cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25497/d7w889
title: CERP Site 1 Impoundment - Phase 1 Construction Turbidity Monitoring

description: As a condition of the construction permit, environmental monitoring during the Site 1 Impoundment Project phase 1 construction is required. It is required that contractors conduct operations in a manner that will minimize turbidity, therefor turbidity must be monitored on a daily basis throughout the construction phase of the project.
DOI: 10.25497/d7ws3k
title: CERP - DECOMP - WCA 3 Decompartmentalization and Sheetflow Enhancement - PROJ 12

description: The DECOMP Physical Model (DPM) is a large-scale field test designed to address uncertainties associated with the Comprehensive Everglades Restoration Project (CERP) Water Conservation Area (WCA) 3 Decompartmentalization and Sheet Flow Enhancement Project (DECOMP), specifically to reduce the environmental risks and aid alternative selections associated with Project Implementation Reports (PIR) 2 and 3. The project couples the construction and operation of hydrologic features and design alternatives with a comprehensive hydrological and ecological monitoring plan. The intent is to coordinate the operation of the hydraulic features with the collection of monitoring data in a statistically robust manner to reduce uncertainty. An objective of the DPM is to build the structural features that will cause a range of surface water velocities to occur in a marginally degraded portion of the natural system in order to verify the critical velocity threshold necessary to entrain and redistribute particles and nutrients in the landscape, which is thought to be a fundamental process needed to maintain the historic ridge and slough pattern. The creation of this flow fieldshould allow evaluation of the spatial variability of particle and nutrient transport. The objectives are to begin to assess the benefits of sheet flow study by evaluating surface flows, vegetation interactions, and particle entrainment and redistribution along a spatial and temporal gradient of surface flow velocities. The study will test 13 flow hypotheses to determine the role of flow in structuring and maintaining ridge and slough landscape pattern, as outlined in the Science Plan (DPMST 2010). This is a field based hydrological, sedimentological, and biological experimental and monitoring program to address uncertainties associated with canal backfilling and flow thresholds utilizing the physical features and structures of the DPM. Pulsed flows will be conducted in an operational window that extends from the end of October through January when the hydrologic gradient, water quality conditions, and other operational constraints are ideal. The DPM tasks for Hydrologic Monitoring, Particle Transport, and Biological Monitoring (described below) involve the following key components: a) operation and maintenance of field instrumentation for the collection of water level and environmental data; b) processing of stage records; c) implementation of large and local scale tracer studies; d) sediment transport studies; e) vegetation assessment; f) biogeochemical characterizations; g) environmental assessment; and h) quality assurance, quality control, data release and publication. Data will be collected using a BACI (before, after, control, impact) sampling design involving sample collection before and one after experimental flow releases at locations affected by the flow release and control sites outside the footprint of the flow release.Keywords:
DOI: 10.25497/d7zk5w
title: CERP - Aquifer Storage and Recovery Regional Study-PROJ 44

description: In April 1999, the Comprehensive Everglades Restoration Plan (CERP) proposed large-scale development of Aquifer Storage and Recovery (ASR) facilities as the preferred method of providing additional freshwater storage required for overall restoration success. Six ASR components will collectively form the proposed CERP ASR System, which includes a total of 333 ASR wells and related surface facilities at the general locations in attached Figure A. All proposed ASR wells have a target capacity of 5 mgd (million gallons per day). Water treatment facilities were also included in the conceptual CERP ASR components. Total cost of the proposed CERP ASR System is approximately $1,700,000,000. The United States Army Corps of Engineers (USACE), Jacksonville District and the South Florida Water Management District (SFWMD) are 50/50 cost sharing partners for design studies required prior to implementation of any large-scale CERP ASR facilities.
DOI: 10.25497/d7zp4j
title: CERP Picayune Strand - NRCS Groundwater Monitoring

