Broadband hyperspectral imaging for breast tumor detection using spectral and spatial information

Complete tumor removal during breast-conserving surgery remains challenging due to the lack of optimal intraoperative margin assessment techniques. Here, we use hyperspectral imaging for tumor detection in fresh breast tissue. We evaluated different wavelength ranges and two classification algorithms; a pixel-wise classification algorithm and a convolutional neural network that combines spectral and spatial information. The highest classification performance was obtained using the full wavelength range (450-1650nm). Adding spatial information mainly improved the differentiation of tissue classes within the malignant and healthy classes. High sensitivity and specificity were accomplished, which offers potential for hyperspectral imaging as a margin assessment technique to improve surgical outcome. (C) 2019 Optical Society of America under the terms of the OSA Open Access Publishing Agreemen

Method for coregistration of optical measurements of breast tissue with histopathology : the importance of accounting for tissue deformations

For the validation of optical diagnostic technologies, experimental results need to be benchmarked against the gold standard. Currently, the gold standard for tissue characterization is assessment of hematoxylin and eosin (H&E)-stained sections by a pathologist. When processing tissue into H&E sections, the shape of the tissue deforms with respect to the initial shape when it was optically measured. We demonstrate the importance of accounting for these tissue deformations when correlating optical measurement with routinely acquired histopathology. We propose a method to register the tissue in the H&E sections to the optical measurements, which corrects for these tissue deformations. We compare the registered H&E sections to H&E sections that were registered with an algorithm that does not account for tissue deformations by evaluating both the shape and the composition of the tissue and using microcomputer tomography data as an independent measure. The proposed method, which did account for tissue deformations, was more accurate than the method that did not account for tissue deformations. These results emphasize the need for a registration method that accounts for tissue deformations, such as the method presented in this study, which can aid in validating optical techniques for clinical use. (C) The Authors. Published by SPIE under a Creative Commons Attribution 4.0 Unported License

Written informed consent and selection bias in observational studies using medical records: systematic review

Objectives To determine whether informed consent introduces selection bias in prospective observational studies using data from medical records, and consent rates for such studies

A unified approach for the solution of the Fokker-Planck equation

This paper explores the use of a discrete singular convolution algorithm as a unified approach for numerical integration of the Fokker-Planck equation. The unified features of the discrete singular convolution algorithm are discussed. It is demonstrated that different implementations of the present algorithm, such as global, local, Galerkin, collocation, and finite difference, can be deduced from a single starting point. Three benchmark stochastic systems, the repulsive Wong process, the Black-Scholes equation and a genuine nonlinear model, are employed to illustrate the robustness and to test accuracy of the present approach for the solution of the Fokker-Planck equation via a time-dependent method. An additional example, the incompressible Euler equation, is used to further validate the present approach for more difficult problems. Numerical results indicate that the present unified approach is robust and accurate for solving the Fokker-Planck equation.Comment: 19 page

Fluvial organic carbon fluxes from oil palm plantations on tropical peatland

Intact tropical peatlands are dense long-term stores of carbon. However, the future security of these ecosystems is at risk from land conversion and extensive peatland drainage. This can enhance peat oxidation and convert long-term carbon sinks into significant carbon sources. In Southeast Asia, the largest land use on peatland is for oil palm plantation agriculture. Here, we present the first annual estimate of exported fluvial organic carbon in the drainage waters of four peatland oil palm plantation areas in Sarawak, Malaysia. Total organic carbon (TOC) fluxes from the plantation second- and third-order drains were dominated (91 %) by dissolved organic carbon (DOC) and ranged from 34.4 ± 9.7 C m−2 yr−1 to 57.7 %, 16.3 g C m−2 yr−1 (± 95 % confidence interval). These fluxes represent a single-year survey which was strongly influenced by an El Ninõ event and therefore lower discharge than usual was observed. The magnitude of the flux was found to be influenced by water table depth, with higher TOC fluxes observed from more deeply drained sites. Radiocarbon dating on the DOC component indicated the presence of old (pre-1950s) carbon in all samples collected, with DOC at the most deeply drained site having a mean age of 735 years. Overall, our estimates suggest fluvial TOC contributes ∼ 5 % of total carbon losses from oil palm plantations on peat. Maintenance of high and stable water tables in oil palm plantations appears to be key to minimising TOC losses. This reinforces the importance of considering all carbon loss pathways, rather than just CO2 emissions from the peat surface, in studies of tropical peatland land conversion

