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1.	Ahmad, Shahzad, et al. (författare) CDH6 and HAGH protein levels in plasma associate with Alzheimer’s disease in APOE ε4 carriers 2020 Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 10:1 Tidskriftsartikel (refereegranskat)abstract Many Alzheimer’s disease (AD) genes including Apolipoprotein E (APOE) are found to be expressed in blood-derived macrophages and thus may alter blood protein levels. We measured 91 neuro-proteins in plasma from 316 participants of the Rotterdam Study (incident AD = 161) using Proximity Extension Ligation assay. We studied the association of plasma proteins with AD in the overall sample and stratified by APOE. Findings from the Rotterdam study were replicated in 186 AD patients of the BioFINDER study. We further evaluated the correlation of these protein biomarkers with total tau (t-tau), phosphorylated tau (p-tau) and amyloid-beta (Aβ) 42 levels in cerebrospinal fluid (CSF) in the Amsterdam Dementia Cohort (N = 441). Finally, we conducted a genome-wide association study (GWAS) to identify the genetic variants determining the blood levels of AD-associated proteins. Plasma levels of the proteins, CDH6 (β = 0.638, P = 3.33 × 10−4) and HAGH (β = 0.481, P = 7.20 × 10−4), were significantly elevated in APOE ε4 carrier AD patients. The findings in the Rotterdam Study were replicated in the BioFINDER study for both CDH6 (β = 1.365, P = 3.97 × 10−3) and HAGH proteins (β = 0.506, P = 9.31 × 10−7) when comparing cases and controls in APOE ε4 carriers. In the CSF, CDH6 levels were positively correlated with t-tau and p-tau in the total sample as well as in APOE ε4 stratum (P < 1 × 10−3). The HAGH protein was not detected in CSF. GWAS of plasma CDH6 protein levels showed significant association with a cis-regulatory locus (rs111283466, P = 1.92 × 10−9). CDH6 protein is implicated in cell adhesion and synaptogenesis while HAGH protein is related to the oxidative stress pathway. Our findings suggest that these pathways may be altered during presymptomatic AD and that CDH6 and HAGH may be new blood-based biomarkers.
2.	Householder, John Ethan, et al. (författare) One sixth of Amazonian tree diversity is dependent on river floodplains 2024 Ingår i: NATURE ECOLOGY & EVOLUTION. - 2397-334X. Tidskriftsartikel (refereegranskat)abstract Amazonia's floodplain system is the largest and most biodiverse on Earth. Although forests are crucial to the ecological integrity of floodplains, our understanding of their species composition and how this may differ from surrounding forest types is still far too limited, particularly as changing inundation regimes begin to reshape floodplain tree communities and the critical ecosystem functions they underpin. Here we address this gap by taking a spatially explicit look at Amazonia-wide patterns of tree-species turnover and ecological specialization of the region's floodplain forests. We show that the majority of Amazonian tree species can inhabit floodplains, and about a sixth of Amazonian tree diversity is ecologically specialized on floodplains. The degree of specialization in floodplain communities is driven by regional flood patterns, with the most compositionally differentiated floodplain forests located centrally within the fluvial network and contingent on the most extraordinary flood magnitudes regionally. Our results provide a spatially explicit view of ecological specialization of floodplain forest communities and expose the need for whole-basin hydrological integrity to protect the Amazon's tree diversity and its function.
