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opencc-by-4.0Jun 2022View details →

A dataset of anonymised hospitalised COVID-19 patient data: outcomes, demographics and biomarker measurements for two New York hospitals

These datasets are for a cohort of n=1540 anonymised hospitalised COVID-19 patients, and the data provide information on outcomes (i.e. patient death or discharge), demographics and biomarker measurements for two New York hospitals: State University of New York (SUNY) Downstate Health Sciences University and Maimonides Medical Center. The file "demographics_both_hospitals.csv" contains the ultimate outcomes of hospitalisation (whether a patient was discharged or died), demographic information and known comorbidities for each of the patients. The file "dynamics_clean_both_hospitals.csv" contains cleaned dynamic biomarker measurements for the n=1233 patients where this information was available and the data passed our various checks (see https://doi.org/10.1101/2021.11.12.21266248 for information of these checks and the cleaning process). Patients can be matched to demographic data via the "id" column. Study approval and data collection Study approval was obtained from the State University of New York (SUNY) Downstate Health Sciences University Institutional Review Board (IRB\#1595271-1) and Maimonides Medical Center Institutional Review Board/Research Committee (IRB\#2020-05-07). A retrospective query was performed among the patients who were admitted to SUNY Downstate Medical Center and Maimonides Medical Center with COVID-19-related symptoms, which was subsequently confirmed by RT PCR, from the beginning of February 2020 until the end of May 2020. Stratified randomization was used to select at least 500 patients who were discharged and 500 patients who died due to the complications of COVID-19. Patient outcome was recorded as a binary choice of “discharged” versus “COVID-19 related mortality”. Patients whose outcome was unknown were excluded. Demographic, clinical history and laboratory data was extracted from the hospital’s electronic health records.

opencc-by-4.0Nov 2020View details →

Data to accompany "Automatic text clustering for audio attribute elicitation experiment responses", AES 143rd Convention, New York, NY, USA, 2017

This work was supported by the EPSRC Programme Grant S3A: Future Spatial Audio for an Immersive Listener Experience at Home (EP/L000539/1) and the BBC as part of the BBC Audio Research Partnership. Details about the data underlying this work, along with the terms for data access, are available from http://dx.doi.org/10.15126/surreydata.00841589. If you use the data, please cite the following paper: J. Francombe, T. Brookes, and R. Mason, “Automatic text clustering for audio attribute elicitation experiment responses”, AES 143rd Convention, New York, NY, USA, 2017

Figure 6 in A new Late Eocene cassiduloid (Echinoidea) from Yorke Peninsula, South Australia

Figure 6. Comparative drawings of A, Late Eocene Rhynchopygus? janchrisorum sp. nov. from Yorke Peninsula, South Australia; B, Late Cretaceous (Late Maastrichtian) R. donetzensis from the Severny Donetz Basin, Ukraine (adapted from Smith and Jeffery, 2000); C1, Late Cretaceous (Late? Santonian) R. marmini from La Richardière, Dissay, France; C2, posterior profile of Late Cretaceous (Late Campanian) R. marmini from near Royan and St Palais-sur-Mer, France. Based on published illustrations, latter profile typical of Maastrichtian R. marmini specimens in general. Scale bars 5 mm.

Figure 4 in A new Late Eocene cassiduloid (Echinoidea) from Yorke Peninsula, South Australia

Figure 4. Rhynchopygus? janchrisorum sp. nov. A–C, reconstruction of adapical, right lateral and posterior characteristics of holotype NMV P145616 (actual specimen outline shown with broken line). Scale bar 10 mm.

Figure 2 in A new Late Eocene cassiduloid (Echinoidea) from Yorke Peninsula, South Australia

Figure 2. Rhynchopygus? janchrisorum sp. nov. A–C, adapical, right lateral and posterior views of holotype NMV P145616; D, adoral view of paratype NMV P312115; E, adoral view of paratype NMV P312114; F, adapical view of paratype NMV P312113. All specimens form the Late Eocene Muloowurtie Formation, Yorke Peninsula, South Australia. Scale bar 10 mm.

Figure 1. A and B in A new Late Eocene cassiduloid (Echinoidea) from Yorke Peninsula, South Australia

Figure 1. A and B, general location maps; C, map of St Vincent Basin in relation to Yorke Peninsula, Kangaroo Island and the Fleurieu Peninsula (Maslin Bay), South Australia; D, location of the northernmost exposure (1), and southernmost exposure (2), of the Muloowurtie Formation, west side of Gulf St Vincent.

