Longitudinal spin polarization and symmetries in low-energy-electron diffraction: Experiment and theory for Pt(111)

Bauer P, Feder R, Müller N. Longitudinal spin polarization and symmetries in low-energy-electron diffraction: Experiment and theory for Pt(111). Solid State Communications. 1980;36(3):249-251.In low-energy electron diffraction from Pt(111), the longitudinal component of the spin polarization vector and its transverse component normal to the scattering plane were measured by a Mott detector and found to agree very well with corresponding theoretical results. Rotation diagrams of the longitudinal and transverse components exhibit only a three-fold symmetry in contrast to the six-fold symmetry, which time reversal invariance dictates for intensities

Speckle from phase ordering systems

The statistical properties of coherent radiation scattered from phase-ordering materials are studied in detail using large-scale computer simulations and analytic arguments. Specifically, we consider a two-dimensional model with a nonconserved, scalar order parameter (Model A), quenched through an order-disorder transition into the two-phase regime. For such systems it is well established that the standard scaling hypothesis applies, consequently the average scattering intensity at wavevector _k and time t' is proportional to a scaling function which depends only on a rescaled time, t ~ |_k|^2 t'. We find that the simulated intensities are exponentially distributed, with the time-dependent average well approximated using a scaling function due to Ohta, Jasnow, and Kawasaki. Considering fluctuations around the average behavior, we find that the covariance of the scattering intensity for a single wavevector at two different times is proportional to a scaling function with natural variables mt = |t_1 - t_2| and pt = (t_1 + t_2)/2. In the asymptotic large-pt limit this scaling function depends only on z = mt / pt^(1/2). For small values of z, the scaling function is quadratic, corresponding to highly persistent behavior of the intensity fluctuations. We empirically establish a connection between the intensity covariance and the two-time, two-point correlation function of the order parameter. This connection allows sensitive testing, either experimental or numerical, of existing theories for two-time correlations in systems undergoing order-disorder phase transitions. Comparison between theory and our numerical results requires no adjustable parameters.Comment: 18 pgs RevTeX, to appear in PR

Highly sensitive liquid biopsy Duplex sequencing complements tissue biopsy to enhance detection of clinically relevant genetic variants

BackgroundLiquid biopsy (LB) is a promising complement to tissue biopsy for detection of clinically relevant genetic variants in cancer and mosaic diseases. A combined workflow to enable parallel tissue and LB analysis is required to maximize diagnostic yield for patients.MethodsWe developed and validated a cost-efficient combined next-generation sequencing (NGS) workflow for both tissue and LB samples, and applied Duplex sequencing technology for highly accurate detection of low frequency variants in plasma. Clinically relevant cutoffs for variant reporting and quantification were established.ResultsWe investigated assay performance characteristics for very low amounts of clinically relevant variants. In plasma, the assay achieved 100% sensitivity and 92.3% positive predictive value (PPV) for single nucleotide variants (SNVs) and 91.7% sensitivity and 100% PPV for insertions and deletions (InDel) in clinically relevant hotspots with 0.5-5% variant allele frequencies (VAFs). We further established a cutoff for reporting variants (i.e. Limit of Blank, LOB) at 0.25% VAF and a cutoff for quantification (i.e. Limit of Quantification, LOQ) at 5% VAF in plasma for accurate clinical interpretation of analysis results. With our LB approach, we were able to identify the molecular cause of a clinically confirmed asymmetric overgrowth syndrome in a 10-year old child that would have remained undetected with tissue analysis as well as other molecular diagnostic approaches.ConclusionOur flexible and cost-efficient workflow allows analysis of both tissue and LB samples and provides clinically relevant cutoffs for variant reporting and precise quantification. Complementing tissue analysis by LB is likely to increase diagnostic yield for patients with molecular diseases

Ribose 2′-O-methylation provides a molecular signature for the distinction of self and non-self mRNA dependent on the RNA sensor Mda5

The 5'-cap-structures of higher eukaryote mRNAs are ribose 2'-O-methylated. Likewise, a number of viruses replicating in the cytoplasm of eukayotes have evolved 2'-O-methyltransferases to modify autonomously their mRNAs. However, a defined biological role of mRNA 2'-O-methylation remains elusive. Here we show that viral mRNA 2'-O-methylation is critically involved in subversion of type-I-interferon (IFN-I) induction. We demonstrate that human and murine coronavirus 2'-O-methyltransferase mutants induce increased IFN-I expression, and are highly IFN-I sensitive. Importantly, IFN-I induction by 2'-O-methyltransferase-deficient viruses is dependent on the cytoplasmic RNA sensor melanoma differentiation-associated gene 5 (MDA5). This link between MDA5-mediated sensing of viral RNA and mRNA 2'-O-methylation suggests that RNA modifications, such as 2'-O-methylation, provide a molecular signature for the discrimination of self and non-self mRNA

Building an Aerial-Ground Robotics System for Precision Farming: An Adaptable Solution

The application of autonomous robots in agriculture is gaining increasing popularity thanks to the high impact it may have on food security, sustainability, resource use efficiency, reduction of chemical treatments, and the optimization of human effort and yield. With this vision, the Flourish research project aimed to develop an adaptable robotic solution for precision farming that combines the aerial survey capabilities of small autonomous unmanned aerial vehicles (UAVs) with targeted intervention performed by multi-purpose unmanned ground vehicles (UGVs). This paper presents an overview of the scientific and technological advances and outcomes obtained in the project. We introduce multi-spectral perception algorithms and aerial and ground-based systems developed for monitoring crop density, weed pressure, crop nitrogen nutrition status, and to accurately classify and locate weeds. We then introduce the navigation and mapping systems tailored to our robots in the agricultural environment, as well as the modules for collaborative mapping. We finally present the ground intervention hardware, software solutions, and interfaces we implemented and tested in different field conditions and with different crops. We describe a real use case in which a UAV collaborates with a UGV to monitor the field and to perform selective spraying without human intervention.Comment: Published in IEEE Robotics & Automation Magazine, vol. 28, no. 3, pp. 29-49, Sept. 202

Cold truths: how winter drives responses of terrestrial organisms to climate change

Winter is a key driver of individual performance, community composition, and ecological interactions in terrestrial habitats. Although climate change research tends to focus on performance in the growing season, climate change is also modifying winter conditions rapidly. Changes to winter temperatures, the variability of winter conditions, and winter snow cover can interact to induce cold injury, alter energy and water balance, advance or retard phenology, and modify community interactions. Species vary in their susceptibility to these winter drivers, hampering efforts to predict biological responses to climate change. Existing frameworks for predicting the impacts of climate change do not incorporate the complexity of organismal responses to winter. Here, we synthesise organismal responses to winter climate change, and use this synthesis to build a framework to predict exposure and sensitivity to negative impacts. This framework can be used to estimate the vulnerability of species to winter climate change. We describe the importance of relationships between winter conditions and performance during the growing season in determining fitness, and demonstrate how summer and winter processes are linked. Incorporating winter into current models will require concerted effort from theoreticians and empiricists, and the expansion of current growing-season studies to incorporate winter

Unraveling genetic predisposition to familial or early onset gastric cancer using germline whole-exome sequencing

Recognition of individuals with a genetic predisposition to gastric cancer (GC) enables preventive measures. However, the underlying cause of genetic susceptibility to gastric cancer remains largely unexplained. We performed germline whole-exome sequencing on leukocyte DNA of 54 patients from 53 families with genetically unexplained diffuse-type and intestinal-type GC to identify novel GC-predisposing candidate genes. As young age at diagnosis and familial clustering are hallmarks of genetic tumor susceptibility, we selected patients that were diagnosed below the age of 35, patients from families with two cases of GC at or below age 60 and patients from families with three GC cases at or below age 70. All included individuals were tested negative for germline CDH1 mutations before or during the study. Variants that were possibly deleterious according to in silico predictions were filtered using several independent approaches that were based on gene function and gene mutation burden in controls. Despite a rigorous search, no obvious candidate GC predisposition genes were identified. This negative result stresses the importance of future research studies in large, homogeneous cohorts

Spin polarization in low-energy electron diffraction from Pt(111): experiment and theory

Bauer P, Feder R, Müller N. Spin polarization in low-energy electron diffraction from Pt(111): experiment and theory. Surface Science Letters. 1980;99(2):L395-L401.Spin polarization in low-energy electron diffraction from the (111) surface of platinum, which is geometrically unreconstructed, was measured by means of a Mott detector. Corresponding relativistic calculations yield mostly excellent agreement with the data and clearly favour an ion-core scattering potential model containing an energy-dependent exchange approximation