3.	Luize, Bruno Garcia, et al. (författare) Geography and ecology shape the phylogenetic composition of Amazonian tree communities 2024 Ingår i: JOURNAL OF BIOGEOGRAPHY. - 0305-0270 .- 1365-2699. Tidskriftsartikel (refereegranskat)abstract Aim: Amazonia hosts more tree species from numerous evolutionary lineages, both young and ancient, than any other biogeographic region. Previous studies have shown that tree lineages colonized multiple edaphic environments and dispersed widely across Amazonia, leading to a hypothesis, which we test, that lineages should not be strongly associated with either geographic regions or edaphic forest types. Location: Amazonia. Taxon: Angiosperms (Magnoliids; Monocots; Eudicots). Methods: Data for the abundance of 5082 tree species in 1989 plots were combined with a mega-phylogeny. We applied evolutionary ordination to assess how phylogenetic composition varies across Amazonia. We used variation partitioning and Moran's eigenvector maps (MEM) to test and quantify the separate and joint contributions of spatial and environmental variables to explain the phylogenetic composition of plots. We tested the indicator value of lineages for geographic regions and edaphic forest types and mapped associations onto the phylogeny. Results: In the terra firme and v & aacute;rzea forest types, the phylogenetic composition varies by geographic region, but the igap & oacute; and white-sand forest types retain a unique evolutionary signature regardless of region. Overall, we find that soil chemistry, climate and topography explain 24% of the variation in phylogenetic composition, with 79% of that variation being spatially structured (R-2 = 19% overall for combined spatial/environmental effects). The phylogenetic composition also shows substantial spatial patterns not related to the environmental variables we quantified (R-2 = 28%). A greater number of lineages were significant indicators of geographic regions than forest types. Main Conclusion: Numerous tree lineages, including some ancient ones (>66 Ma), show strong associations with geographic regions and edaphic forest types of Amazonia. This shows that specialization in specific edaphic environments has played a long-standing role in the evolutionary assembly of Amazonian forests. Furthermore, many lineages, even those that have dispersed across Amazonia, dominate within a specific region, likely because of phylogenetically conserved niches for environmental conditions that are prevalent within regions.
4.	ter Steege, Hans, et al. (författare) Mapping density, diversity and species-richness of the Amazon tree flora 2023 Ingår i: COMMUNICATIONS BIOLOGY. - 2399-3642. ; 6:1 Tidskriftsartikel (refereegranskat)abstract Using 2.046 botanically-inventoried tree plots across the largest tropical forest on Earth, we mapped tree species-diversity and tree species-richness at 0.1-degree resolution, and investigated drivers for diversity and richness. Using only location, stratified by forest type, as predictor, our spatial model, to the best of our knowledge, provides the most accurate map of tree diversity in Amazonia to date, explaining approximately 70% of the tree diversity and species-richness. Large soil-forest combinations determine a significant percentage of the variation in tree species-richness and tree alpha-diversity in Amazonian forest-plots. We suggest that the size and fragmentation of these systems drive their large-scale diversity patterns and hence local diversity. A model not using location but cumulative water deficit, tree density, and temperature seasonality explains 47% of the tree species-richness in the terra-firme forest in Amazonia. Over large areas across Amazonia, residuals of this relationship are small and poorly spatially structured, suggesting that much of the residual variation may be local. The Guyana Shield area has consistently negative residuals, showing that this area has lower tree species-richness than expected by our models. We provide extensive plot meta-data, including tree density, tree alpha-diversity and tree species-richness results and gridded maps at 0.1-degree resolution. A study mapping the tree species richness in Amazonian forests shows that soil type exerts a strong effect on species richness, probably caused by the areas of these forest types. Cumulative water deficit, tree density and temperature seasonality affect species richness at a regional scale.
5.	Zamora, Juan Carlos, et al. (författare) Considerations and consequences of allowing DNA sequence data as types of fungal taxa 2018 Ingår i: IMA Fungus. - : INT MYCOLOGICAL ASSOC. - 2210-6340 .- 2210-6359. ; 9:1, s. 167-185 Tidskriftsartikel (refereegranskat)abstract Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity). Two proposals to amend the International Code of Nomenclature for algae, fungi, and plants (ICN), allowing DNA sequences alone (of any region and extent) to serve as types of taxon names for voucherless fungi (mainly putative taxa from environmental DNA sequences), have been submitted to be voted on at the 11th International Mycological Congress (Puerto Rico, July 2018). We consider various genetic processes affecting the distribution of alleles among taxa and find that alleles may not consistently and uniquely represent the species within which they are contained. Should the proposals be accepted, the meaning of nomenclatural types would change in a fundamental way from physical objects as sources of data to the data themselves. Such changes are conducive to irreproducible science, the potential typification on artefactual data, and massive creation of names with low information content, ultimately causing nomenclatural instability and unnecessary work for future researchers that would stall future explorations of fungal diversity. We conclude that the acceptance of DNA sequences alone as types of names of taxa, under the terms used in the current proposals, is unnecessary and would not solve the problem of naming putative taxa known only from DNA sequences in a scientifically defensible way. As an alternative, we highlight the use of formulas for naming putative taxa (candidate taxa) that do not require any modification of the ICN.
