More Like this

1. Phosphorus availability and leaching losses in annual and perennial cropping systems in an upper US Midwest landscape

   https://doi.org/10.5061/dryad.8sf7m0cpx  

   Hussain, Mir Zaman ; Hamilton, Stephen ; Robertson, G. Philip ; Basso, Bruno ( January 2021 , Dryad)

   Excessive phosphorus (P) applications to croplands can contribute to eutrophication of surface waters through surface runoff and subsurface (leaching) losses. We analyzed leaching losses of total dissolved P (TDP) from no-till corn, hybrid poplar (Populus nigra X P. maximowiczii), switchgrass (Panicum virgatum), miscanthus (Miscanthus giganteus), native grasses, and restored prairie, all planted in 2008 on former cropland in Michigan, USA. All crops except corn (13 kg P ha−1 year−1) were grown without P fertilization. Biomass was harvested at the end of each growing season except for poplar. Soil water at 1.2 m depth was sampled weekly to biweekly for TDP determination during March–November 2009–2016 using tension lysimeters. Soil test P (0–25 cm depth) was measured every autumn. Soil water TDP concentrations were usually below levels where eutrophication of surface waters is frequently observed (> 0.02 mg L−1) but often higher than in deep groundwater or nearby streams and lakes. Rates of P leaching, estimated from measured concentrations and modeled drainage, did not differ statistically among cropping systems across years; 7-year cropping system means ranged from 0.035 to 0.072 kg P ha−1 year−1 with large interannual variation. Leached P was positively related to STP, which decreased over the 7 years in all systems. These results indicate that both P-fertilized and unfertilized cropping systems may leach legacy P from past cropland management. Experimental details The Biofuel Cropping System Experiment (BCSE) is located at the W.K. Kellogg Biological Station (KBS) (42.3956° N, 85.3749° W; elevation 288 m asl) in southwestern Michigan, USA. This site is a part of the Great Lakes Bioenergy Research Center (www.glbrc.org) and is a Long-term Ecological Research site (www.lter.kbs.msu.edu). Soils are mesic Typic Hapludalfs developed on glacial outwash54 with high sand content (76% in the upper 150 cm) intermixed with silt-rich loess in the upper 50 cm55. The water table lies approximately 12–14 m below the surface. The climate is humid temperate with a mean annual air temperature of 9.1 °C and annual precipitation of 1005 mm, 511 mm of which falls between May and September (1981–2010)56,57. The BCSE was established as a randomized complete block design in 2008 on preexisting farmland. Prior to BCSE establishment, the field was used for grain crop and alfalfa (Medicago sativa L.) production for several decades. Between 2003 and 2007, the field received a total of ~ 300 kg P ha−1 as manure, and the southern half, which contains one of four replicate plots, received an additional 206 kg P ha−1 as inorganic fertilizer. The experimental design consists of five randomized blocks each containing one replicate plot (28 by 40 m) of 10 cropping systems (treatments) (Supplementary Fig. S1; also see Sanford et al.58). Block 5 is not included in the present study. Details on experimental design and site history are provided in Robertson and Hamilton57 and Gelfand et al.59. Leaching of P is analyzed in six of the cropping systems: (i) continuous no-till corn, (ii) switchgrass, (iii) miscanthus, (iv) a mixture of five species of native grasses, (v) a restored native prairie containing 18 plant species (Supplementary Table S1), and (vi) hybrid poplar. Agronomic management Phenological cameras and field observations indicated that the perennial herbaceous crops emerged each year between mid-April and mid-May. Corn was planted each year in early May. Herbaceous crops were harvested at the end of each growing season with the timing depending on weather: between October and November for corn and between November and December for herbaceous perennial crops. Corn stover was harvested shortly after corn grain, leaving approximately 10 cm height of stubble above the ground. The poplar was harvested only once, as the culmination of a 6-year rotation, in the winter of 2013–2014. Leaf emergence and senescence based on daily phenological images indicated the beginning and end of the poplar growing season, respectively, in each year. Application of inorganic fertilizers to the different crops followed a management approach typical for the region (Table 1). Corn was fertilized with 13 kg P ha−1 year−1 as starter fertilizer (N-P-K of 19-17-0) at the time of planting and an additional 33 kg P ha−1 year−1 was added as superphosphate in spring 2015. Corn also received N fertilizer around the time of planting and in mid-June at typical rates for the region (Table 1). No P fertilizer was applied to the perennial grassland or poplar systems (Table 1). All perennial grasses (except restored prairie) were provided 56 kg N ha−1 year−1 of N fertilizer in early summer between 2010 and 2016; an additional 77 kg N ha−1 was applied to miscanthus in 2009. Poplar was