relative to the level of HLA expression. Then, the migration of alloCTL will be examined in SCID mice with intracranial human breast tumor foci. We will evaluate the spread of alloCTL after intratumoral injection and the trafficking to distant tumor foci in the brain. Finally, the efficacy of alloCTL in eradicating breast tumor foci in the brain will be determined by volumetric analyses.

 AlloCTL have never been evaluated fosr the treatment of breast cancer metastasis to the brain. Therefore the proposed project is novel and unique. However, alloCTL technology has been worked out in the context of primary brain tumors and we are very hopeful that similar conditions can be found for the treatment of breast cancer metastasis to the brain. In this regard the proposed project is feasible and its translation into the clinic will not require any technological leaps.
Amphilophus viridis Recknagel, Kusche, Elmer & Meyer 2013
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
Cichlidae
Amphilophus
Amphilophus viridis

description: Amphilophus viridis Recknagel, Kusche, Elmer & Meyer 2013. Green Midas Cichlid; Mojarra Verde
Vouchers: (other collections) AMCK 13138 (1), 13177 (1), 13178 (1), 13180 (1), 13181 (1), 13269 (1), 13270 (1), 13271 (1), 13639 (1), BMNH 2012.9.2.5 (1) and 2012.9.2.6-7 (1). Distribution: Central America; endemic to the Lago Xiloá, Nicaragua; (Nicaragua) LN (Atlantic); 45– 45 masl; Sec, Pot. Occurrence and conservation status: Nat, End; VU D2 (2020), population trend stable. Literature: Recknagel et al. (2013: 217; original description).
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 50, DOI: 10.11646/zootaxa.5376.1.1, http://zenodo.org/record/10208788
3 T Two-Dimensional Cerebral MRS in HIV Youths
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: HIV in adults and children has become a chronic illness and there is a critical need to develop noninvasive, reliable techniques to detect brain involvement with the virus and prevent further damage. Magnetic resonance spectroscopy (MRS) permits the study of HIV effects on brain chemicals, called cerebral metabolites, which are markers for the health of both the nerve cells in the brain (neurons) and the support cells (glial cells). Most previous investigations have used 1.5 Tesla scanners and one –dimensional MRS (1D-MRS) techniques. The goals of this study are to improve detection of abnormal cerebral metabolites in HIV – infected patients by using a new technique, two –dimensional magnetic resonance spectroscopy (2D-MRS) with an MRI scanner that uses a stronger magnetic (3 Tesla) compared to the standard 1.5 Tesla scanner. When abnormalities are detected in the brain of patients, it is important to see if there are also abnormalities evident on tests of brain function (neurocognitive tests) and we will correlate performance and brain metabolite levels. A 3 T scanner detects brain chemicals more precisely than the 1.5 T scanner. The 2D-MRS technique is also more sensitive than the standard 1D-MRS and allows the detection of many additional brain metabolites. Of particular interest among the cerebral metabolites are GABA, an inhibitory neurotransmitter, and myo-inositol (mI), a glial cell marker for which elevation suggests ongoing inflammation. Metabolite ratios to reference metabolites will be determined. Creatine is an energy reference marker and choline is also a reference metabolite. The 3 Tesla scanner combined with two dimensional magnetic resonance spectroscopy also provides the ability to study other chemicals, such as glutathione and choline groups, potentially additional markers of central nervous system (CNS) damage by the HIV virus. The specific aims of this study are to compare GABA, mI, choline groups, and other metabolites in the left frontal brain and basal ganglia of 15 HIV-infected patients and 15 control youths. Both of these areas of the brain have been documented by autopsy studies and MRS to be commonly damaged by HIV. The hypotheses are that GABA and mI ratios will be increased in HIV-infected patients and that elevation of these metabolites will correlate with poorer performance on a panel of neurocognitive tests of executive funtioning, fine motor activity, and attention. Reliable identification of adult or adolescent HIV-infected patients by 2D-MRS (3T) with abnormal brain metabolites and sub clinical brain involvement may require starting therapy earlier than CD4 count criteria would indicate or changing existing HAART therapy to antiretroviral medications with improved levels in the brain. This study may potentially improve the quality of life of HIV-infected patients and preserve the health of the brain.
Glossodrilus loksai Zicsi 1989
Creators: name: Csuzdi, Csaba
name: Szederjesi, Tímea
name: Sherlock, Emma
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Animalia
Annelida
Clitellata
Haplotaxida
Glossoscolecidae
Glossodrilus
Glossodrilus loksai

