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opencc-by-4.0Dec 2021View details →

Modeling Crash Severity and Collision Types Using Machine Learning

Traffic safety analysis is the fundamental step for reducing economic, social, and environmental cost incurred due to traffic accidents. The essence of traffic safety is understanding the factors affecting crash occurrence, injury severity and collision type and their underlying relationships and predict-prevent future crash instances. Crash injury severity studies in past have utilized numerous statistical, econometric and Machine Learning (ML) and Artificial Intelligence (AI) tools to extract the underlying relationship between the crash causal factors and the consequent severity or collision type. The study aims to explore the Multi-Label Classification (MLC) tool from the domain of Artificial Intelligence (AI) for classification problems in the setting of traffic safety. MLC finds its application primarily in protein function, semantic scene, and music categorization problems. In the real world, multiple heterogenous subjective factors decide the extent of damage/severity of a particular crash instance. Theoretically, the traffic collision type and crash severity type can be correlated, and thus, it is intuitive to model them simultaneously. The ability of MLC to categorize an entity under analysis to more than one labels, correlated or uncorrelated, provides the approach an edge over the single-class (binary) or multi-class classification approach. The MLC based classification model was calibrated and tested using the historical crash data extracted for the state of Texas. The selection of study area was based on a link-level unsupervised principal component analysis-based clustering approach. Similar clustering approach was also tested at the county-level to understand the spatial behavior and thus transferability of the MLC approach to other key cities in the state. The performance of the proposed approach was tested, compared, and quantified with the conventional binary/multi-class classification tools used in the traffic safety domain. Inferences from the preliminary numerical analysis indicates that the proposed multi-label classification approach has promising performance compared to the traditional classification approaches, specifically found in traffic safety literatures.

opencc-by-4.0Jun 2022View details →

Towards Developing and Analysing The Metric-Based Software Defect Severity Prediction Model

This is a metric based approach to solve software defect severity prediction problem. In addition to that, this work proposes a new evaluation scheme that comprised of five metrics to analyze the performances.

opencc-by-4.0Jan 2022View details →

Variables from several snapshots of 0% net helicity driven sunspot simulation

The included dataset is from an magnetohydrodynamic simulation of a sunspot that is driven by photospheric motions. Several snapshots in time are extracted, and the magnetic field, velocity, and current from those snapshots is stored in the attached dataset, along with the three coordinate arrays. The datafiles are in HDF5 format, which is easily read in all major programming languages. The simulation is largely described in https://ui.adsabs.harvard.edu/abs/2017ApJ...851L..17K/abstract. The files are read directly from the restart files and the variables reside at their original grid locations. The files labeled fieldline.* are fortran unformatted datasets of magnetic field lines traced from the boundary of the simulation at these time steps. The dimensions of the traced field lines are 401x401x400x3.

opencc-zeroJul 2022View details →

An ordinal severity scale for COVID-19 retrospective studies using electronic health record data

Objectives: Although the World Health Organization (WHO) Clinical Progression Scale for COVID-19 is useful in prospective clinical trials, it cannot be effectively used with retrospective Electronic Health Record (EHR) datasets. Modifying the existing WHO Clinical Progression Scale, we developed an ordinal severity scale (OS) and assessed its usefulness in the analyses of COVID-19 patient outcomes using retrospective EHR data. Results: The data set used in this analysis consists of 2,880,456 patients. PCA of the day-to-day variation in OS levels over the totality of the 28-day period revealed contrasting patterns of variation in disease severity within the first and second 14 days and illustrated the importance of evaluation over the full 28-day period. Discussion: An OS with well-defined, robust features, based on discrete EHR data elements, is useful for assessments of COVID-19 patient outcomes, providing insights on progression of COVID-19 disease severity over time. Conclusion: The OS provides a framework which can facilitate better understanding of the course of acute COVID-19, informing clinical decision-making and resource allocation.

opencc-zeroJul 2022View details →

Beyond bold versus shy: Zebrafish exploratory behavior falls into several behavioral clusters and is influenced by strain and sex

Individual differences in exploratory behavior have been found across a range of taxa and are thought to contribute to evolutionary fitness. Animals that explore more of a novel environment and visit areas of high predation risk are considered bold, whereas animals with the opposite behavioral pattern are shy. Here, we determined whether this bimodal characterization of bold versus shy adequately captures the breadth of behavioral variation in zebrafish or if there are more than these two subtypes. To identify behavioral categories, we applied unsupervised machine to three-dimensional swim traces from over 400 adult zebrafish across four strains (AB, TL, TU, and WIK) and both sexes. We found that behavior stratified into four distinct clusters: previously described bold and shy behavior and two new behavioral types we call wall-huggers and active explorers. Clusters were stable across time and influenced by strain and sex where we found that TLs were shy, female TU fish were bold, male TU fish were active explorers, and male ABs were wall-huggers. Our work suggests that zebrafish exploratory behavior has greater complexity than previously recognized and lays the groundwork for the use of zebrafish in understanding the biological basis of individual differences in behavior.

opencc-zeroAug 2022View details →

The gut microbiome variability of a butterflyfish increases on severely degraded Caribbean reefs

Environmental degradation has the potential to alter key mutualisms that underlie the structure and function of ecological communities. How microbial communities associated with fishes vary across populations and in relation to habitat characteristics remains largely unknown despite their fundamental roles in host nutrition and immunity. We find significant differences in the gut microbiome composition of a facultative coral-feeding butterflyfish (Chaetodon capistratus) across Caribbean reefs that differ markedly in live coral cover (∼0–30%). Fish gut microbiomes were significantly more variable at degraded reefs, a pattern driven by changes in the relative abundance of the most common taxa potentially associated with stress. We also demonstrate that fish gut microbiomes on severely degraded reefs have a lower abundance of Endozoicomonas and a higher diversity of anaerobic fermentative bacteria, which may suggest a less coral dominated diet. The observed shifts in fish gut bacterial communities across the habitat gradient extend to a small set of potentially beneficial host associated bacteria (i.e., the core microbiome) suggesting essential fish-microbiome interactions may be vulnerable to severe coral degradation.