fertilized once with 157 kg N ha−1 in 2010 after the canopy had closed. Sampling of subsurface soil water and soil for P determination Subsurface soil water samples were collected beneath the root zone (1.2 m depth) using samplers installed at approximately 20 cm into the unconsolidated sand of 2Bt2 and 2E/Bt horizons (soils at the site are described in Crum and Collins54). Soil water was collected from two kinds of samplers: Prenart samplers constructed of Teflon and silica (http://www.prenart.dk/soil-water-samplers/) in replicate blocks 1 and 2 and Eijkelkamp ceramic samplers (http://www.eijkelkamp.com) in blocks 3 and 4 (Supplementary Fig. S1). The samplers were installed in 2008 at an angle using a hydraulic corer, with the sampling tubes buried underground within the plots and the sampler located about 9 m from the plot edge. There were no consistent differences in TDP concentrations between the two sampler types. Beginning in the 2009 growing season, subsurface soil water was sampled at weekly to biweekly intervals during non-frozen periods (April–November) by applying 50 kPa of vacuum to each sampler for 24 h, during which the extracted water was collected in glass bottles. Samples were filtered using different filter types (all 0.45 µm pore size) depending on the volume of leachate collected: 33-mm dia. cellulose acetate membrane filters when volumes were less than 50 mL; and 47-mm dia. Supor 450 polyethersulfone membrane filters for larger volumes. Total dissolved phosphorus (TDP) in water samples was analyzed by persulfate digestion of filtered samples to convert all phosphorus forms to soluble reactive phosphorus, followed by colorimetric analysis by long-pathlength spectrophotometry (UV-1800 Shimadzu, Japan) using the molybdate blue method60, for which the method detection limit was ~ 0.005 mg P L−1. Between 2009 and 2016, soil samples (0–25 cm depth) were collected each autumn from all plots for determination of soil test P (STP) by the Bray-1 method61, using as an extractant a dilute hydrochloric acid and ammonium fluoride solution, as is recommended for neutral to slightly acidic soils. The measured STP concentration in mg P kg−1 was converted to kg P ha−1 based on soil sampling depth and soil bulk density (mean, 1.5 g cm−3). Sampling of water samples from lakes, streams and wells for P determination In addition to chemistry of soil and subsurface soil water in the BCSE, waters from lakes, streams, and residential water supply wells were also sampled during 2009–2016 for TDP analysis using Supor 450 membrane filters and the same analytical method as for soil water. These water bodies are within 15 km of the study site, within a landscape mosaic of row crops, grasslands, deciduous forest, and wetlands, with some residential development (Supplementary Fig. S2, Supplementary Table S2). Details of land use and cover change in the vicinity of KBS are given in Hamilton et al.48, and patterns in nutrient concentrations in local surface waters are further discussed in Hamilton62. Leaching estimates, modeled drainage, and data analysis Leaching was estimated at daily time steps and summarized as total leaching on a crop-year basis, defined from the date of planting or leaf emergence in a given year to the day prior to planting or emergence in the following year. TDP concentrations (mg L−1) of subsurface soil water were linearly interpolated between sampling dates during non-freezing periods (April–November) and over non-sampling periods (December–March) based on the preceding November and subsequent April samples. Daily rates of TDP leaching (kg ha−1) were calculated by multiplying concentration (mg L−1) by drainage rates (m3 ha−1 day−1) modeled by the Systems Approach for Land Use Sustainability (SALUS) model, a crop growth model that is well calibrated for KBS soil and environmental conditions. SALUS simulates yield and environmental outcomes in response to weather, soil, management (planting dates, plant population, irrigation, N fertilizer application, and tillage), and genetics63. The SALUS water balance sub-model simulates surface runoff, saturated and unsaturated water flow, drainage, root water uptake, and evapotranspiration during growing and non-growing seasons63. The SALUS model has been used in studies of evapotranspiration48,51,64 and nutrient leaching20,65,66,67 from KBS soils, and its predictions of growing-season evapotranspiration are consistent with independent measurements based on growing-season soil water drawdown53 and evapotranspiration measured by eddy covariance68. Phosphorus leaching was assumed insignificant on days when SALUS predicted no drainage. Volume-weighted mean TDP concentrations in leachate for each crop-year and for the entire 7-year study period were calculated as the total dissolved P leaching flux (kg ha−1) divided by the total drainage (m3 ha−1). One-way ANOVA with time (crop-year) as the fixed factor was conducted to compare total annual drainage rates, P leaching rates, volume-weighted mean TDP concentrations, and maximum aboveground biomass among the