description: Glossodrilus loksai Zicsi, 1989
Glossodrilus loksai Zicsi, 1989b Acta Zool. Hung. 35: 172.
Glossodrilus loksai: Zicsi 1995a Opusc. Zool. (Budapest) 27–28: 94.
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 20, DOI: 10.11646/zootaxa.4496.1.4, http://zenodo.org/record/1447011
“Just don't call it a book club”
Creators: name: Lattanzi, James A.
Publisher: name: No Publisher Supplied
Year: 2014

description: Much has been written about the “boy crisis” in the last two decades in regards to achievement in school and the struggles boys face in literacy learning.  The National Assessment of Educational Progress (NAEP) data demonstrate that girls consistently outperform boys in reading and writing (Educational Alliance, 2006). Therefore, the importance of reading engagement and wide reading cannot be undervalued.  It is commonly accepted that frequent and wide reading leads to increases in student achievement (Guthrie & Alvermann, 1999).    The purpose of this study was to capture and understand how an informal book club for boys might lead to insights about their reading motivation and engagement in order to inform literacy instruction, to obtain the perspectives of middle school boys in what may motivate them to read widely outside of school-based assignments, and to understand how social interactions influence their desire to read.    A purposeful sample of seven middle school boys who demonstrated a range of resistance to reading was the basis for selection.  Book club meetings were based on three novels of the boys’ choosing which were read and discussed. Observations were used to note changes in attitudes and spontaneous comments about reading and school.  Three focus group interviews were conducted to provide data on boys’ perspectives on reading experience in school and the book club.  Additional data was obtained through individual interviews reflecting on the book club experience approximately a month after the book club stopped meeting.  The data suggest that the boys in the study may reject reading because of the pressure they feel as a result of the various tasks, in particular writing tasks, which are attached to their personal choice reading.  The boys found it difficult to get lost in books even of their own choosing because of these tasks.  They were also unable to share their reading in school and felt disconnected from their teachers.  The book club model allowed the boys to forge relationships, build competence, and find enjoyment in reading through the autonomy of free flowing deep discussions and humor about a shared text.
Amphilophus xiloaensis Stauffer & McKaye 2002
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
Cichlidae
Amphilophus
Amphilophus xiloaensis

description: Amphilophus xiloaensis Stauffer & McKaye 2002. Xiloá Cichlid; Mojarra de Xiloá
Vouchers: LSUMZ 16989 (10); other collections: PSU 3381 (1), 3381.1 (1) and 3384 (5). Distribution: Central America; endemic to the Lago Xiloá, Nicaragua; (Nicaragua) LN (Atlantic); 45– 45 masl; Sec, Pot. Occurrence and conservation status: Nat, End; VU D2 (2020), population trend stable. Literature: Stauffer & McKaye (2002: 9; original description), Stauffer et al. (2008: 117; comparative morphological data and information on distribution) and Recknagel et al. (2013: 209; comparative morphological data, including an identification key, and 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 50, DOI: 10.11646/zootaxa.5376.1.1, http://zenodo.org/record/10208788
Mechanisms of Daxx-Mediated Apoptosis in 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: Daxx is a protein that suppresses cell accumulation by promoting cell death, through a mechanism called “apoptosis.” A loss of the normal cell turnover mechanisms that keep cell numbers in check is a common feature of breast cancer. The way that Daxx (also called “death associated protein 6”) promotes apoptosis is unclear, and we plan to focus this research on the Daxx-initiated epigenetic changes that may underlie its role in breast cancer. Recent evidence linking epigenetic processes with cancer is extremely compelling. Epigenetics is a process that alters gene activity without changing the DNA sequence. DNA methylation, a chemical modification involving addition or removal of methyl groups from DNA, is a common type of epigenetic mechanism that can “silence” genes, especially tumor suppressors and apoptosis genes that would otherwise block disease progression. Global changes in DNA methylation are known to occur during progression of breast cancer. Examples of such genes associated with breast cancer initiation and progression that undergo epigenetic modifications include the estrogen and progesterone receptors. Daxx is known to bind DNA methyltransferases (DNMTs), proteins responsible for DNA methylation.

