cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Amphilophus chancho Stauffer, McCrary & Black 2008
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 chancho

description: Amphilophus chancho Stauffer, McCrary & Black 2008. Chancho Cichlid; Mojarra Chancho
Vouchers: (other collections) AMNH 240556 (4), PSU 4500 (1), 4500.1 (1), 4501 (1), 4502 (1), 4503 (1), 4504 (1), 4505 (1), 4506 (1), 4507 (1), 4508 (1), 4509 (1), 4510 (1), 4511 (1), 4512 (1), 4513 (1) and 4514 (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: Stauffer et al. (2008: 119; 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 48, DOI: 10.11646/zootaxa.5376.1.1, http://zenodo.org/record/10208788
Prevention or perpetuation
Creators: name: Buckley, Kimberly Rose
Publisher: name: No Publisher Supplied
Year: 2014

description: In the United States today, at least one-third of women will experience some form of sexual violence, typically before they reach the age of thirty. In order to make sense of such an alarming trend, this thesis aims to explore current sexual violence prevention programs meant to address this phenomenon within youth populations in the United States.  The thesis seeks to identify the characteristics of youth sexual violence prevention programs to determine how comprehensive these programs are, what may be missing from them, and to evaluate the degree to which these programs reflect current theories and best practices. The primary method of this study is qualitative content analysis. Use of this method in the research reveals that there are recognizable strengths as well as discernible gaps in existing sexual violence prevention programs targeted at youth. These findings indicate the potential for further study of these gaps in content and a need for an updated approach to sexual violence prevention, one that is situated at the intersection of theory and best practices.  The paper concludes with implications and considerations for future research and practice.
Microchaetus decipiens Michaelsen 1899
Creators: name: Jadwiga Danuta Plisko
Publisher: name: Zenodo
Year: 2006
Subjects: Biodiversity
Taxonomy
Animalia
Annelida
Clitellata
Haplotaxida
Glossoscolecidae
Microchaetus
Microchaetus decipiens

description: Microchaetus decipiens Michaelsen, 1899
Microchaeta decipiens: Michaelsen 1899 a: 113.
Microchaeta rappi: Michaelsen 1891: 207 [partim].
Microchaetus decipiens: Michaelsen 1900: 452; Reynolds & Cook 1976: 93; Plisko 1991 b: 301; 1992: 340; 1998: 294; 2003: 281.
Microchaetus microchaetus var. decipiens: Michaelsen 1910: 161; 1913 a: 538; 1918: 318; Reynolds & Cook 1976: 93.
Known from the type locality, Grahamstown, Eastern Cape.
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 38, DOI: 10.5281/zenodo.160162
Characterizing the role of mitochondria in the toxicity of trichothecenes produced by Fusarium graminearum
Creators: name: Bin Umer, Mohamed Anwar
Publisher: name: No Publisher Supplied
Year: 2014

description: Fusarium graminearum is a toxigenic fungal pathogen infecting economically significant cereal crops. Trichothecenes are a large family of low molecular weight sesquiterpenoid mycotoxins synthesized by F. graminearum and other fungi and are among the most toxic compounds known to man. These mycotoxins and their producers are encountered worldwide in the environment as natural contaminants of cereal grains presenting a high food safety risk for humans and cattle and threaten the global food supply. Trichothecene mycotoxicosis was primarily associated with their inhibitory effects on translation. However, these highly stable toxins also inhibit other cellular processes which contribute to their toxicity. In this work, using yeast as a model organism, a genome wide approach has been applied to obtain a comprehensive understanding of the molecular mechanism of the type A and B trichothecene toxicity. Due to their prevalence and impact, T-2 toxin and diacetoxyscirpenol (DAS) are used as representative type A toxins while trichothecin (Tcin) and deoxynivalenol (DON) are used as representative type B toxins. The yeast knockout collection of nonessential genes was initially used to identify mutant strains that exhibited increased resistance or susceptibility to trichothecenes. This screening led to identification of the role of mitochondria during trichothecene toxicity. The largest group of mutants exhibiting resistance was affected in their mitochondrial functions. Mitochondrial translation was directly inhibited, independent of total translation, and the trichothecene-treated cells exhibited severe fragmentation of mitochondrial membrane. Furthermore, actively respiring cells with functional mitochondria were essential for trichothecene cytotoxicity suggesting a critical role for mitochondria. A large fraction of the highly susceptible strains exhibited very high levels of reactive oxygen species (ROS) upon trichothecene treatment. Antioxidants increased cell survival and reduced mitochondrial membrane damage in trichothecene-treated cells. The direct role for ROS in mediating trichothecene cytotoxicity was confirmed when two novel Arabidopsis nonspecific lipid transfer proteins that mediated resistance to trichothecenes in A. thaliana exhibited antioxidant property and rescued trichothecene-treated yeast cells. Rapamycin-induced mitophagy reduced ROS levels and increased survival in trichothecene-treated cells suggesting mitophagy as a novel prosurvival cellular mechanism during oxidative stress in trichothecene-treated cells.
Fimoscolex angai subsp. minor Zicsi & Csuzdi 1987
Creators: name: Csuzdi, Csaba
name: Szederjesi, Tímea
name: Sherlock, Emma
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Animalia
Annelida
Clitellata
Haplotaxida
Glossoscolecidae
Fimoscolex
Fimoscolex angai
Fimoscolex angai minor zicsi & csuzdi, 1987

