pinecone/core-2020-05-10-deduplication huggingface dataset:
Chromosomal in situ suppression hybridization of immunologically classified mitotic cells in hematologic malignancies

Chromosomal in situ suppression (CISS) hybridization was performed with library DNA from sorted human chromosomes 8, 9, 15, 17, 21, and 22 on immunologically stained bone marrow cells of four patients with a hematologic neoplasm, including two patients with myelodysplastic syndrome and trisomy 8, one patient with promyelocytic leukemia bearing the translocation t(15;17)(q22;q11-12), and one patient with chronic myeloid leukemia and the translocation t(9;22)(q34;q11). In all patients, the results of conventional karyotype analysis could be confirmed by one- or two-color CISS hybridization using the appropriate chromosome-specific libraries. Our results show that CISS hybridization can detect both numerical and structural chromosome changes in immunologically classified cells with high specificity and reliability. The fact that chromosome spreads of very poor quality can now be included in such analyses is a decisive advantage of this approach. In addition, the suitability of this approach for interphase cytogenetics is discussed.
Translocation of BCR to chromosome 9: A new cytogenetic variant detected by FISH in two Ph-negative, BCR-positive patients with chronic myeloid leukemia

Leukemic cells from two patients with Philadelphia-negative chronic myeloid leukemia (CML) were investigated: I) Cytogenetics showed a normal 46.XY karyotype in both cases, 2) molecular studies revealed rearrangement of the M-BCR region and formation of BCR-ABL fusion mRNA with b2a2 (patient I) or b3a2 (patient 2) configuration, and 3) fluorescence in situ hybridization (FISH) demonstrated relocation of the 5′ BCR sequences from one chromosome 22 to one chromosome 9. The ABL probe hybridized to both chromosomes 9 at band q34, while two other probes which map centromeric and telomeric of BCR on 22q 11 hybridized solely with chromosome 22. For the first time, a BCR-ABL rearrangement is shown to take place on 9q34 instead of in the usual location on 22q 11. A rearrangement in the latter site is found in all Ph-positive CML and in almost all investigated CML with variant Ph or Ph-negative, BCR-positive cases. The few aberrant chromosomal localizations of BCR-ABL recombinant genes found previously were apparently the result of complex and successive changes. Furthermore in patient 2, both chromosomes 9 showed positive FISH signals with both ABL and BCR probes. Restriction fragment length polymorphism (RFLP) analysis indicated that mitotic recombination had occurred on the long arm of chromosome 9 and that the rearranged chromosome 9 was of paternal origin. The leukemic cells of this patient showed a duplication of the BCR-ABL gene, analogous to duplication of the Ph chromosome in classic CML. In addition they had lost the maternal alleles of the 9q34 chromosomal region. The lymphocytes of patient 2 carried the maternal chromosome 9 alleles and were Ph-negative as evidenced by RFLP and FISH analyses, respectively. © 1993 Wiley-Liss, Inc
Expression of the Wilms' tumor gene WT1 in human malignant mesothelioma cell lines and relationship to platelet-derived growth factor A and insulin- like growth factor 2 expression

