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We present a measurement of inclusive J/ψ production in p-Pb collisions at sNN−−−√ = 5.02 TeV as a function of the centrality of the collision, as estimated from the energy deposited in the Zero Degree Calorimeters. The measurement is performed with the ALICE detector down to zero transverse momentum, pT, in the backward (−4.46<ycms<−2.96) and forward (2.03<ycms<3.53) rapidity intervals in the dimuon decay channel and in the mid-rapidity region (−1.37<ycms<0.43) in the dielectron decay channel. The backward and forward rapidity intervals correspond to the Pb-going and p-going direction, respectively. The pT-differential J/ψ production cross section at backward and forward rapidity is measured for several centrality classes, together with the corresponding average pT and p2T values. The nuclear modification factor, QpPb, is presented as a function of centrality for the three rapidity intervals, and, additionally, at backward and forward rapidity, as a function of pT for several centrality classes. At mid- and forward rapidity, the J/ψ yield is suppressed up to 40% compared to that in pp interactions scaled by the number of binary collisions. The degree of suppression increases towards central p-Pb collisions at forward rapidity, and with decreasing pT of the J/ψ. At backward rapidity, the QpPb is compatible with unity within the total uncertainties, with an increasing trend from peripheral to central p-Pb collisions.
Transverse momentum (pT) spectra of pions, kaons, and protons up to pT=20 GeV/c have been measured in Pb-Pb collisions at sNN−−−√=2.76 TeV using the ALICE detector for six different centrality classes covering 0-80%. The proton-to-pion and the kaon-to-pion ratios both show a distinct peak at pT≈3 GeV/c in central Pb-Pb collisions that decreases towards more peripheral collisions. For pT>10 GeV/c, the nuclear modification factor is found to be the same for all three particle species in each centrality interval within systematic uncertainties of 10-20%. This suggests there is no direct interplay between the energy loss in the medium and the particle species composition in the hard core of the quenched jet. For pT<10 GeV/c, the data provide important constraints for models aimed at describing the transition from soft to hard physics.
Transverse momentum (pT) spectra of pions, kaons, and protons up to pT=20 GeV/c have been measured in Pb-Pb collisions at sNN−−−√=2.76 TeV using the ALICE detector for six different centrality classes covering 0-80%. The proton-to-pion and the kaon-to-pion ratios both show a distinct peak at pT≈3 GeV/c in central Pb-Pb collisions that decreases towards more peripheral collisions. For pT>10 GeV/c, the nuclear modification factor is found to be the same for all three particle species in each centrality interval within systematic uncertainties of 10-20%. This suggests there is no direct interplay between the energy loss in the medium and the particle species composition in the hard core of the quenched jet. For pT<10 GeV/c, the data provide important constraints for models aimed at describing the transition from soft to hard physics.
Background: Alzheimer's disease is a common debilitating dementia with known heritability, for which 20 late onset susceptibility loci have been identified, but more remain to be discovered. This study sought to identify new susceptibility genes, using an alternative gene-wide analytical approach which tests for patterns of association within genes, in the powerful genome-wide association dataset of the International Genomics of Alzheimer's Project Consortium, comprising over 7 m genotypes from 25,580 Alzheimer's cases and 48,466 controls.
Principal findings: In addition to earlier reported genes, we detected genome-wide significant loci on chromosomes 8 (TP53INP1, p = 1.4×10−6) and 14 (IGHV1-67 p = 7.9×10−8) which indexed novel susceptibility loci.
Significance: The additional genes identified in this study, have an array of functions previously implicated in Alzheimer's disease, including aspects of energy metabolism, protein degradation and the immune system and add further weight to these pathways as potential therapeutic targets in Alzheimer's disease.
Direct photon production at mid-rapidity in Pb–Pb collisions at √sNN=2.76 TeV was studied in the transverse momentum range 0.9<pT<14 GeV/c. Photons were detected with the highly segmented electromagnetic calorimeter PHOS and via conversions in the ALICE detector material with the e+e− pair reconstructed in the central tracking system. The results of the two methods were combined and direct photon spectra were measured for the 0–20%, 20–40%, and 40–80% centrality classes. For all three classes, agreement was found with perturbative QCD calculations for pT≳5 GeV/c. Direct photon spectra down to pT≈1 GeV/c could be extracted for the 20–40% and 0–20% centrality classes. The significance of the direct photon signal for 0.9<pT<2.1 GeV/c is 2.6σ for the 0–20% class. The spectrum in this pT range and centrality class can be described by an exponential with an inverse slope parameter of (297±12stat±41syst) MeV. State-of-the-art models for photon production in heavy-ion collisions agree with the data within uncertainties.
