Hardware Implementation of a Fixed-Point Decoder for Low-Density Lattice Codes

This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.This paper describes a field-programmable gate array (FPGA) implementation of a fixed-point low-density lattice code (LDLC) decoder where the Gaussian mixture messages that are exchanged during the iterative decoding process are approxi- mated to a single Gaussian. A detailed quantization study is first performed to find the minimum number of bits required for the fixed-point decoder to attain a frame error rate (FER) performance similar to floating-point. Then efficient numeri- cal methods are devised to approximate the required non-linear functions. Finally, the paper presents a comparison of the performance of the different decoder architectures as well as a detailed analysis of the resource requirements and through- put trade-offs of the primary design blocks for the different architectures. A novel pipelined LDLC decoder architecture is proposed where resource re-utilization along with pipelining allows for a parallelism equivalent to 50 variable nodes on the target FPGA device. The pipelined architecture attains a throughput of 10.5 Msymbols/sec at a distance of 5 dB from capacity which is a 1.8× improvement in throughput compared to an implementation with 20 parallel variable nodes without pipelining. This implementation also achieves 24× improvement in throughput over a baseline serial decoder.NSERC || CMC Microsystem

Machine Learning in the Nuclear Medicine: Part 2-Neural Networks and Clinical Aspects

COPYRIGHT © 2021 by the Society of Nuclear Medicine and Molecular Imaging.This article is the second part in our machine learning series. Part 1 provided a general overview of machine learning in nuclear medicine. Part 2 focuses on neural networks. We start with an example illustrating how neural networks work and a discussion of potential applications. Recognizing that there is a spectrum of applications, we focus on recent publications in the areas of image reconstruction, low-dose PET, disease detection, and models used for diagnosis and outcome prediction. Finally, since the way machine learning algo- rithms are reported in the literature is extremely variable, we conclude with a call to arms regarding the need for standardized reporting of design and outcome metrics and we propose a basic checklist our community might follow going forward

Exploratory Assessment of K-means Clustering to Classify 18F-Flutemetamol Brain PET as Positive or Negative

Copyright © 2021 Wolters Kluwer Health, Inc. All rights reserved.Rationale: We evaluated K-means clustering to classify amyloid brain PETs as positive or negative. Patients and Methods: Sixty-six participants (31 men, 35 women; age range, 52–81 years) were recruited through a multicenter observational study: 19 cognitively normal, 25 mild cognitive impairment, and 22 demen- tia (11 Alzheimer disease, 3 subcortical vascular cognitive impairment, and 8 Parkinson–Lewy Body spectrum disorder). As part of the neurocognitive and imaging evaluation, each participant had an 18F-flutemetamol (Vizamyl, GE Healthcare) brain PET. All studies were processed using Cortex ID soft- ware (General Electric Company, Boston, MA) to calculate SUV ratios in 19 regions of interest and clinically interpreted by 2 dual-certified radiologists/ nuclear medicine physicians, using MIM software (MIM Software Inc, Cleveland, OH), blinded to the quantitative analysis, with final interpreta- tion based on consensus. K-means clustering was retrospectively used to classify the studies from the quantitative data. Results: Based on clinical interpretation, 46 brain PETs were negative and 20 were positive for amyloid deposition. Of 19 cognitively normal partici- pants, 1 (5%) had a positive 18F-flutemetamol brain PET. Of 25 participants with mild cognitive impairment, 9 (36%) had a positive 18F-flutemetamol brain PET. Of 22 participants with dementia, 10 (45%) had a positive 18F-flutemetamol brain PET; 7 of 11 participants with Alzheimer disease (64%), 1 of 3 participants with vascular cognitive impairment (33%), and 2 of 8 participants with Parkinson–Lewy Body spectrum disorder (25%) had a positive 18F-flutemetamol brain PET. Using clinical interpretation as the criterion standard, K-means clustering (K = 2) gave sensitivity of 95%, specificity of 98%, and accuracy of 97%. Conclusions: K-means clustering may be a powerful algorithm for classifying amyloid brain PET.This is a multisite project of the Toronto Dementia Research Alli- ance (www.tdra.utoronto.ca) partly funded by Brain Canada, The Edward Foundation, the Canadian Institutes of Health Research (FDN 159910), the LC Campbell Cognitive Neurology Research Unit, Sunnybrook Research Institute, and the Dr Sandra Black Cen- tre for Brain Resilience and Recovery. M.F. received support from the Saul A. Silverman Family Foundation as a Canada Interna- tional Scientific Exchange Program and the Morris Kerzner Memo- rial Fund. We gratefully acknowledge GE Healthcare and the CAMH Brain Health Imaging Centre for manufacturing and sup- plying the ligand. We are also grateful to GE Healthcare for provid- ing the software to calculate the brain region of interest SUV ratios. The study protocol, Brain Eye Amyloid Memory study (BEAM), is registered at https://clinicaltrials.gov/ct2/show/NCT02524405? term=beam+sandra+black&rank=1