Outcome of severe COVID-19: spotlight on fatigue, fatiguability, multidomain complaints and pattern of cognitive deficits in a case series without prior brain dysfunction and without COVID-19-related stroke and/or cardiac arrest

Outcome of severe COVID-19: spotlight on fatigue, fatiguability, multidomain complaints and pattern of cognitive deficits in a case series without prior brain dysfunction and without COVID-19-related stroke and/or cardiac arrest Valérie Beaud1, Sonia Crottaz-Herbette1, Vincent Dunet2, Jean-François Knebel1, Pierre-Alexandre Bart3, Stephanie Clarke1 1 Service of Neuropsychology and Neurorehabilitation, Lausanne University Hospital and University of Lausanne, 1011 Lausanne, Switzerland 2 Service of Diagnostic and Interventional Radiology, Lausanne University Hospital and University of Lausanne, 1011 Lausanne, Switzerland 3 Service of Internal Medicine, Lausanne University Hospital and University of Lausanne, 1011 Lausanne, Switzerland ABSTRACT Background: Cognitive deficits were often reported during the acute and post-acute stages of severe COVID-19 and were often, but not always, associated with signs of brain damage. Population-wide surveys highlighted the need for investigations into the nature, the severity and the evolution of cognitive, behavioural and psychiatric deficits. Case presentation: We report the outcome at 12 months after severe COVID-19 involving intensive care unit stay and mechanical ventilation in six patients. None of the patients had history of prior brain dysfunction and none sustained stroke and/or cardiac arrest during COVID-19. A pervading mental and physical fatigue was consistently reported as well as numerous multidomain complaints, which affect to some extend everyday life, and for some of the patients a mental fatiguability, a certain degree of neurobehavioural (apathy) and/or psychiatric (anxiety) dysfunction. Standardized neuropsychological tests revealed for 4 of the 6 patients the occurrence relatively isolated of cognitive dysfunction or performance at the lower limit of the norm in some, but not all attentional, executive and/or working memory tests. Somatic scales highlighted the presence of dyspnoea, muscle weakness, olfactory disorder and/or minor sleep problems in some but not all patients. Conclusion: Fatigue, fatiguability, multidomain complaints, which affect to some extend everyday life, cognitive dysfunction or performance at the lower limit of the norm and a certain degree of neurobehavioural and/or psychiatric and/or somatic dysfunction can occur in the aftermath of severe COVID-19 even in the absence of neurological antecedents or of COVID-19-related stroke and/or cardiac arrest.

opencc-zeroSep 2022View details →

Integrated plasma proteomic and single-cell immune signaling network signatures demarcate mild, moderate, and severe COVID-19

The biological determinants underlying the range of COVID-19 clinical manifestations are not fully understood. Here, over 1400 plasma proteins and 2600 single-cell immune features comprising cell phenotype, endogenous signaling activity, and signaling responses to inflammatory ligands are cross-sectionally assessed in peripheral blood from 97 patients with mild, moderate, and severe COVID-19 and 40 uninfected patients. Using an integrated computational approach to analyze the combined plasma and single-cell proteomic data, we identify and independently validate a multivariate model classifying COVID-19 severity (multi-class AUCtraining = 0.799, p-value = 4.2e-6; multi-class AUCvalidation = 0.773, p-value = 7.7e-6). Examination of informative model features reveals novel biological signatures of COVID-19 severity, including the dysregulation of JAK/STAT, MAPK/mTOR, and NF-κB immune signaling networks in addition to recapitulating known hallmarks of COVID-19. These results provide a set of early determinants of COVID-19 severity that may point to therapeutic targets for prevention and/or treatment of COVID-19 progression.

opencc-zeroAug 2022View details →

Discrete fire events, their severity, and their ignitions, as derived from MODIS MCD 14ML active-fire detection data for Indonesia, 2002-2019