Unique features of a global human ectoparasite identified through sequencing of the bed bug genome
(2016)
The bed bug, Cimex lectularius, has re-established itself as a ubiquitous human ectoparasite throughout much of the world during the past two decades. This global resurgence is likely linked to increased international travel and commerce in addition to widespread insecticide resistance. Analyses of the C. lectularius sequenced genome (650 Mb) and 14,220 predicted protein-coding genes provide a comprehensive representation of genes that are linked to traumatic insemination, a reduced chemosensory repertoire of genes related to obligate hematophagy, host–symbiont interactions, and several mechanisms of insecticide resistance. In addition, we document the presence of multiple putative lateral gene transfer events. Genome sequencing and annotation establish a solid foundation for future research on mechanisms of insecticide resistance, human–bed bug and symbiont–bed bug associations, and unique features of bed bug biology that contribute to the unprecedented success of C. lectularius as a human ectoparasite.
Non-standard errors
(2021)
In statistics, samples are drawn from a population in a data-generating process (DGP). Standard errors measure the uncertainty in sample estimates of population parameters. In science, evidence is generated to test hypotheses in an evidence-generating process (EGP). We claim that EGP variation across researchers adds uncertainty: non-standard errors. To study them, we let 164 teams test six hypotheses on the same sample. We find that non-standard errors are sizeable, on par with standard errors. Their size (i) co-varies only weakly with team merits, reproducibility, or peer rating, (ii) declines significantly after peer-feedback, and (iii) is underestimated by participants.
In this paper we test previous claims concerning the universality of patterns of polysemy and semantic change in perception verbs. Implicit in such claims are two elements: firstly, that the sharing of two related senses A and B by a given form is cross-linguistically widespread, and matched by a complementary lack of some rival polysemy, and secondly that the explanation for the ubiquity of a given pattern of polysemy is ultimately rooted in our shared human cognitive make-up. However, in comparison to the vigorous testing of claimed universals that has occurred in phonology, syntax and even basic lexical meaning, there has been little attempt to test proposed universals of semantic extension against a detailed areal study of non-European languages. To address this problem we examine a broad range of Australian languages to evaluate two hypothesized universals: one by Viberg (1984), concerning patterns of semantic extension across sensory modalities within the domain of perception verbs (i .e. intra-field extensions), and the other by Sweetser (1990), concerning the mapping of perception to cognition (i.e. trans-field extensions). Testing against the Australian data allows one claimed universal to survive, but demolishes the other, even though both assign primacy to vision among the senses.
Acesta excavata (Fabricius, 1779) is a slow growing bivalve from the Limidae family and is often found associated with cold-water coral reefs along the European continental margin. Here we present the compositional variability of frequently used proxy elemental ratios (Mg/ Ca, Sr/Ca, Na/Ca) measured by laser-ablation mass spectrometry (LA-ICP-MS) and com- pare it to in-situ recorded instrumental seawater parameters such as temperature and salin- ity. Shell Mg/Ca measured in the fibrous calcitic shell section was overall not correlated with seawater temperature or salinity; however, some samples show significant correlations with temperature with a sensitivity that was found to be unusually high in comparison to other marine organisms. Mg/Ca and Sr/Ca measured in the fibrous calcitic shell section display significant negative correlations with the linear extension rate of the shell, which indicates strong vital effects in these bivalves. Multiple linear regression analysis indicates that up to 79% of elemental variability is explicable with temperature and salinity as independent pre- dictor values. Yet, the overall results clearly show that the application of Element/Ca (E/Ca) ratios in these bivalves to reconstruct past changes in temperature and salinity is likely to be complicated due to strong vital effects and the effects of organic material embedded in the shell. Therefore, we suggest to apply additional techniques, such as clumped isotopes, in order to exactly determine and quantify the underlying vital effects and possibly account for these. We found differences in the chemical composition between the two calcitic shell lay- ers that are possibly explainable through differences of the crystal morphology. Sr/Ca ratios also appear to be partly controlled by the amount of magnesium, because the small magne- sium ions bend the crystal lattice which increases the space for strontium incorporation. Oxi- dative cleaning with H2O2 did not significantly change the Mg/Ca and Sr/Ca composition of the shell. Na/Ca ratios decreased after the oxidative cleaning, which is most likely a leaching effect and not caused by the removal of organic matter.
