More Like this

1. Differences between gridded population data impact measures of geographic access to healthcare in sub-Saharan Africa

   https://doi.org/10.1038/s43856-022-00179-4  

   Hierink, Fleur ; Boo, Gianluca ; Macharia, Peter M. ; Ouma, Paul O. ; Timoner, Pablo ; Levy, Marc ; Tschirhart, Kevin ; Leyk, Stefan ; Oliphant, Nicholas ; Tatem, Andrew J. ; et al ( December 2022 , Communications Medicine)

   Abstract Background Access to healthcare is imperative to health equity and well-being. Geographic access to healthcare can be modeled using spatial datasets on local context, together with the distribution of existing health facilities and populations. Several population datasets are currently available, but their impact on accessibility analyses is unknown. In this study, we model the geographic accessibility of public health facilities at 100-meter resolution in sub-Saharan Africa and evaluate six of the most popular gridded population datasets for their impact on coverage statistics at different administrative levels. Methods Travel time to nearest health facilities was calculated by overlaying health facility coordinates on top of a friction raster accounting for roads, landcover, and physical barriers. We then intersected six different gridded population datasets with our travel time estimates to determine accessibility coverages within various travel time thresholds (i.e., 30, 60, 90, 120, 150, and 180-min). Results Here we show that differences in accessibility coverage can exceed 70% at the sub-national level, based on a one-hour travel time threshold. The differences are most notable in large and sparsely populated administrative units and dramatically shape patterns of healthcare accessibility at national and sub-national levels. Conclusions The results of this study show how valuable and critical a comparative analysis between population datasets is for the derivation of coverage statistics that inform local policies and monitor global targets. Large differences exist between the datasets and the results underscore an essential source of uncertainty in accessibility analyses that should be systematically assessed. 

   more » « less
2. Opioid Treatment Deserts: Concept development and application in a US Midwestern urban county

   https://doi.org/10.1371/journal.pone.0250324  

   Hyder, Ayaz ; Lee, Jinhyung ; Dundon, Ashley ; Southerland, Lauren T. ; All, David ; Hammond, Gretchen ; Miller, Harvey J. ( May 2021 , PLOS ONE)

   West, Brooke (Ed.)

   Objectives An Opioid Treatment Desert is an area with limited accessibility to medication-assisted treatment and recovery facilities for Opioid Use Disorder. We explored the concept of Opioid Treatment Deserts including racial differences in potential spatial accessibility and applied it to one Midwestern urban county using high resolution spatiotemporal data. Methods We obtained individual-level data from one Emergency Medical Services (EMS) agency (Columbus Fire Department) in Franklin County, Ohio. Opioid overdose events were based on EMS runs where naloxone was administered from 1/1/2013 to 12/31/2017. Potential spatial accessibility was measured as the time (in minutes) it would take an individual, who may decide to seek treatment after an opioid overdose, to travel from where they had the overdose event, which was a proxy measure of their residential location, to the nearest opioid use disorder (OUD) treatment provider that provided medically-assisted treatment (MAT). We estimated accessibility measures overall, by race and by four types of treatment providers (any type of MAT for OUD, Buprenorphine, Methadone, or Naltrexone). Areas were classified as an Opioid Treatment Desert if the estimate travel time to treatment provider (any type of MAT for OUD) was greater than a given threshold. We performed sensitivity analysis using a range of threshold values based on multiple modes of transportation (car and public transit) and using only EMS runs to home/residential location types. Results A total of 6,929 geocoded opioid overdose events based on data from EMS agencies were used in the final analysis. Most events occurred among 26–35 years old (34%), identified as White adults (56%) and male (62%). Median travel times and interquartile range (IQR) to closest treatment provider by car and public transit was 2 minutes (IQR: 3 minutes) and 17 minutes (IQR: 17 minutes), respectively. Several neighborhoods in the study area had limited accessibility to OUD treatment facilities and were classified as Opioid Treatment Deserts. Travel time by public transit for most treatment provider types and by car for Methadone-based treatment was significantly different between individuals who were identified as Black adults and White adults based on their race. Conclusions Disparities in access to opioid treatment exist at the sub-county level in specific neighborhoods and across racial groups in Columbus, Ohio and can be quantified and visualized using local public safety data (e.g., EMS runs). Identification of Opioid Treatment Deserts can aid multiple stakeholders better plan and allocate resources for more equitable access to MAT for OUD and, therefore, reduce the burden of the opioid epidemic while making better use of real-time public safety data to address a public health epidemic that has turned into a public safety crisis. 