description: This hydrologic monitoring study was a component of a 1996 cooperative agreement between the Big Cypress Basin of the South Florida Water Management District (District) and the U.S. Department of Agriculture, Natural Resources Conservation Service (NRCS) to procure data and analyses of the soils, vegetation, topography, and water table fluctuations in the Picayune Strand State Forest (PSSF) and the Ten Thousand Islands National Wildlife Refuge (TTINWR). The goal of the study was to update an earlier analysis of the proposed hydrologic restoration strategy using more detailed site-specific data and to predict the effects of the proposed strategy on the existing plant communities in the study area. In addition, data acquired during this study can serve as a “baseline” that can be augmented to track hydrological and biological changes that occur in the PSSF and TTINWR over the duration of the hydrologic restoration process. Field surveys of plant communities, soils, and surficial aquifer levels were conducted at 39 selected sites; the enclosed dataset encompasses the first 27 sites. In order to show fluctuations in the shallow water table at the survey sites, shallow surficial aquifer monitoring wells were installed at all study area sites and at a comparison site within the Belle Meade tract. Well water levels were monitored by Conservancy of Southwest Florida volunteers (NRCS Earth Team volunteers) until October 2000, when monitoring duties were transferred to Picayune Strand State Forest (PSSF). A copy of the final report for this study can be found in DOCUMENTUM SOUTH at the following location: Cabinets/CERP Project/Picayune Strand Restoration/11 Project Implementation Monitoring/11.02 Inland Monitoring/Hydrology/Ground Water/NRCS/Report
DOI: 10.34945/f51g60
title: Delayed viral vector mediated delivery of neurotrophin-3 improves skilled hindlimb placement on the horizontal ladder, hindlimb coordination during swimming, and stability walking in the open field after T9 thoracic contusion in female rats

description: STUDY PURPOSE: Restoration of skilled function is a key objective for spinal cord injury (SCI) patients. Intramuscular injections of viral (adeno-associated viral vector 1; AAV1) Neurotrophin-3 (NT-3) into the rat hindlimb 24 hours following thoracic T9 contusion has been shown to restore some functional locomotor activity, aid spinal neuroplasticity, and reduce spasms. Here, we test the hypothesis that injection of AAV1-CMV-NT3 to the rat abdominal and hindlimb muscles 48-hours following severe T9 contusion will enable functional recovery of skilled locomotive activity and reduced hyper reflexivity in female rats. DATA COLLECTED: The dataset includes n=29 female Sprague Dawley rats, injured at 8 weeks of age. Animals received either: 1) a 250 kDyne thoracic level 9 (T9) contusion via the Infinite Horizon impactor; or 2) a Sham injury (all surgical procedures including the laminectomy, apart from the injury itself). 48-hours following injury contused animals received bilateral injections of either PBS vehicle or AAV1-CMV-NT3 into their tibialis anterior, gastrocnemius and rectus abdominus muscles. Experimental groups were thus defined as: 1) NT3 (contusion and AAV1-CMV-NT3 injection); 2) PBS (contusion and PBS injection; and 3) Sham (Sham injured). Animals were assessed for recovery over 10 weeks. Functional recovery was assessed prior to injury and then weekly using the Basso, Beattie and Bresnahan (BBB) locomotor rating scale, and horizontal ladder. At prior to injury and then at 4 and 9 weeks post injury the animals were assessed for coordination, spasm, and the number of hindlimb strokes in the swimming task. Spasm activity was assessed at 10 weeks post injury through H-reflex recordings. At 11 weeks post injury, CtB injections were made into the lateral head of the gastrocnemius in the left hindlimb to retrogradely trace innervating motor neurons. At the experimental (end-point 11 weeks following injury), blood samples were taken from which levels of NT3 protein in serum could be assessed. Following an overdose of anesthetic (sodium pentobarbital), animals were transcardially perfused. Magnetic resonance imaging (MRI) was used on intact cord following animal perfusion to determine the lesion volumetrics. Following ex vivo MRI, spinal cords were washed, sectioned and stained to histologically assess levels of vGlut1+ and NeuN. DATA USAGE NOTES:
DOI: 10.34945/f51p49
title: Aggregated animal subject metadata from 11 UCSF preclinical TBI publications and 1 ODC-TBI published dataset