1. PUBLICATION CORRESPONDING TO THESE DATA Sloan, Sean*; Locatelli, Bruno; Andela, Niels; Cattau, Megan E.; Gaveau, David; Tacconi, Luca. 2022 'Declining Severe Fire Activity on Managed Lands in Equatorial Asia'. Communications Earth & Environment. DOI: 10.1038/s43247-022-00522-6. *Corresponding author email: sean.sloan@viu.ca 2. ABSTRACT OF THE DATA The GIS data and corresponding attribute data described here pertain to discrete fire events, their severity, and their ignitions, as derived on the basis of daily MODIS Collection 6 MCD14ML active-fire detections (AFDs). Data on fire events and their ignitions are provided separately, as two data files. These data files on fire events and ignitions may however be linked to each other by the data user. Fire-event severity is quantified per fire event and reported in the data file for fire events. A fire event is a cluster of MODIS Collection 6 MCD14ML active-fire detections (AFDs) wherein each AFD has a spatial (<=1-km) and temporal (<=4-day) proximity to another AFD in the same fire event, inferring thus a relational co-occurrence amongst AFDs in time and space. In other words, a fire event is considered a likely occasion of burning wherein all constituent AFDs are related to each other in time and space, either directly (as for proximate AFDs) or indirectly (as in the case of a large area of fire activity that spread progressively over time and space from an initial source). Each fire event has a designated ignition AFD, being the AFD of the fire event with the earliest detection date. A given fire event can have more than one ignition AFD if the ignitions all share same earliest detection date. The ignition AFD(s) is the nominal initial source of the burning described by the corresponding fire event. All other, non-ignition AFDs of a fire event are deemed its 'propagation' AFDs, since these AFDs follow from the ignitions, temporally and spatially. See Figure 4 in the publication by Sloan et al. for an illustration of the geography of fire events and their ignition AFDs. Fire events and their ignitions were derived from standard science-quality MODIS Collection 6 MCD 14ML AFD data, commonly referred to as fire 'hotspot' data. Data were detected by both the Terra and Aqua satellite sensors daily for Indonesia between July 2002 and December 2019. Information on these input data are provide by the two citations below. The publication of Sloan et al. provides methodological details on how the MODIS Collection 6 MCD 14ML AFD data were processed into discrete fire events and ignitions. EarthData. MODIS Collection 6 Active-Fire Detections standard scientific data (MCD14ML), NASA EarthData, https://earthdata.nasa.gov/firms (2019). Giglio, L., Schroeder, W. & Justice, C. O. The Collection 6 MODIS active fire detection algorithm and fire products. Remote Sensing of Environment 178, 31-41, (2016). 3. DATA FILES Two data files are distributed here – one for discrete fire events, and another for the ignition AFDs of each fire event. The data files are provided in a GIS-compatible format, and also as a generic text format, as described below. 3.1 GIS VERSION Data files in GIS-compatible format are provided as 'feature classes' within an ArcGIS file geodatabase 'Sloan_MODIS_FireEvents_Ignitions_2002_2019.gdb'. These data files can be viewed and manipulated using either ArcGIS Desktop or ArcGIS Pro software. There is one feature class for fire events, and another file for ignitions. Sloan_MODIS_FireEvents_Ignitions_2002_2019.gdb\nfire4_all_spatial_fire_2002_2019_joins_sp_LC This file pertains to fire events. All AFDs of a given fire event are included, without differentiation as to whether the AFDs are ignition AFDs or other (propagation) AFDs. Fire events are assigned unique ID values and basic attribute data. Sloan_MODIS_FireEvents_Ignitions_2002_2019.gdb\nfire4_all_spatial_fire_2002_2019_igs_sp_LC This file pertains to ignitions. Only ignition AFDs are included for a given fire event. Fire events corresponding to the ignitions are assigned unique ID values and basic attribute data. 3.2 CSV TEXT VERSION Both data files are also supplied as comma-separated value (CSV) text files for viewing and manipulation in non-GIS software, such as Excel, text editors, or any statistical software. The text files can also be read into various GIS software. CSV-formatted files have the same file name and attribute fields as the corresponding GIS-formatted data files. These CSV-formatted data files (as well as the GIS-formatted data files) include attribute data on the latitude and the longitude of each AFD. Attribute field names are included as the first row of values in a CSV file. No 'text qualifiers' like quotations (" ") or inverted commas ('') are used to designate text/string values within the CSV file. Text values appear directly between commas in the CSV data file, e.g., …,Kalimantan_Southern,… . Note two points of caution for working with these CSV data: i) Microsoft Excel may be used for a partial view of the data file nfire4_all_spatial_fire_2002_2019_joins_sp_LC.csv, but it is not recommended for working with this data file. This is because the number of records/rows in this csv file slightly exceeds that maximum that may be read by Excel, which is just over 1 million. This limitation does not apply to the other csv file, however. ii) The GIS-formatted data files employ 'null values' in their attribute tables, and so the corresponding 'values' in the CSV-formatted data files are similarly null. For null values, no value whatsoever is ascribed, not even 0. In the syntax of a CSV file (apparent upon opening the file in any text editor like Microsoft Notepad), a null value is denoted by two consecutive commas without any value, text, or space between them. If a CSV file were opened in Excel, a cell assigned a null value would be blank, not 0 or otherwise. This denotes the correct transcription of the GIS-formatted data. This feature will not impede the correct reading of these CSV data by whatever software. Users are made aware of this feature merely to ensure the proper input of these data into whatever software. 