   more » « less
3. Can Tanker Water Services Contribute to Sustainable Access to Water? A Systematic Review of Case Studies in Urban Areas

   https://doi.org/10.3390/su141711029  

   Zozmann, Heinrich ; Morgan, Alexander ; Klassert, Christian ; Klauer, Bernd ; Gawel, Erik ( September 2022 , Sustainability)

   Tanker water markets (TWM) supply water services in many urban areas, including those unconnected to public infrastructures. Notwithstanding, they have been associated with outcomes in conflict with sustainability goals of water policy, e.g., through inequitable and unaffordable supply or by contributing to groundwater overexploitation. So far, the literature dedicated to TWM has primarily conducted case studies embedded in diverse local contexts, which impedes the comparison and transfer of insights. In this article, we systematically summarize existing empirical knowledge on TWM and assess to what extent normative claims about the impacts of TWM on sustainability goals are supported by evidence. We use the concept of sustainable access, which combines notions of what constitutes access to water and what characterizes sustainable supply of services. The available evidence suggests that TWM have two key functions in urban water systems: (1) They provide services at otherwise unavailable levels, particularly with respect to the temporal availability and spatial accessibility of the service, and (2) they extend access to areas without or with low-quality network supply, typically low-income communities on the fringe of cities. From the perspective of sustainable access, we find that TWM can provide high service levels and thus fill a specific gap in the landscape of urban water services. Due to comparatively high prices, however, it is unlikely that these services are affordable for all. The combination of heterogeneous access to cheaper (subsidized) piped water and marginal pricing in TWM results in allocation outcomes that are not coherent with existing notions of equitable access to water. However, there is little convincing evidence that TWM necessarily result in unsustainable water use. The literature indicates that urban water governance in the studied areas is frequently characterized by a lack of effective institutions, which impedes the regulation or formalization of TWM. 

   more » « less
4. Assessing Trauma Center Accessibility for Healthcare Equity Using an Anti-Covering Approach

   https://doi.org/10.3390/ijerph19031459  

   Chea, Heewon ; Kim, Hyun ; Shaw, Shih-Lung ; Chun, Yongwan ( February 2022 , International Journal of Environmental Research and Public Health)

   Motor vehicle accidents are one of the most prevalent causes of traumatic injury in patients needing transport to a trauma center. Arrival at a trauma center within an hour of the accident increases a patient’s chances of survival and recovery. However, not all vehicle accidents in Tennessee are accessible to a trauma center within an hour by ground transportation. This study uses the anti-covering location problem (ACLP) to assess the current placement of trauma centers and explore optimal placements based on the population distribution and spatial pattern of motor vehicle accidents in 2015 through 2019 in Tennessee. The ACLP models seek to offer a method of exploring feasible scenarios for locating trauma centers that intend to provide accessibility to patients in underserved areas who suffer trauma as a result of vehicle accidents. The proposed ACLP approach also seeks to adjust the locations of trauma centers to reduce areas with excessive service coverage while improving coverage for less accessible areas of demand. In this study, three models are prescribed for finding optimal locations for trauma centers: (a) TraCt: ACLP model with a geometric approach and weighted models of population, fatalities, and spatial fatality clusters of vehicle accidents; (b) TraCt-ESC: an extended ACLP model mitigating excessive service supply among trauma center candidates, while expanding services to less served areas for more beneficiaries using fewer facilities; and (c) TraCt-ESCr: another extended ACLP model exploring the optimal location of additional trauma centers. 

   more » « less
5. The Temple University Digital Pathology Corpus: The Breast Tissue Subset

   https://doi.org/10.1109/SPMB52430.2021.9672275  

   Wevodau, Z. ; Doshna, B. ; Jhala, N. ; Akhtar, I. ; Obeid, I. ; Picone, J. ( December 2021 , Proceedings of the IEEE Signal Processing in Medicine and Biology Symposium (SPMB))

   Obeid, I. (Ed.)

