An open-source deep learning algorithm for efficient and fully-automatic analysis of the choroid in optical coherence tomography

Purpose: To develop an open-source, fully-automatic deep learning algorithm, DeepGPET, for choroid region segmentation in optical coherence tomography (OCT) data. Methods: We used a dataset of 715 OCT B-scans (82 subjects, 115 eyes) from 3 clinical studies related to systemic disease. Ground truth segmentations were generated using a clinically validated, semi-automatic choroid segmentation method, Gaussian Process Edge Tracing (GPET). We finetuned a UNet with MobileNetV3 backbone pre-trained on ImageNet. Standard segmentation agreement metrics, as well as derived measures of choroidal thickness and area, were used to evaluate DeepGPET, alongside qualitative evaluation from a clinical ophthalmologist. Results: DeepGPET achieves excellent agreement with GPET on data from 3 clinical studies (AUC=0.9994, Dice=0.9664; Pearson correlation of 0.8908 for choroidal thickness and 0.9082 for choroidal area), while reducing the mean processing time per image on a standard laptop CPU from 34.49s ($\pm$15.09) using GPET to 1.25s ($\pm$0.10) using DeepGPET. Both methods performed similarly according to a clinical ophthalmologist, who qualitatively judged a subset of segmentations by GPET and DeepGPET, based on smoothness and accuracy of segmentations. Conclusions :DeepGPET, a fully-automatic, open-source algorithm for choroidal segmentation, will enable researchers to efficiently extract choroidal measurements, even for large datasets. As no manual interventions are required, DeepGPET is less subjective than semi-automatic methods and could be deployed in clinical practice without necessitating a trained operator. DeepGPET addresses the lack of open-source, fully-automatic and clinically relevant choroid segmentation algorithms, and its subsequent public release will facilitate future choroidal research both in ophthalmology and wider systemic health.Comment: 8 pages, 2 figures, 3 tables. Currently in submission to ARVO TVST (Association for Research in Vision and Ophthalmology, Translational Vision Science & Technology). GitHub link to codebase provided upon publicatio

Radio Astronomy

Contains table of contents and reports on seven research projects.National Science Foundation (Grant AST 86-17172)National Aeronautics and Space AdministrationJet Propulsion LaboratoryNASA/Goddard Space Flight Center (Grant NAG5-10)SM Systems and Research, Inc.U.S. Navy Office of Naval Research (Contract N00014-86-C-2114)Center for Advanced Television StudiesNASA/Goddard Space Flight Center (Grant NAG5-537

Radio Astronomy

Contains table of contents for Section 4 and reports on twelve research projects.National Science Foundation Grant AST 88-19848Jet Propulsion Laboratory Contract 957687National Aeronautics and Space Administration Grant NAGW 1386National Science Foundation Grant AST 88-19848Annie Jump Cannon AwardSM Systems and Research, Inc.U.S. Navy Office of Naval Research Contract N00014-88-K-2016NASA/Goddard Space Flight Center Grant NAG 5-537NASA/Goddard Space Flight Center Grant NAG 5-10Woods Hole Oceanographic Institution Contract SC-28860Leaders for Manufacturing Progra

Radio Astronomy

Contains reports on nine research projects.National Science Foundation (Grant AST 86-17172)National Aeronautics and Space Administration (Contract NAS7-918)Jet Propulsion Laboratory (Contract 958048)U.S. Navy - Office of Naval Research (Contract N00014-84-C-2082)U.S. Navy - Office of Naval Research (Contract N00014-86-C-2114)SM Systems and Research, Inc.National Aeronautics and Space Administration/Goddard Space Flight Center (Grant NAG5-10)Center for Advanced Television StudiesBrazil, Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (Grant 300.832-82)National Aeronautics and Space Administration/Goddard Space Flight Center (Grant NAG5-537

Rare coding variants in PLCG2, ABI3, and TREM2 implicate microglial-mediated innate immunity in Alzheimer's disease

We identified rare coding variants associated with Alzheimer’s disease (AD) in a 3-stage case-control study of 85,133 subjects. In stage 1, 34,174 samples were genotyped using a whole-exome microarray. In stage 2, we tested associated variants (P<1×10-4) in 35,962 independent samples using de novo genotyping and imputed genotypes. In stage 3, an additional 14,997 samples were used to test the most significant stage 2 associations (P<5×10-8) using imputed genotypes. We observed 3 novel genome-wide significant (GWS) AD associated non-synonymous variants; a protective variant in PLCG2 (rs72824905/p.P522R, P=5.38×10-10, OR=0.68, MAFcases=0.0059, MAFcontrols=0.0093), a risk variant in ABI3 (rs616338/p.S209F, P=4.56×10-10, OR=1.43, MAFcases=0.011, MAFcontrols=0.008), and a novel GWS variant in TREM2 (rs143332484/p.R62H, P=1.55×10-14, OR=1.67, MAFcases=0.0143, MAFcontrols=0.0089), a known AD susceptibility gene. These protein-coding changes are in genes highly expressed in microglia and highlight an immune-related protein-protein interaction network enriched for previously identified AD risk genes. These genetic findings provide additional evidence that the microglia-mediated innate immune response contributes directly to AD development