Figure 5 in A new Late Eocene cassiduloid (Echinoidea) from Yorke Peninsula, South Australia

Figure 5. Rhynchopygus? janchrisorum sp. nov. Drawing of adapical surface of NMV P312113 showing plate structure distal to petals. Scale bar 10 mm.

opencc-zeroJun 2024View details →

Dataset: New York Mortgage Trust, Inc. (NYMTL) Stock Performance

This dataset provides historical stock market performance data for specific companies. It enables users to analyze and understand the past trends and fluctuations in stock prices over time. This information can be utilized for various purposes such as investment analysis, financial research, and market trend forecasting.

opencc-by-nc-sa-4.0Oct 2018View details →

Green Roofs Footprints for New York City, Assembled from Available Data and Remote Sensing

Summary: The files contained herein represent green roof footprints in NYC visible in 2016 high-resolution orthoimagery of NYC (described at <a href="https://github.com/CityOfNewYork/nyc-geo-metadata/blob/master/Metadata/Metadata_AerialImagery.md">https://github.com/CityOfNewYork/nyc-geo-metadata/blob/master/Metadata/Metadata_AerialImagery.md</a>). Previously documented green roofs were aggregated in 2016 from multiple data sources including from NYC Department of Parks and Recreation and the NYC Department of Environmental Protection, greenroofs.com, and greenhomenyc.org. Footprints of the green roof surfaces were manually digitized based on the 2016 imagery, and a sample of other roof types were digitized to create a set of training data for classification of the imagery. A Mahalanobis distance classifier was employed in Google Earth Engine, and results were manually corrected, removing non-green roofs that were classified and adjusting shape/outlines of the classified green roofs to remove significant errors based on visual inspection with imagery across multiple time points. Ultimately, these initial data represent an estimate of where green roofs existed as of the imagery used, in 2016. These data are associated with an existing GitHub Repository, <a href="https://github.com/tnc-ny-science/NYC_GreenRoofMapping">https://github.com/tnc-ny-science/NYC_GreenRoofMapping</a>, and as needed and appropriate pending future work, versioned updates will be released here. Terms of Use: The Nature Conservancy and co-authors of this work shall not be held liable for improper or incorrect use of the data described and/or contained herein. Any sale, distribution, loan, or offering for use of these digital data, in whole or in part, is prohibited without the approval of The Nature Conservancy and co-authors. The use of these data to produce other GIS products and services with the intent to sell for a profit is prohibited without the written consent of The Nature Conservancy and co-authors. All parties receiving these data must be informed of these restrictions. Authors of this work shall be acknowledged as data contributors to any reports or other products derived from these data. Associated Files: As of this release, the specific files included here are: <ul> <li>GreenRoofData2016_20180917.geojson is in the human-readable, GeoJSON format, in geographic coordinates (Lat/Long, WGS84; EPSG 4263).</li> <li>GreenRoofData2016_20180917.gpkg is in the GeoPackage format, which is an Open Standard readable by most GIS software including Esri products (tested on ArcMap 10.3.1 and multiple versions of QGIS). This dataset is in the New York State Plan Coordinate System (units in feet) for the Long Island Zone, North American Datum 1983, EPSG 2263.</li> <li>GreenRoofData2016_20180917_Shapefile.zip is a zipped folder containing a Shapefile and associated files. Please note that some field names were truncated due to limitations of Shapefiles, but columns are in the same order as for other files and in the same order as listed below. This dataset is in the New York State Plan Coordinate System (units in feet) for the Long Island Zone, North American Datum 1983, EPSG 2263.</li> <li>GreenRoofData2016_20180917.csv is a comma-separated values file (CSV) with coordinates for centroids for the green roofs stored in the table itself. This allows for easily opening the data in a tool like spreadsheet software (e.g., Microsoft Excel) or a text editor.