description: STUDY PURPOSE: The dataset was created to provide descriptions of the animal subjects with data uploaded to the ODC-TBI (but not necessarily published yet). DATA COLLECTED: The metadata was aggregated from 11 papers published from the labs of Susanna Rosi, Michael S Beattie, Jacqueline C Bresnahan, and Adam R Ferguson from UCSF as well as the dataset published by Bridget E Hawkins through the ODC-TBI (DOI:10.34945/F51591). The animal species, strain, sex, genotype and age at time of injury are included in addition to the preclinical TBI model used, the experimental group the subject was assigned to, and the time post-injury of the data entry. The dataset contains a total of N=1250 animals with 3313 observations total. Subject IDs are provided to align this data to the corresponding datasets when they are published. DATA USAGE NOTES: The data was summarized to describe a cohort of animals with data uploaded by January 2021.
DOI: 10.34945/f52g69
title: Lung immunity after complete thoracic spinal cord transection in female mice

description: STUDY PURPOSE: Pulmonary infection is a leading cause of morbidity and mortality after spinal cord injury (SCI). Although SCI causes atrophy and dysfunction in primary and secondary lymphoid tissues with a corresponding decrease in the number and function of circulating leukocytes, it is unknown if this SCI-dependent systemic immune suppression also affects the unique tissue-specific antimicrobial defense mechanisms that protect the lung. Here, we test the hypothesis that SCI directly impairs pulmonary immunity and subsequently increases the risk for developing pneumonia. DATA COLLECTED: The dataset includes n=242 C57/Bl6 female mice aged 9-13 weeks. Mice received a complete transection SCI at either the thoracic level 1 (T1Tx) or 3 (T3Tx). Sham mice underwent a laminectomy only at the appropriate thoracic level. Flow cytometry was used to assess lung immune cells (neutrophils, T- and B-lymphocytes, alveolar macrophages, CD45+ immune cells) at 12h ((n=8-12 T3Tx, n=8-12 T3 sham), 3d (n=12 T3Tx, n=12 T3 sham, n=7 T1Tx, n=7 T1 sham), and 28d (n=12 T3Tx, n=12 T3 sham) post- injury. Corresponding cultures of lung homogenate on blood agar (n=7 12h & 3dpi T3Tx and 3dpi T3 Sham, n=12-14 28dpi T3 Sham mice, n=12-14 28dpi T3Tx, n=18 T1Tx, n=13 T1 Sham) and CHROMagar ™ plates (n=18 T1Tx, n=13 T1 Sham) at these timepoints were also used to assess pulmonary bacterial burden after injury. The drug AMD3100, a CXCR4 antagonist (1mg/mouse given subcutaneously 1h post-injury then daily for either 3d or 7d), was also tested in T1Tx mice to see if the drug improved pulmonary immune function as measured by flow cytometry (n=10 T1Tx vehicle and n= 13 T1Tx AMD3100 mice), altered blood immune cell counts (n=8 T1 sham, n=9 T1Tx vehicle and n=10 T1Tx AMD3100) or reduced bacteria load (n=21 T1Tx vehicle and n=23 T1Tx AMD3100 for 3dpi studies, n=9 T1Tx vehicle and n=10 T1Tx AMD3100 for 7dpi studies). A subset of AMD3100 treated mice also underwent an induced pneumonia procedure (n=11 T3Tx vehicle + pneumonia and n=11 T3TxAMD3100 + pneumonia). Finally, n=4 mice were pooled from T3 Sham or T3Tx groups to perform a PCR array for lung immunity genes and RT-qPCR on 10 identified hub genes at 12h and 3d post-injury. DATA USAGE NOTES:
DOI: 10.34945/f5588x
title: Immune phenotyping SCI patients versus healthy controls