description: Fimoscolex angai minor Zicsi & Csuzdi, 1987
Fimoscolex angai minor Zicsi & Csuzdi, 1987 Acta Zool. Hung. 33: 272.
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 19, DOI: 10.11646/zootaxa.4496.1.4, http://zenodo.org/record/1447011
Glossodrilus antisanae 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 antisanae

description: Glossodrilus antisanae Zicsi, 1989
Glossodrilus antisanae Zicsi, 1989b Acta Zool. Hung. 35: 181.
Glossodrilus antisanae: 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 19, DOI: 10.11646/zootaxa.4496.1.4, http://zenodo.org/record/1447011
Antiquité et anachronisme chez deux poètes contemporains
Creators: name: Belova, Olga
Publisher: name: No Publisher Supplied
Year: 2014

description: This work studies the paradoxical nature of cultural transmission through the particular prism of contemporary poetry.  On the one hand, this poetry is conscious of being shaped and informed by the culture of the past; on the other, it actively intervenes in the shaping of that culture and thus plays a central part in its transmission and survival. In order to understand the stakes of this tension, the dissertation analyses representations of Antiquity and the figure of anachronism in the works of the French poet and philosopher Michel Deguy and the Russian-American poet and literary critic Joseph Brodsky.  These two authors have very different cultural, political and linguistic backgrounds and their views on cultural transmission are correspondingly antithetical; while Deguy insists on “reinventing” the meaning of  “relics” from the past through a play of poetic “profanation,” Brodsky believes that memory must be carried by forms and works aiming to recreate “cultural continuity.” A comparative analysis of these two poets’ writings allows us to show that their relation to the culture of the past is heavily influenced by the circumstances they encounter in the present. The thesis demonstrates how their respective selection of specific elements drawn from the tradition of Antiquity and the use of different poetic devices to integrate these elements within their poetic texts are historically determined, and correspond to diverse ways of “reading” and interrogating the present world.     Each of these poets creates his own particular “anachronization system” through the intellectual and poetic gesture of transmitting the culture of Antiquity. A close examination of these different systems takes us to the core of a peculiar encounter between past and present, and helps us understand the relations that exemplary texts and, more generally, contemporary poetics maintain with culture as a whole.
Repression of HMGA2 by BRCA1 Prevents Mammary Tumorigenesis
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: BRCA1 gene mutations account for 50% of hereditary breast cancer. In sporadic breast cancers, although the BRCA1 gene is intact, the protein expression is often reduced. BRCA1 is known to play an essential role in maintaining genomic integrity mainly through direct involvement in repairing damaged DNA and monitoring cell proliferation. However, these functions of BRCA1 do not adequately explain how its deficiency accelerates breast cancer progression. It is postulated that BRCA1 is also important for cell growth and differentiation by its ability to regulate genes critical for these processes. We recently demonstrated that BRCA1 has a direct role in regulating the expression of an array of genes involved in tumor progression, one of which is HMGA2.

 HMGA2 (High Mobility Group AT-hook2) plays an important role during embryonic development, when cells are undergoing extensive cell growth. HMGA2 expression in adult tissue is almost undetectable, but the inappropriate expression of HMGA2 in adult tissue is observed in many types of benign and malignant tumors. Intriguingly, elevated HMGA2 mRNA expression is found in the peripheral blood of breast cancer patients and may serve as a biomarker for metastasis and poor prognosis. However, it is still unknown whether up-regulation of HMGA2 expression has a direct role in development and progression of breast cancer.

 Thus, the aim of this project is to show that loss of HMGA2 gene repression by BRCA1 is a key pathway in accelerating breast cancer progression. Our methods include gene regulatory promoter analysis, luciferase assays, and ChIP (chromatin immunoprecipitation) assays to understand the mechanisms of BRCA1-dependent transcriptional regulation of HMGA2. Next, we plan to express HMGA2 in normal mammary epithelial cells via retrovirus-mediated gene transfer and assess the oncogenic consequences. Lastly, we will deplete HMGA2 by a technique, called RNA inference (RNAi), in breast cancer cells to demonstrate whether this suppresses breast tumor formation in a mouse model.