6.	Abelev, Betty, et al. (författare) Long-range angular correlations on the near and away side in p-Pb collisions at root S-NN=5.02 TeV 2013 Ingår i: Physics Letters. Section B: Nuclear, Elementary Particle and High-Energy Physics. - : Elsevier BV. - 0370-2693. ; 719:1-3, s. 29-41 Tidskriftsartikel (refereegranskat)abstract Angular correlations between charged trigger and associated particles are measured by the ALICE detector in p-Pb collisions at a nucleon-nucleon centre-of-mass energy of 5.02 TeV for transverse momentum ranges within 0.5 < P-T,P-assoc < P-T,P-trig < 4 GeV/c. The correlations are measured over two units of pseudorapidity and full azimuthal angle in different intervals of event multiplicity, and expressed as associated yield per trigger particle. Two long-range ridge-like structures, one on the near side and one on the away side, are observed when the per-trigger yield obtained in low-multiplicity events is subtracted from the one in high-multiplicity events. The excess on the near-side is qualitatively similar to that recently reported by the CMS Collaboration, while the excess on the away-side is reported for the first time. The two-ridge structure projected onto azimuthal angle is quantified with the second and third Fourier coefficients as well as by near-side and away-side yields and widths. The yields on the near side and on the away side are equal within the uncertainties for all studied event multiplicity and p(T) bins, and the widths show no significant evolution with event multiplicity or p(T). These findings suggest that the near-side ridge is accompanied by an essentially identical away-side ridge. (c) 2013 CERN. Published by Elsevier B.V. All rights reserved.
7.	Abelev, Betty, et al. (författare) Measurement of prompt J/psi and beauty hadron production cross sections at mid-rapidity in pp collisions at root s=7 TeV 2012 Ingår i: Journal of High Energy Physics. - 1029-8479. ; :11 Tidskriftsartikel (refereegranskat)abstract The ALICE experiment at the LHC has studied J/psi production at mid-rapidity in pp collisions at root s = 7 TeV through its electron pair decay on a data sample corresponding to an integrated luminosity L-int = 5.6 nb(-1). The fraction of J/psi from the decay of long-lived beauty hadrons was determined for J/psi candidates with transverse momentum p(t) > 1,3 GeV/c and rapidity vertical bar y vertical bar < 0.9. The cross section for prompt J/psi mesons, i.e. directly produced J/psi and prompt decays of heavier charmonium states such as the psi(2S) and chi(c) resonances, is sigma(prompt J/psi) (p(t) > 1.3 GeV/c, vertical bar y vertical bar < 0.9) = 8.3 +/- 0.8(stat.) +/- 1.1 (syst.)(-1.4)(+1.5) (syst. pol.) mu b. The cross section for the production of b-hadrons decaying to J/psi with p(t) > 1.3 GeV/c and vertical bar y vertical bar < 0.9 is a sigma(J/psi <- hB) (p(t) > 1.3 GeV/c, vertical bar y vertical bar < 0.9) = 1.46 +/- 0.38 (stat.)(-0.32)(+0.26) (syst.) mu b. The results are compared to QCD model predictions. The shape of the p(t) and y distributions of b-quarks predicted by perturbative QCD model calculations are used to extrapolate the measured cross section to derive the b (b) over bar pair total cross section and d sigma/dy at mid-rapidity.
8.	Abelev, Betty, et al. (författare) Underlying Event measurements in pp collisions at root s=0.9 and 7 TeV with the ALICE experiment at the LHC 2012 Ingår i: Journal of High Energy Physics. - 1029-8479. ; :7 Tidskriftsartikel (refereegranskat)abstract We present measurements of Underlying Event observables in pp collisions at root s = 0 : 9 and 7 TeV. The analysis is performed as a function of the highest charged-particle transverse momentum p(T),L-T in the event. Different regions are defined with respect to the azimuthal direction of the leading (highest transverse momentum) track: Toward, Transverse and Away. The Toward and Away regions collect the fragmentation products of the hardest partonic interaction. The Transverse region is expected to be most sensitive to the Underlying Event activity. The study is performed with charged particles above three different p(T) thresholds: 0.15, 0.5 and 1.0 GeV/c. In the Transverse region we observe an increase in the multiplicity of a factor 2-3 between the lower and higher collision energies, depending on the track p(T) threshold considered. Data are compared to PYTHIA 6.4, PYTHIA 8.1 and PHOJET. On average, all models considered underestimate the multiplicity and summed p(T) in the Transverse region by about 10-30%.