cropping systems over all seven crop-years as well as with TDP concentrations from local lakes, streams, and groundwater wells. When a significant (α = 0.05) difference was detected among the groups, we used the Tukey honest significant difference (HSD) post-hoc test to make pairwise comparisons among the groups. In the case of maximum aboveground biomass, we used the Tukey–Kramer method to make pairwise comparisons among the groups because the absence of poplar data after the 2013 harvest resulted in unequal sample sizes. We also used the Tukey–Kramer method to compare the frequency distributions of TDP concentrations in all of the soil leachate samples with concentrations in lakes, streams, and groundwater wells, since each sample category had very different numbers of measurements. Individual spreadsheets in “data table_leaching_dissolved organic carbon and nitrogen.xls” 1.    annual precip_drainage 2.    biomass_corn, perennial grasses 3.    biomass_poplar 4.    annual N leaching _vol-wtd conc 5.    Summary_N leached 6.    annual DOC leachin_vol-wtd conc 7.    growing season length 8.    correlation_nh4 VS no3 9.    correlations_don VS no3_doc VS don Each spreadsheet is described below along with an explanation of variates. Note that ‘nan’ indicate data are missing or not available. First row indicates header; second row indicates units 1. Spreadsheet: annual precip_drainage Description: Precipitation measured from nearby Kellogg Biological Station (KBS) Long Term Ecological Research (LTER) Weather station, over 2009-2016 study period. Data shown in Figure 1; original data source for precipitation (https://lter.kbs.msu.edu/datatables/7). Drainage estimated from SALUS crop model. Note that drainage is percolation out of the root zone (0-125 cm). Annual precipitation and drainage values shown here are calculated for growing and non-growing crop periods. Variate    Description year    year of the observation crop    “corn” “switchgrass” “miscanthus” “nativegrass” “restored prairie” “poplar” precip_G    precipitation during growing period (milliMeter) precip_NG    precipitation during non-growing period (milliMeter) drainage_G    drainage during growing period (milliMeter) drainage_NG    drainage during non-growing period (milliMeter)      2. Spreadsheet: biomass_corn, perennial grasses Description: Maximum aboveground biomass measurements from corn, switchgrass, miscanthus, native grass and restored prairie plots in Great Lakes Bioenergy Research Center (GLBRC) Biomass Cropping System Experiment (BCSE) during 2009-2015. Data shown in Figure 2.   Variate    Description year    year of the observation date    day of the observation (mm/dd/yyyy) crop    “corn” “switchgrass” “miscanthus” “nativegrass” “restored prairie” “poplar” replicate    each crop has four replicated plots, R1, R2, R3 and R4 station    stations (S1, S2 and S3) of samplings within the plot. For more details, refer to link (https://data.sustainability.glbrc.org/protocols/156) species    plant species that are rooted within the quadrat during the time of maximum biomass harvest. See protocol for more information, refer to link (http://lter.kbs.msu.edu/datatables/36) For maize biomass, grain and whole biomass reported in the paper (weed biomass or surface litter are excluded). Surface litter biomass not included in any crops; weed biomass not included in switchgrass and miscanthus, but included in grass mixture and prairie. fraction    Fraction of biomass biomass_plot    biomass per plot on dry-weight basis (Grams_Per_SquareMeter) biomass_ha    biomass (megaGrams_Per_Hectare) by multiplying column biomass per plot with 0.01 3. Spreadsheet: biomass_poplar Description: Maximum aboveground biomass measurements from poplar plots in Great Lakes Bioenergy Research Center (GLBRC) Biomass Cropping System Experiment (BCSE) during 2009-2015. Data shown in Figure 2. Note that poplar biomass was estimated from crop growth curves until the poplar was harvested in the winter of 2013-14. Variate    Description year    year of the observation method    methods of poplar biomass sampling date    day of the observation (mm/dd/yyyy) replicate    each crop has four replicated plots, R1, R2, R3 and R4 diameter_at_ground    poplar diameter (milliMeter) at the ground diameter_at_15cm    poplar diameter (milliMeter) at 15 cm height biomass_tree    biomass per plot (Grams_Per_Tree) biomass_ha    biomass (megaGrams_Per_Hectare) by multiplying biomass per tree with 0.01 4. Spreadsheet: annual N leaching_vol-wtd conc Description: Annual leaching rate (kiloGrams_N_Per_Hectare) and volume-weighted mean N concentrations (milliGrams_N_Per_Liter) of nitrate (no3) and dissolved organic nitrogen (don) in the leachate samples collected from corn, switchgrass, miscanthus, native grass, restored prairie and poplar plots in Great Lakes Bioenergy Research Center (GLBRC) Biomass Cropping System Experiment (BCSE) during 2009-2016. Data for nitrogen leached and volume-wtd mean N concentration shown in Figure 3a and Figure 3b, respectively. Note that ammonium (nh4) concentration were much lower and often undetectable (<0.07 milliGrams_N_Per_Liter). Also note that in 2009 and 2010 crop-years, data from some replicates are missing.    