 These studies will provide the mechanistic basis on the regulation of HMGA2 expression by BRCA1 and demonstrate the biological consequence upon loss of regulation by BRCA1. This finding will augment our understanding of BRCA1-associated breast cancer and identify a potential target for treatment and detection of the disease.
Glossodrilus baloghi 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 baloghi

description: Glossodrilus baloghi Zicsi, 1988
Glossodrilus baloghi Zicsi, 1988a Acta Zool. Hung. 34 (2–3): 318.
Glossodrilus baloghi: Zicsi 1995a Opusc. Zool. (Budapest) 27–28: 96.
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 19, DOI: 10.11646/zootaxa.4496.1.4, http://zenodo.org/record/1447011
Amphilophus erythraeus
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 erythraeus

description: Amphilophus erythraeus (Günther 1867). Xolotlán Cichlid, Red Midas Cichlid; Mojarra de Xolotlán, Cíclido Midas Rojo
Vouchers: FMNH 5974 (1). Distribution: Central America; endemic to the Lago Xolotlán (Managua), Nicaragua; (Nicaragua) LN (Atlantic); 41– 41 masl; Sec, Pot. Occurrence and conservation status: Nat, End; NE, population trend unknown. Literature: Meek (1907: 124, as Cichlasoma erythraeus —synonym; brief description, including an identification key, and information on distribution and ecology), Stauffer & McKaye (2002: 8; comparative morphological data and information on distribution) and Stauffer et al. (2008: 117; comparative morphological data 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 49, DOI: 10.11646/zootaxa.5376.1.1, http://zenodo.org/record/10208788
Endogenous Nuclear Retrotransposition Antagonists
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: Ty3 is a retroviruslike element in Saccharomyces cerevisiae which can be used as a model system to understand the interaction of retroviruses and their hosts. A recent screen of the nonessential yeast gene knockout collection has led to the identification of 130 yeast genes that are required for wild-type (wt) frequencies of Ty3 retrotransposition. Among the genes that were identified are ones encoding nuclear factors involved in DNA maintenance, genes for checkpoint proteins, helicases, and components of clamp loaders which support DNA polymerase processivity. Interestingly, almost all of these deletions were associated with increased frequency of Ty3 transposition, indicating that they act, directly or indirectly, to antagonize retrotransposition. The objective of the current one-year proposal is to determine whether the effects we observe are mediated directly by DNA maintenance factors interacting with Ty3 DNA. If DNA maintenance factors act directly to control Ty3 replication, their homologs in mammalian cells might act as host restriction factors for retroviral replication. Identification of such factors could contribute to development of new anti-retrovirals and will increase our understanding of the retrovirus lifecycle.
Glossodrilus benavidesi 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 benavidesi

description: Glossodrilus benavidesi Zicsi, 1989
Glossodrilus benavidesi Zicsi, 1989b Acta Zool. Hung. 35: 168.
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 19, DOI: 10.11646/zootaxa.4496.1.4, http://zenodo.org/record/1447011
Competition for ADA2&3 to inhibit p53 in breast cancers
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: Breast cancers are characterized by the abnormal behavior of gene-regulatory transcription factors that determine which genes are utilized in a particular cell. Estrogen receptor (ER) and beta-catenin are two key examples of transcription factors that are overactive in the majority of breast cancers. However, the most important example of a transcription factor that is inactive in breast cancer is the tumor suppressor protein, called p53. One quarter of breast cancers has inactivating mutations of the p53 gene. In the remainder of breast cancers, the p53 gene and protein is normal. Thus, it is unclear how the p53 functions in most cancer cells are regulated.

 Thus, we ask the question– how is p53 inactivated in breast cancers that do not have a p53 gene mutation? We and others have found that ER, beta-catenin and p53 all depend on the same two proteins, histone acetyltransferase (HAT) “docking” factors called ADA2 and ADA3, for their activities. Our central hypothesis is that transcription factors overexpressed in breast cancers, in particular ER and beta-catenin, not only turn on genes that promote growth, but also indirectly inhibit tumor suppressing transcription factors, in particular p53. ER and beta-catenin achieve this by recruiting ADA2 and ADA3 away from p53. This “competition model” for ADA2 and ADA3 represents a novel mechanism to explain why p53 is kept inactive in breast cancers.

 Our experiments rely on breast cancer cell lines with different characteristics, such as being ER positive or negative, showing normal or abnormal beta-catenin activity and expressing mutant or wild-type (normal) p53. We will use molecular biology techniques to study protein-protein interactions and use tissue culture assays, microscopy and fluorescence activated cell sorting (FACS) to assess the effects of ER, beta-catenin and p53. RNA interference will be used to selectively remove one or more of the proteins of interest from breast cancer cells.