9.	Aprile, E., et al. (författare) Constraining the Spin-Dependent WIMP-Nucleon Cross Sections with XENON1T 2019 Ingår i: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 122:14 Tidskriftsartikel (refereegranskat)abstract We report the first experimental results on spin-dependent elastic weakly interacting massive particle (WIMP) nucleon scattering from the XENON1T dark matter search experiment. The analysis uses the full ton year exposure of XENON1T to constrain the spin-dependent proton-only and neutron-only cases. No significant signal excess is observed, and a profile likelihood ratio analysis is used to set exclusion limits on the WIMP-nucleon interactions. This includes the most stringent constraint to date on the WIMP-neutron cross section, with a minimum of 6.3 x 10(-42) cm(2) at 30 GeV/c(2) and 90% confidence level. The results are compared with those from collider searches and used to exclude new parameter space in an isoscalar theory with an axial-vector mediator.
10.	Aprile, E., et al. (författare) Dark Matter Search Results from a One Ton-Year Exposure of XENON1T 2018 Ingår i: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 121:11 Tidskriftsartikel (refereegranskat)abstract We report on a search for weakly interacting massive particles (WIMPs) using 278.8 days of data collected with the XENON1T experiment at LNGS. XENON1T utilizes a liquid xenon time projection chamber with a fiducial mass of (1.30 +/- 0.01) ton, resulting in a 1.0 ton yr exposure. The energy region of interest, [1.4; 10.6] keV(ee) ([4.9; 40.9] keV(nr)), exhibits an ultralow electron recoil background rate of [82(-3)(+5) (syst) +/- 3 stat)] events/ton yr keV(ee)). No significant excess over background is found, and a profile likelihood analysis parametrized in spatial and energy dimensions excludes new parameter space for the WIMP-nucleon spin-independent elastic scatter cross section for WIMP masses above 6 GeV/c(2), with a minimum of 4.1 x 10(-47) cm(2) at 30 GeV/c(2) and a 90% confidence level.
11.	Aprile, E., et al. (författare) Effective Field Theory and Inelastic Dark Matter Results from XENON1T Annan publikation (övrigt vetenskapligt/konstnärligt)abstract In this work we expand on the XENON1T nuclear recoil searches and study the individual signals of Dark Matter interactions from operators up to dimension-eight in a Chiral Effective Field Theory (ChEFT) as well as a model of inelastic Dark Matter using data from the two science runs of the detector totalling 1 tonne*year exposure. For these analyses we extended the region of interest from [4.9, 40.9]keVnr to [4.9, 54.4]keVnr to enhance our sensitivity for signals that peak at nonzero energies. We show that the data is consistent with a background only hypothesis, with small excesses in the models which peak between 20 and 50keVnr, obtaining a maximum local discovery significance of 1.7 for the VVs ChEFT model for a WIMP mass of 70GeV/c2, and 1.8 for an iDM particle of 50GeV/c2 with a mass splitting of 100keV/c2. For each model we report 90% confidence level upper limits. We also report limits on three benchmark models of WIMP interaction using ChEFT for which we investigate the effect of isospin breaking interactions, reporting up to 6 orders of magnitude weaker limits with respect to the isospin conserving case driven by cancellations in the expected rate.
