Light and propagule pressure affect invasion intensity of Prunus serotina in a 14-tree species forest common garden experiment

Experiments testing multiple factors that affect the rate of invasions in forests are scarce. We aimed to assess how the biomass of invasive Prunus serotina changed over eight years and how this change was affected by light availability, tree stand growth, and propagule pressure. The study was conducted in Siemianice Experimental Forest (W Poland), a common garden forest experiment with 14 tree species. We investigated aboveground biomass and density of P. serotina within 53 experimental plots with initial measurements in 2005 and repeated in 2013. We also measured light availability and distance from seed sources. We used generalized additive models to assess the impact of particular predictors on P. serotina biomass in 2013 and its relative change over eight years. The relative biomass increments of P. serotina ranged from 0 to 22,000-fold. The success of P. serotina, expressed as aboveground biomass and biomass increment, varied among different tree species stands, but was greater under conifers. Total biomass of P. serotina depended on light and propagule availability while biomass increment depended on the change in tree stand biomass, a metric corresponding to tree stand maturation. Our study quantified the range of invasion intensity, expressed as biomass increment, in a forest common garden experiment with 14 tree species. Canopy cover was the most important variable to reduce susceptibility to invasion by P. serotina. Even a modest decrease of overstory biomass, e.g. caused by dieback of coniferous species, may be risky in areas with high propagule pressure from invasive tree species. Thus, P. serotina control may include maintaining high canopy closure and supporting natural regeneration of tree species with high leaf area index, which shade the understory

Towards virtual histology with X-ray grating interferometry

Breast cancer is the most common type of cancer worldwide. Diagnosing breast cancer relies on clinical examination, imaging and biopsy. A core-needle biopsy enables a morphological and biochemical characterization of the cancer and is considered the gold standard for breast cancer diagnosis. A histopathological examination uses high-resolution microscopes with outstanding contrast in the 2D plane, but the spatial resolution in the third, Z-direction, is reduced. In the present paper, we propose two high-resolution table-top systems for phase-contrast X-ray tomography of soft-tissue samples. The first system implements a classical Talbot-Lau interferometer and allows to perform ex-vivo imaging of human breast samples with a voxel size of 5.57 μm. The second system with a comparable voxel size relies on a Sigray MAAST X-ray source with structured anode. For the first time, we demonstrate the applicability of the latter to perform X-ray imaging of human breast specimens with ductal carcinoma in-situ. We assessed image quality of both setups and compared it to histology. We showed that both setups made it possible to target internal features of breast specimens with better resolution and contrast than previously achieved, demonstrating that grating-based phase-contrast X-ray CT could be a complementary tool for clinical histopathology

Frequency and phenotype associations of rare variants in 5 monogenic cerebral small vessel disease genes in 200,000 UK Biobank participants

BACKGROUND AND OBJECTIVES: Based on previous case reports and disease-based cohorts, a minority of patients with cerebral small vessel disease (cSVD) have a monogenic cause, with many also manifesting extracerebral phenotypes. We investigated the frequency, penetrance, and phenotype associations of putative pathogenic variants in cSVD genes in the UK Biobank (UKB), a large population-based study. METHODS: We used a systematic review of previous literature and ClinVar to identify putative pathogenic rare variants in CTSA, TREX1, HTRA1, and COL4A1/2. We mapped phenotypes previously attributed to these variants (phenotypes-of-interest) to disease coding systems used in the UKB's linked health data from UK hospital admissions, death records, and primary care. Among 199,313 exome-sequenced UKB participants, we assessed the following: the proportion of participants carrying ≥1 variant(s); phenotype-of-interest penetrance; and the association between variant carrier status and phenotypes-of-interest using a binary (any phenotype present/absent) and phenotype burden (linear score of the number of phenotypes a participant possessed) approach. RESULTS: Among UKB participants, 0.5% had ≥1 variant(s) in studied genes. Using hospital admission and death records, 4%–20% of variant carriers per gene had an associated phenotype. This increased to 7%–55% when including primary care records. Only COL4A1 variant carrier status was significantly associated with having ≥1 phenotype-of-interest and a higher phenotype score (OR = 1.29, p = 0.006). DISCUSSION: While putative pathogenic rare variants in monogenic cSVD genes occur in 1:200 people in the UKB population, only approximately half of variant carriers have a relevant disease phenotype recorded in their linked health data. We could not replicate most previously reported gene-phenotype associations, suggesting lower penetrance rates, overestimated pathogenicity, and/or limited statistical power