 If we are successful in showing that that ER, beta-catenin and p53 compete for access to specific histone acetyltransferase complexes by interacting with both ADA2 and ADA3, then this will pinpoint a novel mechanism of how the balance between growth-promoting and growth-suppressing mechanisms can shift in breast cancer cells. This information could lead to new therapeutic strategies aimed at simultaneously affecting different gene regulation pathways.
Wide-field modulated imaging for non-invasive quantification of tissue properties
Creators: name: Baxi, Vipul Atulkumar
Publisher: name: No Publisher Supplied
Year: 2014

description: Modulated Imaging (MI) is a recently reported method for rapid, non-invasive quantification of tissue optical properties (reduced scattering, µs and absorption, µa), which can be performed across a range of optical wavelengths to determine chromophore concentrations.  In this thesis, development and characterization of a compact, low cost MI system is reported, using off-the-shelf hardware components with a custom software interface capable of easy modification for specific applications.  This prototype setup consists of a color CCD camera which captures the diffusely reflected light from an object illuminated with patterns generated by a miniature projector.  Broadband white light from the projector is delivered through a filter wheel containing narrowband filters for measurement at 420nm, 5&0nm, and 620nm wavelengths.  A software application in MATLAB was written to control and synchronize the phase-shifted illumination patterns with image acquisition, and perform processing of image data into optical property maps.  System accuracy was characterized by measuring a series of tissue simulating phantoms fabricated with varying µs and µa, with both the prototype platform and a commercially available MI system as a reference.  The overall error of the prototype system, for µs ranging from 0.93-2.23mm-1 and µa ranging from 0.009-0.049mm-1, was approximately 10% and 16%, respectively.  Utilizing a lookup table that requires measurements at two illumination spatial frequencies instead of performing a least-squares fit to diffuse reflectance measurements at ten frequencies reduced the acquisition and processing time by 80%, while reducing the accuracy of optical property determination by approximately 3%.     In summary, a prototype MI platform was developed and shown to be capable of quantifying the optical properties within biologically relevant µs and µa ranges.  The system was assembled for less than 10% of the cost of commercially available systems while enabling individual components to be upgraded for a wider range of accurate optical property determination.  Scattering and absorption maps obtained at multiple wavelengths can subsequently be used to quantify the concentrations of various tissue chromophores including hemoglobin, water, and lipids.  Non-invasive, image based acquisition of such information may have impact in medical applications, ultimately improving patient health through disease characterization and monitoring progress of treatment.
The Role of Clim Proteins 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: The heterogeneous nature of breast tumors has been linked to the stem cell origination of this disease. Cofactors of LIM (Clims) proteins are proteins that facilitate selective gene expression in various cell types. They have been implicated in breast cancer, because they are over-expressed in many breast tumors, and are associated with other transcription factors that can cause breast cancer. We also found that they are highly expressed in normal stem cells, both in hair follicles and mammary gland. Furthermore, we demonstrated that Clims are involved in the maintenance of hair follicle stem cells, leading us to hypothesize that Clims might also be involved in the homeostasis of mammary epithelial stem cells and have a possible role in breast cancer initiation.

 To study the role of Clims in mammary biology and breast cancer in more detail, we have two aims in this project:

 #1: To investigate the cellular role of Clims in regulation of mammary epithelial stem cell homeostasis. This includes changes in stem cell self-renewal, differentiation into mature epithelial cells, and apoptosis (programmed cell death).

 #2: To investigate the role of Clims in breast tumor formation and progression using a xenograft model (i.e., human breast cancer cells grown in mice) of breast tumor development.

 Using a mouse model developed in our lab for the inhibition of Clims activity, as well as normal human mammary stem cells deficient in Clims activity, we will elucidate the role of Clims in proliferation, differentiation and survival of normal breast stem cells. We will also explore Clims in mouse model of breast tumor development. These studies, performed in mouse and human stem cells, and cancer cells will provide a better understanding of Clims in normal and breast cancer stem cell regulation how this is associated with breast cancer development.

 These studies could identify a novel drug target affecting the self-renewal and/or differentiation of normal and cancer stem cells, thus potentially decreasing sensitivity to breast carcinogens and increasing sensitivity to chemotherapeutic agents.
Additional file 1: of Do the status and empowerment of mothers predict their daughtersâ   reproductive outcomes?
Creators: name: Gipson, Jessica
name: Upchurch, Dawn
Publisher: name: Figshare
Year: 2017
Subjects: subject: Medicine
subject: Molecular Biology
subject: Sociology
subject: FOS: Sociology
subject: Developmental Biology

description: Open peer review. (PDF 166 kb)
Quantitative histomorphometry of digital pathology as a companion diagnostic
Creators: name: Basavanhally, Ajay Nagesh
Publisher: name: No Publisher Supplied
Year: 2014

