Anne Riches
Ontology highlight
ABSTRACT:
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PROVIDER: S-EPMC554080 | biostudies-literature | 2005 Mar
REPOSITORIES: biostudies-literature
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| S-EPMC416655 | biostudies-literature
Project description:The genetic, epigenetic, and physiological differences among cells in clonal microbial colonies are underexplored opportunities for discovery. A recently developed genetic assay reveals that transient losses of heterochromatic repression, a heritable form of gene silencing, occur throughout the growth of Saccharomyces colonies. This assay requires analyzing two-color fluorescence patterns in yeast colonies, which is qualitatively appealing but quantitatively challenging. In this paper, we developed a suite of automated image processing, visualization, and classification algorithms (MORPHE) that facilitated the analysis of heterochromatin dynamics in the context of colonial growth and that can be broadly adapted to many colony-based assays in Saccharomyces and other microbes. Using the features that were automatically extracted from fluorescence images, our classification method distinguished loss-of-silencing patterns between mutants and wild type with unprecedented precision. Application of MORPHE revealed subtle but significant differences in the stability of heterochromatic repression between various environmental conditions, revealed that haploid cells experienced higher rates of silencing loss than diploids, and uncovered the unexpected contribution of a sirtuin to heterochromatin dynamics.
| S-EPMC4878510 | biostudies-literature
Project description:Urbanisation brings with it rapid socio-economic change with volatile livelihoods and unstable ownership of assets. Yet, current measures of wealth are based predominantly on static livelihoods found in rural areas. We sought to assess the extent to which seven common measures of wealth appropriately capture vulnerability to poverty in urban areas. We then sought to develop a measure that captures the characteristics of one urban area in Nepal. We collected and analysed data from 1,180 households collected during a survey conducted between November 2017 and January 2018 and designed to be representative of the Kathmandu valley. A separate survey of a sub set of households was conducted using participatory qualitative methods in slum and non-slum neighbourhoods. A series of currently used indices of deprivation were calculated from questionnaire data. We used bivariate statistical methods to examine the association between each index and identify characteristics of poor and non-poor. Qualitative data was used to identify characteristics of poverty from the perspective of urban poor communities which were used to construct an Urban Poverty Index that combined asset and consumption focused context specific measures of poverty that could be proxied by easily measured indicators as assessed through multivariate modelling. We found a strong but not perfect association between each measure of poverty. There was disagreement when comparing the consumption and deprivation index on the classification of 19% of the sample. Choice of short-term monetary and longer-term capital approaches accounted for much of the difference. Those who reported migrating due to economic necessity were most likely to be categorised as poor. A combined index was developed to capture these dimension of poverty and understand urban vulnerability. A second version of the index was constructed that can be computed using a smaller range of variables to identify those in poverty. Current measures may hide important aspects of urban poverty. Those who migrate out of economic necessity are particularly vulnerable. A composite index of socioeconomic status helps to capture the complex nature of economic vulnerability.
| S-EPMC7001899 | biostudies-literature
Project description:Purpose of reviewAcute myeloid leukemia (AML) is an aggressive malignancy of the bone marrow that has a poor prognosis with traditional cytotoxic chemotherapy, especially in elderly patients. In recent years, small molecule inhibitors targeting AML-associated IDH1, IDH2, and FLT3 mutations have been FDA approved. However, the majority of AML cases do not have a targetable mutation. A variety of novel agents targeting both previously untargetable mutations and general pathways in AML are currently being investigated. Herein, we review selected new targeted therapies currently in early-phase clinical investigation in AML.Recent findingsThe DOT1L inhibitor pinometostat in KMT2A-rearranged AML, the menin inhibitors KO-539 and SYNDX-5613 in KMT2Ar and NPM1-mutated AML, and the mutant TP53 inhibitor APR-246 are examples of novel agents targeting specific mutations in AML. In addition, BET inhibitors, polo-like kinase inhibitors, and MDM2 inhibitors are promising new drug classes for AML which do not depend on the presence of a particular mutation. AML remains in incurable disease for many patients but advances in genomics, epigenetics, and drug discovery have led to the development of many potential novel therapeutic agents, many of which are being investigated in ongoing clinical trials. Additional studies will be necessary to determine how best to incorporate these novel agents into routine clinical treatment of AML.
| S-EPMC8515252 | biostudies-literature
Project description:Comprehensive genomic and transcriptomic analysis demonstrate that tumor-infiltrating T lymphocytes that react to mutated neoepitopes could be identified in recurrent ovarian cancer. Two of these T-cell populations reacted against TP53 hotspot missense mutations that are present in a wide variety of malignancies. Clin Cancer Res; 24(22); 5493-5. ©2018 AACR See related article by Deniger et al., p. 5562.
| S-EPMC6215482 | biostudies-literature