Mutations in the WT1 tumor suppressor gene are known to contribute to the development of Wilms' tumor (WT) and associated gonadal abnormalities. WT1 is expressed principally in the fetal kidney, developing gonads, and spleen and also in the mesothelium, which lines the coelomic cavities. These tissues develop from mesenchymal components that have subsequently become epithelialized, and it has therefore been proposed that WT1 may play a role in this transition of cell types. To test the possible involvement of this gene in malignant mesothelioma, we have first studied its expression in a panel of human normal and malignant mesothelial cell lines. WT1 mRNA expression levels varied greatly between the cell lines and no specific chromosomal aberration on 11p, which could be related to the variation in WT1 expression in these cell lines, was observed. Furthermore, no gross deletions, rearrangements, or functionally inactivating point mutations in the WT1 coding region were identified. All four WT1 splice variants were observed at similar levels in these cell lines. The WT1 gene encodes a zinc-finger transcription factor and the four protein isoforms are each believed to act as transcriptional repressors of certain growth factor genes. Lack of WT1 expression is thus predicted to result in growth stimulation of tumor cells. Binding of one particular WT1 isoform construct to the insulin-like growth factor 2 (IGF2) and platelet-derived growth factor A (PDGFA) gene promoters has been demonstrated to result in repression of these genes in transient transfection studies. Analysis of IGF2 and PDGFA mRNA expression levels compared with WT1 mRNA expression levels failed to demonstrate an inverse correlation in the mesothelial cell lines, which endogenously express these genes. Finally, the putative role of WT1 in the transition of cell types was investigated. No obvious correlation between WT1 expression levels and cell morphology of the malignant mesothelial cell lines was evident from this study. Moreover, no change in WT1 expression was observed in normal mesothelial cells which were, by alteration of culture conditions, manipulated to switch from the mesenchymal to epithelial morphology
N- and KRAS mutations in primary testicular germ cell tumors: Incidence and possible biological implications

Recently, conflicting results have been reported on the incidence of RAS mutations in primary testicular germ cell tumors of adults (TGCTs). In four studies a low incidence of mutations (less than 15%) in a variety of TGCTs or derived cell lines was found, whereas in two other studies a high incidence of N- or KRAS mutations (over 40%) was shown. A total of 62 testicular seminomas (SE) and 34 nonseminomatous TGCTs (NS) were studied thus far. The largest series consisted of 42 TGCTs, studied on paraffin embedded tissue. We present the results of analysis for the presence of N- and KRAS mutations, in codons 12, 13, and 61, in snap frozen samples of 100 primary TGCTs, comprising 40 SE and 60 NS. Using the polymerase chain reaction (PCR) and allele specific oligonucleotide hybridization (ASO), mutations were found in five SE (three in NRAS and two in KRAS, all codon 12), and in one NS (KRAS, codon 12). To exclude underestimation of the incidence of RAS mutations in TGCTs due to the presence of an excess of wild type alleles in the analyzed sample, a PCR technique preferentially amplifying KRAS alleles with a mutation in codon 12 was applied to all SE. This approach, allowing a 250 times more sensitive assay, resulted in the detection of only one additional SE with a mutation. Based on a critical analysis of published data and on our results from the largest series of frozen samples investigated thus far, we conclude that N- or KRAS mutations are rare and apparently not essential for initiation or progression of TGCTs
Reliable, resilient and sustainable water management: the Safe & SuRe approach

This is the final version of the article. Available from Wiley via the DOI in this record.Global threats such as climate change, population growth, and rapid urbanization pose a huge future challenge to water management, and, to ensure the ongoing reliability, resilience and sustainability of service provision, a paradigm shift is required. This paper presents an overarching framework that supports the development of strategies for reliable provision of services while explicitly addressing the need for greater resilience to emerging threats, leading to more sustainable solutions. The framework logically relates global threats, the water system (in its broadest sense), impacts on system performance, and social, economic, and environmental consequences. It identifies multiple opportunities for intervention, illustrating how mitigation, adaptation, coping, and learning each address different elements of the framework. This provides greater clarity to decision makers and will enable better informed choices to be made. The framework facilitates four types of analysis and evaluation to support the development of reliable, resilient, and sustainable solutions: “top-down,” “bottom-up,” “middle based,” and “circular” and provides a clear, visual representation of how/when each may be used. In particular, the potential benefits of a middle-based analysis, which focuses on system failure modes and their impacts and enables the effects of unknown threats to be accounted for, are highlighted. The disparate themes of reliability, resilience and sustainability are also logically integrated and their relationships explored in terms of properties and performance. Although these latter two terms are often conflated in resilience and sustainability metrics, the argument is made in this work that the performance of a reliable, resilient, or sustainable system must be distinguished from the properties that enable this performance to be achieved.This work forms part of a 5-year fellowship for the first author funded by the UK Engineering & Physical Sciences Research Council (EP/K006924/1) and supported by the Welsh Government, the Environment Agency, the Consumer Council for Water, the Environmental Sustainability Knowledge Transfer Network, the Water Industry Forum, Severn Trent Water, Northumbrian Water, Arup, Black & Veatch, Arcadis, and ACO Technologies
Frugal energy innovations for developing countries - a framework