description: STUDY PURPOSE: Following a spinal cord injury (SCI), an inflammatory immune reaction is triggered which results in advanced secondary tissue damage. The systemic post-SCI immune response is poorly understood. This study aimed to extensively analyse the circulating immune cell composition in traumatic SCI patients in relation to clinical parameters. DATA COLLECTED: High-dimensional flow cytometry was performed on peripheral blood mononuclear cells of 18 traumatic SCI patients and 18 healthy controls to determine immune cell subsets. SCI blood samples were collected at multiple time points in the (sub)acute (0 days to 3 weeks post-SCI, (s)aSCI) and chronic (6 to &gt;18 weeks post-SCI, cSCI) disease phase. Not all time points were available for every included SCI patient due to organizational issues (late inclusion) or withdrawal of subjects from the study. Twelve SCI patients presented with a cervical injury, 5 with a thoracic injury and 1 with a lumbar injury. We first analyzed the major immune cell subsets in PBMC of HC, (s)aSCI patients and cSCI patients. These included CD14+ monocytes, natural killer (NK) cells, which are classically divided into cytotoxic CD56loCD16+ and highly cytokine producing CD56hiCD16+/- subsets, CD19+ B cells and CD3+ T cells, divided into CD4+ helper and CD8+ cytotoxic subsets. Next, the following subsets were studied in both CD4+ and CD8+ T cells: naive (Tnaive, CD45RA+CD45RO-), memory (Tm, CD45RA-CD45RO+), effector memory (Tem, CD45RA-CCR7-), central memory (Tcm, CD45RA-CCR7+), effector memory re-expressing CD45RA (Temra, CD45RA+CCR7-) and regulatory (Treg, CD25+CD127low). CD19+ B cells were studied in more detail by analysis of CD24hiCD38hi transitional, IgD+CD27- naive, IgD+CD27+ non class-switched memory (NCSM), IgD-CD27+ class-switched memory (CSM), IgM+IgD-CD27+ IgM only and IgD-CD27- double negative (DN) subsets. IgM, IgG and IgA were included to further define memory responses. DATA USAGE NOTES:
DOI: 10.6075/j09p31tf
title: GCM Modification Code. In Data and Code from: Buoyancy Forcing Dominates the Cross-Equatorial Ocean Heat Transport Response to Northern Hemisphere Extratropical Cooling

description: Fortran source code developed to override wind stress in the Community Earth System Model (CESM) v. 1.2, as described in Luongo et al. (2022).
description: Community Earth System Model (CESM), v 1.2.2.1: National Center for Atmospheric Research (NCAR), Boulder, CO, USA.
DOI: 10.34945/f56887
title: Genetic deletion of the glucocorticoid receptor in Cx3cr1+ myeloid cells is neuroprotective and improves motor recovery in female mice after 75 kdyne T9 contusion spinal cord injury

description: STUDY PURPOSE: Glucocorticoid receptors (GRs), part of the nuclear receptor superfamily of transcription factors (TFs), are ubiquitously expressed in all cell types and regulate cellular responses to glucocorticoids (e.g., cortisol in humans; corticosterone in rodents). In myeloid cells, glucocorticoids binding to GRs can enhance or repress gene transcription, thereby imparting distinct and context-dependent functions in macrophages at sites of inflammation. In experimental models and in humans, glucocorticoids are widely used as anti-inflammatory treatments to promote recovery of function after SCI. Thus, we predicted that deleting GR in mouse myeloid lineage cells (i.e., microglia and monocyte-derived macrophages) would enhance inflammation at the site of injury and worsen functional recovery after traumatic spinal cord injury (SCI). DATA COLLECTED: The dataset includes n=29 female mice with genotype of GRf/f (Macrophage GR intact) or Cx3cr1-Cre;GRf/f (Macrophage GR deleted). Mice received a 75 kdyne T9 IH contusion SCI or sham (laminectomy only) surgery. The Basso Mouse Scale (BMS) main score and sub-score were used to assess motor function. At 35 dpi, animals were perfused with 0.1M PBS followed by 4% PFA, and spinal tissues were cryopreserved in OCT at -80oC. Tissues were cut in serial sections on a cryostat, 12 um thick along the coronal axis. Spared myelin (EC), spared axons (NFH), and vessel sparing (CD31) were assessed using immunohistochemical staining. GFAP, Iba1, MBP, CD68, and Oil Red O staining was performed in coronal spinal histological sections at 35 days post-injury (dpi). Injury parameters are included for all injured mice. For validation of GR knockout in myeloid cells, we used additional male and female uninjured Cx3cr1-Cre;TdT mice (n=6) and uninjured TdTomato controls (n=4). DATA USAGE NOTES:
DOI: 10.34945/f5b012
title: Microglia coordinate cellular interactions during spinal cord repair after contusion or crush spinal cord injury in female mice

