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1. Assessing resilience of hospitals to cyberattack

   https://doi.org/10.1177/20552076211059366  

   Ghayoomi, Hadi ; Laskey, Kathryn ; Miller-Hooks, Elise ; Hooks, Charles ; Tariverdi, Mersedeh ( January 2021 , DIGITAL HEALTH)

   Objective This paper investigates the impact on emergency hospital services from initiation through recovery of a ransomware attack affecting the emergency department, intensive care unit and supporting laboratory services. Recovery strategies of paying ransom to the attackers with follow-on restoration and in-house full system restoration from backup are compared. Methods A multi-unit, patient-based and resource-constrained discrete-event simulation model of a typical U.S. urban tertiary hospital is adapted to model the attack, its impacts, and tested recovery strategies. The model is used to quantify the hospital's resilience to cyberattack. Insights were gleaned from systematically designed numerical experiments. Results While paying the ransom was found to result in some short-term gains assuming the perpetrators actually provide the decryption key as promised, in the longer term, the results of this study suggest that paying the ransom does not pay off. Rather, paying the ransom, when considered at the end of the event when services are fully restored, precluded significantly more patients from receiving critically needed care. Also noted was a lag in recovery for the intensive care unit as compared with the emergency department. Such a lag must be considered in preparedness plans. Conclusion Vulnerability to cyberattacks is a major challenge to themore »healthcare system. This paper provides a methodology for assessing the resilience of a hospital to cyberattacks and analyzing the effects of different response strategies. The model showed that paying the ransom resulted in short-term gains but did not pay off in the longer term.« less
2. Reduction in urban water use leads to less wastewater and fewer emissions:analysis of three representative U.S. cities

   https://doi.org/10.1088/1748-9326/ab8dd8  

   Gursel, Aysegul Petek ; Chaudron, Camille ; Kavvada, Ioanna ; Horvath, Arpad ( July 2020 , Environmental Research Letters)

   Electricity consumption and greenhouse gas (GHG) emissions associated with wastewater flows from residential and commercial water use in three major cities of the United States are analyzed and compared for the period 2010–2018. Contributions of unit wastewater treatment processes and electricity sources to the overall emissions are considered. Tucson (Arizona), Denver (Colorado), and Washington, DC were chosen for their distinct locations, climatic conditions, raw water sources, wastewater treatment technologies, and electric power mixes. Denver experienced a 20% reduction in treated wastewater volumes per person despite a 16% increase in population. In Washington, DC, the reduction was 19%, corresponding to a 16% increase in population, and in Tucson 14% despite a population growth of 3%. The electricity intensity per volume of treated wastewater was higher in Tucson (1 kWh m⁻³) than in Washington, DC (0.7 kWh m⁻³) or Denver (0.5 kWh m⁻³). Tucson’s GHG emissions per person were about six times higher compared to Denver and four times higher compared to Washington, DC. Wastewater treatment facilities in Denver and Washington, DC generated a quarter to third of their electricity needs from onsite biogas and lowered their GHG emissions by offsetting purchases from the grid, including coal-generated electricity. The higher GHGmore »emission intensity in Tucson is a reflection of coal majority in the electricity mix in the period, gradually replaced with natural gas, solar, and biogas. In 2018, the GHG reduction was 20% when the share of solar electricity increased to 14% from zero in 2016. In the analysis period, reduced wastewater volumes relative to the 2010 baseline saved Denver 44 000 MWh, Washington, DC 11 000 MWh and Tucson 7000 MWh of electricity. As a result, Washington, DC managed to forgo 21 000 metric tons of CO_2-eqand Denver 34 000 metric tons, while Tucson’s cumulative emissions increased by 22 000 metric tons of CO_2-eq. This study highlights the variability observed in water systems and the opportunities that exist with water savings to allow for wastewater generation reduction, recovering energy from onsite biogas, and using energy-efficient wastewater treatment technologies.