A highly stable atomic vector magnetometer based on free spin precession

We present a magnetometer based on optically pumped Cs atoms that measures the magnitude and direction of a 1 $\mu$T magnetic field. Multiple circularly polarized laser beams were used to probe the free spin precession of the Cs atoms. The design was optimized for long-time stability and achieves a scalar resolution better than 300 fT for integration times ranging from 80 ms to 1000 s. The best scalar resolution of less than 80 fT was reached with integration times of 1.6 to 6 s. We were able to measure the magnetic field direction with a resolution better than 10 $\mu$rad for integration times from 10 s up to 2000 s

Revised experimental upper limit on the electric dipole moment of the neutron

We present for the first time a detailed and comprehensive analysis of the experimental results that set the current world sensitivity limit on the magnitude of the electric dipole moment (EDM) of the neutron. We have extended and enhanced our earlier analysis to include recent developments in the understanding of the effects of gravity in depolarizing ultracold neutrons; an improved calculation of the spectrum of the neutrons; and conservative estimates of other possible systematic errors, which are also shown to be consistent with more recent measurements undertaken with the apparatus. We obtain a net result of dn=−0.21±1.82×10−26  e cm, which may be interpreted as a slightly revised upper limit on the magnitude of the EDM of 3.0×10−26  e cm (90% C.L.) or 3.6×10−26  e cm (95% C.L.)

Gravitational depolarization of ultracold neutrons: comparison with data

We compare the expected effects of so-called gravitationally enhanced depolarization of ultracold neutrons to measurements carried out in a spin-precession chamber exposed to a variety of vertical magnetic-field gradients. In particular, we have investigated the dependence upon these field gradients of spin-depolarization rates and also of shifts in the measured neutron Larmor precession frequency. We find excellent qualitative agreement, with gravitationally enhanced depolarization accounting for several previously unexplained features in the data

Measurement of the permanent electric dipole moment of the neutron

We present the result of an experiment to measure the electric dipole moment EDM) of the neutron at the Paul Scherrer Institute using Ramsey's method of separated oscillating magnetic fields with ultracold neutrons (UCN). Our measurement stands in the long history of EDM experiments probing physics violating time reversal invariance. The salient features of this experiment were the use of a Hg-199 co-magnetometer and an array of optically pumped cesium vapor magnetometers to cancel and correct for magnetic field changes. The statistical analysis was performed on blinded datasets by two separate groups while the estimation of systematic effects profited from an unprecedented knowledge of the magnetic field. The measured value of the neutron EDM is d_{\rm n} = (0.0\pm1.1_{\rm stat}\pm0.2_{\rmsys})\times10^{-26}e\,{\rm cm}

Whole-genome sequencing reveals host factors underlying critical COVID-19

Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care(1) or hospitalization(2-4) after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes-including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)-in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease.Peer reviewe

Observation of gravitationally induced vertical striation of polarized ultracold neutrons by spin-echo spectroscopy

We describe a spin-echo method for ultracold neutrons (UCNs) confined in a precession chamber and exposed to a |B 0 |=1  μT magnetic field. We have demonstrated that the analysis of UCN spin-echo resonance signals in combination with knowledge of the ambient magnetic field provides an excellent method by which to reconstruct the energy spectrum of a confined ensemble of neutrons. The method takes advantage of the relative dephasing of spins arising from a gravitationally induced striation of stored UCNs of different energies, and also permits an improved determination of the vertical magnetic-field gradient with an exceptional accuracy of 1.1  pT/cm . This novel combination of a well-known nuclear resonance method and gravitationally induced vertical striation is unique in the realm of nuclear and particle physics and should prove to be invaluable for the assessment of systematic effects in precision experiments such as searches for an electric dipole moment of the neutron or the measurement of the neutron lifetime

A multi-tissue atlas of regulatory variants in cattle:Cattle Genotype-Tissue Expression Atlas

Characterization of genetic regulatory variants acting on the livestock gene expression is essential for interpreting the molecular mechanisms underlying traits of economic value and for increasing the rate of genetic gain through artificial selection. Here we build a Cattle Genotype-Tissue Expression atlas (CattleGTEx) as part of the pilot phase of Farm animal GTEx (FarmGTEx) project for the research community based on publicly available 7,180 RNA-Seq samples. We describe the transcriptomic landscape of over 100 tissues/cell types and report hundreds of thousands of genetic associations with gene expression and alternative splicing for 23 distinct tissues. We evaluate the tissue-sharing patterns of these genetic regulatory effects, and functionally annotate them using multi-omics data. Finally, we link gene expression in different tissues to 43 economically important traits using both transcriptome-wide association and colocalization analyses to decipher the molecular regulatory mechanisms underpinning such agronomic traits in cattle