Frugal innovations have recently emerged to feature low-cost technologies and busi-ness innovations to serve consumers in emerging markets and improve their qualityof life. Although the concept of frugality is well known, the present literature on frugalenergy innovations, or energy frugality, is scarce, which could lead to overlooking itstrue characteristics. Therefore, we propose a framework for deﬁning energy frugalitybased on a detailed analysis of several low-cost sustainable energy technologies. Theﬁve-criteria assessment method developed will help to identify potential frugal energyinnovations and will increase the adoption of these technologies through bettermatching to local needs. Fuel-efﬁcient biomass cooking stoves, small-scale photovol-taic systems, and pico-grids are examples of such frugal energy technologies.Peer reviewe
Global health governance in the sustainable development goals : is it grounded in the right to health?

This paper explores the extent to which global health governance – in the context of the early implementation of the Sustainable Development Goals is grounded in the right to health. The essential components of the right to health in relation to global health are unpacked. Four essential functions of the global health system are assessed from a normative, rights-based, analysis on how each of these governance functions should operate. These essential functions are: the production of global public goods, the management of externalities across countries, the mobilization of global solidarity, and stewardship. The paper maps the current reality of global health governance now that the post-2015 Sustainable Development Goals are beginning to be implemented. In theory, the existing human rights legislation would enable the principles and basis for the global governance of health beyond the premise of the state. In practice, there is a governance gap between the human rights framework and practices in global health and development policies. This gap can be explained by the political determinants of health that shape the governance of these global policies. Current representations of the right to health in the Sustainable Development Goals are insufficient and superficial, because they do not explicitly link commitments or right to health discourse to binding treaty obligations for duty-bearing nation states or entitlements by people. If global health policy is to meaningfully contribute to the realization of the right to health and to rights based global health governance then future iterations of global health policy must bridge this gap. This includes scholarship and policy debate on the structure, politics, and agency to overcome existing global health injustices
From Targets to Action : Rolling up our Sleeves after Paris

At the United Nations Climate Change Conference in Paris in 2015 ambitious targets for responding to the threat of climate change have been set: limiting global temperature increase to “well below 2 °C […] and to pursue efforts to limit the temperature increase to 1.5 °C”. However, calculating the CO2 budget for 1.5 °C, it becomes clear that there is nearly no room left for future emissions. Scenarios suggest that negative emission technologies will play an even more important role for 1.5 °C than they already play for 2 °C. Especially against this background the feasibility of the target(s) is hotly debated, but this debate does not initiate the next steps that are urgently needed. Already the negotiations have featured the move from targets to implementation which is needed in the coming decade. Most importantly, there is an urgent need to develop and implement instruments that incentivize the rapid decarbonization. Moreover, it needs to be worked out how to link the climate and development agenda and prevent a buildup of coal power causing lock-in effects. Short term entry points into climate policy should now be in the focus instead of the fruitless debate on the feasibility of targets
Crossing the death valley to transfer environmental decision support systems to the water market