12.	Aprile, E., et al. (författare) First Results on the Scalar WIMP-Pion Coupling, Using the XENON1T Experiment 2019 Ingår i: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 122:7 Tidskriftsartikel (refereegranskat)abstract We present first results on the scalar coupling of weakly interacting massive particles (WIMPs) to pions from 1 t yr of exposure with the XENON1T experiment. This interaction is generated when the WIMP couples to a virtual pion exchanged between the nucleons in a nucleus. In contrast to most nonrelativistic operators, these pion-exchange currents can be coherently enhanced by the total number of nucleons and therefore may dominate in scenarios where spin-independent WIMP-nucleon interactions are suppressed. Moreover, for natural values of the couplings, they dominate over the spin-dependent channel due to their coherence in the nucleus. Using the signal model of this new WIMP-pion channel, no significant excess is found, leading to an upper limit cross section of 6.4 x 10(-46) cm(2) (90% confidence level) at 30 GeV/c(2) WIMP mass.
13.	Aprile, E., et al. (författare) Light Dark Matter Search with Ionization Signals in XENON1T 2019 Ingår i: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 123:25 Tidskriftsartikel (refereegranskat)abstract We report constraints on light dark matter (DM) models using ionization signals in the XENON1T experiment. We mitigate backgrounds with strong event selections, rather than requiring a scintillation signal, leaving an effective exposure of (22 +/- 3) tonne day. Above similar to 0.4 keV(ee), we observe <1 event/(tonne day keV(ee)), which is more than 1000 times lower than in similar searches with other detectors. Despite observing a higher rate at lower energies, no DM or CEvNS detection may be claimed because we cannot model all of our backgrounds. We thus exclude new regions in the parameter spaces for DM-nucleus scattering for DM masses m(chi) within 3-6 GeV/c(2), DM-electron scattering for m(chi) > 30 MeV/c(2), and absorption of dark photons and axionlike particles for m(chi) within 0.186-1 keV/c(2).
14.	Aprile, E., et al. (författare) Observation of two-neutrino double electron capture in 124Xe with XENON1T 2019 Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 568:7753, s. 532-535 Tidskriftsartikel (refereegranskat)abstract Two-neutrino double electron capture (2νECEC) is a second-order weak-interaction process with a predicted half-life that surpasses the age of the Universe by many orders of magnitude. Until now, indications of 2νECEC decays have only been seen for two isotopes, 78Kr and 130Ba, and instruments with very low background levels are needed to detect them directly with high statistical significance. The 2νECEC half-life is an important observable for nuclear structure models and its measurement represents a meaningful step in the search for neutrinoless double electron capture—the detection of which would establish the Majorana nature of the neutrino and would give access to the absolute neutrino mass. Here we report the direct observation of 2νECEC in 124Xe with the XENON1T dark-matter detector. The significance of the signal is 4.4 standard deviations and the corresponding half-life of 1.8 × 1022 years (statistical uncertainty, 0.5 × 1022 years; systematic uncertainty, 0.1 × 1022 years) is the longest measured directly so far. This study demonstrates that the low background and large target mass of xenon-based dark-matter detectors make them well suited for measuring rare processes and highlights the broad physics reach of larger next-generation experiments.
15.	Aprile, E., et al. (författare) Search for bosonic super-WIMP interactions with the XENON100 experiment 2017 Ingår i: Physical Review D. - 2470-0010 .- 2470-0029. ; 96:12 Tidskriftsartikel (refereegranskat)abstract We present results of searches for vector and pseudoscalar bosonic super-weakly interacting massive particles (WIMPs), which are dark matter candidates with masses at the keV-scale, with the XENON100 experiment. XENON100 is a dual-phase xenon time projection chamber operated at the Laboratori Nazionali del Gran Sasso. A profile likelihood analysis of data with an exposure of 224.6 live days x34 kg showed no evidence for a signal above the expected background. We thus obtain new and stringent upper limits in the (8-125) keV/c(2) mass range, excluding couplings to electrons with coupling constants of g(ae) > 3 x 10(-13) for pseudo-scalar and alpha'/alpha > 2 x 10(-28) for vector super-WIMPs, respectively. These limits are derived under the assumption that super-WIMPs constitute all of the dark matter in our galaxy.
