| 1. |
- Egelhofer, Thea A, et al.
(author)
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An assessment of histone-modification antibody quality
- 2011
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In: Nature Structural & Molecular Biology. - : Springer Science and Business Media LLC. - 1545-9993 .- 1545-9985. ; 18:1, s. 91-93
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Journal article (peer-reviewed)abstract
- We have tested the specificity and utility of more than 200 antibodies raised against 57 different histone modifications in Drosophila melanogaster, Caenorhabditis elegans and human cells. Although most antibodies performed well, more than 25% failed specificity tests by dot blot or western blot. Among specific antibodies, more than 20% failed in chromatin immunoprecipitation experiments. We advise rigorous testing of histone-modification antibodies before use, and we provide a website for posting new test results (http://compbio.med.harvard.edu/antibodies/).
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| 2. |
- Fonseca, Catarina, et al.
(author)
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Survey data of public awareness on climate change and the value of marine and coastal ecosystems
- 2023
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In: Data in Brief. - : Elsevier BV. - 2352-3409. ; 47
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Journal article (peer-reviewed)abstract
- The long-term provision of ocean ecosystem services depends on healthy ecosystems and effective sustainable management. Understanding public opinion about marine and coastal ecosystems is important to guide decision-making and inform specific actions. However, available data on public perceptions on the interlinked effects of climate change, human impacts and the value and management of marine and coastal ecosystems are rare. This dataset presents raw data from an online, self-administered, public awareness survey conducted between November 2021 and February 2022 which yielded 709 responses from 42 countries. The survey was released in four languages (English, French, Spanish and Italian) and consisted of four main parts: (1) perceptions about climate change; (2) perceptions about the value of, and threats to, coasts, oceans and their wildlife, (3) perceptions about climate change response; and (4) socio-demographic information. Participation in the survey was voluntary and all respondents provided informed consent after reading a participant information form at the beginning of the survey. Responses were anonymous unless respondents chose to provide contact information. All identifying information has been removed from the dataset. The dataset can be used to conduct quantitative analyses, especially in the area of public perceptions of the interlinkages between climate change, human impacts and options for sustainable management in the context of marine and coastal ecosystems. The dataset is provided with this article, including a copy of the survey and participant information forms in all four languages, data and the corresponding codebook.
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| 3. |
- Nobre, Liana, et al.
(author)
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Outcomes of BRAF V600E pediatric gliomas treated with targeted BRAF inhibition
- 2020
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In: JCO Precision Oncology. - 2473-4284. ; 3, s. 561-571
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Journal article (peer-reviewed)abstract
- © 2020 by American Society of Clinical Oncology PURPOSE Children with pediatric gliomas harboring a BRAF V600E mutation have poor outcomes with current chemoradiotherapy strategies. Our aim was to study the role of targeted BRAF inhibition in these tumors. PATIENTS AND METHODS We collected clinical, imaging, molecular, and outcome information from patients with BRAF V600E–mutated glioma treated with BRAF inhibition across 29 centers from multiple countries. RESULTS Sixty-seven patients were treated with BRAF inhibition (pediatric low-grade gliomas [PLGGs], n = 56; pediatric high-grade gliomas [PHGGs], n = 11) for up to 5.6 years. Objective responses were observed in 80% of PLGGs, compared with 28% observed with conventional chemotherapy (P, .001). These responses were rapid (median, 4 months) and sustained in 86% of tumors up to 5 years while receiving therapy. After discontinuation of BRAF inhibition, 76.5% (13 of 17) of patients with PLGG experienced rapid progression (median, 2.3 months). However, upon rechallenge with BRAF inhibition, 90% achieved an objective response. Poor prognostic factors in conventional therapies, such as concomitant homozygous deletion of CDKN2A, were not associated with lack of response to BRAF inhibition. In contrast, only 36% of those with PHGG responded to BRAF inhibition, with all but one tumor progressing within 18 months. In PLGG, responses translated to 3-year progression-free survival of 49.6% (95% CI, 35.3% to 69.5%) versus 29.8% (95% CI, 20% to 44.4%) for BRAF inhibition versus chemotherapy, respectively (P = .02). CONCLUSION Use of BRAF inhibition results in robust and durable responses in BRAF V600E–mutated PLGG. Prospective studies are required to determine long-term survival and functional outcomes with BRAF inhibitor therapy in childhood gliomas.