 Thus, our goal is to identify how Daxx promotes apoptosis of breast cancer cells, and to define the role that epigenetic modifications play in this process. Recent data from our laboratory shows that Daxx interacts with and suppresses RelB, a DNA-binding protein that controls the activity of several anti-apoptotic genes, and which is hyperactive in many aggressive breast cancers. To confirm this observation, I will seek to elucidate the molecular mechanism by which Daxx suppresses RelB function using breast cancer cells and focus on the role that DNA methylation plays in the process. I will map the association sites in the Daxx and RelB protein sequence that are necessary for their binding and test for function by making mutant proteins that should lose binding activity. I will then determine whether Daxx binding to RelB is required for suppression of RelB target genes. I will next study the role that DNA methylation plays in this process. Finally, I will explore whether chemical and immunological agents known to activate Daxx suppress RelB target gene activity and promote breast cancer cell death.

 Very few examples exist in literature that would explain how the specific genes are silenced by DNA methylation in cancer, and none exists in breast cancer. Identifying and characterizing Daxx-triggered epigenetic modifications may enable us to utilize Daxx’s functions as weapons to pharmacologically manipulate the Daxx-dependent cell death pathway for breast cancer treatment.
Geogenia caementerii Michaelsen 1913, comb. n.
Creators: name: Jadwiga Danuta Plisko
Publisher: name: Zenodo
Year: 2006
Subjects: Biodiversity
Taxonomy
Animalia
Annelida
Clitellata
Haplotaxida
Microchaetidae
Geogenia
Geogenia caementerii

description: Geogenia caementerii (Michaelsen, 1913), comb. n.
Microchaetus papillatus var. caementerii: Michaelsen 1913 c: 429; Reynolds & Cook 1976: 83.
Microchaetus caementerii: Michaelsen 1918: 321; Pickford 1975: 23; Plisko 1991 a: 282 [redescription of the paratype housed in the Natal Museum]; 1992: 340; 1995 b: 49; 1998: 260; 2003: 288; Reynolds & Cook 1993: 23.
The species was known from a few localities in the Pietermaritzburg district, but may
now be extinct. Midlands of KwaZulu-Natal.
description: Published as part of Jadwiga Danuta Plisko, 2006, A systematic reassessment of the genus Microchaetus Rapp, 1849: its amended definition, reinstatement of Geogenia Kinberg, 1867, and erection of a new genus Kazimierzus (Oligochaeta: Microchaetidae), pp. 31-56 in African Invertebrates 47 (1) on page 43, DOI: 10.5281/zenodo.160162
MOESM1 of An accurate description of Aspergillus niger organic acid batch fermentation through dynamic metabolic modelling
Creators: name: Upton, Daniel
name: McQueen-Mason, Simon
name: A. Wood
Publisher: name: Figshare
Year: 2017
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Pharmacology
subject: Biotechnology
subject: Evolutionary Biology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Developmental Biology
subject: Computational Biology