Abstract:
The mid Miocene represents an important target for paleoclimatic study because the atmospheric CO2 concentration ranged from near modern values to ∼800 ppm, while a large, dynamic Antarctic ice sheet was likely to have been present throughout much of this interval. In this special issue, Modestou et al. (2020) (doi.org/10.1029/2020PA003927) reconstruct deep ocean warmth based on the clumped isotopic composition of benthic foraminifera, a technique that allows the ice volume and thermal components of the benthic oxygen isotope stack to be separated. These data reveal a very warm deep ocean while simultaneously suggesting that continental ice volume may, at times, have been greater than today. Here, I review these results in the context of recent developments in geochemical proxies and ice sheet modeling, and explore how the presence of a large Miocene ice sheet could be reconciled with CO2 at least as high as present. More broadly, I argue that many of the 'paradoxes' that pepper the paleoclimate literature result as much from our imperfect understanding of the proxies, as from our understanding of the climate system. Robust proxies with a well-understood mechanistic basis, as employed by Modestou et al. (2020), as well as advances in model-data comparability usher in a new era of palaeoclimate research; an exciting future of untangling Earth's myriad past climate states awaits.
Plain Language Summary:
Reconstructing climate variation in Earth's geologic past informs us of the broad features of warm climates, which is relevant to preparing for climate change over the coming centuries. Moreover, these data can be compared to state-of-the-art climate models, which provides a test of the degree to which our models can reproduce warm climate states. A paper recently published in this journal applies a new method in order to reconstruct the temperature of the deep ocean in the middle Miocene (between 17 and 12 million years ago), when the atmospheric CO2 concentration was naturally similar to or higher than it is today. Coupled with decades of previous study, these exciting results depict an unfamiliar world characterized by a warm deep ocean, and yet a large ice sheet was present on Antarctica. Both models and data agree that the Antarctic ice sheet in the Miocene was highly responsive to changes in the atmospheric CO2 concentration, a clear cause of concern in the context of ongoing anthropogenic climate change.
Hyrrokkin sarcophaga is a parasitic foraminifera that is commonly found in cold-water coral reefs where it infests the file clam Acesta excavata and the scleractinian coral Desmophyllum pertusum (formerly known as Lophelia pertusa). Here, we present measurements of the trace element and isotopic composition of these parasitic foraminifera, analyzed by inductively coupled optical emission spectrometry (ICP-OES), electron probe microanalysis (EPMA) and mass spectrometry (gas-source MS and inductively-coupled-plasma MS). Our results reveal that the geochemical signature of H. sarcophaga depends on the host organism it infests. Sr / Ca ratios are 1.1 mmol mol−1 higher in H. sarcophaga that infest D. pertusum, which could be an indication that dissolved host carbonate material is utilized in shell calcification, given that the aragonite of D. pertusum has a naturally higher Sr concentration compared to the calcite of A. excavata. Similarly, we measure 3.1 ‰ lower δ13C and 0.25 ‰ lower δ18O values in H. sarcophaga that lived on D. pertusum, which might be caused by the direct uptake of the host's carbonate material with a more negative isotopic composition or different pH regimes in these foraminifera (pH can exert a control on the extent of CO2 hydration/hydroxylation) due to the uptake of body fluids of the host. We also observe higher Mn / Ca ratios in foraminifera that lived on A. excavata but did not penetrate the host shell compared to specimen that penetrated the shell, which could be interpreted as a change in food source, changes in the calcification rate, Rayleigh fractionation or changing oxygen conditions. While our measurements provide an interesting insight into the calcification process of this unusual foraminifera, these data also indicate that the geochemistry of this parasitic foraminifera is unlikely to be a reliable indicator of paleoenvironmental conditions using Sr / Ca, Mn / Ca, δ18O or δ13C unless the host organism is known and its geochemical composition can be accounted for.
A quantitative analysis of any environment older than the instrumental record relies on proxies. Uncertainties associated with proxy reconstructions are often underestimated, which can lead to artificial conflict between different proxies, and between data and models. In this paper, using ordinary least squares linear regression as a common example, we describe a simple, robust and generalizable method for quantifying uncertainty in proxy reconstructions. We highlight the primary controls on the magnitude of uncertainty, and compare this simple estimate to equivalent estimates from Bayesian, nonparametric and fiducial statistical frameworks. We discuss when it may be possible to reduce uncertainties, and conclude that the unexplained variance in the calibration must always feature in the uncertainty in the reconstruction. This directs future research toward explaining as much of the variance in the calibration data as possible. We also advocate for a “data-forward” approach, that clearly decouples the presentation of proxy data from plausible environmental inferences.