</li> </ul> Column Information for the datasets: Some, but not all fields were joined to the green roof footprint data based on building footprint and tax lot data; those datasets are embedded as hyperlinks below. <ul> <li>fid - Unique identifier</li> <li>bin - NYC Building ID Number based on overlap between green roof areas and a building footprint dataset for NYC from August, 2017. (Newer building footprint datasets do not have linkages to the tax lot identifier (bbl), thus this older dataset was used). The most current building footprint dataset should be available at: <a href="https://data.cityofnewyork.us/Housing-Development/Building-Footprints/nqwf-w8eh">https://data.cityofnewyork.us/Housing-Development/Building-Footprints/nqwf-w8eh</a>. Associated metadata for fields from that dataset are available at <a href="https://github.com/CityOfNewYork/nyc-geo-metadata/blob/master/Metadata/Metadata_BuildingFootprints.md">https://github.com/CityOfNewYork/nyc-geo-metadata/blob/master/Metadata/Metadata_BuildingFootprints.md</a>.</li> <li>bbl - Boro Block and Lot number as a single string. This field is a tax lot identifier for NYC, which can be tied to the Digital Tax Map (<a href="http://gis.nyc.gov/taxmap/map.htm">http://gis.nyc.gov/taxmap/map.htm</a>) and PLUTO/MapPLUTO (<a href="https://www1.nyc.gov/site/planning/data-maps/open-data/dwn-pluto-mappluto.page">https://www1.nyc.gov/site/planning/data-maps/open-data/dwn-pluto-mappluto.page</a>). Metadata for fields pulled from PLUTO/MapPLUTO can be found in the PLUTO Data Dictionary found on the aforementioned page. All joins to this bbl were based on MapPLUTO version 18v1.</li> <li>gr_area - Total area of the footprint of the green roof as per this data layer, in square feet, calculated using the projected coordinate system (EPSG 2263).</li> <li>bldg_area - Total area of the footprint of the associated building, in square feet, calculated using the projected coordinate system (EPSG 2263).</li> <li>prop_gr - Proportion of the building covered by green roof according to this layer (gr_area/bldg_area).</li> <li>cnstrct_yr - Year the building was constructed, pulled from the Building Footprint data.</li> <li>doitt_id - An identifier for the building assigned by the NYC Dept. of Information Technology and Telecommunications, pulled from the Building Footprint Data.</li> <li>heightroof - Height of the roof of the associated building, pulled from the Building Footprint Data.</li> <li>feat_code - Code describing the type of building, pulled from the Building Footprint Data.</li> <li>groundelev - Lowest elevation at the building level, pulled from the Building Footprint Data.</li> <li>qa - Flag indicating a positive QA/QC check (using multiple types of imagery); all data in this dataset should have 'Good'</li> <li>notes - Any notes about the green roof taken during visual inspection of imagery; for example, it was noted if the green roof appeared to be missing in newer imagery, or if there were parts of the roof for which it was unclear whether there was green roof area or potted plants.</li> <li>classified - Flag indicating whether the green roof was detected image classification. (1 for yes, 0 for no)</li> <li>digitized - Flag indicating whether the green roof was digitized prior to image classification and used as training data. (1 for yes, 0 for no)</li> <li>newlyadded - Flag indicating whether the green roof was detected solely by visual inspection after the image classification and added. (1 for yes, 0 for no)</li> <li>original_source - Indication of what the original data source was, whether a specific website, agency such as NYC Dept. of Parks and Recreation (DPR), or NYC Dept. of Environmental Protection (DEP). Multiple sources are separated by a slash.</li> <li>address - Address based on MapPLUTO, joined to the dataset based on bbl.</li> <li>borough - Borough abbreviation pulled from MapPLUTO.</li> <li>ownertype - Owner type field pulled from MapPLUTO.</li> <li>zonedist1 - Zoning District 1 type pulled from MapPLUTO.</li> <li>spdist1 - Special District 1 pulled from MapPLUTO.</li> <li>bbl_fixed - Flag to indicate whether bbl was manually fixed. Since tax lot data may have changed slightly since the release of the building footprint data used in this work, a small percentage of bbl codes had to be manually updated based on overlay between the green roof footprint and the MapPLUTO data, when no join was feasible based on the bbl code from the building footprint data. (1 for yes, 0 for no)</li> </ul> For GreenRoofData2016_20180917.csv there are two additional columns, representing the coordinates of centroids in geographic coordinates (Lat/Long, WGS84; EPSG 4263): <ul> <li>xcoord - Longitude in decimal degrees.</li> <li>ycoord - Latitude in decimal degrees.</li> </ul> Acknowledgements: This work was primarily supported through funding from the J.M. Kaplan Fund, awarded to the New York City Program of The Nature Conservancy, with additional support from the New York Community Trust, through New York City Audubon and the Green Roof Researchers Alliance.