description: Additional file 1: Table S1. Biomass equation parameters altered to fit empirical data. Table S2. Putative phosphate transporters in ATCC 1015. Top BLASTP hits with phosphate transporters in SwissProt database are given.
Additional file 3: of Barriers to HPV self-sampling and cytology among low-income indigenous women in rural areas of a middle-income setting: a qualitative study
Creators: name: Betania Allen-Leigh
name: Uribe-Zúñiga, Patricia
name: León-Maldonado, Leith
name: Brown, Brandon
name: Lörincz, Attila
name: Salmeron, Jorge
name: Lazcano-Ponce, Eduardo
Publisher: name: Figshare
Year: 2017
Subjects: subject: Biotechnology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Developmental Biology
subject: Cancer
subject: Science Policy
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: Codes used for qualitative analysis-Allen-Leigh. Codes applied to qualitative data (field-notes taken during discussion groups, transcriptions of interviews and focus groups) in study on HPV and cytology among rural, indigenous women in Mexico. (DOCX 121 kb)
Graphic novels and the common core
Creators: name: Jakubik, Tara Lynn
Publisher: name: No Publisher Supplied
Year: 2014

description: State tests, which assess reading comprehension, ask students to make inferences and connections beyond the text.  The problem of practice in which this study is situated is that students are having difficulty making meaningful connections and developing inferences in relation to the material that is read aloud together in class or assigned for homework.  Indicators of their struggle include post-reading assessments such as reading comprehension tests with multiple choice and open-ended questions similar to those used on high-stakes tests.  The dissertation describes a research project in which graphic novels were incorporated into the curriculum to provide students with an opportunity to work with a nontraditional literary genre.  Data sources included video recordings of student think-alouds, video recordings of literature circles; and the NJ High School Proficiency Assessment (NJ HSPA) test scores. Descriptive statistics informed the analysis of the data.  The constructs of the research were examined through forms of behavior such as student performance during individual and small group work (e.g. think-alouds and literature circles.)  The think-aloud and the literature circles were coded by text features for the reading comprehension strategies and student behavior and allowed for reflective analysis.  Findings suggested that readers made connections to the Common Core Standards when reading graphic novels.  The research also found correlations between NJ HSPA scores and reading strategies used and behaviors enacted.  The research also indicated that students, of varying Language Arts proficiency levels, supported one another in reading comprehension in small group settings.
The Regulation of SATB1 in Metastatic 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: Metastasis occurs when tumor cells travel to distal organs and create new tumors in the body. There is strong evidence to suggest that a protein in the cell, SATB1 (Special AT Sequence Binding Protein 1), regulates the tumor-initiating and metastatic potential of breast cancer cells. Adding this protein (SATB1) to non-aggressive breast cancer cell lines causes these cells to now have the ability to form tumors and metastasize. Depleting this protein from highly aggressive breast cancer cell lines reduces the metastatic potential and tumor-initiating ability of these cells. Additionally, the presence of SATB1 in primary breast tumors is strongly associated with an aggressive cancer phenotype and a poor prognosis, independent of the lymph-node status. Tumors are comprised of many different types of cells, and only a small percentage of these cells (i.e., cancer stem cells) have the ability to initiate new tumors and metastasize. Not every cancer cell in a primary tumor has the SATB1 protein, but these experiments provide evidence to support the hypothesis that cells with SATB1 are an aggressive, metastatic, sub-population of tumor-initiating cells.

 There are three aims for this project: (1) screen for cytokines, chemokines, and growth factors that are involved in the activation and expression of SATB1 in metastatic breast cancer, (2) screen for transcription factors and signaling pathways that are involved in the activation and expression of SATB1 in metastatic breast cancer, and (3) study the relationship between SATB1 expression and progenitor breast cancer cells. A main approach will be non-biased, genome-wide RNAi screening to discover candidate genes that activate or maintain SATB1 expression in cancer cells. To define the relationship between SATB1 expression and cancer stem cells, I will use FACS analysis to characterize SATB1-expressing cells relative to cancer stem cell markers and employ mice models of breast cancer to determine the metastatic potential of different stem cell-containing populations.

 These experiments will establish whether SATB1 expression is necessary and sufficient to convert a non-aggressive breast cancer cell to a metastatic cancer stem cell. If we can learn what molecules and pathways are important for the generation and/or persistence of cancer stem cells, we can effectively target these processes and develop more effective cancer therapies. This research is necessary to learn whether SATB1 will be an effective therapeutic target.