The use of random forests to classify amyloid brain PET

Copyright © 2019 Wolters Kluwer Health, Inc. All rights reserved.Purpose: To evaluate random forests (RFs) as a supervised machine learning algorithm to classify amyloid brain PET as positive or negative for amyloid deposition and identify key regions of interest for stratification. Methods: The data set included 57 baseline 18F-florbetapir (Amyvid; Lilly, Indianapolis, IN) brain PET scans in participants with severe white matter disease, presenting with either transient ischemic attack/lacunar stroke or mild cognitive impairment from early Alzheimer disease, enrolled in a multicenter prospective observational trial. Scans were processed using the MINC toolkit to generate SUV ratios, normalized to cerebellar gray matter, and clinically read by 2 nuclear medicine physicians with interpretation based on consensus (35 negative, 22 positive). SUV ratio data and clinical reads were used for super- vised training of an RF classifier programmed in MATLAB. Results: A 10,000-tree RF, each tree using 15 randomly selected cases and 20 randomly selected features (SUV ratio per region of interest), with 37 cases for training and 20 cases for testing, had sensitivity = 86% (95% confidence in- terval [CI], 42%–100%), specificity = 92% (CI, 64%–100%), and classification accuracy = 90% (CI, 68%–99%). The most common features at the root node (key regions for stratification) were (1) left posterior cingulate (1039 trees), (2) left middle frontal gyrus (1038 trees), (3) left precuneus (857 trees), (4) right an- terior cingulate gyrus (655 trees), and (5) right posterior cingulate (588 trees). Conclusions: Random forests can classify brain PET as positive or negative for amyloid deposition and suggest key clinically relevant, regional features for classification.CIHR MITNEC C6 || Linda C Campbell Foundation || Lilly-Avid Radiopharmaceuticals

The Use of Random Forests to Identify Brain Regions on Amyloid and FDG PET Associated With MoCA Score

Copyright © 2020 Wolters Kluwer Health, Inc. All rights reserved.Purpose: The aim of this study was to evaluate random forests (RFs) to identify ROIs on 18F-florbetapir and 18F-FDG PET associated with Montreal Cognitive Assessment (MoCA) score. Materials and Methods: Fifty-seven subjects with significant white matter disease presenting with either transient ischemic attack/lacunar stroke or mild cognitive impairment from early Alzheimer disease, enrolled in a mul- ticenter prospective observational trial, had MoCA and 18F-florbetapir PET; 55 had 18F-FDG PET. Scans were processed using the MINC toolkit to gen- erate SUV ratios, normalized to cerebellar gray matter (18F-florbetapir PET), or pons (18F-FDG PET). SUV ratio data and MoCA score were used for su- pervised training of RFs programmed in MATLAB. Results: 18F-Florbetapir PETs were randomly divided into 40 training and 17 testing scans; 100 RFs of 1000 trees, constructed from a random subset of 16 training scans and 20 ROIs, identified ROIs associated with MoCA score: right posterior cingulate gyrus, right anterior cingulate gyrus, left precuneus, left posterior cingulate gyrus, and right precuneus. Amyloid in- creased with decreasing MoCA score. 18F-FDG PETs were randomly di- vided into 40 training and 15 testing scans; 100 RFs of 1000 trees, each tree constructed from a random subset of 16 training scans and 20 ROIs, identified ROIs associated with MoCA score: left fusiform gyrus, left precuneus, left posterior cingulate gyrus, right precuneus, and left middle orbitofrontal gyrus. 18F-FDG decreased with decreasing MoCA score. Conclusions: Random forests help pinpoint clinically relevant ROIs associ- ated with MoCA score; amyloid increased and 18F-FDG decreased with de- creasing MoCA score, most significantly in the posterior cingulate gyrus.CIHR MITNEC C6 || Linda C Campbell Foundation || Lilly-Avid Radiopharmaceuticals