16.	Aprile, E., et al. (författare) Search for Light Dark Matter Interactions Enhanced by the Migdal Effect or Bremsstrahlung in XENON1T 2019 Ingår i: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 123:24 Tidskriftsartikel (refereegranskat)abstract Direct dark matter detection experiments based on a liquid xenon target are leading the search for dark matter particles with masses above similar to 5 GeV/c(2), but have limited sensitivity to lighter masses because of the small momentum transfer in dark matter-nucleus elastic scattering. However, there is an irreducible contribution from inelastic processes accompanying the elastic scattering, which leads to the excitation and ionization of the recoiling atom (the Migdal effect) or the emission of a bremsstrahlung photon. In this Letter, we report on a probe of low-mass dark matter with masses down to about 85 MeV/c(2) by looking for electronic recoils induced by the Migdal effect and bremsstrahlung using data from the XENON1T experiment. Besides the approach of detecting both scintillation and ionization signals, we exploit an approach that uses ionization signals only, which allows for a lower detection threshold. This analysis significantly enhances the sensitivity of XENON1T to light dark matter previously beyond its reach.
17.	Aprile, E., et al. (författare) Signal yields of keV electronic recoils and their discrimination from nuclear recoils in liquid xenon 2018 Ingår i: Physical Review D. - 2470-0010 .- 2470-0029. ; 97:9 Tidskriftsartikel (refereegranskat)abstract We report on the response of liquid xenon to low energy electronic recoils below 15 keV from beta decays of tritium at drift fields of 92 V/cm, 154 V/cm and 366 V/cm using the XENON100 detector. A data-to-simulation fitting method based on Markov Chain Monte Carlo is used to extract the photon yields and recombination fluctuations from the experimental data. The photon yields measured at the two lower fields are in agreement with those from literature; additional measurements at a higher field of 366 V/cm are presented. The electronic and nuclear recoil discrimination as well as its dependence on the drift field and photon detection efficiency are investigated at these low energies. The results provide new measurements in the energy region of interest for dark matter searches using liquid xenon.
18.	Aprile, E., et al. (författare) The XENON1T dark matter experiment 2017 Ingår i: European Physical Journal C. - : Springer Science and Business Media LLC. - 1434-6044 .- 1434-6052. ; 77:12 Tidskriftsartikel (refereegranskat)abstract The XENON1T experiment at the Laboratori Nazionali del Gran Sasso (LNGS) is the first WIMP dark matter detector operating with a liquid xenon target mass above the ton-scale. Out of its 3.2t liquid xenon inventory, 2.0t constitute the active target of the dual-phase time projection chamber. The scintillation and ionization signals from particle interactions are detected with low-background photomultipliers. This article describes the XENON1T instrument and its subsystems as well as strategies to achieve an unprecedented low background level. First results on the detector response and the performance of the subsystems are also presented.
19.	Aprile, E., et al. (författare) The XENON1T data acquisition system 2019 Ingår i: Journal of Instrumentation. - 1748-0221. ; 14 Tidskriftsartikel (refereegranskat)abstract The XENON1T liquid xenon time projection chamber is the most sensitive detector built to date for the measurement of direct interactions of weakly interacting massive particles with normal matter. The data acquisition system (DAQ) is constructed from commercial, open source, and custom components to digitize signals from the detector and store them for later analysis. The system achieves an extremely low signal threshold by triggering each channel independently, achieving a single photoelectron acceptance of (93 +/- 3)%, and deferring the global trigger to a later, software stage. The event identification is based on MongoDB database queries and has over 98% efficiency at recognizing interactions at the analysis threshold in the center of the target. A readout bandwidth over 300 MB/s is reached in calibration modes and is further expandable via parallelization. This DAQ system was successfully used during three years of operation of XENON1T.
20.	Aprile, E., et al. (författare) XENON1T dark matter data analysis : Signal and background models and statistical inference 2019 Ingår i: Physical Review D. - 2470-0010 .- 2470-0029. ; 99:11 Tidskriftsartikel (refereegranskat)abstract The XENON1T experiment searches for dark matter particles through their scattering off xenon atoms in a 2 metric ton liquid xenon target. The detector is a dual-phase time projection chamber, which measures simultaneously the scintillation and ionization signals produced by interactions in target volume, to reconstruct energy and position, as well as the type of the interaction. The background rate in the central volume of XENON1T detector is the lowest achieved so far with a liquid xenon-based direct detection experiment. In this work we describe the response model of the detector, the background and signal models, and the statistical inference procedures used in the dark matter searches with a 1 metric ton x year exposure of XENON1T data, that leads to the best limit to date on WIMP-nucleon spin-independent elastic scatter cross section for WIMP masses above 6 GeV/c(2).
