Comprehensive single-cell genome analysis at nucleotide resolution using the PTA Analysis Toolbox

Detection of somatic mutations in single cells has been severely hampered by technical limitations of whole-genome amplification. Novel technologies including primary template-directed amplification (PTA) significantly improved the accuracy of single-cell whole-genome sequencing (WGS) but still generate hundreds of artifacts per amplification reaction. We developed a comprehensive bioinformatic workflow, called the PTA Analysis Toolbox (PTATO), to accurately detect single base substitutions, insertions-deletions (indels), and structural variants in PTA-based WGS data. PTATO includes a machine learning approach and filtering based on recurrence to distinguish PTA artifacts from true mutations with high sensitivity (up to 90%), outperforming existing bioinformatic approaches. Using PTATO, we demonstrate that hematopoietic stem cells of patients with Fanconi anemia, which cannot be analyzed using regular WGS, have normal somatic single base substitution burdens but increased numbers of deletions. Our results show that PTATO enables studying somatic mutagenesis in the genomes of single cells with unprecedented sensitivity and accuracy.</p

Non-founder human capital and the long-run growth and survival of high-tech ventures

This paper considers the impact of non-founder human capital on high-tech firms' long-run growth and survival. Drawing upon threshold theory, we explore how lack of access to complementary skills at different points in the life course impacts founders' thresholds for exit. We examine these factors using a unique longitudinal dataset tracking the performance and survival of a sample of UK high-tech firms over thirteen years as the firms move from youth into maturity. We find that firms that survive but do not grow are characterized by difficulty in accessing complementary managerial skills in youth, while firms that grow but subsequently exit are characterized by shortfalls of specialized complementary skills during adolescence. Firms that grow and survive do not report skills shortfalls. We discuss the implications of these resource constraints for entrepreneurs’ decisions to persist or exit through the life course

Comprehensive single-cell genome analysis at nucleotide resolution using the PTA Analysis Toolbox

Detection of somatic mutations in single cells has been severely hampered by technical limitations of whole-genome amplification. Novel technologies including primary template-directed amplification (PTA) significantly improved the accuracy of single-cell whole-genome sequencing (WGS) but still generate hundreds of artifacts per amplification reaction. We developed a comprehensive bioinformatic workflow, called the PTA Analysis Toolbox (PTATO), to accurately detect single base substitutions, insertions-deletions (indels), and structural variants in PTA-based WGS data. PTATO includes a machine learning approach and filtering based on recurrence to distinguish PTA artifacts from true mutations with high sensitivity (up to 90%), outperforming existing bioinformatic approaches. Using PTATO, we demonstrate that hematopoietic stem cells of patients with Fanconi anemia, which cannot be analyzed using regular WGS, have normal somatic single base substitution burdens but increased numbers of deletions. Our results show that PTATO enables studying somatic mutagenesis in the genomes of single cells with unprecedented sensitivity and accuracy

Detection and localization of early- and late-stage cancers using platelet RNA

Cancer patients benefit from early tumor detection since treatment outcomes are more favorable for less advanced cancers. Platelets are involved in cancer progression and are considered a promising biosource for cancer detection, as they alter their RNA content upon local and systemic cues. We show that tumor-educated platelet (TEP) RNA-based blood tests enable the detection of 18 cancer types. With 99% specificity in asymptomatic controls, thromboSeq correctly detected the presence of cancer in two-thirds of 1,096 blood samples from stage I–IV cancer patients and in half of 352 stage I–III tumors. Symptomatic controls, including inflammatory and cardiovascular diseases, and benign tumors had increased false-positive test results with an average specificity of 78%. Moreover, thromboSeq determined the tumor site of origin in five different tumor types correctly in over 80% of the cancer patients. These results highlight the potential properties of TEP-derived RNA panels to supplement current approaches for blood-based cancer screening

Emission factors for heavy metals from diesel and petrol used in European vehicles

Heavy metals constitute an important group of persistent toxic pollutants occurring in ambient air and other media. One of the suspected sources of these metals in the atmosphere is combustion of transport fuels in road vehicles. However estimates of the emissions of these metals from road vehicles as reported in national emission inventories show a very high variability in emission factors used. This paper provides high quality data on concentrations of heavy metals in fuels and derives default emission factors from these. The paper discusses these values against the emission estimates presently reported by the Parties to the LRTAP Convention. The measured concentrations of heavy metals in petrol and diesel fuel show a high variability between different samples taken at gas stations throughout Europe. Metal concentrations in road transport fuels vary over two orders of magnitude, but all remain in the ppb region (a few tenths of a ppb to a few hundred ppb for all metals). The frequency distributions of the measurements could be approximated by lognormal distributions. We could not detect a significant difference between samples from different countries. The fuel based emission factors as derived in this study are compared with those related to lubricant use as published by Winther and Slentø (2010). For most HMs studied here, this would lead to an two to fourfold increase of the tailpipe emissions as derived from the fuel concentrations. The emission factors, including 95 percent confidence intervals were derived from a statistical analysis of the survey data. The proposed emission factors were generally lower than previously published emission factors. National emissions of heavy metals from vehicle exhaust, estimated in this study therefore are in many cases considerably lower than those reported by the countries for this source

Anthropogenic Rare Earth Element in rivers: Gadolinium and lanthanum. Partitioning between the dissolved and particulate phases in the Rhine River and spatial propagation through the Rhine-Meuse Delta (the Netherlands)

International audienceIn this study, we report for the first time lanthanum and gadolinium anomalies at the catchment scale (Rhine-Meuse River system) together with the partitioning of their anthropogenic contents between the dissolved and the particulate phases. We compare the dissolved and total REE patterns of samples taken at 9 locations in the Rhine Branches including Lobith (situated at the German Dutch border where the Rhine is not yet divided in three Branches), in surface water fed by the Rhine Branches (canals and lake IJsselmeer and Ketelmeer) and 3 locations where the water is derived from the river Meuse (originating from Belgium and France).We demonstrate that the anthropogenic input of lanthanum in the German part of the Rhine River identified by Kulaksiz and Bau (2011) can be traced in the complex Rhine-Meuse Delta up to the North Sea. In the Dutch Branches of the Rhine River, in contrast to the German part of the Rhine River, the anthropogenic lanthanum (La-ANTHRO) is mainly present in the particulate phase (SPM) and not in the dissolved phase (defined as the <0.45 mu m fraction). In the Meuse River no anthropogenic lanthanum was found. The amount of La-ANTHRO transported by the Rhine River at the Lobith station (German-Dutch border) varies from 2008 to 2010 between 3.7 and 5.2 tons/y in the dissolved phase, and between 28.8 and 37.4 tons/y in the particulate phase. However, a big discrepancy is evidenced when we compare the La-ANTHRO load calculated on bases of the total water samples with the La-ANTHRO load calculated as the sum of the particulate and dissolved load: the total La-ANTHRO load is roughly 2 times larger than the La-ANTHRO load calculated as the sum of the dissolved and particulate La-ANTHRO load. The difference between the two calculated fluxes is most likely caused by not sampling the finest fraction of the particulate pool in the SPM samples with an overflow centrifuge.The anthropogenic gadolinium identified by high gadolinium anomalies in the REE patterns originates from numerous point sources (waste water treatment plant effluents) and can thus be considered as diffuse pollution when compared to anthropogenic lanthanum clearly resulting from a single source. The amount of anthropogenic gadolinium measured in the dissolved phase (main carrier of Gd) increases or decreases along the Rhine and Meuse Rivers depending whether or not the mixing water contains anthropogenic gadolinium, i.e. receives waste water effluents

Oceanic Exchanges: Transnational Textual Migration And Viral Culture

Abstract of paper 0234 presented at the Digital Humanities Conference 2019 (DH2019), Utrecht , the Netherlands 9-12 July, 2019