Variate    Description crop    “corn” “switchgrass” “miscanthus” “nativegrass” “restored prairie” “poplar” crop-year    year of the observation replicate    each crop has four replicated plots, R1, R2, R3 and R4 no3 leached    annual leaching rates of nitrate (kiloGrams_N_Per_Hectare) don leached    annual leaching rates of don (kiloGrams_N_Per_Hectare) vol-wtd no3 conc.    Volume-weighted mean no3 concentration (milliGrams_N_Per_Liter) vol-wtd don conc.    Volume-weighted mean don concentration (milliGrams_N_Per_Liter) 5. Spreadsheet: summary_N leached Description: Summary of total amount and forms of N leached (kiloGrams_N_Per_Hectare) and the percent of applied N lost to leaching over the seven years for corn, switchgrass, miscanthus, native grass, restored prairie and poplar plots in Great Lakes Bioenergy Research Center (GLBRC) Biomass Cropping System Experiment (BCSE) during 2009-2016. Data for nitrogen amount leached shown in Figure 4a and percent of applied N lost shown in Figure 4b. Note the fraction of unleached N includes in harvest, accumulation in root biomass, soil organic matter or gaseous N emissions were not measured in the study. Variate    Description crop    “corn” “switchgrass” “miscanthus” “nativegrass” “restored prairie” “poplar” no3 leached    annual leaching rates of nitrate (kiloGrams_N_Per_Hectare) don leached    annual leaching rates of don (kiloGrams_N_Per_Hectare) N unleached    N unleached (kiloGrams_N_Per_Hectare) in other sources are not studied % of N applied N lost to leaching    % of N applied N lost to leaching 6. Spreadsheet: annual DOC leachin_vol-wtd conc Description: Annual leaching rate (kiloGrams_Per_Hectare) and volume-weighted mean N concentrations (milliGrams_Per_Liter) of dissolved organic carbon (DOC) in the leachate samples collected from corn, switchgrass, miscanthus, native grass, restored prairie and poplar plots in Great Lakes Bioenergy Research Center (GLBRC) Biomass Cropping System Experiment (BCSE) during 2009-2016. Data for DOC leached and volume-wtd mean DOC concentration shown in Figure 5a and Figure 5b, respectively. Note that in 2009 and 2010 crop-years, water samples were not available for DOC measurements.     Variate    Description crop    “corn” “switchgrass” “miscanthus” “nativegrass” “restored prairie” “poplar” crop-year    year of the observation replicate    each crop has four replicated plots, R1, R2, R3 and R4 doc leached    annual leaching rates of nitrate (kiloGrams_Per_Hectare) vol-wtd doc conc.    volume-weighted mean doc concentration (milliGrams_Per_Liter) 7. Spreadsheet: growing season length Description: Growing season length (days) of corn, switchgrass, miscanthus, native grass, restored prairie and poplar plots in the Great Lakes Bioenergy Research Center (GLBRC) Biomass Cropping System Experiment (BCSE) during 2009-2015. Date shown in Figure S2. Note that growing season is from the date of planting or emergence to the date of harvest (or leaf senescence in case of poplar).   Variate    Description crop    “corn” “switchgrass” “miscanthus” “nativegrass” “restored prairie” “poplar” year    year of the observation growing season length    growing season length (days) 8. Spreadsheet: correlation_nh4 VS no3 Description: Correlation of ammonium (nh4+) and nitrate (no3-) concentrations (milliGrams_N_Per_Liter) in the leachate samples from corn, switchgrass, miscanthus, native grass, restored prairie and poplar plots in Great Lakes Bioenergy Research Center (GLBRC) Biomass Cropping System Experiment (BCSE) during 2013-2015. Data shown in Figure S3. Note that nh4+ concentration in the leachates was very low compared to no3- and don concentration and often undetectable in three crop-years (2013-2015) when measurements are available. Variate    Description crop    “corn” “switchgrass” “miscanthus” “nativegrass” “restored prairie” “poplar” date    date of the observation (mm/dd/yyyy) replicate    each crop has four replicated plots, R1, R2, R3 and R4 nh4 conc    nh4 concentration (milliGrams_N_Per_Liter) no3 conc    no3 concentration (milliGrams_N_Per_Liter)   9. Spreadsheet: correlations_don VS no3_doc VS don Description: Correlations of don and nitrate concentrations (milliGrams_N_Per_Liter); and doc (milliGrams_Per_Liter) and don concentrations (milliGrams_N_Per_Liter) in the leachate samples of corn, switchgrass, miscanthus, native grass, restored prairie and poplar plots in Great Lakes Bioenergy Research Center (GLBRC) Biomass Cropping System Experiment (BCSE) during 2013-2015. Data of correlation of don and nitrate concentrations shown in Figure S4 a and doc and don concentrations shown in Figure S4 b. Variate    Description crop    “corn” “switchgrass” “miscanthus” “nativegrass” “restored prairie” “poplar” year    year of the observation don    don concentration (milliGrams_N_Per_Liter) no3     no3 concentration (milliGrams_N_Per_Liter) doc    doc concentration (milliGrams_Per_Liter) 

