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1. SES Grants, 2000-2015

   https://doi.org/10.7910/DVN/QCA35O  

   Kaiser, Kendra ; Braswell, Anna ; Fork, Megan ; Fork, Megan ( January 2022 , Harvard Dataverse)

   Information about grants funded by NSF to support SES research from 2000-2015. The grants included in this dataset are a subset that we identified as having an SES research focus from a set of grants accessed using the Dimensions platform (https://dimensions.ai). CSV file with 35 columns and names in header row: "Grant Searched" lists the granting NSF program (text); "Grant Searched 2" lists a secondary granting NSF program, if applicable (text); "Grant ID" is the ID from the Dimensions platform (string); "Grant Number" is the NSF Award number (integer); "Number of Papers (NSF)" is the count of publications listed under "PUBLICATIONS PRODUCED AS A RESULT OF THIS RESEARCH" in the NSF Award Search page for the grant (integer); "Number of Pubs Tracked" is the count of publications from "Number of Papers (NSF)" included in our analysis (integer); "Publication notes" are our notes about the publication information. We used "subset" to denote when a grant was associated with >10 publications and we used a random sample of 10 publications in our analysis (text); "Unique ID" is our unique identifier for each grant in the dataset (integer); "Collaborative/Cross Program" denotes whether the grant was submitted as part of a set of collaborative or cross-program proposals. In this case, all linked proposals are given the same unique identifier and treated together in the analysis. (text); "Title" is the title of the grant (text); "Title translated" is the title of the grant translated to English, where applicable (text); "Abstract" is the abstract of the grant (text); "Abstract translated" is the abstract of the grant translated to English, where applicable (text); "Funding Amount" is the numeric value of funding awarded to the grant (integer); "Currency" is the currency associated with the field "Funding Amount" (text); "Funding Amount in USD" is the numeric value of funding awarded to the grant expressed in US Dollars (integer); "Start Date" is the start date of the grant (mm/dd/yyyy); "Start Year" is the year in which grant funding began (year); "End Date" is the end date of the grant (mm/dd/yyyy); "End Year" is the year in which the term of the grant expired (year); "Researchers" lists the Principal Investigators on the grant in First Name Last Name format, separated by semi-colons (text); "Research Organization - original" gives the affiliation of the lead PI as listed in the grant (text); "Research Organization - standardized" gives the affiliation of each PI in the list, separated by semi-colons (text); "GRID ID" is a list of the unique identifier for each the Research Organization in the Global Research Identifier Database [https://grid.ac/?_ga=2.26738100.847204331.1643218575-1999717347.1643218575], separated by semi-colons (string); "Country of Research organization" is a list of the countries in which each Research Organization is located, separated by semi-colons (text); "Funder" gives the NSF Directorate that funded the grant (text); "Source Linkout" is a link to the NSF Award Search page with information about the grant (URL); "Dimensions URL" is a link to information about the grant in Dimensions (URL); "FOR (ANZSRC) Categories" is a list of Field of Research categories [from the Australian and New Zealand Standard Research Classification (ANZSRC) system] associated with each grant, separated by semi-colons (string); "FOR [1-5]" give the FOR categories separated. "NOTES" provide any other notes added by the authors of this dataset during our processing of these data. 

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2. Journal Aims Scope and Further Details

   https://doi.org/10.7910/DVN/ASMDSA  

   Kaiser, Kendra ; Braswell, Anna ; Fork, Megan ; Fork, Megan ( January 2022 , Harvard Dataverse)