4. DATA STRUCTURE / GEOGRAPHY The GIS-formatted data files are 'point data', i.e., they map the geography of AFDs as individual 'points', in keeping with how these MODIS MCD14ML AFD data were originally structured. For the GIS-formatted data files, each record/row in its corresponding attribute tables corresponds geographically to single AFD 'point', regardless of whether that AFD belongs to a fire event comprised of many AFDs. In the parlance of GIS files, the files depict 'single-part' point features. The unique ID field [nfireID2] serves to denote the fire event to which a given AFD belongs. Similarly, for the CSV-formatted data files, each record/row of values corresponds to a single AFD. There are 1,232,377 records for the data file 'nfire4_all_spatial_fire_2002_2019_joins_sp_LC'. There are 720795 records for the data file 'nfire4_all_spatial_fire_2002_2019_igs_sp_LC'. 5. ATTRIBUTE FIELDS In the data files, while some attribute fields pertain to the individual AFD as the unit of observation (e.g., the land-cover class coincident with the AFD), other attribute fields correspond to the larger 'fire event' to which the individual AFD belongs (e.g., the total duration of fire activity for the fire event). Accordingly, for certain attribute fields pertaining to the fire event as a whole, their values will appear 'duplicated' in the data file amongst those individual AFDs (records) that constitute the fire event in question. Whether a given attribute field pertains to the individual AFD or to its constituent fire event is denoted below for each field. Each AFD is assigned a unique ID field denoting its constituent fire event, [nfireID2]. This field is consistent between both data files, so that attribute data for a given fire event may be 'matched' to attribute data for its corresponding ignition AFD(s), and vice versa, on the basis of the common value of the field [nfireID2]. Note that many attributes below are as originally defined/measured by the input MCD 14ML data, or are derived directly thereof. 5.1 DATASET nfire4_all_spatial_fire_2002_2019_joins_sp_LC <table class="MsoTableGrid"> <tbody> <tr> <td> Field Name </td> <td> Geography of Attribute Value </td> <td> Definition </td> </tr> <tr> <td> OID </td> <td> AFD </td> <td> Object ID value. Unique values for each AFD (record) in the GIS-formatted data file when viewed in ArcGIS. Field values are -1 in the CSV-formatted data file. </td> </tr> <tr> <td> Peat </td> <td> AFD </td> <td> Denotes whether the AFD occurs on peatlands (value=1) as defined in Sloan et al. </td> </tr> <tr> <td> MIN_CONFIDE </td> <td> Fire Event </td> <td> The minimum detection confidence of all AFDs in the fire event, where confidence ranges from 1-100%. </td> </tr> <tr> <td> MAX_CONFIDE </td> <td> Fire Event </td> <td> The maximum detection confidence of all AFDs in the fire event, where confidence ranges from 1-100%. </td> </tr> <tr> <td> MEAN_CONFIDE </td> <td> Fire Event </td> <td> The mean detection confidence of all AFDs in the fire event, where confidence ranges from 1-100%. </td> </tr> <tr> <td> STD_CONFIDE </td> <td> Fire Event </td> <td> The standard deviation of detection confidence of all AFDs in the fire event, where confidence ranges from 1-100%. </td> </tr> <tr> <td> SUM_FRP </td> <td> Fire Event </td> <td> The sum total of all fire-radiative power (FRP) measures for all AFDs in the fire event. Units are megawatts. </td> </tr> <tr> <td> MEAN_FRP </td> <td> Fire Event </td> <td> The mean of all fire-radiative power (FRP) measures for all AFDs in the fire event. Units are megawatts. </td> </tr> <tr> <td> MIN_FRP </td> <td> Fire Event </td> <td> The minimum of all fire-radiative power (FRP) measures for all AFDs in the fire event. Units are megawatts. </td> </tr> <tr> <td> MAX_FRP </td> <td> Fire Event </td> <td> The maximum of all fire-radiative power (FRP) measures for all AFDs in the fire event. Units are megawatts. </td> </tr> <tr> <td> MEAN_LATITUD </td> <td> Fire Event </td> <td> The mean latitude of all AFDs in the fire event. </td> </tr> <tr> <td> MEAN_LONGITU </td> <td> Fire Event </td> <td> The mean longitude of all AFDs in the fire event. </td> </tr> <tr> <td> MIN_ACQ_DAT </td> <td> Fire Event </td> <td> The minimum acquisition date of all AFDs in the fire event (i.e., the ignition AFD detection date). </td> </tr> <tr> <td> MAX_ACQ_DAT </td> <td> Fire Event </td> <td> The maximum acquisition date of all AFDs in the fire event (i.e., the ignition AFD detection date). </td> </tr> <tr> <td> MIN_acq_yer </td> <td> Fire Event </td> <td> The year in which the earliest AFD of the fire event was detected. </td> </tr> <tr> <td> MIN_acq_mnt </td> <td> Fire Event </td> <td> The month in which the earliest AFD of the fire event (i.e., ignition AFD) was detected. Months are coded numerically, e.g., 1=January, 12=December. </td> </tr> <tr> <td> MAX_acq_mnt </td> <td> Fire Event </td> <td> The month in which the latest AFD of the fire event was detected. Months are coded numerically, e.g., 1=January, 12=December. </td> </tr> <tr> <td> MIN_yday </td> <td> Fire Event </td> <td> The detection day of year of the earliest AFD of the fire event, i.e., ignition AFD. Day of year is denoted numerically, where 1=January 1 and 365=December 31. </td> </tr> <tr> <td> MAX_yday </td> <td> Fire Event </td> <td> The detection day of year of the latest AFD of the fire event, i.e., ignition AFD. Day of year is denoted numerically, where 1=January 1 and 365=December 31. </td> </tr> <tr> <td> RANGE_yday </td> <td> Fire Event </td> <td> The number of days of duration of the fire event, defined as [MAX_yday]-[MIN_yday] </td> </tr> <tr> <td> FIRST_subst_r </td> <td> AFD </td> <td> Text labels denoting the Indonesian island/region of data processing, e.g., Kalimantan, Papua. </td> </tr> <tr> <td> AF_Count </td> <td> Fire Event </td> <td> Number of AFDs in the fire event. </td> </tr> <tr> <td> nfireID2 </td> <td> Fire Event </td> <td> The unique ID of the fire event to which the AFD belongs. </td> </tr> <tr> <td> Island </td> <td> AFD </td> <td> Numerical values coding for major Indonesian islands/region: 1000000=Sumatra; 2000000=Kalimantan; 3000000=Sulawesi; 4000000=Papua. </td> </tr> <tr> <td> FRP_Days </td> <td> Fire Event </td> <td> The severity of the fire event, as defined by Sloan et al., equal to [Sum_FRP] * ([Range_yday]+1). </td> </tr> <tr> <td> IG_Count </td> <td> Fire Event </td> <td> Number of ignition AFDs in the fire event </td> </tr> <tr> <td> CCI_LC2002 </td> <td> </td> <td> The land-cover class coincident with the AFD. The class is coded by a numerical value as per the left-most column in the table in Section 5.3. The class is that observed for the calendar year in which the AFD occurred, where the year #### is denoted in the field name 'CCI_LC####'. The land-cover data source is as described in Section 5.3. </td> </tr> <tr> <td> CCI_LC2003 </td> <td> </td> </tr> <tr> <td> CCI_LC2004 </td> <td> </td> </tr> <tr> <td> CCI_LC2005 </td> <td> </td> </tr> <tr> <td> CCI_LC2006 </td> <td> </td> </tr> <tr> <td> CCI_LC2007 </td> <td> </td> </tr> <tr> <td> CCI_LC2008 </td> <td> </td> </tr> <tr> <td> CCI_LC2009 </td> <td> </td> </tr> <tr> <td> CCI_LC2010 </td> <td> </td> </tr> <tr> <td> CCI_LC2011 </td> <td> </td> </tr> <tr> <td> CCI_LC2012 </td> <td> </td> </tr> <tr> <td> CCI_LC2013 </td> <td> </td> </tr> <tr> <td> CCI_LC2014 </td> <td> </td> </tr> <tr> <td> CCI_LC2015 </td> <td> </td> </tr> <tr> <td> CCI_LC2016 </td> <td> </td> </tr> <tr> <td> CCI_LC2017 </td> <td> </td> </tr> <tr> <td> CCI_LC2018 </td> <td> </td> </tr> <tr> <td> CCI_LC2019 </td> <td> </td> </tr> <tr> <td> Region </td> <td> AFD </td> <td> Text labels denote whether the AFD occurs within one of the two focal regions of Sloan et al.: Southern Kalimantan, or Central South Sumatra. </td> </tr> <tr> <td> POINT_X </td> <td> AFD </td> <td> Longitude, given as decimal degrees with WGS84 datum. </td> </tr> <tr> <td> POINT_Y </td> <td> AFD </td> <td> Latitude, given as decimal degrees with WGS84 datum. </td> </tr> <tr> <td> POINT_Z </td> <td> -- </td> <td> Ignore. </td> </tr> <tr> <td> POINT_M </td> <td> -- </td> <td> Ignore. </td> </tr> </tbody> </table> 5.2 DATASET nfire4_all_spatial_fire_2002_2019_igs_sp_LC <table class="MsoTableGrid"> <tbody> <tr> <td> Field Name </td> <td> Geography of Attribute Value </td> <td> Definition </td> </tr> <tr> <td> OID </td> <td> AFD </td> <td> Object ID value. Unique values for each AFD (record) in the GIS-formatted data file when viewed in ArcGIS. Field values are -1 in the CSV-formatted data file. </td> </tr> <tr> <td> IG_Count </td> <td> Fire Event </td> <td> Number of ignition AFDs in the fire event. </td> </tr> <tr> <td> MIN_acq_yer </td> <td> Fire Event </td> <td> The year in which the earliest AFD of the fire event was detected. </td> </tr> <tr> <td> MIN_acq_mnt </td> <td> Fire Event </td> <td> The month in which the earliest AFD of the fire event (i.e., ignition AFD) was detected. Months are coded numerically, e.g., 1=January, 12=December. </td> </tr> <tr> <td> FIRST_subst_r </td> <td> AFD </td> <td> Text labels denoting the Indonesian island/region of data processing, e.g., Kalimantan, Papua. </td> </tr> <tr> <td> MIN_yday </td> <td> Fire Event </td> <td> The detection day of year of the earliest AFD of the fire event, i.e., ignition AFD. Day of year is denoted numerically, where 1=January 1 and 365=December 31. </td> </tr> <tr> <td> nfireID2 </td> <td> Fire Event </td> <td> The unique ID of the fire event to which the AFD belongs. </td> </tr> <tr> <td> CCI_LC2002 </td> <td> AFD </td> <td> The land-cover class coincident with the AFD. The class is coded by a numerical value as per the left-most column in the table in Section 5.3. The class is that observed for the calendar year in which the AFD occurred, where the year #### is denoted in the field name 'CCI_LC####'. The land-cover data source is as described in Section 5.3. </td> </tr> <tr> <td> CCI_LC2003 </td> <td> AFD </td> </tr> <tr> <td> CCI_LC2004 </td> <td> AFD </td> </tr> <tr> <td> CCI_LC2005 </td> <td> AFD </td> </tr> <tr> <td> CCI_LC2006 </td> <td> AFD </td> </tr> <tr> <td> CCI_LC2007 </td> <td> AFD </td> </tr> <tr> <td> CCI_LC2008 </td> <td> AFD </td> </tr> <tr> <td> CCI_LC2009 </td> <td> AFD </td> </tr> <tr> <td> CCI_LC2010 </td> <td> AFD </td> </tr> <tr> <td> CCI_LC2011 </td> <td> AFD </td> </tr> <tr> <td> CCI_LC2012 </td> <td> AFD </td> </tr> <tr> <td> CCI_LC2013 </td> <td> AFD </td> </tr> <tr> <td> CCI_LC2014 </td> <td> AFD </td> </tr> <tr> <td> CCI_LC2015 </td> <td> AFD </td> </tr> <tr> <td> CCI_LC2016 </td> <td> AFD </td> </tr> <tr> <td> CCI_LC2017 </td> <td> AFD </td> </tr> <tr> <td> CCI_LC2018 </td> <td> AFD </td> </tr> <tr> <td> CCI_LC2019 </td> <td> AFD </td> </tr> <tr> <td> Region </td> <td> AFD </td> <td> Text labels denote whether the AFD occurs within one of the two focal regions of Sloan et al.: Southern Kalimantan, or Central South Sumatra. </td> </tr> <tr> <td> Peat </td> <td> AFD </td> <td> Denotes whether the AFD occurs on peatlands (value=1) as defined in Sloan et al. </td> </tr> <tr> <td> POINT_X </td> <td> AFD </td> <td> Longitude, given as decimal degrees with WGS84 datum. </td> </tr> <tr> <td> POINT_Y </td> <td> AFD </td> <td> Latitude, given as decimal degrees with WGS84 datum. </td> </tr> <tr> <td> POINT_Z </td> <td> -- </td> <td> Ignore. </td> </tr> <tr> <td> POINT_M </td> <td> -- </td> <td> Ignore. </td> </tr> </tbody> </table> 5.3. LAND-COVER ATTRIBUTE DATA As noted in Section 5.1 and Section 5.2, the nominal values of the attribute fields 'CCI_LC####' correspond to column 1 of the table below. These hierarchical values, and their corresponding land-cover classes labels in column 2 of the table, pertain to the land-cover classification of the Copernicus Climate Change Initiative Land-Cover Product of the European Space Agency. This classification has an annual temporal resolution and 300-meter spatial resolution. Pertinent citations for these land-cover data are below: ESA. Annual land-cover product, 1992 to 2019/present, based on MERIS 300-m and ancillary SPOT, AVHRR, Sentinel-3 and PROB-V satellite data. European Space Agency (ESA) European Centre for Medium-Range Weather Forecasts (ECMFW) Copernicus Climate Change Service (C3S) Climate Change Initiative (CCI), <a href="https://cds.climate.copernicus.eu/cdsapp#!