   The Neural Engineering Data Consortium (NEDC) is developing the Temple University Digital Pathology Corpus (TUDP), an open source database of high-resolution images from scanned pathology samples [1], as part of its National Science Foundation-funded Major Research Instrumentation grant titled “MRI: High Performance Digital Pathology Using Big Data and Machine Learning” [2]. The long-term goal of this project is to release one million images. We have currently scanned over 100,000 images and are in the process of annotating breast tissue data for our first official corpus release, v1.0.0. This release contains 3,505 annotated images of breast tissue including 74 patients with cancerous diagnoses (out of a total of 296 patients). In this poster, we will present an analysis of this corpus and discuss the challenges we have faced in efficiently producing high quality annotations of breast tissue. It is well known that state of the art algorithms in machine learning require vast amounts of data. Fields such as speech recognition [3], image recognition [4] and text processing [5] are able to deliver impressive performance with complex deep learning models because they have developed large corpora to support training of extremely high-dimensional models (e.g., billions of parameters). Other fields that do not have access to such data resources must rely on techniques in which existing models can be adapted to new datasets [6]. A preliminary version of this breast corpus release was tested in a pilot study using a baseline machine learning system, ResNet18 [7], that leverages several open-source Python tools. The pilot corpus was divided into three sets: train, development, and evaluation. Portions of these slides were manually annotated [1] using the nine labels in Table 1 [8] to identify five to ten examples of pathological features on each slide. Not every pathological feature is annotated, meaning excluded areas can include focuses particular to these labels that are not used for training. A summary of the number of patches within each label is given in Table 2. To maintain a balanced training set, 1,000 patches of each label were used to train the machine learning model. Throughout all sets, only annotated patches were involved in model development. The performance of this model in identifying all the patches in the evaluation set can be seen in the confusion matrix of classification accuracy in Table 3. The highest performing labels were background, 97% correct identification, and artifact, 76% correct identification. A correlation exists between labels with more than 6,000 development patches and accurate performance on the evaluation set. Additionally, these results indicated a need to further refine the annotation of invasive ductal carcinoma (“indc”), inflammation (“infl”), nonneoplastic features (“nneo”), normal (“norm”) and suspicious (“susp”). This pilot experiment motivated changes to the corpus that will be discussed in detail in this poster presentation. To increase the accuracy of the machine learning model, we modified how we addressed underperforming labels. One common source of error arose with how non-background labels were converted into patches. Large areas of background within other labels were isolated within a patch resulting in connective tissue misrepresenting a non-background label. In response, the annotation overlay margins were revised to exclude benign connective tissue in non-background labels. Corresponding patient reports and supporting immunohistochemical stains further guided annotation reviews. The microscopic diagnoses given by the primary pathologist in these reports detail the pathological findings within each tissue site, but not within each specific slide. The microscopic diagnoses informed revisions specifically targeting annotated regions classified as cancerous, ensuring that the labels “indc” and “dcis” were used only in situations where a micropathologist diagnosed it as such. Further differentiation of cancerous and precancerous labels, as well as the location of their focus on a slide, could be accomplished with supplemental immunohistochemically (IHC) stained slides. When distinguishing whether a focus is a nonneoplastic feature versus a cancerous growth, pathologists employ antigen targeting stains to the tissue in question to confirm the diagnosis. For example, a nonneoplastic feature of usual ductal hyperplasia will display diffuse staining for cytokeratin 5 (CK5) and no diffuse staining for estrogen receptor (ER), while a cancerous growth of ductal carcinoma in situ will have negative or focally positive staining for CK5 and diffuse staining for ER [9]. Many tissue samples contain cancerous and non-cancerous features with morphological overlaps that cause variability between annotators. The informative fields IHC slides provide could play an integral role in machine model pathology diagnostics. Following the revisions made on all the annotations, a second experiment was run using ResNet18. Compared to the pilot study, an increase of model prediction accuracy was seen for the labels indc, infl, nneo, norm, and null. This increase is correlated with an increase in annotated area and annotation accuracy. Model performance in identifying the suspicious label decreased by 25% due to the decrease of 57% in the total annotated area described by this label. A summary of the model performance is given in Table 4, which shows the new prediction accuracy and the absolute change in error rate compared to Table 3. The breast tissue subset we are developing includes 3,505 annotated breast pathology slides from 296 patients. The average size of a scanned SVS file is 363 MB. The annotations are stored in an XML format. A CSV