Crosstalk Correction in Atomic Force Microscopy

Commercial atomic force microscopes usually use a four-segmented photodiode to detect the motion of the cantilever via laser beam deflection. This read-out technique enables to measure bending and torsion of the cantilever separately. A slight angle between the orientation of the photodiode and the plane of the readout beam, however, causes false signals in both readout channels, so-called crosstalk, that may lead to misinterpretation of the acquired data. We demonstrate this fault with images recorded in contact mode on ferroelectric crystals and present an electronic circuit to compensate for it, thereby enabling crosstalk-free imaging

Contrast Mechanisms for the Detection of Ferroelectric Domains with Scanning Force Microscopy

We present a full analysis of the contrast mechanisms for the detection of ferroelectric domains on all faces of bulk single crystals using scanning force microscopy exemplified on hexagonally poled lithium niobate. The domain contrast can be attributed to three different mechanisms: i) the thickness change of the sample due to an out-of-plane piezoelectric response (standard piezoresponse force microscopy), ii) the lateral displacement of the sample surface due to an in-plane piezoresponse, and iii) the electrostatic tip-sample interaction at the domain boundaries caused by surface charges on the crystallographic y- and z-faces. A careful analysis of the movement of the cantilever with respect to its orientation relative to the crystallographic axes of the sample allows a clear attribution of the observed domain contrast to the driving forces respectively.Comment: 8 pages, 8 figure

Critical Casimir effect in classical binary liquid mixtures

If a fluctuating medium is confined, the ensuing perturbation of its fluctuation spectrum generates Casimir-like effective forces acting on its confining surfaces. Near a continuous phase transition of such a medium the corresponding order parameter fluctuations occur on all length scales and therefore close to the critical point this effect acquires a universal character, i.e., to a large extent it is independent of the microscopic details of the actual system. Accordingly it can be calculated theoretically by studying suitable representative model systems. We report on the direct measurement of critical Casimir forces by total internal reflection microscopy (TIRM), with femto-Newton resolution. The corresponding potentials are determined for individual colloidal particles floating above a substrate under the action of the critical thermal noise in the solvent medium, constituted by a binary liquid mixture of water and 2,6-lutidine near its lower consolute point. Depending on the relative adsorption preferences of the colloid and substrate surfaces with respect to the two components of the binary liquid mixture, we observe that, upon approaching the critical point of the solvent, attractive or repulsive forces emerge and supersede those prevailing away from it. Based on the knowledge of the critical Casimir forces acting in film geometries within the Ising universality class and with equal or opposing boundary conditions, we provide the corresponding theoretical predictions for the sphere-planar wall geometry of the experiment. The experimental data for the effective potential can be interpreted consistently in terms of these predictions and a remarkable quantitative agreement is observed.Comment: 30 pages, 17 figure

Collective magnetism at multiferroic vortex domain walls

Topological defects have been playgrounds for many emergent phenomena in complex matter such as superfluids, liquid crystals, and early universe. Recently, vortex-like topological defects with six interlocked structural antiphase and ferroelectric domains merging into a vortex core were revealed in multiferroic hexagonal manganites. Numerous vortices are found to form an intriguing self-organized network. Thus, it is imperative to find out the magnetic nature of these vortices. Using cryogenic magnetic force microscopy, we discovered unprecedented alternating net moments at domain walls around vortices that can correlate over the entire vortex network in hexagonal ErMnO3 The collective nature of domain wall magnetism originates from the uncompensated Er3+ moments and the correlated organization of the vortex network. Furthermore, our proposed model indicates a fascinating phenomenon of field-controllable spin chirality. Our results demonstrate a new route to achieving magnetoelectric coupling at domain walls in single-phase multiferroics, which may be harnessed for nanoscale multifunctional devices.Comment: 18 pages, 10 figure

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment

Climate Change, Foodborne Pathogens, and Illness in Higher Income Countries

Purpose of review: We present a review of the likely consequences of climate change for foodborne pathogens and associated human illness in higher income countries. Recent findings: The relationships between climate and food are complex and hence the impacts of climate change uncertain. This makes it difficult to know which foodborne pathogens will be most affected, what the specific effects will be, and on what timescales changes might occur. Hence, a focus upon current capacity and adaptation potential against foodborne pathogens is essential. We highlight a number of developments that may enhance preparedness for climate change. These include: • Adoption of novel surveillance methods, such as syndromic methods, to speed up detection and increase the fidelity of intervention in foodborne outbreaks • Genotype based approaches to surveillance of food pathogens to enhance spatio-temporal resolution in tracing and tracking of illness • Ever increasing integration of plant, animal and human surveillance systems, one-health, to maximize potential for identifying threats • Increased commitment to cross-border (global) information initiatives (including big data) • Improved clarity regarding the governance of complex societal issues such as the conflict between food safety and food waste • Strong user centric (social) communications strategies to engage diverse stakeholder groups Summary: The impact of climate change upon foodborne pathogens and associated illness is uncertain. This emphasises the need to enhance current capacity and adaptation potential against foodborne illness. A range of developments are explored in this paper to enhance preparedness