description: STUDY PURPOSE: Traumatic spinal cord injury (SCI) triggers a neuro-inflammatory response dominated by tissue-resident microglia and monocyte derived macrophages (MDMs). To better understand the specific role of microglia in SCI, we pharmacologically depleted microglia using the CSF1R antagonist PLX5622 (1200 ppm). We used behavioral, anatomical, histopathological, tract tracing, bulk RNA sequencing and single cell RNA sequencing techniques to reveal the cellular and molecular responses to SCI that are controlled by microglia. We also reconstituted mice with or without microglia, with recombinant CCL2 (rCCL2, 50 ng intraspinally at 2 dpi) and/or a TLR2 agonist (500 ng intraspinally at 2 dpi and/or 50 ug/kg i.p. at 3 dpi). We also collected baseline behavior and challenged mice with lipopolysaccharide (LPS, 1 mg/kg daily for four consecutive days) to determine whether PLX5622 has any off-target effects. DATA COLLECTED: The dataset includes n=230 female mice aged 10-12-weeks on a C57BL/6J background. Mice received a 75 kdyne T9 IH contusion SCI, sham surgery, or a L1 or T9 complete forceps crush SCI. Mice were fed PLX5622 (1200 ppm) or Vehicle chow from 2 weeks before surgery/ intervention until the experimental end point of 3d, 4d, 7d, 14d, 21d, 28d or 35d after surgery/intervention. The Basso Mouse Scale (BMS) main score and sub-score were used to assess motor function at baseline and 1, 3, 7, 10, 14, 21, 28, and 35 days post-injury. The horizontal ladder task was performed at baseline and day 20, 27 and 34 post-injury. Lesion volume, lesion length, spared myelin, spared axons, astrogliosis, NG2 cell presence, microglia and macrophage presence were analyzed in histological sections using standard immunohistochemical techniques. Dividing cells were identified based on Bromodeoxyuridine (BrdU) labeling (50 mg/kg i.p BrdU administered daily in a subset of mice from 1-7 dpi). Biotinylated dextran amine (BDA, 1 ul, 10% solution) was injected into the motor cortex at 14 dpi to assess the distance of corticospinal tract retraction from a T9 crush SCI at 28 dpi. Injury parameters for all mice, including those used for bulk RNA sequencing or single cell RNA sequencing experiments, are provided. Gene expression datasets are available on Gene Expression Omnibus (GSE196928) and code is available on GitHub at https://github.com/OSU-BMBL/Spinal-cord-scRNAseq. Additional uninjured mice were used to establish baseline behavior and immune responses to LPS challenge in mice on PLX5622 diet. We used the BMS scale, hot plate and Von Frey tasks to assess motor and sensory function in uninjured mice. DATA USAGE NOTES:
DOI: 10.34945/f5d01p
title: Studying Sex as a Biological Variable: Considerations of weight, anemia and mortality following thoracic spinal cord contusion injury in male and female mice