A regional informatics platform for coordinated antibiotic resistant infection tracking, alerting and prevention

Background. We developed and assessed the impact of a patient registry and electronic admission notification system relating to regional antimicrobial resistance (AMR) on regional AMR infection rates over time. We conducted an observational cohort study of all patients identified as infected or colonized with methicillin-resistant Staphylococcus aureus (MRSA) and/or vancomycin-resistant enterococci (VRE) on at least 1 occasion by any of 5 healthcare systems between 2003 and 2010. The 5 healthcare systems included 17 hospitals and associated clinics in the Indianapolis, Indiana, region. Methods. We developed and standardized a registry of MRSA and VRE patients and created Web forms that infection preventionists (IPs) used to maintain the lists. We sent e-mail alerts to IPs whenever a patient previously infected or colonized with MRSA or VRE registered for admission to a study hospital from June 2007 through June 2010. Results. Over a 3-year period, we delivered 12 748 e-mail alerts on 6270 unique patients to 24 IPs covering 17 hospitals. One in 5 (22%–23%) of all admission alerts was based on data from a healthcare system that was different from the admitting hospital; a few hospitals accounted for most of this crossover among facilities and systems. Conclusions. Regional patient registries identify an important patient cohort with relevant prior antibiotic-resistant infection data from different healthcare institutions. Regional registries can identify trends and interinstitutional movement not otherwise apparent from single institution data. Importantly, electronic alerts can notify of the need to isolate early and to institute other measures to prevent transmission

Taking monocrystalline silicon to the ultimate lifetime limit

A central quantity to assess the high quality of monocrystalline silicon (on scales beyond mere purity) is the minority charge carrier lifetime. We demonstrate that the lifetime in high purity float zone material can be improved beyond existing observations, thanks to a deeper understanding of grown-in defects and how they can be permanently annihilated. In a first step we investigate the influence of several process sequences on the lifetime by applying a low temperature superacid passivation treatment. We find that a pre-treatment consisting of an oxidation at 1050 °C followed by a POCl3 diffusion at 900 °C can improve the lifetime by deactivating or eliminating grown-in defects. Then, pre-treated wafers of different float zone materials are passivated with three state-of-the-art layer stacks. Very high effective lifetime values are measured, thereby demonstrating the high quality of the surface passivation schemes and the pre-treated silicon wafers. The measured effective lifetimes exceed previous records, and we report an effective lifetime of 225 ms measured on a 200 µm thick 100 Ω cm n-type silicon wafer symmetrically passivated with a layer stack of a thin thermally grown oxide and a polycrystalline layer (the TOPCon layer stack)

Quantitative model for inferring dynamic regulation of the tumour suppressor gene p53

Background: The availability of various "omics" datasets creates a prospect of performing the study of genome-wide genetic regulatory networks. However, one of the major challenges of using mathematical models to infer genetic regulation from microarray datasets is the lack of information for protein concentrations and activities. Most of the previous researches were based on an assumption that the mRNA levels of a gene are consistent with its protein activities, though it is not always the case. Therefore, a more sophisticated modelling framework together with the corresponding inference methods is needed to accurately estimate genetic regulation from "omics" datasets. Results: This work developed a novel approach, which is based on a nonlinear mathematical model, to infer genetic regulation from microarray gene expression data. By using the p53 network as a test system, we used the nonlinear model to estimate the activities of transcription factor (TF) p53 from the expression levels of its target genes, and to identify the activation/inhibition status of p53 to its target genes. The predicted top 317 putative p53 target genes were supported by DNA sequence analysis. A comparison between our prediction and the other published predictions of p53 targets suggests that most of putative p53 targets may share a common depleted or enriched sequence signal on their upstream non-coding region. Conclusions: The proposed quantitative model can not only be used to infer the regulatory relationship between TF and its down-stream genes, but also be applied to estimate the protein activities of TF from the expression levels of its target genes