Environmental decision support systems (EDSSs) are attractive tools to cope with the complexity of environmental global challenges. Several thoughtful reviews have analyzed EDSSs to identify the key challenges and best practices for their development. One of the major criticisms is that a wide and generalized use of deployed EDSSs has not been observed. The paper briefly describes and compares four case studies of EDSSs applied to the water domain, where the key aspects involved in the initial conception and the use and transfer evolution that determine the final success or failure of these tools (i.e., market uptake) are identified. Those aspects that contribute to bridging the gap between the EDSS science and the EDSS market are highlighted in the manuscript. Experience suggests that the construction of a successful EDSS should focus significant efforts on crossing the death-valley toward a general use implementation by society (the market) rather than on development.The authors would like to thank the Catalan Water Agency (Agència Catalana de l’Aigua), Besòs River Basin Regional Administration\ud
(Consorci per la Defensa de la Conca del Riu Besòs), SISLtech, and Spanish Ministry of Science and Innovation for providing funding\ud
(CTM2012-38314-C02-01 and CTM2015-66892-R). LEQUIA, KEMLG, and\ud
ICRA were recognized as consolidated research groups by the Catalan\ud
Government under the codes 2014-SGR-1168, 2013-SGR-1304 and\ud
2014-SGR-291.Peer ReviewedPostprint (published version
The Mars Analysis Correction Data Assimilation (MACDA) dataset V1.0

The Mars Analysis Correction Data Assimilation (MACDA) dataset version 1.0 contains the reanalysis of fundamental atmospheric and surface variables for the planet Mars covering a period of about three Martian years (a Martian year is about 1.88 terrestrial years). This has been produced by data assimilation of observations from NASA's Mars Global Surveyor (MGS) spacecraft during its science mapping phase (February 1999–August 2004). In particular, we have used retrieved thermal profiles and total dust optical depths from the Thermal Emission Spectrometer (TES) on board MGS. Data have been assimilated into a Mars global climate model (MGCM) using the Analysis Correction scheme developed at the UK Meteorological Office. The MGCM used is the UK spectral version of the Laboratoire de Météorologie Dynamique (LMD, Paris, France) MGCM. MACDA is a joint project of the University of Oxford and The Open University in the UK
Implementation of a webGIS service platform for high mountain climate research: the SHARE GeoNetwork project

The implementation of a webGIS service platform dedicated to the management and sharing of climatological data acquired by\ud
high elevation stations is the core of the Station at High Altitude for Research on the Environment (SHARE) GeoNetwork project,\ud
promoted by the Ev-K2 CNR Committee. The web platform basically will provide three types of services: structured metadata\ud
archive, data and results from high-altitude environments research and projects; access to high-altitude Ev-K2 CNR stations and\ud
creation of a network of existing stations; dedicated webGIS for geo-referenced data collected during the research. High elevation\ud
environmental and territorial data and metadata are catalogued in a single integrated platform to get access to the information\ud
heritage of the SHARE project, using open-source tools: Geonetwork for the metadata catalogue and webGIS resources, and the\ud
open-source Weather and Water Database (WDB), developed by the Norwegian Meteorological Institute, for the database information\ud
system implementation. The information system is designed to have a main node, with the possibility to install relocated\ud
subsystems based on the same technology, named focal point of SHARE, which will contain metadata and data connected to the\ud
main node. In this study, a new structure of metadata for the description of the climatological stations is proposed and WDB\ud
adaptation and data preprocessing are described in detail, giving code and script samples
Sea surface temperature datasets for climate applications from Phase 1 of the European Space Agency Climate Change Initiative (SST CCI)

Sea surface temperature (SST) datasets have been generated from satellite observations for the period 1991–2010, intended for use in climate science applications. Attributes of the datasets specifically relevant to climate applications are: first, independence from in situ observations; second, effort to ensure homogeneity and stability through the time-series; third, context-specific uncertainty estimates attached to each SST value; and, fourth, provision of estimates of both skin SST (the fundamental measurement, relevant to air-sea fluxes) and SST at standard depth and local time (partly model mediated, enabling comparison with historical in situ datasets). These attributes in part reflect requirements solicited from climate data users prior to and during the project. Datasets consisting of SSTs on satellite swaths are derived from the Along-Track Scanning Radiometers (ATSRs) and Advanced Very High Resolution Radiometers (AVHRRs). These are then used as sole SST inputs to a daily, spatially complete, analysis SST product, with a latitude-longitude resolution of 0.05°C and good discrimination of ocean surface thermal features. A product user guide is available, linking to reports describing the datasets' algorithmic basis, validation results, format, uncertainty information and experimental use in trial climate applications. Future versions of the datasets will span at least 1982–2015, better addressing the need in many climate applications for stable records of global SST that are at least 30 years in length.Peer-reviewedPublisher Versio
A daily Azores–Iceland North Atlantic Oscillation index back to 1850