   more » « less
2. Monthly and Annual contour lines of the zero and the positive maximum of the Wind Stress Curl over Western North Atlantic during 1980-2019 and the Gulf Stream path during 1993-2019.

   https://doi.org/10.5281/zenodo.8217388  

   Gifford, Ian ; Silver, Adrienne ; Gangopadhyay, Avijit ; Andres, Magdalena ; Gawarkiewicz, Glen ; Oliver, Hilde ( January 2023 , Zenodo)

   This dataset includes multiple fields: (i) files for monthly and annual fields for the max curl line and the zero curl line at 0.1 degree longitudinal resolutions; (ii) files for monthly and annual GS path obtained from Altimetry and originally processed by Andres (2016) at 0.1 degree longitudinal resolution. The maximum curl line (MCL) and the zero curl line (ZCL) calculations are briefly described here and are based on the original wind data (at 1.25 x 1.25 degree) provided by the Japanese reanalysis (JRA-55; Kobayashi et al., 2015) and available at https://zenodo.org/record/8200832 (Gifford et al. 2023). For details see Gifford, 2023. 

   The wind stress curl (WSC) fields used for the MCL and ZCL calculations extend from 80W to 45W and 30N to 45N at the 1.25 by 1.25-degree resolution.  The MCL is defined as the maximum WSC values greater than zero within the domain per 1.25 degree longitude. As such, it is a function of longitude and is not a constant WSC value unlike the zero contour. High wind stress curl values that occurred near the coast were not included within this calculation. After MCL at the 1.25 resolution was obtained the line was smoothed with a gaussian smoothing and interpolated on to a 0.1 longitudinal resolution. The smoothed MCL lines at 0.1 degree resolution are provided in separate files for monthly and annual averages (2 files). Similarly, 2 other files (monthly and annual) are provided for the ZCL.    

   Like the MCL, the ZCL is a line derived from 1.25 degree longitude throughout the domain under the condition that it's the line of zero WSC. The ZCL is constant at 0 and does not vary spatially like the MCL. If there are more than one location of zero curl for a given longitude the first location south of the MCL is selected. Similar to the MCL, the ZCL was smoothed with a gaussian smoothing and interpolated on to a 0.1 longitudinal resolution.   

   The above files span the years from 1980 through 2019. So, the monthly files have 480 months starting January 1980, and the annual files have 40 years of data. The files are organized with each row being a new time step and each column being a different longitude. Therefore, the monthly MCL and ZCL files are each 480 x 351 for the 0.1 resolution data. Similarly, the annual files are 40 x 351 for the 0.1 degree resolution data.  