Identification of a BRCA2-Specific modifier locus at 6p24 related to breast cancer risk

Common genetic variants contribute to the observed variation in breast cancer risk for BRCA2 mutation carriers; those known to date have all been found through population-based genome-wide association studies (GWAS). To comprehensively identify breast cancer risk modifying loci for BRCA2 mutation carriers, we conducted a deep replication of an ongoing GWAS discovery study. Using the ranked P-values of the breast cancer associations with the imputed genotype of 1.4 M SNPs, 19,029 SNPs were selected and designed for inclusion on a custom Illumina array that included a total of 211,155 SNPs as part of a multi-consortial project. DNA samples from 3,881 breast cancer affected and 4,330 unaffected BRCA2 mutation carriers from 47 studies belonging to the Consortium of Investigators of Modifiers of BRCA1/2 were genotyped and available for analysis. We replicated previously reported breast cancer susceptibility alleles in these BRCA2 mutation carriers and for several regions (including FGFR2, MAP3K1, CDKN2A/B, and PTHLH) identified SNPs that have stronger evidence of association than those previously published. We also identified a novel susceptibility allele at 6p24 that was inversely associated with risk in BRCA2 mutation carriers (rs9348512; per allele HR = 0.85, 95% CI 0.80-0.90, P = 3.9×10−8). This SNP was not associated with breast cancer risk either in the general population or in BRCA1 mutation carriers. The locus lies within a region containing TFAP2A, which encodes a transcriptional activation protein that interacts with several tumor suppressor genes. This report identifies the first breast cancer risk locus specific to a BRCA2 mutation background. This comprehensive update of novel and previously reported breast cancer susceptibility loci contributes to the establishment of a panel of SNPs that modify breast cancer risk in BRCA2 mutation carriers. This panel may have clinical utility for women with BRCA2 mutations weighing options for medical prevention of breast cancer

Genome-Wide Association Study in BRCA1 Mutation Carriers Identifies Novel Loci Associated with Breast and Ovarian Cancer Risk

BRCA1-associated breast and ovarian cancer risks can be modified by common genetic variants. To identify further cancer risk-modifying loci, we performed a multi-stage GWAS of 11,705 BRCA1 carriers (of whom 5,920 were diagnosed with breast and 1,839 were diagnosed with ovarian cancer), with a further replication in an additional sample of 2,646 BRCA1 carriers. We identified a novel breast cancer risk modifier locus at 1q32 for BRCA1 carriers (rs2290854, P = 2.7×10-8, HR = 1.14, 95% CI: 1.09-1.20). In addition, we identified two novel ovarian cancer risk modifier loci: 17q21.31 (rs17631303, P = 1.4×10-8, HR = 1.27, 95% CI: 1.17-1.38) and 4q32.3 (rs4691139, P = 3.4×10-8, HR = 1.20, 95% CI: 1.17-1.38). The 4q32.3 locus was not associated with ovarian cancer risk in the general population or BRCA2 carriers, suggesting a BRCA1-specific associat

Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)1.

In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field