We present the construction of a continuous, daily (09:00 UTC), station-based (Azores–Iceland) North Atlantic Oscillation (NAO) Index back to 1871 which is extended back to 1850 with additional daily mean data. The constructed index more than doubles the length of previously existing, widely available, daily NAO time series. The index is created using entirely observational sea-level pressure (SLP) data from Iceland and 73.5% of observational SLP data from the Azores – the remainder being filled in via reanalysis (Twentieth Century Reanalysis Project and European Mean Sea Level Pressure) SLP data. Icelandic data are taken from the Southwest Iceland pressure series. We construct and document a new Ponta Delgada SLP time series based on recently digitized and newly available data that extend back to 1872. The Ponta Delgada time series is created by splicing together several fractured records (from Ponta Delgada, Lajes, and Santa Maria) and filling in the major gaps (pre-1872, 1888–1905, and 1940–1941) and occasional days (145) with reanalysis data. Further homogeneity corrections are applied to the Azores record, and the daily (09:00 UTC) NAO index is then calculated. The resulting index, with its extended temporal length and daily resolution, is the first reconstruction of daily NAO back into the 19th Century and therefore is useful for researchers across multiple disciplines
Missing data in spatiotemporal datasets: the UK rainfall chemistry network

Rainfall chemistry networks inevitably report some missing data, caused by contamination or loss of samples. However, there are no universally accepted rules about how such data, particularly from samples contaminated in the field, are identified and reported, leading to uncertainties in data usage by third parties, and possible incorrect inferences based on the reported data. This paper describes how the UK rainfall chemistry network data have been analysed for contamination, and how missing values can be estimated based on cross-correlations in time and space, using data from 20 sites over 26 years. The final flagged dataset is available through the CEH Environmental Information Data Centre (EIDC). Erroneous data values are identified through consideration of ion balance (internal consistency), and evidence of contamination by birds or windblown dust based on the reported chemical analysis. Overall data capture with the erroneous data excluded and no replacement of missing data was 86%, but with much smaller data capture at some sites in some years, to less than 30% in some cases. The use of estimated data to replace missing values resulted in an increase in overall data capture to 96%, with only one site having data capture less than 70% in an individual year, and all sites achieving a data capture of 88% or more over the full period. The implications of using the reported ‘official’ annual data, as opposed to the dataset with missing values replaced by estimates, are illustrated by consideration of the temporal trend in nitrate at one site, which shows twice the value in the ‘official’ reported annual data compared with the ‘estimated’ data, part of a consistent pattern across all sites. Use of the uncorrected ‘raw’ sample data leads to large errors
The International Surface Pressure Databank version 2

The International Surface Pressure Databank (ISPD) is the world's largest collection of global surface and sea-level pressure observations. It was developed by extracting observations from established international archives, through international cooperation with data recovery facilitated by the Atmospheric Circulation Reconstructions over the Earth (ACRE) initiative, and directly by contributing universities, organizations, and countries. The dataset period is currently 1768–2012 and consists of three data components: observations from land stations, marine observing systems, and tropical cyclone best track pressure reports. Version 2 of the ISPD (ISPDv2) was created to be observational input for the Twentieth Century Reanalysis Project (20CR) and contains the quality control and assimilation feedback metadata from the 20CR. Since then, it has been used for various general climate and weather studies, and an updated version 3 (ISPDv3) has been used in the ERA-20C reanalysis in connection with the European Reanalysis of Global Climate Observations project (ERA-CLIM). The focus of this paper is on the ISPDv2 and the inclusion of the 20CR feedback metadata. The Research Data Archive at the National Center for Atmospheric Research provides data collection and access for the ISPDv2, and will provide access to future versions