/dataset/satellite-land-cover?tab=overview">https://cds.climate.copernicus.eu/cdsapp#!/dataset/satellite-land-cover?tab=overview</a>; <a href="http://maps.elie.ucl.ac.be/CCI/viewer/download.php">http://maps.elie.ucl.ac.be/CCI/viewer/download.php</a>; <a href="http://www.esa-landcover-cci.org/">http://www.esa-landcover-cci.org/</a> (2020). Pérez-Hoyos, A., Rembold, F., Kerdiles, H. & Gallego, J. Comparison of global land cover datasets for cropland monitoring. Remote Sensing 9, (2017). Columns 3 and 4 in the table below illustrate how the original land-cover classes of the Copernicus Climate Change Initiative Land-Cover Product were reclassified for analysis in Sloan et al. <table class="MsoNormalTable"> <tbody> <tr> <td> 1. CCI-LC Class Value </td> <td> 2. CCI-LC Class Label </td> <td> 3. New Class Value for Sloan et al. </td> <td> 4. New Class Label for Sloan et al. </td> </tr> <tr> <td> 0 </td> <td> No Data </td> <td> 0 </td> <td> No Data </td> </tr> <tr> <td> 10 </td> <td> Cropland, rainfed </td> <td> 1 </td> <td> Cleared/Cultivated </td> </tr> <tr> <td> 11 </td> <td> Herbaceous cover </td> <td> 1 </td> <td> Cleared/Cultivated </td> </tr> <tr> <td> 12 </td> <td> Tree or shrub cover </td> <td> 1 </td> <td> Cleared/Cultivated </td> </tr> <tr> <td> 20 </td> <td> Cropland, irrigated or post‐flooding </td> <td> 1 </td> <td> Cleared/Cultivated </td> </tr> <tr> <td> 30 </td> <td> Mosaic cropland (>50%) / natural vegetation (tree, shrub, herbaceous cover) (<50%) </td> <td> 2 </td> <td> Mosaic Cropland </td> </tr> <tr> <td> 40 </td> <td> Mosaic natural vegetation (tree, shrub, herbaceous cover) (>50%) / cropland (<50%) </td> <td> 3 </td> <td> Mosaic Natural Veg </td> </tr> <tr> <td> 50 </td> <td> Tree cover, broadleaved, evergreen, closed to open (>15%) </td> <td> 4 </td> <td> Forest </td> </tr> <tr> <td> 60 </td> <td> Tree cover, broadleaved, deciduous, closed to open (>15%) </td> <td> 4 </td> <td> Forest </td> </tr> <tr> <td> 61 </td> <td> Tree cover, broadleaved, deciduous, closed (>40%) </td> <td> 4 </td> <td> Forest </td> </tr> <tr> <td> 62 </td> <td> Tree cover, broadleaved, deciduous, open (15‐40%) </td> <td> 4 </td> <td> Forest </td> </tr> <tr> <td> 70 </td> <td> Tree cover, needleleaved, evergreen, closed to open (>15%) </td> <td> 4 </td> <td> Forest </td> </tr> <tr> <td> 71 </td> <td> Tree cover, needleleaved, evergreen, closed (>40%) </td> <td> 4 </td> <td> Forest </td> </tr> <tr> <td> 72 </td> <td> Tree cover, needleleaved, evergreen, open (15‐40%) </td> <td> 4 </td> <td> Forest </td> </tr> <tr> <td> 80 </td> <td> Tree cover, needleleaved, deciduous, closed to open (>15%) </td> <td> 4 </td> <td> Forest </td> </tr> <tr> <td> 81 </td> <td> Tree cover, needleleaved, deciduous, closed (>40%) </td> <td> 4 </td> <td> Forest </td> </tr> <tr> <td> 82 </td> <td> Tree cover, needleleaved, deciduous, open (15‐40%) </td> <td> 4 </td> <td> Forest </td> </tr> <tr> <td> 90 </td> <td> Tree cover, mixed leaf type (broadleaved and needleleaved) </td> <td> 4 </td> <td> Forest </td> </tr> <tr> <td> 100 </td> <td> Mosaic tree and shrub (>50%) / herbaceous cover (<50%) </td> <td> 5 </td> <td> Mosaic Shrubland </td> </tr> <tr> <td> 110 </td> <td> Mosaic herbaceous cover (>50%) / tree and shrub (<50%) </td> <td> 5 </td> <td> Mosaic Shrubland </td> </tr> <tr> <td> 120 </td> <td> Shrubland </td> <td> 6 </td> <td> Low/Sparse Vegetation </td> </tr> <tr> <td> 121 </td> <td> Evergreen shrubland </td> <td> 6 </td> <td> Low/Sparse Vegetation </td> </tr> <tr> <td> 122 </td> <td> Deciduous shrubland </td> <td> 6 </td> <td> Low/Sparse Vegetation </td> </tr> <tr> <td> 130 </td> <td> Grassland </td> <td> 6 </td> <td> Low/Sparse Vegetation </td> </tr> <tr> <td> 140 </td> <td> Lichens and mosses </td> <td> 6 </td> <td> Low/Sparse Vegetation </td> </tr> <tr> <td> 150 </td> <td> Sparse vegetation (tree, shrub, herbaceous cover) (<15%) </td> <td> 6 </td> <td> Low/Sparse Vegetation </td> </tr> <tr> <td> 151 </td> <td> Sparse tree (<15%) </td> <td> 6 </td> <td> Low/Sparse Vegetation </td> </tr> <tr> <td> 152 </td> <td> Sparse shrub (<15%) </td> <td> 6 </td> <td> Low/Sparse Vegetation </td> </tr> <tr> <td> 153 </td> <td> Sparse herbaceous cover (<15%) </td> <td> 6 </td> <td> Low/Sparse Vegetation </td> </tr> <tr> <td> 160 </td> <td> Tree cover, flooded, fresh or brakish water </td> <td> 7 </td> <td> Flooded Vegetation </td> </tr> <tr> <td> 170 </td> <td> Tree cover, flooded, saline water </td> <td> 7 </td> <td> Flooded Vegetation </td> </tr> <tr> <td> 180 </td> <td> Shrub or herbaceous cover, flooded, fresh/saline/brakish water </td> <td> 7 </td> <td> Flooded Vegetation </td> </tr> <tr> <td> 190 </td> <td> Urban areas </td> <td> 8 </td> <td> Other </td> </tr> <tr> <td> 200 </td> <td> Bare areas </td> <td> 8 </td> <td> Other </td> </tr> <tr> <td> 201 </td> <td> Consolidated bare areas </td> <td> 8 </td> <td> Other </td> </tr> <tr> <td> 202 </td> <td> Unconsolidated bare areas </td> <td> 8 </td> <td> Other </td> </tr> <tr> <td> 210 </td> <td> Water bodies </td> <td> 8 </td> <td> Other </td> </tr> </tbody> </table>