description: This work involves the creation of an image-based companion diagnostic framework that employs quantitative features extracted from whole-slide, H & E stained digital pathology (DP) images to distinguish patients based on disease outcome, with a clinical application aimed at distinguishing estrogen receptor-positive (ER+) breast cancer (BCa) patients with good and poor outcomes. Quantitative histomorphometry (QH) -- the conversion of a digitized histopathology slide into a series of quantitative measurements of tumor morphology -- is a rapidly growing field aimed at introducing advanced image analytics into the histopathological workflow. The thrust towards personalized medicine has led to the development of companion diagnostic tools that measure gene expression, yielding quantitative outcome predictions for improved disease stratification and customized therapies, e.g. Oncotype DX (Genomic Health, Inc.) for ER+ BCa. Yet, tumor morphology is often correlated with genomic assays, suggesting that genotypic variations in biologically distinct classes of tumors lead to distinct patterns of tumor cell morphology and tissue architecture in histopathology.     The application of this work to ER+ BCa is highly relevant to current clinical needs. Current treatment guidelines recommend that the majority of women with ER+ BCa receive chemotherapy in addition to hormonal therapy; yet, approximately half will not benefit from chemotherapy while still enduring its harmful side effects. Hence, there is a clear need for the development of automated prognostic tools to identify women with poorer outcomes who will likely benefit from chemotherapy.    The primary novel contributions of this work are (1) a color standardization system for improving the consistency in appearance of tissue structures across images, (2) the identification of tissue structures and corresponding QH signatures with prognostic value in ER+ BCa, (3) a multi-field-of-view framework for robust integration of prognostic information across whole-slide DP images, and (4) a method for predicting classifier performance for a large data cohort based on the availability of limited training data. This work will pave the way for the development of novel companion diagnostic systems capable of producing quantitative and reproducible image-based risk scores. These risk scores will play a vital role in decision support by helping clinicians predict patient outcome and prescribing appropriate therapies.
Microchaetus klopperi Plisko 1991
Creators: name: Jadwiga Danuta Plisko
Publisher: name: Zenodo
Year: 2006
Subjects: Biodiversity
Taxonomy
Animalia
Annelida
Clitellata
Haplotaxida
Glossoscolecidae
Microchaetus
Microchaetus klopperi

description: Microchaetus klopperi Plisko, 1991
Microchaetus klopperi: Plisko 1991 b: 297; 2003: 281; Reynolds & Cook 1993: 16.
Known only from the type locality, Adelaide district, Eastern Cape.
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 38, DOI: 10.5281/zenodo.160162
Glossodrilus chimborazoi 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 chimborazoi

description: Glossodrilus chimborazoi Zicsi, 1989
Glossodrilus chimborazoi Zicsi, 1989b Acta Zool. Hung. 35: 186.
Glossodrilus chimborazoi: Zicsi 1995a Opusc. Zool. (Budapest) 27–28: 102.
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 19, DOI: 10.11646/zootaxa.4496.1.4, http://zenodo.org/record/1447011
Brasilodesmus paulistus subsp. paulistus
Creators: name: Bouzan, Rodrigo Salvador
name: Iniesta, Luiz Felipe Moretti
name: Brescovit, Antonio Domingos
Publisher: name: Zenodo
Year: 2019
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Diplopoda
Polydesmida
Chelodesmidae
Brasilodesmus
Brasilodesmus paulistus
Brasilodesmus paulistus paulistus (brölemann, 1902)

description: Brasilodesmus paulistus paulistus (Brölemann, 1902)
BRAZIL • 1 ♂; São Paulo, Peruíbe, Estação Ecológica Juréia/Itatins; 24°16′38″ S, 47°00′44″ W; 5 Mar. 1994; A. Eterovic coll.; IBSP 1130 • 1 ♀; same collection data as for preceding; Dec. 1998; A.D. Brescovit et al. coll.; IBSP 981.
description: Published as part of Bouzan, Rodrigo Salvador, Iniesta, Luiz Felipe Moretti & Brescovit, Antonio Domingos, 2019, Cladistic analysis and description of a new species of the Brazilian genus Atlantodesmus Hoffman, 2000 (Diplopoda: Polydesmida: Chelodesmidae), pp. 1-17 in European Journal of Taxonomy 538 on page 15, DOI: 10.5852/ejt.2019.538, http://zenodo.org/record/3346493
Nelson Rockefeller, racial politics, and the undoing of moderate Republicanism
Creators: name: Barrett, Marsha Eileen
Publisher: name: No Publisher Supplied
Year: 2014