   Note that the monthly MCLs and ZCLs are obtained from the monthly wind-stress curl fields. The annual MCLs and ZCLs are obtained from the annual wind-stress curl fields.

   Since the monthly curl fields preserves more atmospheric mesoscales than the annual curl fields, the 12-month average of the monthly MCLs and ZCLs will not match with the annual MCLs and ZCLs derived from the annual curl field.  The annual MCLs and ZCLs provided here are obtained from the annual curl fields and representative metrics of the wind forcing on an annual time-scale. 

   Furthermore, the monthly Gulf Stream axis path (25 cm isoheight from Altimeter, reprocessed by Andres (2016) technique) from 1993 through 2019 have been made available here. A total of 324 monthly paths of the Gulf Stream are tabulated. In addition, the annual GS paths for these 27 years (1993-2019) of altimetry era have been put together for ease of use. The monthly Gulf Stream paths have been resampled and reprocessed for uniqueness at every 0.1 degree longitude from 75W to 50W and smoothed with a 100 km (10 point) running average via matlab. The uniqueness has been achieved by using Consolidator algorithm (D’Errico, 2023). 

   Each monthly or annual GS path has 251 points between 75W to 50W at 0.1 degree resolution.  

   Please contact igifford@earth.miami.edu for any queries. {"references": ["Andres, M., 2016. On the recent destabilization of the Gulf Stream path downstream of Cape Hatteras. Geophysical Research Letters, 43(18), 9836-9842.", "D'Errico, J., 2023. Consolidator (https://www.mathworks.com/matlabcentral/fileexchange/ 8354-consolidator), MATLAB Central File Exchange. Retrieved June 17, 2023.", "Gifford, Ian. H., 2023. The Synchronicity of the Gulf Stream Free Jet and the Wind Induced Cyclonic Vorticity Pool. MS Thesis, University of Massachusetts Dartmouth. 75pp.", "Gifford, Ian, H., Avijit Gangopadhyay, Magdalena Andres, Glen Gawarkiewicz, Hilde Oliver, Adrienne Silver, 2023. Wind Stress, Wind Stress Curl, and Upwelling Velocities in the Northwest Atlantic (80-45W, 30-45N) during 1980-2019, https://zenodo.org/record/8200832.", "Kobayashi, S., Ota, Y., Harada, Y., Ebita, A., Moriya, M., Onoda, H., Onogi, K., Kamahori, H., Kobayashi, C., Endo, H. and Miyaoka, K., 2015. The JRA-55 reanalysis: General specifications and basic characteristics.\u202fJournal of the Meteorological Society of Japan. Ser. II,\u202f93(1), pp.5-48. Kobayashi, S., Ota, Y., Harada, Y., Ebita, A., Moriya, M., Onoda, H., Onogi, K., Kamahori, H., Kobayashi, C., Endo, H. and Miyaoka, K., 2015. The JRA-55 reanalysis: General specifications and basic characteristics.\u202fJournal of the Meteorological Society of Japan. Ser. II,\u202f93(1), pp.5-48."]} 

   more » « less
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. 

   more » « less
4. Point-hyperplane Incidence Geometry and the Log-rank Conjecture

   https://doi.org/10.1145/3543684  

   Singer, Noah ; Sudan, Madhu ( June 2022 , ACM Transactions on Computation Theory)