opencc-by-4.0Apr 2021View details →

Fig. 1. Phylogenetic relationships between 74 in Prevalence and molecular characterization of novel species of the Diplomonad genus Octomitus (Diplomonadida: Giardiinae) from wildlife in a New York watershed

Fig. 1. Phylogenetic relationships between 74 sequences of Octomitus representing 14 genotypes estimated by maximum likelihood analysis. The GTR + I + G model (gamma shape = 0.338, prop. invariable sites = 0.619) was chosen by jModelTest2 to be the best-fitting evolutionary model. Branches with less than 70% bootstrap support were not considered statistically robust and were collapsed during manual editing of the visualization. Inset: ML phylogeny computed from Octomitus genotypes aligned with the homologous region of available Diplomonad 18S rDNA sequences from Giardia, Spironucleus, Hexamita, Trimitus, and Enteromonas.

Fig. 9 in Givetian (Middle Devonian) sharks from Cairo, New York (USA): Evidence of early cosmopolitanism

Fig. 9. Incomplete fin spine with compound chondrichthyan scales that are comparable to Type 1 sensu Liao et al. (2007) from the Givetian of the Aragonian Pyrenees, Spain, NYSM 17790. A. Specimen whitened with ammonium chloride. B. Close-up view of associated spine, associated to compound chondrichthyan scales Type 1 sensu Liao et al. (2007). C. Transversal section extracted from a reconstruction of the specimen from micro CT scan data (exposure time: 1650 ms; accelerating voltage: 65kV; current: 120 μA), showing the internal canals. D. Sections extracted from the reconstruction of the fin spine tip from micro-tomodensitometry data; lateral (D1) and dorsal (D2) views, showing the system of internal canals. E. 3D reconstructions of the fin spine tip from micro CT scan data (exposure time: 1650 ms; accelerating voltage: 65kV; current: 120 μA), in lateral (E1) and dorso-lateral (E2) views.

Fig. 6 in Givetian (Middle Devonian) sharks from Cairo, New York (USA): Evidence of early cosmopolitanism

Fig. 6. Internal structure of the teeth of omalodontid shark Portalodus mannoliniae sp. nov. from the Givetian of the Cairo quarry, New York, for the adult (A–E) and the juvenile (F–H) morphotypes. A–C. NYSM 17718; images acquired by micro CT-scan (exposure time: 1300 ms; accelerating voltage: 75kV; current: 106 μA). A. Coronal planes angled through the crown and the base, near the lingual margin, with the base horizontal (A1) and along the plane of the cusps (A2), black arrow indicates a possible growth line in the orthodentine outer layer. B. Transverse planes through the right (B1) and the left (B2) cusps when looking from the labial side. C. Horizontal plane through the base. D–E. NYSM 17716; images acquired by SEM. D. Break facet of the right cusp when looking from the labial side. E. Close-up view of the margin of the left cusp (when looking from the labial side) (E1) and of the orthodentine external layer (E2); white arrow indicates the enamel outer layer, black arrow shows separation line between the two main orthodentine layers. F–H. NYSM 17699; images acquired by micro CT-scan (exposure time: 1000 ms; accelerating voltage: 70kV; current: 114 μA). F. Coronal plane angled through the crown and the base. G. Horizontal planes through the base, near the bottom of the base (G1), at about mid-base (G2), and at the bottom of the crown, underneath the forking of the cusps (G3). H. Planes along the labio-lingual axis through the left cusp (when looking from the labial side), near its median side (H1), and inbetween the two cusps (H2).

Fig. 3 in Givetian (Middle Devonian) sharks from Cairo, New York (USA): Evidence of early cosmopolitanism

Fig. 3. Juvenile morphotype of the teeth of omalodontid shark Portalodus mannoliniae sp. nov. from the Givetian of the Cairo quarry, New York, USA. A. NYSM 17736, paratype, in labial (A1), lingual (A2), occlusal (A3), and lateral (A4) views. B. NYSM 17756, in occlusal (B1) and lingual (B2) views. C. NYSM 17752, in occlusal (C1) and lingual (C2) views.

Fig. 2 in Givetian (Middle Devonian) sharks from Cairo, New York (USA): Evidence of early cosmopolitanism

Fig. 2. Generalized stratigraphic section of the Plattekill Formation at Cairo quarry. Chondrichthyan specimens described herein originate from the 5-m level. The fish horizon at 7.35 m corresponds to the level of the fossilized forest mentioned by Cloutier et al. (2010).

Fig. 10 in Givetian (Middle Devonian) sharks from Cairo, New York (USA): Evidence of early cosmopolitanism

Fig. 10. Scales of Elasmobranchii indet. fam., gen. et sp. B sensu Burrow et al. 2009 from the Givetian of the Cairo quarry, New York, tentatively assigned to omalodontid shark Portalodus mannoliniae sp. nov. A. NYSM 17899. B. NYSM 17898. C. NYSM 17900. D. NYSM 17958. E. NYSM 17791. F. NYSM 17796. G. NYSM 17927. H. NYSM 17795. I. NYSM 17944. J. NYSM 17798. K. NYSM 17934, white arrows indicate the superposed internal layers in the crown. L. NYSM 17918 (L1), with magnification of framed section (L2); the close-up on the bundle of fibres (L3) corresponds to the section identified by the arrow in L2. In crown (A1–J1), lateral (A2–C2, E2–H2, J2, L), postero-lateral (D2), antero-lateral (I2), and anterior (K) views.

0.0 0.2 0.4 0.6 0.8 1.0 in Givetian (Middle Devonian) sharks from Cairo, New York (USA): Evidence of early cosmopolitanism

0.0 0.2 0.4 0.6 0.8 1.0 Base width (latero-medial) (log10 (x + 1)) Fig. 5. Relationship between width and length of the tooth base for Portalodus mannoliniae sp. nov. Regression lines are represented for the juvenile (n = 32 teeth) and adult (n = 43 teeth) morphotypes as well as for the complete sample.