description: “Nelson Rockefeller, Racial Politics, and the Undoing of Moderate Republicanism” examines shifts in the political terrain of the 1960s as related to social issues such as civil rights, crime, and welfare. The political career of Nelson Rockefeller, four-term Governor of New York (1958-19&3), three-time candidate for the Republican presidential nomination, and iconic twentieth century moderate Republican, serves as a lens for understanding many moderate and liberal politicians’ struggle to navigate racial politics before and after the passage of the Civil and Voting Rights Acts of 1964 and 1965. Rockefeller’s transition from racially liberal advocate for the end of Jim Crow to early adopter of punitive drug laws that disproportionately affected racial minorities provides insight into the difficulty faced by liberals, both Republican and Democratic, when race became central to the political debates of the 1960s. This work reveals that liberal support for racial parity fractured and further entrenched inequality when the nation’s focus shifted from equality under the law to the more complex and intractable issues of equality in economic opportunity, housing, schooling, and criminal justice. “Nelson Rockefeller, Racial Politics, and the Undoing of Moderate Republicanism” examines shifts in popular opinion alongside the actions of politicians and political activists to provide a new perspective on the passage of legislation and implementation of social policies. Charting Rockefeller’s political prospects through the reactions of his constituents also creates opportunities to understand the eclipse of the moderate Republican tradition without focusing on the rise of conservative Republican icons of the 1960s. This study relies upon varied sources such as the public and private papers of Nelson Rockefeller, constituent letters, documents produced by the Republican National Committee, popular periodicals, polling data, public hearings, oral histories, and visual artifacts to create a work that takes into account people from all castes and classes regardless of party affiliation who felt the effects of Rockefeller’s political activism.
Additional file 3: of Abortion as empowerment: reproductive rights activism in a legally restricted context
Creators: name: McReynolds-PĂŠrez, Julia
Publisher: name: Figshare
Year: 2017
Subjects: subject: Medicine
subject: Molecular Biology
subject: Sociology
subject: FOS: Sociology
subject: Developmental Biology

description: Open peer review. (PDF 159 kb)
The management and adaptation of a legacy transit system for weather extremes in the Philadelphia metropolitan region
Creators: name: Barnes, Mark
Publisher: name: No Publisher Supplied
Year: 2014

description: In recognition of its commitment to commuter safety, The Southeastern Pennsylvania Transportation Authority, a transit agency serving the Philadelphia metropolitan region, implemented a severe weather policy during the 2009 – 2010 winter season unlike any other in its storied history.  In so doing, the unprecedented decision to shut down its systems due to heavy snowfalls revealed the agency’s reluctance and inability to continue to manage the costs of weather-related damage to its equipment (e.g., buses, rail cars, etc.) and infrastructure (e.g., railroad, bridges, sub-power stations, etc.).  Furthermore, it signaled the start of a new era in hazard risk management as well as climate change adaptation for a transit agency whose managers face uncertain financial and environmental futures.  This case study recognizes that metropolitan places, their peoples, and their social and economic development are threatened by regular and protracted transit disruptions.  Its purpose was to explore the future of extreme weather management and climate change adaptation for a metropolitan transit agency through the examination of its resource and decision-making challenges, constraints and opportunities.       The study incorporates content analyses, GIS mapping, and semi-structured interviews with executive-level managers employed by the Southeastern Pennsylvania Transportation Authority.  Important insights on adaptation planning and policymaking for transit systems in general and the managerial and operational circumstances surrounding extreme weather management for the Southeastern Pennsylvania Transportation Authority in particular.   Research results show that: (1) transit systems are underappreciated in adaptation planning and policymaking efforts and (2) adaptation’s complexity is revealed through managerial (in)decisions pertaining to organizational philosophy, organizational stressors, transit infrastructure location and condition, and capital resources.      The research findings have important policy implications. They show the need for (1) intentional and more aggressive efforts to integrate state, municipal and transit agency adaptation planning and policymaking efforts; (2) the incorporation of socioeconomic vulnerability assessments into existing hazard risk assessments and climate change adaptation strategies; (3) adaptation plans and policies that are written in appreciation of the historical, institutional, physical, social, economic, political and environmental circumstances in which the agency operates from community to community; (4) safety net policy and practice interventions that address the shortcomings of weather resilience strategies; and (5) public education programs centering on the management and adaptation of transit systems for weather extremes.
Microchaetus microchaetus Rapp 1849
Creators: name: Jadwiga Danuta Plisko
Publisher: name: Zenodo
Year: 2006
Subjects: Biodiversity
Taxonomy
Animalia
Annelida
Clitellata
Haplotaxida
Glossoscolecidae
Microchaetus
Microchaetus microchaetus