   We study the log-rank conjecture from the perspective of point-hyperplane incidence geometry. We formulate the following conjecture: Given a point set in ℝ d that is covered by constant-sized sets of parallel hyperplanes, there exists an affine subspace that accounts for a large (i.e., 2 –polylog( d ) ) fraction of the incidences, in the sense of containing a large fraction of the points and being contained in a large fraction of the hyperplanes. In other words, the point-hyperplane incidence graph for such configurations has a large complete bipartite subgraph. Alternatively, our conjecture may be interpreted linear-algebraically as follows: Any rank- d matrix containing at most O (1) distinct entries in each column contains a submatrix of fractional size 2 –polylog( d ) , in which each column is constant. We prove that our conjecture is equivalent to the log-rank conjecture; the crucial ingredient of this proof is a reduction from bounds for parallel k -partitions to bounds for parallel ( k -1)-partitions. We also introduce an (apparent) strengthening of the conjecture, which relaxes the requirements that the sets of hyperplanes be parallel. Motivated by the connections above, we revisit well-studied questions in point-hyperplane incidence geometry without structural assumptions (i.e., the existence of partitions). We give an elementary argument for the existence of complete bipartite subgraphs of density Ω (ε 2 d / d ) in any d -dimensional configuration with incidence density ε, qualitatively matching previous results proved using sophisticated geometric techniques. We also improve an upper-bound construction of Apfelbaum and Sharir [ 2 ], yielding a configuration whose complete bipartite subgraphs are exponentially small and whose incidence density is Ω (1/√ d ). Finally, we discuss various constructions (due to others) of products of Boolean matrices which yield configurations with incidence density Ω (1) and complete bipartite subgraph density 2 -Ω (√ d ) , and pose several questions for this special case in the alternative language of extremal set combinatorics. Our framework and results may help shed light on the difficulty of improving Lovett’s Õ(√ rank( f )) bound [ 20 ] for the log-rank conjecture. In particular, any improvement on this bound would imply the first complete bipartite subgraph size bounds for parallel 3-partitioned configurations which beat our generic bounds for unstructured configurations. 

   more » « less
5. Unveiling the warm and dense ISM in z  > 6 quasar host galaxies via water vapor emission

   https://doi.org/10.1051/0004-6361/202243406  

   Pensabene, A. ; van der Werf, P. ; Decarli, R. ; Bañados, E. ; Meyer, R. A. ; Riechers, D. ; Venemans, B. ; Walter, F. ; Weiß, A. ; Brusa, M. ; et al ( November 2022 , Astronomy & Astrophysics)

   Water vapor (H₂O) is one of the brightest molecular emitters after carbon monoxide (CO) in galaxies with high infrared (IR) luminosity, allowing us to investigate the warm and dense phase of the interstellar medium (ISM) where star formation occurs. However, due to the complexity of its radiative spectrum, H₂O is not frequently exploited as an ISM tracer in distant galaxies. Therefore, H₂O studies of the warm and dense gas at high-zremain largely unexplored. In this work, we present observations conducted with the Northern Extended Millimeter Array (NOEMA) toward threez > 6 IR-bright quasarsJ2310+1855,J1148+5251, andJ0439+1634targeted in their multiple para- and ortho-H₂O transitions (3₁₂ − 3₀₃, 1₁₁ − 0₀₀, 2₂₀ − 2₁₁, and 4₂₂ − 4₁₃), as well as their far-IR (FIR) dust continuum. By combining our data with previous measurements from the literature, we estimated the dust masses and temperatures, continuum optical depths, IR luminosities, and star formation rates (SFR) from the FIR continuum. We modeled the H₂O lines using the MOLPOP-CEP radiative transfer code, finding that water vapor lines in our quasar host galaxies are primarily excited in the warm, dense (with a gas kinetic temperature and density ofT_kin = 50 K,n_H2 ∼ 10^4.5 − 10⁵ cm⁻³) molecular medium with a water vapor column density ofN_H2O ∼ 2 × 10¹⁷ − 3 × 10¹⁸ cm⁻³. High-JH₂O lines are mainly radiatively pumped by the intense optically-thin far-IR radiation field associated with a warm dust component at temperatures ofT_dust ∼ 80 − 190 K that account for < 5 − 10% of the total dust mass. In the case of J2310+1855, our analysis points to a relatively high value of the continuum optical depth at 100 μm (τ₁₀₀ ∼ 1). Our results are in agreement with expectations based on the H₂O spectral line energy distribution of local and high-zultra-luminous IR galaxies and active galactic nuclei (AGN). The analysis of the Boltzmann diagrams highlights the interplay between collisions and IR pumping in populating the high H₂O energy levels and it allows us to directly compare the excitation conditions in the targeted quasar host galaxies. In addition, the observations enable us to sample the high-luminosity part of the H₂O–total-IR (TIR) luminosity relations (L_H2O − L_TIR). Overall, our results point to supralinear trends that suggest H₂O–TIR relations are likely driven by IR pumping, rather than the mere co-spatiality between the FIR continuum- and line-emitting regions. The observedL_H2O/L_TIRratios in ourz > 6 quasars do not show any strong deviations with respect to those measured in star-forming galaxies and AGN at lower redshifts. This supports the notion that H₂O can be likely used to trace the star formation activity buried deep within the dense molecular clouds.

    

   more » « less