21.	Aprile, E., et al. (författare) XENON1T dark matter data analysis : Signal reconstruction, calibration, and event selection 2019 Ingår i: Physical Review D. - 2470-0010 .- 2470-0029. ; 100:5 Tidskriftsartikel (refereegranskat)abstract The XENON1T experiment at the Laboratori Nazionali del Gran Sasso is the most sensitive direct detection experiment for dark matter in the form of weakly interacting particles (WIMPs) with masses above 6 GeV/c(2) scattering off nuclei. The detector employs a dual-phase time projection chamber with 2.0 metric tons of liquid xenon in the target. A one metric ton x year exposure of science data was collected between October 2016 and February 2018. This article reports on the performance of the detector during this period and describes details of the data analysis that led to the most stringent exclusion limits on various WIMP-nucleon interaction models to date. In particular, signal reconstruction, event selection, and calibration of the detector response to nuclear and electronic recoils in XENON1T are discussed.
22.	Baumeister, Hannah, et al. (författare) A generalizable data-driven model of atrophy heterogeneity and progression in memory clinic settings Ingår i: Brain : a journal of neurology. - 1460-2156. ; 147:7, s. 2400-2413 Tidskriftsartikel (refereegranskat)abstract Memory clinic patients are a heterogeneous population representing various aetiologies of pathological aging. It is unknown if divergent spatiotemporal progression patterns of brain atrophy, as previously described in Alzheimer's disease (AD) patients, are prevalent and clinically meaningful in this group of older adults. To uncover distinct atrophy subtypes, we applied the Subtype and Stage Inference (SuStaIn) algorithm to baseline structural MRI data from 813 participants enrolled in the DELCODE cohort (mean ± SD age = 70.67 ± 6.07 years, 52% females). Participants were cognitively unimpaired (CU; n = 285) or fulfilled diagnostic criteria for subjective cognitive decline (SCD; n = 342), mild cognitive impairment (MCI; n = 118), or dementia of the Alzheimer's type (n = 68). Atrophy subtypes were compared in baseline demographics, fluid AD biomarker levels, the Preclinical Alzheimer Cognitive Composite (PACC-5), as well as episodic memory and executive functioning. PACC-5 trajectories over up to 240 weeks were examined. To test if baseline atrophy subtype and stage predicted clinical trajectories before manifest cognitive impairment, we analysed PACC-5 trajectories and MCI conversion rates of CU and SCD participants. Limbic-predominant and hippocampal-sparing atrophy subtypes were identified. Limbic-predominant atrophy first affected the medial temporal lobes, followed by further temporal and, finally, the remaining cortical regions. At baseline, this subtype was related to older age, more pathological AD biomarker levels, APOE ε4 carriership, and an amnestic cognitive impairment. Hippocampal-sparing atrophy initially occurred outside the temporal lobe with the medial temporal lobe spared up to advanced atrophy stages. This atrophy pattern also affected individuals with positive AD biomarkers and was associated with more generalised cognitive impairment. Limbic-predominant atrophy, in all and in only unimpaired participants, was linked to more negative longitudinal PACC-5 slopes than observed in participants without or with hippocampal-sparing atrophy and increased the risk of MCI conversion. SuStaIn modelling was repeated in a sample from the Swedish BioFINDER-2 cohort. Highly similar atrophy progression patterns and associated cognitive profiles were identified. Cross-cohort model generalizability, both on the subject and group level, were excellent, indicating reliable performance in previously unseen data. The proposed model is a promising tool for capturing heterogeneity among older adults at early at-risk states for AD in applied settings. The implementation of atrophy subtype- and stage-specific end-points may increase the statistical power of pharmacological trials targeting early AD.