Hyrrokkin sarcophaga is a parasitic foraminifer that is commonly found in cold-water coral reefs where it infests the file clam Acesta excavata and the scleractinian coral Lophelia pertusa. Here, we present measurements of the elemental and isotopic composition of this parasitic foraminifer for the first time, analyzed by inductively coupled optical emission spectrometry (ICP-OES), electron probe micro analysis (EPMA) and mass spectrometry (MS). Our results reveal that the geochemical signature of H. sarcophaga depends on the host organism it infests. Sr/Ca ratios are 1.1 mmol mol-1 higher in H. sarcophaga that infest L. pertusa, which could be an indication that dissolved host carbonate material is utilised in shell calcification, given that the aragonite of L. pertusa has a naturally higher Sr concentration compared to the calcite of A. excavata.Similarly, we measure 3.1 ‰ lower δ13C and 0.25 ‰ lower δ18O values in H. sarcophaga that lived on20 L. pertusa, which might be caused by the direct uptake of the host’s carbonate material with a more negative isotopic composition or different pH regimes in these foraminifera (pH can exert a control on the extent of CO2 hydration/hydroxylation) due to the uptake of body fluids of the host. We also observe higher Mn/Ca ratios in foraminifers that lived on A. excavata but did not penetrate the host shell compared to specimen that penetrated the shell, which could be interpreted as a change in food source, changes in the calcification rate, Rayleigh fractionation or changing oxygen conditions. While our measurements provide an interesting insight into the calcification process of this unusual foraminifer, these data also indicate that the geochemistry of this parasitic foraminifer is unlikely to be a reliable indicator of paleoenvironmental conditions using Sr/Ca, Mn/Ca, δ18O or δ13C unless the host organism is known and its geochemical composition can be accounted for.
Here we present a comprehensive attempt to correlate aragonitic Na∕Ca ratios from Desmophyllum pertusum (formerly known as Lophelia pertusa), Madrepora oculata and a caryophylliid cold-water coral (CWC) species with different seawater parameters such as temperature, salinity and pH. Living CWC specimens were collected from 16 different locations and analyzed for their Na∕Ca ratios using solution-based inductively coupled plasma-optical emission spectrometry (ICP-OES) measurements.
The results reveal no apparent correlation with salinity (30.1–40.57 g kg−1) but a significant inverse correlation with temperature (−0.31±0.04 mmolmol−1∘C−1). Other marine aragonitic organisms such as Mytilus edulis (inner aragonitic shell portion) and Porites sp. exhibit similar results highlighting the consistency of the calculated CWC regressions. Corresponding Na∕Mg ratios show a similar temperature sensitivity to Na∕Ca ratios, but the combination of two ratios appears to reduce the impact of vital effects and domain-dependent geochemical variation. The high degree of scatter and elemental heterogeneities between the different skeletal features in both Na∕Ca and Na∕Mg, however, limit the use of these ratios as a proxy and/or make a high number of samples necessary. Additionally, we explore two models to explain the observed temperature sensitivity of Na∕Ca ratios for an open and semi-enclosed calcifying space based on temperature-sensitive Na- and Ca-pumping enzymes and transport proteins that change the composition of the calcifying fluid and consequently the skeletal Na∕Ca ratio.
Here we present a comprehensive attempt to correlate aragonitic Na / Ca ratios from Lophelia pertusa, Madrepora oculata and a caryophylliid cold-water coral (CWC) species with different seawater parameters such as temperature, salinity and pH. Living CWC specimens were collected from 16 different locations and analyzed for their Na / Ca content using solution-based inductively coupled plasma-optical emission spectrometry (ICP-OES) measurements. The results reveal no apparent correlation with salinity (30.1–40.57 g/kg) but a significant inverse correlation with temperature (−0.31 mmol/mol/°C). Other marine aragonitic organisms such as Mytilus edulis (inner aragonitic shell portion) and Porites sp. exhibit similar results highlighting the consistency of the calculated CWC regressions. Corresponding Na / Mg ratios show a similar temperature sensitivity to Na / Ca ratios, but the combination of two ratios appear to reduce the impact of vital effects and domain-dependent geochemical variation. The high degree of scatter and elemental heterogeneities between the different skeletal features in both Na / Ca and Na / Mg however limit the use of these ratios as a proxy and/or make a high number of samples necessary. Additionally, we explore two models to explain the observed temperature sensitivity of Na / Ca ratios for an open and semi-enclosed calcifying space based on temperature sensitive Na and Ca pumping enzymes and transport proteins that change the composition of the calcifying fluid and consequently the skeletal Na / Ca ratio.