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3. 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 notmore »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.« less
4. Spatial Life Cycle Analysis of Soybean-Based Biodiesel Production in Indiana, USA Using Process Modeling

   https://doi.org/10.3390/pr8040392  

   Vunnava, Venkata Sai ; Singh, Shweta ( April 2020 , Processes)

   Life Cycle Analysis (LCA) has long been utilized for decision making about the sustainability of products. LCA provides information about the total emissions generated for a given functional unit of a product, which is utilized by industries or consumers for comparing two products with regards to environmental performance. However, many existing LCAs utilize data that is representative of an average system with regards to life cycle stage, thus providing an aggregate picture. It has been shown that regional variation may lead to large variation in the environmental impacts of a product, specifically dealing with energy consumption, related emissions and resource consumptions. Hence, improving the reliability of LCA results for decision making with regards to environmental performance needs regional models to be incorporated for building a life cycle inventory that is representative of the origin of products from a certain region. In this work, we present the integration of regionalized data from process systems models and other sources to build regional LCA models and quantify the spatial variations per unit of biodiesel produced in the state of Indiana for environmental impact. In order to include regional variation, we have incorporated information about plant capacity for producing biodiesel from North and Centralmore »Indiana. The LCA model built is a cradle-to-gate. Once the region-specific models are built, the data were utilized in SimaPro to integrate with upstream processes to perform a life cycle impact assessment (LCIA). We report the results per liter of biodiesel from northern and central Indiana facilities in this work. The impact categories studied were global warming potential (kg CO2 eq) and freshwater eutrophication (kg P eq). While there were a lot of variations at individual county level, both regions had a similar global warming potential impact and the northern region had relatively lower eutrophication impacts.« less
5. A Spatially Detailed and Economically Complete Blue Water Footprint of the United States

   https://doi.org/10.5194/hess-2017-650  

   Rushforth, Richard R. ; Ruddell, Benjamin L. ( January 2017 , Hydrology and Earth System Sciences Discussions)

   This paper quantifies and maps a spatially detailed and economically complete blue water footprint for the United States, utilizing the National Water Economy Database version 1.1 (NWED). NWED utilizes multiple mesoscale federal data resources from the United States Geological Survey (USGS), the United States Department of Agriculture (USDA), the U.S. Energy Information Administration (EIA), the U.S. Department of Transportation (USDOT), the U.S. Department of Energy (USDOE), and the U.S. Bureau of Labor Statistics (BLS) to quantify water use, economic trade, and commodity flows to construct this water footprint. Results corroborate previous studies in both the magnitude of the U.S. water footprint (F) and in the observed pattern of virtual water flows. The median water footprint (F_CUMed) of the U.S. is 181 966 Mm³ (F_Withdrawal: 400 844 Mm³; F_CUMax: 222 144 Mm³; F_CUMin: 61 117 Mm³) and the median per capita water footprint (F'_CUMed) of the U.S. is 589 m³ capita^−1 (F'_Withdrawal: 1298 m³ capita^−1; F'_CUMax: 720 m³ capita^−1; F'_CUMin: 198 m³ capita^−1). The U.S. hydro-economic network is centered on cities and is dominated by the local and regional scales. Approximately (58 %) of U.S. water consumption is for the direct and indirect use by cities. Further, the water footprint of agriculture and livestock is 93 % of the total U.S. water footprint, and is dominated by irrigated agriculturemore »in the Western U.S. The water footprint of the industrial, domestic, and power economic sectors is centered on population centers, while the water footprint of the mining sector is highly dependent on the location of mineral resources. Owing to uncertainty in consumptive use coefficients alone, the mesoscale blue water footprint uncertainty ranges from 63 % to over 99 % depending on location. Harmonized region-specific, economic sector-specific consumption coefficients are necessary to reduce water footprint uncertainties and to better understand the human economy's water use impact on the hydrosphere.« less