23.	Belloy, Michael E., et al. (författare) Challenges at the APOE locus : a robust quality control approach for accurate APOE genotyping 2022 Ingår i: Alzheimer's Research & Therapy. - : Springer Nature. - 1758-9193. ; 14:1 Tidskriftsartikel (refereegranskat)abstract Background: Genetic variants within the APOE locus may modulate Alzheimer's disease (AD) risk independently or in conjunction with APOE2/3/4 genotypes. Identifying such variants and mechanisms would importantly advance our understanding of APOE pathophysiology and provide critical guidance for AD therapies aimed at APOE. The APOE locus however remains relatively poorly understood in AD, owing to multiple challenges that include its complex linkage structure and uncertainty in APOE2/3/4 genotype quality. Here, we present a novel APOE2/3/4 filtering approach and showcase its relevance on AD risk association analyses for the rs439401 variant, which is located 1801 base pairs downstream of APOE and has been associated with a potential regulatory effect on APOE.Methods: We used thirty-two AD-related cohorts, with genetic data from various high-density single-nucleotide polymorphism microarrays, whole-genome sequencing, and whole-exome sequencing. Study participants were filtered to be ages 60 and older, non-Hispanic, of European ancestry, and diagnosed as cognitively normal or AD (n = 65,701). Primary analyses investigated AD risk in APOE4/4 carriers. Additional supporting analyses were performed in APOE3/4 and 3/3 strata. Outcomes were compared under two different APOE2/3/4 filtering approaches.Results: Using more conventional APOE2/3/4 filtering criteria (approach 1), we showed that, when in-phase with APOE4, rs439401 was variably associated with protective effects on AD case-control status. However, when applying a novel filter that increases the certainty of the APOE2/3/4 genotypes by applying more stringent criteria for concordance between the provided APOE genotype and imputed APOE genotype (approach 2), we observed that all significant effects were lost. Conclusions: We showed that careful consideration of APOE genotype and appropriate sample filtering were crucial to robustly interrogate the role of the APOE locus on AD risk. Our study presents a novel APOE filtering approach and provides important guidelines for research into the APOE locus, as well as for elucidating genetic interaction effects with APOE2/3/4.
24.	Caballero-Pérez, Juan, et al. (författare) Transcriptional landscapes of Axolotl (Ambystoma mexicanum) 2018 Ingår i: Developmental Biology. - : Elsevier. - 0012-1606 .- 1095-564X. ; 433:2, s. 227-239 Tidskriftsartikel (refereegranskat)abstract The axolotl (Ambystoma mexicanum) is the vertebrate model system with the highest regeneration capacity. Experimental tools established over the past 100 years have been fundamental to start unraveling the cellular and molecular basis of tissue and limb regeneration. In the absence of a reference genome for the Axolotl, transcriptomic analysis become fundamental to understand the genetic basis of regeneration.Here we present one of the most diverse transcriptomic data sets for Axolotl by profiling coding and non coding RNAs from diverse tissues. We reconstructed a population of 115,906 putative protein coding mRNAs as full ORFs (including isoforms). We also identified 352 conserved miRNAs and 297 novel putative mature miRNAs.Systematic enrichment analysis of gene expression allowed us to identify tissue-specific protein-coding transcripts. We also found putative novel and conserved microRNAs which potentially target mRNAs which are reported as important disease candidates in heart and liver.
25.	Concepcion Cruz-Santos, Maria, et al. (författare) The Role of microRNAs in Animal Cell Reprogramming 2016 Ingår i: Stem Cells and Development. - : Mary Ann Liebert Inc. - 1547-3287 .- 1557-8534. ; 25:14, s. 1035-1049 Forskningsöversikt (refereegranskat)abstract Our concept of cell reprogramming and cell plasticity has evolved since John Gurdon transferred the nucleus of a completely differentiated cell into an enucleated Xenopus laevis egg, thereby generating embryos that developed into tadpoles. More recently, induced expression of transcription factors, oct4, sox2, klf4, and c-myc has evidenced the plasticity of the genome to change the expression program and cell phenotype by driving differentiated cells to the pluripotent state. Beyond these milestone achievements, research in artificial cell reprogramming has been focused on other molecules that are different than transcription factors. Among the candidate molecules, microRNAs (miRNAs) stand out due to their potential to control the levels of proteins that are involved in cellular processes such as self-renewal, proliferation, and differentiation. Here, we review the role of miRNAs in the maintenance and differentiation of mesenchymal stem cells, epimorphic regeneration, and somatic cell reprogramming to induced pluripotent stem cells.

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