Rationale: Potassium (K) is a major component of several silicate minerals and seawater, and, therefore, constraining past changes in the potassium cycle is a promising way of tracing large-scale geological processes on Earth. However, [K] measurement using inductively coupled plasma mass spectrometry (ICP-MS) is challenging due to an ArH+ interference, which may be of a similar magnitude to the K+ ion beam in samples with <0.1% m/m [K].
Methods: In this work, we investigated the effect of the ArH+ interference on K/Ca data quality by comparing results from laser-ablation (LA)-ICP-MS measured in medium and high mass resolution modes and validating our LA results via solution ICP-optical emission spectroscopy (OES) and solution ICP-MS measurements. To do so, we used a wide range of geological reference materials, with a particular focus on marine carbonates, which are potential archives of past changes in the K cycle but are typically characterised by [K] < 200 μg/g. In addition, we examine the degree to which trace-element data quality is driven by downhole fractionation during LA-ICP-MS measurements.
Results: Our results show that medium mass resolution (MR) mode is sufficiently capable of minimising the effect of the ArH+ interference on K+. However, the rate of downhole fractionation for Na and K varies between different samples as a result of their differing bulk composition, resulting in matrix-specific inaccuracy. We show how this can be accounted for via downhole fractionation corrections, resulting in an accuracy of better than 1% and a long-term reproducibility (intermediate precision) of <6% (relative standard deviation) in JCp-1NP using LA-ICP-MS in MR mode.
Conclusion: Our [K] measurement protocol is demonstrably precise and accurate and applicable to a wide range of materials. The measurement of K/Ca in relatively low-[K] marine carbonates is presented here as a key example of a new application opened up by these advances.
Non-matrix-matched calibration of laser ablation ICPMS (trace/major) element data is a common quantification strategy. However, LA sampling is associated with downhole elemental fractionation, potentially causing inaccuracies if the magnitude of fractionation between the sample and reference material (RM) differs. Here, we estimate fractionation factors (FFs) for different elements (El) in a range of RMs relative to NIST SRM610/612 (FFEl/Ca-NIST) and evaluate element-specific corrections for downhole fractionation using these measured FFEl/Ca-NIST. Significantly different mean El/Ca values were observed before and after correction, particularly for the alkali elements (all RMs), and B, Fe, and Zn (some RMs), notably improving accuracy, especially for the alkali elements. In cases where this methodology does not result in an accuracy improvement, this may help identify underlying issues in reported/reference values for RMs, given that this phenomenon should be accounted for. Overall, we recommend considering routine assessment of FFs and applying a FF correction to enhance data quality.
DNA methylation profiles of aggressive behavior may capture lifetime cumulative effects of genetic, stochastic, and environmental influences associated with aggression. Here, we report the first large meta-analysis of epigenome-wide association studies (EWAS) of aggressive behavior (N = 15,324 participants). In peripheral blood samples of 14,434 participants from 18 cohorts with mean ages ranging from 7 to 68 years, 13 methylation sites were significantly associated with aggression (alpha = 1.2 × 10−7; Bonferroni correction). In cord blood samples of 2425 children from five cohorts with aggression assessed at mean ages ranging from 4 to 7 years, 83% of these sites showed the same direction of association with childhood aggression (r = 0.74, p = 0.006) but no epigenome-wide significant sites were found. Top-sites (48 at a false discovery rate of 5% in the peripheral blood meta-analysis or in a combined meta-analysis of peripheral blood and cord blood) have been associated with chemical exposures, smoking, cognition, metabolic traits, and genetic variation (mQTLs). Three genes whose expression levels were associated with top-sites were previously linked to schizophrenia and general risk tolerance. At six CpGs, DNA methylation variation in blood mirrors variation in the brain. On average 44% (range = 3–82%) of the aggression–methylation association was explained by current and former smoking and BMI. These findings point at loci that are sensitive to chemical exposures with potential implications for neuronal functions. We hope these results to be a starting point for studies leading to applications as peripheral biomarkers and to reveal causal relationships with aggression and related traits.