A novel Alzheimer disease locus located near the gene encoding tau protein

This is the author accepted manuscript. The final version is available from the publisher via the DOI in this recordAPOE ε4, the most significant genetic risk factor for Alzheimer disease (AD), may mask effects of other loci. We re-analyzed genome-wide association study (GWAS) data from the International Genomics of Alzheimer's Project (IGAP) Consortium in APOE ε4+ (10 352 cases and 9207 controls) and APOE ε4- (7184 cases and 26 968 controls) subgroups as well as in the total sample testing for interaction between a single-nucleotide polymorphism (SNP) and APOE ε4 status. Suggestive associations (P<1 × 10-4) in stage 1 were evaluated in an independent sample (stage 2) containing 4203 subjects (APOE ε4+: 1250 cases and 536 controls; APOE ε4-: 718 cases and 1699 controls). Among APOE ε4- subjects, novel genome-wide significant (GWS) association was observed with 17 SNPs (all between KANSL1 and LRRC37A on chromosome 17 near MAPT) in a meta-analysis of the stage 1 and stage 2 data sets (best SNP, rs2732703, P=5·8 × 10-9). Conditional analysis revealed that rs2732703 accounted for association signals in the entire 100-kilobase region that includes MAPT. Except for previously identified AD loci showing stronger association in APOE ε4+ subjects (CR1 and CLU) or APOE ε4- subjects (MS4A6A/MS4A4A/MS4A6E), no other SNPs were significantly associated with AD in a specific APOE genotype subgroup. In addition, the finding in the stage 1 sample that AD risk is significantly influenced by the interaction of APOE with rs1595014 in TMEM106B (P=1·6 × 10-7) is noteworthy, because TMEM106B variants have previously been associated with risk of frontotemporal dementia. Expression quantitative trait locus analysis revealed that rs113986870, one of the GWS SNPs near rs2732703, is significantly associated with four KANSL1 probes that target transcription of the first translated exon and an untranslated exon in hippocampus (P≤1.3 × 10-8), frontal cortex (P≤1.3 × 10-9) and temporal cortex (P≤1.2 × 10-11). Rs113986870 is also strongly associated with a MAPT probe that targets transcription of alternatively spliced exon 3 in frontal cortex (P=9.2 × 10-6) and temporal cortex (P=2.6 × 10-6). Our APOE-stratified GWAS is the first to show GWS association for AD with SNPs in the chromosome 17q21.31 region. Replication of this finding in independent samples is needed to verify that SNPs in this region have significantly stronger effects on AD risk in persons lacking APOE ε4 compared with persons carrying this allele, and if this is found to hold, further examination of this region and studies aimed at deciphering the mechanism(s) are warranted

Developing the assessment literacy of teachers in Chinese language classrooms: A focus on assessment task design

A teacher’s assessment literacy refers to her or his demonstrated understanding of the principles behind selecting and designing tasks, judging student work, and interpreting and using assessment data to support student learning. This study examines the development of the task design aspect of assessment literacy in 12 Chinese language teachers as they participated in a two-year authentic assessment professional development program. By analysing the quality of assessment tasks designed by the teachers over time, we found that, although teachers quickly grasped many aspects of task design, they found it difficult to incorporate certain knowledge manipulation criteria into their assessments. The study provides insights into the contextual and discipline-embedded challenges that face language teachers with regard to assessment.</p

Access to Palliative Care Services: Innovative Development of a Statewide Network

In 2018, the Avera Sacred Heart Hospital and two partners were awarded a planning grant to improve palliative health care services in South Dakota (SD), United States, by assessing palliative care in rural SD communities. Through this effort, a newly formed South Dakota Palliative Care Network (SDPCN) convened statewide partners to develop a palliative care strategy for improving quality palliative care access for individuals with serious illness. Guided by a multidisciplinary governing board, the SDPCN completed needs assessments to (1) better understand the perception of palliative care in SD; (2) assess the palliative care landscape in the state; and (3) explore possible solutions to address the uneven access to palliative care. This article shares the process of network development, considers the future of the SDPCN, and provides a blueprint for improving palliative care in rural areas. The SDPCN sought first to inventory community-based palliative care resources and increase awareness of the need for services followed by addressing gaps identified through a comprehensive assessment. The SDPCN has engaged partners, captured data, and mapped a blueprint for sustaining accessible quality palliative care. Three years since its inception, the SDPCN secured additional funding to sustain the Network and to provide education on palliative care to providers and community members as a first strategic step toward improving overall palliative care in rural communities. The SDPCN currently serves rural SD patients by increasing knowledge of palliative care among health professionals (current and future), fostering Network member engagement, and maintaining an active governing board