version of the annotation file is also available which provides a flat, or simple, annotation that is easy for machine learning researchers to access and interface to their systems. Each patient is identified by an anonymized medical reference number. Within each patient’s directory, one or more sessions are identified, also anonymized to the first of the month in which the sample was taken. These sessions are broken into groupings of tissue taken on that date (in this case, breast tissue). A deidentified patient report stored as a flat text file is also available. Within these slides there are a total of 16,971 total annotated regions with an average of 4.84 annotations per slide. Among those annotations, 8,035 are non-cancerous (normal, background, null, and artifact,) 6,222 are carcinogenic signs (inflammation, nonneoplastic and suspicious,) and 2,714 are cancerous labels (ductal carcinoma in situ and invasive ductal carcinoma in situ.) The individual patients are split up into three sets: train, development, and evaluation. Of the 74 cancerous patients, 20 were allotted for both the development and evaluation sets, while the remain 34 were allotted for train. The remaining 222 patients were split up to preserve the overall distribution of labels within the corpus. This was done in hope of creating control sets for comparable studies. Overall, the development and evaluation sets each have 80 patients, while the training set has 136 patients. In a related component of this project, slides from the Fox Chase Cancer Center (FCCC) Biosample Repository (https://www.foxchase.org/research/facilities/genetic-research-facilities/biosample-repository -facility) are being digitized in addition to slides provided by Temple University Hospital. This data includes 18 different types of tissue including approximately 38.5% urinary tissue and 16.5% gynecological tissue. These slides and the metadata provided with them are already anonymized and include diagnoses in a spreadsheet with sample and patient ID. We plan to release over 13,000 unannotated slides from the FCCC Corpus simultaneously with v1.0.0 of TUDP. Details of this release will also be discussed in this poster. Few digitally annotated databases of pathology samples like TUDP exist due to the extensive data collection and processing required. The breast corpus subset should be released by November 2021. By December 2021 we should also release the unannotated FCCC data. We are currently annotating urinary tract data as well. We expect to release about 5,600 processed TUH slides in this subset. We have an additional 53,000 unprocessed TUH slides digitized. Corpora of this size will stimulate the development of a new generation of deep learning technology. In clinical settings where resources are limited, an assistive diagnoses model could support pathologists’ workload and even help prioritize suspected cancerous cases. ACKNOWLEDGMENTS This material is supported by the National Science Foundation under grants nos. CNS-1726188 and 1925494. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation. REFERENCES [1] N. Shawki et al., “The Temple University Digital Pathology Corpus,” in Signal Processing in Medicine and Biology: Emerging Trends in Research and Applications, 1st ed., I. Obeid, I. Selesnick, and J. Picone, Eds. New York City, New York, USA: Springer, 2020, pp. 67 104. https://www.springer.com/gp/book/9783030368432. [2] J. Picone, T. Farkas, I. Obeid, and Y. Persidsky, “MRI: High Performance Digital Pathology Using Big Data and Machine Learning.” Major Research Instrumentation (MRI), Division of Computer and Network Systems, Award No. 1726188, January 1, 2018 – December 31, 2021. https://www. isip.piconepress.com/projects/nsf_dpath/. [3] A. Gulati et al., “Conformer: Convolution-augmented Transformer for Speech Recognition,” in Proceedings of the Annual Conference of the International Speech Communication Association (INTERSPEECH), 2020, pp. 5036-5040. https://doi.org/10.21437/interspeech.2020-3015. [4] C.-J. Wu et al., “Machine Learning at Facebook: Understanding Inference at the Edge,” in Proceedings of the IEEE International Symposium on High Performance Computer Architecture (HPCA), 2019, pp. 331–344. https://ieeexplore.ieee.org/document/8675201. [5] I. Caswell and B. Liang, “Recent Advances in Google Translate,” Google AI Blog: The latest from Google Research, 2020. [Online]. Available: https://ai.googleblog.com/2020/06/recent-advances-in-google-translate.html. [Accessed: 01-Aug-2021]. [6] V. Khalkhali, N. Shawki, V. Shah, M. Golmohammadi, I. Obeid, and J. Picone, “Low Latency Real-Time Seizure Detection Using Transfer Deep Learning,” in Proceedings of the IEEE Signal Processing in Medicine and Biology Symposium (SPMB), 2021, pp. 1 7. https://www.isip. piconepress.com/publications/conference_proceedings/2021/ieee_spmb/eeg_transfer_learning/. [7] J. Picone, T. Farkas, I. Obeid, and Y. Persidsky, “MRI: High Performance Digital Pathology Using Big Data and Machine Learning,” Philadelphia, Pennsylvania, USA, 2020. https://www.isip.piconepress.com/publications/reports/2020/nsf/mri_dpath/. [8] I. Hunt, S. Husain, J. Simons, I. Obeid, and J. Picone, “Recent Advances in the Temple University Digital Pathology Corpus,” in Proceedings of the IEEE Signal Processing in Medicine and Biology Symposium (SPMB), 2019, pp. 1–4. https://ieeexplore.ieee.org/document/9037859. [9] A. P. Martinez, C. Cohen, K. Z. Hanley, and X. (Bill) Li, “Estrogen Receptor and Cytokeratin 5 Are Reliable Markers to Separate Usual Ductal Hyperplasia From Atypical Ductal Hyperplasia and Low-Grade Ductal Carcinoma In Situ,” Arch. Pathol. Lab. Med., vol. 140, no. 7, pp. 686–689, Apr. 2016. https://doi.org/10.5858/arpa.2015-0238-OA. 

   more » « less