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| 4. |
- Veldman, Sarina
(author)
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Markets, mixtures and molecular methods : Investigating medicinal plant and edible orchid diversity in Tanzania and Zambia
- 2018
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Doctoral thesis (other academic/artistic)abstract
- Medicinal plants are an important source of primary healthcare for many people in Tanzania. These medicinal plants are harvested from the wild, and increasing commercial trade poses a serious threat to local plant populations. Currently it is unknown which species are traded and in what amounts. Across the southwestern border in Zambia, the traditional dish chikanda has transformed from a niche product to being a mainstream delicacy. One of the main ingredients are wild-harvested orchids, and these have become depleted throughout the country as an effect of the increased trade. It is unclear which orchid species are targeted and might be at risk of overharvesting. The aims of my doctorate are to map harvest and trade of Tanzanian medicinal plants and Tanzanian and Zambian edible orchids, to investigate whether species that are traded on local markets can be identified using molecular methods such as DNA barcoding and metabarcoding and identify conservation issues arising from wild-harvesting of medicinal plants and edible orchids.In Paper I DNA metabarcoding analysis of Tanzanian chikanda cake show the presence of 17 different orchids species belonging to the genera Disa, Satyrium and Habenaria, and in Paper V the analysis of chikanda tubers sold on Zambian markets reveals that at least 16 orchid species from 6 different orchid genera are targeted in local orchid trade. Paper II describes a quantitative market survey of the non-woody, non-powdered medicinal plants sold on Kariakoo market in Dar-es-Salaam that shows that a total of 67 species are traded in an annual volume of nearly 31 tonnes of fresh and dried medicinal leaves, seeds and fruits with an estimated value of 200,000 USD. For Paper III 873 medicinal plant products were analysed using DNA barcoding, literature and morphology to determine which species are traded on the Dar-es-Salaam and Tanga markets. In total, 509 identifications could be made corresponding to 91 species, 124 genera and 65 plant families, and several cases of over- and under-differentiation were detected. Paper IV builds upon the identifications in Paper III to determine in what amount the medicinal plant species present at the local markets are traded and to investigate if commercial trade poses a threat to local plant populations. It was found that several of the most highly favored medicinal plants were perceived to becoming more difficult to obtain in the wild.This thesis shows that DNA barcoding is a powerful rapid identification method for morphologically unidentifiable specimens. It also shows that commercialization of wild-harvested plant products threatens local plant populations, and highlights the need for conservation measures to avoid local extinction of economically and socially important plant species.
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| 5. |
- Winther, Jeanete F., et al.
(author)
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Childhood cancer survivor cohorts in Europe
- 2015
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In: Acta Oncologica. - 1651-226X. ; 54:5, s. 655-668
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Research review (peer-reviewed)abstract
- With the advent of multimodality therapy, the overall five-year survival rate from childhood cancer has improved considerably now exceeding 80% in developed European countries. This growing cohort of survivors, with many years of life ahead of them, has raised the necessity for knowledge concerning the risks of adverse long-term sequelae of the life-saving treatments in order to provide optimal screening and care and to identify and provide adequate interventions. Childhood cancer survivor cohorts in Europe. Considerable advantages exist to study late effects in individuals treated for childhood cancer in a European context, including the complementary advantages of large population-based cancer registries and the unrivalled opportunities to study lifetime risks, together with rich and detailed hospital-based cohorts which fill many of the gaps left by the large-scale population-based studies, such as sparse treatment information. Several large national cohorts have been established within Europe to study late effects in individuals treated for childhood cancer including the Nordic Adult Life after Childhood Cancer in Scandinavia study (ALiCCS), the British Childhood Cancer Survivor Study (BCCSS), the Dutch Childhood Oncology Group (DCOG) LATER study, and the Swiss Childhood Cancer Survivor Study (SCCSS). Furthermore, there are other large cohorts, which may eventually become national in scope including the French Childhood Cancer Survivor Study (FCCSS), the French Childhood Cancer Survivor Study for Leukaemia (LEA), and the Italian Study on off-therapy Childhood Cancer Survivors (OTR). In recent years significant steps have been taken to extend these national studies into a larger pan-European context through the establishment of two large consortia - PanCareSurFup and PanCareLIFE. The purpose of this paper is to present an overview of the current large, national and pan-European studies of late effects after childhood cancer. This overview will highlight the strong cooperation across Europe, in particular the EU-funded collaborative research projects PanCareSurFup and PanCareLIFE. Overall goal. The overall goal of these large cohort studies is to provide every European childhood cancer survivor with better care and better long-term health so that they reach their full potential, and to the degree possible, enjoy the same quality of life and opportunities as their peers.
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