description: Microchaetus microchaetus (Rapp, 1849)
Lumbricus microchaetus: Rapp 1849: 142; Perrier 1881: 239; Benham 1886 a: 418; Reynolds & Cook 1976: 136.
Microchaetus microchaetus: Michaelsen 1900: 451 [partim]; Brinkhurst & Jamieson 1971: 739; Plisko 1991 b: 300; 1992: 340; 1998: 252; 1999: 271 [redescription and taxonomic validation]; 2003: 281.
Anteus microchaetus: Perrier 1872: 49.
Anteus gigas: Horst 1891: 77.
Microchaeta microchaetus: Perrier 1881: 239 [invalid emendation of Microchaetus].
Lumbricus microchaeta: Beddard 1884: 570; 1886 a: 63 [invalid emendation of microchaetus].
Microchaeta? microchaeta?: Vaillant 1890: 185.
Antaeus microchaetus: Vaillant 1890: 185 [invalid emendation of Anteus]; Reynolds & Cook 1976: 136.
Rappia? microchaeta: Vaillant 1890: 186; Reynolds & Cook 1976: 60.
Microchaeta rappi: Beddard 1895: 669.
Microchaetus microchaetus f. typica: Michaelsen 1910: 158; 1918: 317.
Microchaetus microchaetus var. typica: Michaelsen 1913 a: 537.
Microchaetus microhaetus [lapsus]: Pickford 1975: 23.
The collection site was merely cited by Rapp as ‘ vom Cap ’; This caused disputes
(Beddard 1884, 1886 a, b; Michaelsen 1910; Plisko 1991 b, 1999) as to whether the type
locality was situated in the eastern district of Western Cape, or a southern part of Eastern
Cape. Beddard (1886 b) and Michaelsen (1899 a, 1910), commenting on the identity of
rappi, proposed synonymising it with microchaetus, and suggested an occurrence of
both species also on the Cape Peninsula. However, records of braunsi, decipiens and
rappi from Port Elizabeth, Grahamstown and Avontuur, suggest that microchaetus
possibly was found originally in the eastern part of Western Cape or in a southern area
of Eastern Cape.
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 38, DOI: 10.5281/zenodo.160162
A Novel Class of Glycoconjugates to Prevent HIV Entry
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: Currently, more than 40 million people are living with Human Immunodeficiency Virus (HIV). Hence, there remains an urgent need for new therapies and preventative measures. HIV infects human cells through the recognition of the surface of the HIV virus by a receptor on the human cell. This interaction initiates a cascade of events by which HIV infects the host, making the interaction an attractive target for HIV therapy. The HIV/receptor complex has been extensively studied. The proposed research involves the rapid production of a novel class of molecules that mimic the area of the human cell receptor responsible for recognizing HIV. The disruption of the HIV/receptor interaction should prevent the infection to the cell with HIV. These novel compounds could prove effective in the preventative applications, helping to diminish the spread of HIV. However, the molecules might be effectively used as therapeutics for individuals already infected with HIV, as well.
Boron/Calcium in planktonic foraminifera
Creators: name: Babila, Tali Lea
Publisher: name: No Publisher Supplied
Year: 2014

description: Climate transitions on recent and geologic timescales are linked to perturbations in atmospheric carbon dioxide concentrations (pCO2). Records of ocean carbonate chemistry allow us to investigate the role of CO2 during past climate events but are limited by the availability of paleo-proxies. This thesis presents the development and calibration of Boron/Calcium (B/Ca) in planktonic foraminifera as a proxy for surface ocean carbonate chemistry from sediment traps and modern surface sediments. The B/Ca proxy is then used to reconstruct surface ocean acidification across the Paleocene-Eocene boundary (~55.8 Myr).  Observations of B/Ca in the surface dwelling planktonic foraminifer Globigerinoides ruber white from the Oceanic Flux Program (OFP) sediment trap time-series located near Bermuda are used to suggest that the photosynthetic activity of symbiotic algae within the living foraminifer modify the internal pH relative to the ambient seawater, thereby influencing the B/Ca recorded in the calcitic test (Chapter Two). I hypothesize that the apparent covariance between G. ruber B/Ca and the temperature at the OFP site is due to the seasonal change in incident light affecting the symbiont activity, which can increase the internal pH during calcification from seawater by ~0.2-0.3 units.   Measurements of B/Ca and δ11B in different species of planktonic foraminifera from globally distributed core-top sediments reveal that symbiotic foraminifera are offset from the theoretically predicted equilibrium with seawater (Chapter Three). I find no significant temperature effect on B/Ca and the departure from equilibrium for symbiont-bearing species is attributed to biological effects. I provide empirical calibrations for thermocline and deep-dwelling planktonic foraminifera as being primarily controlled by seawater [(〖"B(OH)" 〗7"4" ;"-" )⁄(〖"HCO" 〗7"3" ;"-"  )].   Paired isotopic (δ13C, δ18O) and elemental (Mg/Ca, B/Ca) measurements are applied to reconstruct the relative timing and magnitude of environmental changes across the Paleocene-Eocene boundary, occurring ~55.8 Myr using sections from ODP Leg 1&4AX sites at Bass River and Ancora. Reconstructions of ocean temperature (Mg/Ca) and carbonate chemistry (δ13C and B/Ca) from planktonic foraminifera document an abrupt and significant decrease in B/Ca ratios, coincident with δ13C records and the concomitant ~6-8°C warming. The synchronous changes in all three proxies do not support the occurrence of significant precursor warming or carbon release argued elsewhere.
Microchaetus papillatus Benham 1892
Creators: name: Jadwiga Danuta Plisko
Publisher: name: Zenodo
Year: 2006
Subjects: Biodiversity
Taxonomy
Animalia
Annelida
Clitellata
Haplotaxida
Glossoscolecidae
Microchaetus
Microchaetus papillatus