   Detailed information and published mission or aims scope for journals in which 3 or more publications from the dataset Publications associated with SES grants, 2000-2015 appeared. CSV file with 10 columns and names in header row: journal is the name of the scientific journal or outlet in which at least 3 papers were published (text); number of papers is the number of papers from the dataset Publications associated with SES grants, 2000-2015 published in the journal (integer); Impact factor is the most recent available Impact Factor for the journal as of March 2020 (float); Discipline is the broad disciplinary category to which the journal belongs, as identified by the authors of this dataset (text); Stated aimsscope is the text of the journal aimsscope as provided on the journal website (text); Mission includes interdisciplinary? categorizes whether the stated aimsscope of the journal includes dissemination of interdisciplinary research (Y indicates the stated aimsscope explicitly include interdisciplinary research, I indicates that publication of interdisciplinary research is implicit but not directly stated in the aimsscope, N indicates there is no evidence that interdisciplinary research are part of the aimsscope of the journal); Mission includes humans/social? categorizes whether the stated aimsscope of the journal includes dissemination of research about human or social systems (Y indicates the stated aimsscope include some mention of human impacts, social systems, etc., N indicates there is no evidence that research on human or social systems are part of the aimsscope of the journal) Gutcheck Interdisciplinary? is an evaluation of whether the journal publishes interdisciplinary research as a matter of course, as judged by the authors of the dataset (Y indicates the journal publishes interdisciplinary research s a matter of course, N indicates journal does not tend to publish interdisciplinary research, kinda to indicate some history of publishing interdisciplinary research that may not be a major focus of published content. Forward slashes between values show where the dataset authors differed in their assessments.); Gutcheck CNHS? is an evaluation of whether the journal publishes research on socio-environmental systems (social-ecological systems, coupled natural and human systems) as a matter of course, as judged by the authors of the dataset (Y indicates the journal publishes research on socio-environmental systems as a matter of course, N indicates journal does not tend to publish research on socio-environmental systems , kinda to indicate some history of publishing research on socio-environmental systems that may not be a major focus of published content. Forward slashes between values show where the dataset authors differed in their assessments.); Notes provide any other notes added by the authors of this dataset during our processing of these data (text). 

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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 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. 

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4. Warm Core Ring Trajectories in the Northwest Atlantic Slope Sea (2000-2010)

   https://doi.org/10.5281/zenodo.7406675  

   Porter, Nicholas ; Silver, Adrienne ; Gangopadhyay, Avijit ( January 2022 , Zenodo)

   This dataset consists of weekly trajectory information of Gulf Stream Warm Core Rings from 2000-2010. This work builds upon Silver et al. (2022a) ( https://doi.org/10.5281/zenodo.6436380) which contained Warm Core Ring trajectory information from 2011 to 2020. Combining the two datasets a total of 21 years of weekly Warm Core Ring trajectories can be obtained. An example of how to use such a dataset can be found in Silver et al. (2022b).

   The format of the dataset is similar to that of  Silver et al. (2022a), and the following description is adapted from their dataset. This dataset is comprised of individual files containing each ring’s weekly center location and its area for 374 WCRs present between January 1, 2000 and December 31, 2010. Each Warm Core Ring is identified by a unique alphanumeric code 'WEyyyymmddA', where 'WE' represents a Warm Eddy (as identified in the analysis charts); 'yyyymmdd' is the year, month and day of formation; and the last character 'A' represents the sequential sighting of the eddies in a particular year. Continuity of a ring which passes from one year to the next is maintained by the same character in the first sighting.  For example, the first ring in 2002 having a trailing alphabet of 'F' indicates that five rings were carried over from 2001 which were still observed on January 1, 2002. Each ring has its own netCDF (.nc) filename following its alphanumeric code. Each file contains 4 variables, “Lon”- the ring center’s weekly longitude, “Lat”- the ring center’s weekly latitude, “Area” - the rings weekly size in km², and “Date” in days - representing the days since Jan 01, 0000. 

   The process of creating the WCR tracking dataset follows the same methodology of the previously generated WCR census (Gangopadhyay et al., 2019, 2020). The Jenifer Clark’s Gulf Stream Charts used to create this dataset are 2-3 times a week from 2000-2010. Thus, we used approximately 1560 Charts for the 10 years of analysis. All of these charts were reanalyzed between 75° and 55°W using QGIS 2.18.16 (2016) and geo-referenced on a WGS84 coordinate system (Decker, 1986). 

    

   Silver, A., Gangopadhyay, A, & Gawarkiewicz, G. (2022a). Warm Core Ring Trajectories in the Northwest Atlantic Slope Sea (2011-2020) (1.0.0) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.6436380

   Silver, A., Gangopadhyay, A., Gawarkiewicz, G., Andres, M., Flierl, G., & Clark, J. (2022b). Spatial Variability of Movement, Structure, and Formation of Warm Core Rings in the Northwest Atlantic Slope Sea. Journal of Geophysical Research: Oceans, 127(8), e2022JC018737. https://doi.org/10.1029/2022JC018737 

   Gangopadhyay, A., G. Gawarkiewicz, N. Etige, M. Monim and J. Clark, 2019. An Observed Regime Shift in the Formation of Warm Core Rings from the Gulf Stream, Nature - Scientific Reports, https://doi.org/10.1038/s41598-019-48661-9. www.nature.com/articles/s41598-019-48661-9.

   Gangopadhyay, A., N. Etige, G. Gawarkiewicz, A. M. Silver, M. Monim and J. Clark, 2020.  A Census of the Warm Core Rings of the Gulf Stream (1980-2017). Journal of Geophysical Research, Oceans, 125, e2019JC016033. https://doi.org/10.1029/2019JC016033.

   QGIS Development Team. QGIS Geographic Information System (2016).

   Decker, B. L. World Geodetic System 1984. World geodetic system 1984 (1986).

    

   Funded by two NSF US grants OCE-1851242, OCE-212328 {"references": ["Silver, A., Gangopadhyay, A, & Gawarkiewicz, G. (2022). Warm Core Ring Trajectories in the Northwest Atlantic Slope Sea (2011-2020) (1.0.0) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.6436380", "Silver, A., Gangopadhyay, A., Gawarkiewicz, G., Andres, M., Flierl, G., & Clark, J. (2022b). Spatial Variability of Movement, Structure, and Formation of Warm Core Rings in the Northwest Atlantic Slope Sea.\u00a0Journal of Geophysical Research: Oceans,\u00a0127(8), e2022JC018737.\u00a0https://doi.org/10.1029/2022JC018737", "Gangopadhyay, A., G. Gawarkiewicz, N. Etige, M. Monim and J. Clark, 2019. An Observed Regime Shift in the Formation of Warm Core Rings from the Gulf Stream, Nature - Scientific Reports, https://doi.org/10.1038/s41598-019-48661-9. www.nature.com/articles/s41598-019-48661-9.", "Gangopadhyay, A., N. Etige, G. Gawarkiewicz, A. M. Silver, M. Monim and J. Clark, 2020. A Census of the Warm Core Rings of the Gulf Stream (1980-2017). Journal of Geophysical Research, Oceans, 125, e2019JC016033. https://doi.org/10.1029/2019JC016033.", "QGIS Development Team. QGIS Geographic Information System (2016).", "Decker, B. L. World Geodetic System 1984. World geodetic system 1984 (1986)."]} 

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5. Translating interdisciplinary knowledge for gender equity: Quantifying the impact of NSF ADVANCE

   https://doi.org/10.1111/ssqu.13339  

   Gates, Alexander J. ; Gold, Jessica R. ; Nelson, Laura K. ; Zippel, Kathrin ( February 2024 , Social Science Quarterly)

   Interdisciplinarity is often hailed as a necessity for tackling real‐world challenges. We examine the prevalence and impact of interdisciplinarity in the NSF ADVANCE program, which addresses gender equity in STEM.

   Through a quantitative analysis of authorship, references, and citations in ADVANCE publications, we compare the interdisciplinarity of knowledge produced within the program to traditional disciplinary knowledge. We use Simpon's Diversity Index to test for differences across disciplines, and we use negative binomial regression to capture the potential influences of interdisciplinarity on the long‐term impact of ADVANCE publications.

   ADVANCE publications exhibit higher levels of interdisciplinarity across three dimensions of knowledge integration, and cross‐disciplinary ties within ADVANCE successfully integrate social science knowledge into diverse disciplines. Additionally, the interdisciplinarity of publication references positively influences the impact of ADVANCE work, while the interdisciplinarity of authorship teams does not.

   These findings emphasize the significance of interdisciplinarity in problem‐oriented knowledge production, indicating that specific forms of interdisciplinarity can lead to broader impact. By shedding light on the interplay between interdisciplinary approaches, disciplinary structures, and academic recognition, this article contributes to programmatic design to generate impactful problem‐solving knowledge that also adds to the academic community.

    

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