Dendrochonological dataset related to a medieval chest from the city of Antwerp ('Privilegiekom') and several associated wooden boxes, as published by Haneca et al. 2022 in the International Journal of Wood Culture

This repository contains detailed macro-photographs of the wood structure and tree-ring pattern observed on the examined elements of the medieval  ‘Privilegiekom’ chest and individual wooden boxes that were stored inside this chest. On these digital macro-photographs the ring-width pattern could be accuratly measured, and are available in this repository as well. The recorded tree-ring series were further analysed and published by Haneca et al. 2022  in the International Journal of Wood Culture.

opencc-zeroSep 2022View details →

Banding and recovery data on several game bird species to study hunting selectivity

Selective hunting has various impacts that need to be considered for the conservation and management of harvested populations. The consequences of selective harvest have mostly been studied in trophy hunting and fishing, where selection of specific phenotypes is intentional. Recent studies however show that selection can also occur unintentionally. With at least 52 million birds harvested each year in Europe, it is particularly relevant to evaluate the selectivity of hunting on this taxon. Here we considered 211 806 individuals belonging to 7 hunted bird species to study unintentional selectivity in harvest. Using linear mixed models, we compared morphological traits (mass, wing and tarsus size) and body condition at the time of banding between birds that were subsequently recovered from hunting during the same year as their banding, and birds that were not recovered. We did not find any patterns showing systematic differences between recovery categories, among our model species, for the traits we studied. Moreover, when a difference existed between recovery categories, it was so small that its biological relevance can be challenged. Hunting of birds in Europe therefore does not show any form of strong selectivity on the morphological and physiological traits that we studied, and should hence not lead to any change of these traits either by plastic or evolutionary response.

ModelE simulation output used in the study "Severe Global Cooling After Volcanic Supereruptions? The Answer Hinges on Unknown Aerosol Size" in Journal of Climate (2024)

The included files are the GISS ModelE output needed to replicate the figures in McGraw et al 2023, "Severe Global Cooling After Volcanic Supereruptions? The Answer Hinges on Unknown Aerosol Size" Most of the data herein is output from GISS ModelE2.2 simulations that did not include interactive aerosol microphysics and chemistry. Instead, aerosol extinction and effective radius were input into the model from scaled Easy Volcanic Aerosol [Toohey et al, GMD 2016] output, as described in this study's Methods section. To calculate volcanic temperature impacts and forcings at combinations of injected sulfur mass and peak effective radius (Reff) that were not simulated, we used 2D linear interpolation with the scipy function 'Rbf'. Separately included is output from GISS ModelE2.1 with MATRIX interactive aerosol microphysics and chemistry [Bauer et al, ACP 2008]. Note that the injections were scaled to match that a 6.5 Tg sulfur (S) injection in ModelE2.1/MATRIX best replicated the aerosol optical depth (AOD) and effective radius observations of the 1991 Pinatubo event despite this injection being most commonly considered an 9 Tg S injection. Hence, to produce the 1000 Tg S eruption, a 722 Tg S injected was simulated. Such a mismatch has been found in other GCMs (eg Mills et al, JGRA 2016) and may be due to aerosol quick-removal processes not represented in these models. Please note that simulated eruption masses are in this dataset listed in units of Tg S, but in the publication are in Tg SO2 (Tg S x 2). Data from other modeling studies included in Fig. 1 and tree ring estimates in Figs. S2 & S4 can be found within the cited studies. For additional information, please contact zachary.mcgraw@columbia.edu

Measurement of several quality/flow parameters at crop field

DWC_Probe(1:6).csv Sentek soil moisture, temperature and salinity data. -WC[depth cm] = volumetric water content at specified depth. -S[depth cm]  = volumetric ion content. -T[depth cm]  = temperature DWC_GWL(Border,Drip).csv : Groundwater depth measured in the piezometric wells (cm from the soil surface)

Metabolic syndrome severity score and associated cardiovascular risk in postmenopausal women of Bangladesh

This data help to construct metabolic syndrome severity score and seek its association with absolute cardiovascular risk.