description: STUDY PURPOSE: The purpose of this study was to examine functional recovery, morbidity, mortality, etc. as a function of both sex and age in C57Bl/6J mice after thoracic contusion SCI (T9, 60kdyn, IH). Experimental groups consist of young and middle-aged mice (4 or 14 months old at the time of injury) of both sexes, male or female, that underwent contusion or sham injury. The data in this collection and a thorough interpretation of the data was published in manuscript form in Stewart et al., 2020 PMIDs: 32849242; 33193066: Considerations for Studying Sex as a Biological Variable in Spinal Cord Injury. Stewart AN, MacLean SM, Stromberg AJ, Whelan JP, Bailey WM, Gensel JC, Wilson ME. Front Neurol. 2020 Aug 5;11:802. doi:10.3389/fneur.2020.00802. eCollection 2020. DATA COLLECTED: Collectively, data from 8 experimental groups: sex (2) x age (2) x injury (2). Sample sizes range from 5-10 depending upon the outcome measure and time of sacrifice. Data for this study include weights after injury, overall mortality, injury-induced anemia as determined by red blood cell ratios in plasma (28 days post injury), estrous cycle information for females (weekly for 4 weeks) along with endpoint (28 days) plasma estradiol levels, as well as, BMS scores at 1 and 28 days after injury. The data presented is a comprehensive collector of data collected over several years across different experiments utilizing both male and female mice. For this reason, not all outcomes were collected for all subjects (missing or NA is used to indicate data not collected). Not all studies used the same outcome measures (i.e. BMS) so not all outcomes were collected for each subject. DATA USAGE NOTES:
DOI: 10.34945/f5ds3c
title: Comparing the effect of skilled forelimb rehabilitative training after unilateral cervical contusion and dorsal quadrant spinal cord injury in female Lewis rats

description: STUDY PURPOSE: Moderate cervical spinal cord injury (SCI) models target spinal tracts involved in skilled reaching and grasping. Contusion SCIs are often considered the most clinically relevant injuries. They involve lateral gray matter damage and it is unknown whether rats with a cervical contusion can be trained in skilled reaching and grasping task (single pellet reaching, grasping and retrieval; SPRGR). Here we compare the impact of injury size on recovery in a SPRGR task, in rats with cervical unilateral contusion injuries (UCs) with a dorsolateral quadrant transection (DLQ). DATA COLLECTED: Age matched adult female Lewis rats (n = 26 UC and n = 13 DLQ; 200–230 g; Charles River, Canada), were trained to retrieve food pellets. Untrained controls were placed in the training enclosures and received pellets on the floor of the enclosure where they could be licked rather than grasped. Following pre-training 5 days/week, for 6 weeks and baseline testing of the preferred paw all rats received a cervical SCI between C4-5 on the side of the preferred paw For DLQ injuries a dorsolateral quadrant SCI was performed using custom made blades. UC animals received a C5 unilateral contusion, with the tip of the impactor device (2.5 mm diameter, IH-0400 Impactor, Precision Systems and Instrumentation) over the spinal cord at 1.25 mm lateral of the midline. Impact force was set to 125 Kdyn with no dwell-time. Starting 1 week post-injury, rats were divided into untrained and trained groups based on day 4 forelimb injury severity score. A blinded researcher evaluated performance in the trained task at 1, 3, and 5 weeks of training from 10 min videos. After the final day of testing, rats were euthanized, perfused, and spinal cord tissue was harvested. Cervical spinal cords including the lesion site were cut at 25 microns and processed with Cresyl violet and Neurotrace staining. Cresyl violet-stained spinal cord sections were assessed for lesion size using light and fluorescence microscopy. Tissues sections (25 µm) were imaged and quantified, every 200 µm from 2.4 mm rostral to 2.4 mm caudal of injury epicenter, to assess tissue damage. Using ImageJ the corticospinal tract (CST) and the rubrospinal tract (RST) damage was quantified based on the reported projection sites. DATA USAGE NOTES: