A first chronology for the East Greenland Ice-core Project (EGRIP) over the Holocene and last glacial termination

This paper provides the first chronology for the deep ice core from the East Greenland Ice-core Project (EGRIP) over the Holocene and the late last glacial period. We rely mainly on volcanic events and common peak patterns recorded by dielectric profiling (DEP) and electrical conductivity measurement (ECM) for the synchronization between the EGRIP, North Greenland Eemian Ice Drilling (NEEM) and North Greenland Ice Core Project (NGRIP) ice cores in Greenland. We transfer the annual-layer-counted Greenland Ice Core Chronology 2005 (GICC05) from the NGRIP core to the EGRIP ice core by means of 381 match points, typically spaced less than 50 years apart. The NEEM ice core has previously been dated in a similar way and is only included to support the match-point identification. We name our EGRIP timescale GICC05-EGRIP-1. Over the uppermost 1383.84 m, we establish a depth–age relationship dating back to 14 967 years b2k (years before the year 2000 CE). Tephra horizons provide an independent validation of our match points. In addition, we compare the ratio of the annual layer thickness between ice cores in between the match points to assess our results in view of the different ice-flow patterns and accumulation regimes of the different periods and geographical regions. For the next years, this initial timescale will be the basis for climatic reconstructions from EGRIP high-resolution proxy data sets, e.g. stable water isotopes, chemical impurity or dust records

Detection of ice core particles via deep neural networks

Insoluble particles in ice cores record signatures of past climate parameters like vegetation dynamics, volcanic activity, and aridity. For some of them, the analytical detection relies on intensive bench microscopy investigation and requires dedicated sample preparation steps. Both are laborious, require in-depth knowledge, and often restrict sampling strategies. To help overcome these limitations, we present a framework based on flow imaging microscopy coupled to a deep neural network for autonomous image classification of ice core particles. We train the network to classify seven commonly found classes, namely mineral dust, felsic and mafic (basaltic) volcanic ash grains (tephra), three species of pollen (Corylus avellana, Quercus robur, Quercus suber), and contamination particles that may be introduced onto the ice core surface during core handling operations. The trained network achieves 96.8 % classification accuracy at test time. We present the system's potential and its limitations with respect to the detection of mineral dust, pollen grains, and tephra shards, using both controlled materials and real ice core samples. The methodology requires little sample material, is non-destructive, fully reproducible, and does not require any sample preparation procedures. The presented framework can bolster research in the field by cutting down processing time, supporting human-operated microscopy, and further unlocking the paleoclimate potential of ice core records by providing the opportunity to identify an array of ice core particles. Suggestions for an improved system to be deployed within a continuous flow analysis workflow are also presented

TPL-2 negatively regulates interferon-β production in macrophages and myeloid dendritic cells

Stimulation of Toll-like receptors (TLRs) on macrophages and dendritic cells (DCs) by pathogen-derived products induces the production of cytokines, which play an important role in immune responses. Here, we investigated the role of the TPL-2 signaling pathway in TLR induction of interferon-β (IFN-β) and interleukin-10 (IL-10) in these cell types. It has previously been suggested that IFN-β and IL-10 are coordinately regulated after TLR stimulation. However, in the absence of TPL-2 signaling, lipopolysaccharide (TLR4) and CpG (TLR9) stimulation resulted in increased production of IFN-β while decreasing IL-10 production by both macrophages and myeloid DCs. In contrast, CpG induction of both IFN-α and IFN-β by plasmacytoid DCs was decreased in the absence of TPL-2, although extracellular signal-regulated kinase (ERK) activation was blocked. Extracellular signal-related kinase–dependent negative regulation of IFN-β in macrophages was IL-10–independent, required protein synthesis, and was recapitulated in TPL-2–deficient myeloid DCs by retroviral transduction of the ERK-dependent transcription factor c-fos

Magnitude, frequency and climate forcing of global volcanism during the last glacial period as seen in Greenland and Antarctic ice cores (60–9 ka)

Large volcanic eruptions occurring in the last glacial period can be detected by their accompanying sulfuric acid deposition in continuous ice cores. Here we employ continuous sulfate and sulfur records from three Greenland and three Antarctic ice cores to estimate the emission strength, the frequency and the climatic forcing of large volcanic eruptions that occurred during the second half of the last glacial period and the early Holocene, 60–9 kyr before 2000 CE (b2k). Over most of the investigated interval the ice cores are synchronized, making it possible to distinguish large eruptions with a global sulfate distribution from eruptions detectable in one hemisphere only. Due to limited data resolution and large variability in the sulfate background signal, particularly in the Greenland glacial climate, we only list Greenland sulfate depositions larger than 20 kg km−2 and Antarctic sulfate depositions larger than 10 kg km−2. With those restrictions, we identify 1113 volcanic eruptions in Greenland and 737 eruptions in Antarctica within the 51 kyr period – for which the sulfate deposition of 85 eruptions is found at both poles (bipolar eruptions). Based on the ratio of Greenland and Antarctic sulfate deposition, we estimate the latitudinal band of the bipolar eruptions and assess their approximate climatic forcing based on established methods. A total of 25 of the identified bipolar eruptions are larger than any volcanic eruption occurring in the last 2500 years, and 69 eruptions are estimated to have larger sulfur emission strengths than the Tambora, Indonesia, eruption (1815 CE). Throughout the investigated period, the frequency of volcanic eruptions is rather constant and comparable to that of recent times. During the deglacial period (16–9 ka b2k), however, there is a notable increase in the frequency of volcanic events recorded in Greenland and an obvious increase in the fraction of very large eruptions. For Antarctica, the deglacial period cannot be distinguished from other periods. This confirms the suggestion that the isostatic unloading of the Northern Hemisphere (NH) ice sheets may be related to the enhanced NH volcanic activity. Our ice-core-based volcanic sulfate records provide the atmospheric sulfate burden and estimates of climate forcing for further research on climate impact and understanding the mechanism of the Earth system

Psychosocial impact of undergoing prostate cancer screening for men with BRCA1 or BRCA2 mutations.

OBJECTIVES: To report the baseline results of a longitudinal psychosocial study that forms part of the IMPACT study, a multi-national investigation of targeted prostate cancer (PCa) screening among men with a known pathogenic germline mutation in the BRCA1 or BRCA2 genes. PARTICPANTS AND METHODS: Men enrolled in the IMPACT study were invited to complete a questionnaire at collaborating sites prior to each annual screening visit. The questionnaire included sociodemographic characteristics and the following measures: the Hospital Anxiety and Depression Scale (HADS), Impact of Event Scale (IES), 36-item short-form health survey (SF-36), Memorial Anxiety Scale for Prostate Cancer, Cancer Worry Scale-Revised, risk perception and knowledge. The results of the baseline questionnaire are presented. RESULTS: A total of 432 men completed questionnaires: 98 and 160 had mutations in BRCA1 and BRCA2 genes, respectively, and 174 were controls (familial mutation negative). Participants' perception of PCa risk was influenced by genetic status. Knowledge levels were high and unrelated to genetic status. Mean scores for the HADS and SF-36 were within reported general population norms and mean IES scores were within normal range. IES mean intrusion and avoidance scores were significantly higher in BRCA1/BRCA2 carriers than in controls and were higher in men with increased PCa risk perception. At the multivariate level, risk perception contributed more significantly to variance in IES scores than genetic status. CONCLUSION: This is the first study to report the psychosocial profile of men with BRCA1/BRCA2 mutations undergoing PCa screening. No clinically concerning levels of general or cancer-specific distress or poor quality of life were detected in the cohort as a whole. A small subset of participants reported higher levels of distress, suggesting the need for healthcare professionals offering PCa screening to identify these risk factors and offer additional information and support to men seeking PCa screening

Multiple novel prostate cancer susceptibility signals identified by fine-mapping of known risk loci among Europeans

Genome-wide association studies (GWAS) have identified numerous common prostate cancer (PrCa) susceptibility loci. We have fine-mapped 64 GWAS regions known at the conclusion of the iCOGS study using large-scale genotyping and imputation in 25 723 PrCa cases and 26 274 controls of European ancestry. We detected evidence for multiple independent signals at 16 regions, 12 of which contained additional newly identified significant associations. A single signal comprising a spectrum of correlated variation was observed at 39 regions; 35 of which are now described by a novel more significantly associated lead SNP, while the originally reported variant remained as the lead SNP only in 4 regions. We also confirmed two association signals in Europeans that had been previously reported only in East-Asian GWAS. Based on statistical evidence and linkage disequilibrium (LD) structure, we have curated and narrowed down the list of the most likely candidate causal variants for each region. Functional annotation using data from ENCODE filtered for PrCa cell lines and eQTL analysis demonstrated significant enrichment for overlap with bio-features within this set. By incorporating the novel risk variants identified here alongside the refined data for existing association signals, we estimate that these loci now explain ∼38.9% of the familial relative risk of PrCa, an 8.9% improvement over the previously reported GWAS tag SNPs. This suggests that a significant fraction of the heritability of PrCa may have been hidden during the discovery phase of GWAS, in particular due to the presence of multiple independent signals within the same regio

Common Breast Cancer Susceptibility Alleles and the Risk of Breast Cancer for BRCA1 and BRCA2 Mutation Carriers: Implications for Risk Prediction

The known breast cancer (BC) susceptibility polymorphisms in FGFR2, TNRC9/TOX3, MAP3K1,LSP1 and 2q35 confer increased risks of BC for BRCA1 or BRCA2 mutation carriers. We evaluated the associations of three additional SNPs, rs4973768 in SLC4A7/NEK10, rs6504950 in STXBP4/COX11 and rs10941679 at 5p12 and reanalyzed the previous associations using additional carriers in a sample of 12,525 BRCA1 and 7,409 BRCA2 carriers. Additionally, we investigated potential interactions between SNPs and assessed the implications for risk prediction. The minor alleles of rs4973768 and rs10941679 were associated with increased BC risk for BRCA2 carriers (per-allele Hazard Ratio (HR)=1.10, 95%CI:1.03-1.18, p=0.006 and HR=1.09, 95%CI:1.01-1.19, p=0.03, respectively). Neither SNP was associated with BC risk for BRCA1 carriers and rs6504950 was not associated with BC for either BRCA1 or BRCA2 carriers. Of the nine polymorphisms investigated, seven were associated with BC for BRCA2 carriers (FGFR2, TOX3, MAP3K1, LSP1, 2q35, SLC4A7, 5p12, p-values:7×10−11-0.03), but only TOX3 and 2q35 were associated with the risk for BRCA1 carriers (p=0.0049, 0.03 respectively). All risk associated polymorphisms appear to interact multiplicatively on BC risk for mutation carriers. Based on the joint genotype distribution of the seven risk associated SNPs in BRCA2 mutation carriers, the 5% of BRCA2 carriers at highest risk (i.e. between 95th and 100th percentiles) were predicted to have a probability between 80% and 96% of developing BC by age 80, compared with 42-50% for the 5% of carriers at lowest risk. Our findings indicated that these risk differences may be sufficient to influence the clinical management of mutation carriers

TPL2-mediated activation of ERK1 and ERK2 regulates the processing of pre-TNF alpha in LPS-stimulated macrophages

Activation of the TPL2-MKK1/2-ERK1/2 signalling pathway is essential for lipopolysaccharide (LPS)-stimulated production of TNF alpha in macrophages. Here, we demonstrate that, unexpectedly, TPL2-deficient or MKK1-inhibited macrophages produce near normal levels of pre-TNF alpha when TLR2, TLR4 and TLR6 are activated by their respective agonists, but fail to secrete TNF alpha. We show that LPS stimulates the appearance of pre-TNF alpha at the cell surface and that this is prevented by inhibition of MAPK kinases 1 and 2 (MKK1/2) or in TPL2-deficient macrophages. However, the transport of pre-TNF alpha from the Golgi to the plasma membrane is unaffected by inhibition of the TPL2-MKK1/2-ERK1/2 pathway. Finally, we show that TACE, the protease that cleaves pre-TNF alpha to secreted TNF alpha, is phosphorylated by ERK1 and ERK2 (ERK1/2) at Thr735 in LPS-stimulated macrophages. Therefore, although TACE activity per se is not required for the LPS-stimulated cell surface expression of pre-TNF alpha, the phosphorylation of this protease might contribute to, or be required for, the cell surface expression of the pre-TNF alpha-TACE complex.</p

Autonomous detection of ice core particles via deep learning

The presence of insoluble particles in ice cores carry fingerprints of multiple aspects of Earths past climate. Mineral dust records allow the investigation of dust source emissions, atmospheric transport and wind strength variability. Volcanic ash (cryptotephra) particles are emitted during eruptions and deposited as individual layers in the ice. Their detection and characterization is fundamental for reconstructions of past volcanism and as a method to date and synchronize different sedimentary records, such as marine or terrestrial cores. Pollen grains and biological matter are often found in alpine glacial ice records at mid latitudes and are proxies for ecosystem changes and vegetation dynamics. To date, the analytical detection of these particles is often based on intensive manual microscopic investigations and require multiple laborious and often destructive extraction steps. Here, we present an analytical framework that can overcome these limitations, based on flow imaging microscopy coupled to deep learning neural networks for the autonomous detection and quantification of dust, volcanic tephra and pollen grain particles. The network architecture structure joins a Resnet-backbone Convolutional Neural Network and a Fully Connected Net and is trained in supervised mode. We present the developed methodology and the results applied to real ice samples. The network performs particle image classification, thus allowing the simultaneous calculation of particle number concentrations of all classes. Using information on particle size, the framework also allows the quantification of mass concentrations. The network can efficiently identify dust particles with a detection limit of 10 ppb and can thus be deployed as a dust detector in ice core analyses. The network is also able to identify tephra shards, based on trials with known volcanic horizons in the Greenlandic GRIP ice core and is therefore suitable to produce time series of past volcanic activity from ice core records. The analytical routine is non-destructive and can operate in continuous mode, thus applicable in ice core continuous-flow-analysis setups. We believe the proposed framework provides an innovative tool to support human experts across multiple research areas of ice core science