opencc-zeroOct 2022View details →

Resilience of a tropical montane pine forest to fire and severe droughts

1. Higher temperatures, declining precipitation, changing cloud cover, and increased wildfires threaten tropical montane pine forests by overriding the environmental heterogeneity that typically buffers these systems from catastrophic fires. Severe fires threaten to overwhelm forest resilience and tip this biome into alternate vegetation states. 2. This study focused on long-term dynamics of montane Pinus occidentalis forests in the Cordillera Central, Dominican Republic, after a ~1000 km2 fire in 2005, the largest since 1965. We used long-term records to investigate climate before and after the fire and a 19-year dataset of pre- and post-fire vegetation change from a network of 55 permanent plots (20 small 0.05 ha plots and 35 large 0.1 ha plots) established in 1999 to model overstorey and understorey vegetation dynamics. 3. The 2005 fire was synchronized with the most extreme drought in the region in over 60 years. The fire burned from < 1600 to > 3000 m a.s.l. in elevation across windward and leeward slopes, creating a mosaic of low-, moderate-, and high-severity patches. Lower elevations, leeward slopes, and stands with a higher proportion of smaller pine trees all burned at higher severities. 4. Growth rates of trees that survived the fire remained lower than pre-fire rates 13 years after the fire. The highest mortality rates were soon after the fire and in the census immediately after the post-fire droughts. Post-fire pine seedling abundance was significantly greater in stands with higher basal area of live canopy trees and significantly reduced by increased shrub abundance in the understorey. Understorey composition recovered rapidly to pre-fire states in sites affected by low- and moderate-severity fires, but sites affected by high-severity fires remained dissimilar to pre-fire composition 13 years after the fire. Even though high-severity patches had persistently low pine regeneration, 100% of small plots and 96% of large plots had at least one pine sapling or canopy tree recruit by 2018. Shrub taxa survived the fire in higher numbers and recovered to pre-fire densities much faster than the pine, especially in high-severity burns. 5. Synthesis. Climate change has increased the likelihood of wildfires in tropical montane pine forests, with long-lasting effects on vegetation dynamics. However, this biome may prove resilient to increasingly severe fires in the near future, given the ongoing recovery of Pinus occidentalis forests in Hispaniola despite repeated severe droughts. Nevertheless, highly drought- and fire-resistant taxa (e.g. shrubs) may form alternate stable states in drier portions of tropical montane landscapes in the future as droughts and high-severity fires become more common.

opencc-by-4.0Apr 2024View details →

Data from: Signature of altered retinal microstructures and electrophysiology in schizophrenia spectrum disorders is associated with disease severity and polygenic risk

This dataset contains supporting data for the publication:  Boudriot, E. et al. Signature of altered retinal microstructures and electrophysiology in schizophrenia spectrum disorders is associated with disease severity and polygenic risk. Biological Psychiatry <a href="https://doi.org/10.1016/j.biopsych.2024.04.014">https://doi.org/10.1016/j.biopsych.2024.04.014</a>   Files: <ul> <li>clinical.csv contains data from clinical assessment and polygenic risk scores for schizophrenia</li> <li>ophthalmic_examination.csv contains data on spherical equivalent, intraocular pressure and visual acuity</li> <li>oct.csv contains segmentation output from Iowa Reference Algorithms</li> <li>erg.csv contains pre-processed ERG data for the four ERG conditions</li> <li>mri.csv contains ICV-corrected MRI volumes</li> </ul>

opencc-by-4.0Apr 2024View details →

ScintiPi3 data sets for "First observations of severe scintillation over low-to-mid latitudes driven by quiet-time extreme equatorial plasma bubbles: conjugate measurements enabled by citizen science initiatives"

ScintPi 3.0 data sets for "First observations of severe scintillation over low-to-mid latitudes driven by quiet-time extreme equatorial plasma bubbles: conjugate measurements enabled by citizen science initiatives" by Sousasantos et al. (2024).

opencc-zeroApr 2024View details →

Global responses of plant abundance, diversity, and fitness to increased fire severity or frequency

Database of responses of plant abundance, diversity, and fitness to increased fire frequency or severity, collected from published scientific articles or reports. The database includes 394 studies published worldwide between 1962 and 2023. Information on the following variables are also provided: fire regime component (fire frequency or severity), time since the last fire, fire type (wildfire or prescribed fire), historical fire regime type (surface or crown fire), plant life form (woody plant, herb, or bryophyte), habitat type, and climate. The database underpins the meta-analysis 'Global plant responses to intensified fire regimes', published in Global Ecology and Biogeography.

opencc-zeroMay 2024View details →

Data from: Tamm Review: a meta-analysis of thinning, prescribed fire, and wildfire effects on subsequent wildfire severity in conifer dominated forests of the Western US

Increased understanding of how active forest management (i.e., mechanical thinning, prescribed burning, and managed wildfire) affects subsequent wildfire severity is urgently needed as people and forests face a growing wildfire crisis. In response, we reviewed scientific literature for the US West and completed a meta-analysis that answered three questions: (1) How much do treatments reduce wildfire severity within treated areas? (2) How do the effects vary with treatment type, treatment age, and forest type? (3) How does fire weather moderate the effects of treatments? We found overwhelming evidence that mechanical thinning with prescribed burning, mechanical thinning with pile burning, and prescribed burning only are effective at reducing subsequent wildfire severity, resulting in reductions in severity from 62% to 72% relative to untreated areas. In comparison, thinning only was less effective – underscoring the importance of treating surface fuels when mitigating wildfire severity is the management goal. The efficacy of these treatments did not vary among forest types assessed in this study and was high across a range of fire weather conditions. Prior wildfire had more complex impacts on subsequent wildfire severity, which varied with forest type and initial wildfire severity. Across treatment types, we found that effectiveness of treatments declined over time, with the mean reduction in wildfire severity decreasing nearly threefold when wildfire occurred greater than 10 years after initial treatment. Our meta-analysis provides up-to-date information on the extent to which active forest management reduces wildfire severity and facilitates better outcomes for people and forests during future wildfire events.