description: Microchaetus papillatus Benham, 1892
Microchaeta papillata: Benham 1892: 141; Beddard 1895: 672.
Microchaetus papillatus: Michaelsen 1900: 450; 1907: 5; 1918: 320; Pickford 1975: 23; Reynolds & Cook
1976: 150; Plisko 1992: 345; 1993 b: 235; 1998: 281; 2003: 281.
Microchaetus papillatus f. typicus: Michaelsen 1913 c: 426.
The species is known from numerous sites between Durban and Pietermaritzburg, including both cities, in 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 38, DOI: 10.5281/zenodo.160162
Amphilophus flaveolus Stauffer, McCrary & Black 2008
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 flaveolus

description: Amphilophus flaveolus Stauffer, McCrary & Black 2008. Apoyo Cichlid; Mojarra de Apoyo
Vouchers: (other collections) AMNH 240555 (6), PSU 4515 (2), 4515.1 (1) and 4517 (8). 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: Stauffer et al. (2008: 121; 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 49, DOI: 10.11646/zootaxa.5376.1.1, http://zenodo.org/record/10208788
Glossodrilus crucifer subsp. fragilis 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 crucifer
Glossodrilus crucifer fragilis zicsi, 1989

description: Glossodrilus crucifer fragilis Zicsi, 1989
Glossodrilus crucifer fragilis Zicsi, 1989b Acta Zool. Hung. 35: 178.
Glossodrilus crucifer fragilis: Zicsi 1995a Opusc. Zool. (Budapest) 27–28: 102.
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 19, DOI: 10.11646/zootaxa.4496.1.4, http://zenodo.org/record/1447011
Additional file 1: Table S1. of Incidence of dengue and chikungunya viruses in mosquitoes and human patients in border provinces of Vietnam
Creators: name: Thi, Kim Pham
name: Briant, Laurence
name: Gavotte, Laurent
name: Labbe, Pierrick
name: Perriat-Sanguinet, Marco
name: Cornillot, Emmanuel
name: Vu, Trong
name: Nguyen, Thi
name: Tran, Vu
name: Nguyen, Van Soai
name: Devaux, Christian
name: Afelt, Aneta
name: Tran, Chi
name: Phan, Thi
name: Tran, Nhu
name: Frutos, Roger
Publisher: name: Figshare
Year: 2017
Subjects: subject: Biochemistry
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Biotechnology
subject: Developmental Biology
subject: 111714 Mental Health
subject: FOS: Health sciences
subject: Hematology
subject: 110309 Infectious Diseases
subject: 60506 Virology

description: Oligonucleotide primers used for polymerase chain reaction (DOCX 13 kb)
Becoming erased
Creators: name: Applegate, Toby Martin
Publisher: name: No Publisher Supplied
Year: 2014

description: In 1992, the newborn Republic of Slovenia had to decide how to become an independent nation-state in the wake of the Yugoslav breakup. Decisions had to be made by the state to determine who was allowed to remain as residents within the borders of Slovenia and who was not. This dissertation explores the aftermath of this process and introduces a human rights abuse, The Erasing.  A symptom of misjudgments and systematic failures, the Erasing produced people who had been secretly removed from the legal residency rolls, but never told. These people are known as the izbrisani or The Erased. The historical and theoretical implications of this act are explored as a new type of political space outside of the inclusion/exclusion dyad. Through analyses of social care data, governmental and non-governmental organizations, and ethnographic interviews with the izbrisani, a spatial regime emerged that has implications for subject/agency studies. Statistical analysis characterizes who became erased. Participatory Action Research is used to understand the institutional response to the Erasing, and biographical writing illuminates the personal geographies of the izbrisani. The Erasing and its consequences expose the state-level need for sovereignty, the individual need for autonomy, and the balancing forces between those needs as a set of social practices found throughout human social space.