Hudson River Estuary Shallow Water Surveys. Subbottom data was collected November 5 to December 15, 2009, in the estuary north from Saugerties to Troy. Data Collection and Processing: Subbottom Data - Fugro utilized the EdgeTech SB216 Chirp subbottom profiler system for seismic data collection. This system was operated using a swept frequency range of 2-16 KHz, maximizing subsurface resolution within the very shallow near-surface material (1- 5 m beneath seafloor). Subbottom data was processed and interpreted using Discover and SMT Kingdom software. The intent of the processing was to provide the NYSDEC with SEG-Y files that were properly filtered and spatially oriented to allow for near-surface interpretation of sediments in the Hudson River. Processing steps for the subbottom data included swell filtering to compensate for sea conditions during survey operations, compiling correct shotpoint navigation, and adjusting data gains for optimal interpretation. An isopach (sediment thickness) of the unconsolidated surficial sediments was created from the seafloor and mapped sediment horizon base using an acoustic two-way travel time of 1500 meters/second. Subbottom data was used to assist in selecting sediment sampling locations. Graphical sub-bottom profiles for areas of interest were produced and descriptive results will be included in the final report. Points were created every 300th shot (approximately 100 meters). Original contact information: Contact Name: John Ladd Contact Org: Hudson River National Estuarine Research Reserve, NYS DEC Phone: 845-889-4745 Email: jxLadd@gw.dec.state.ny.us

Abstract

In September 2014, the Government of El Salvador created the Consejo Nacional de Seguridad Ciudadana y Convivencia (CNSCC), whose main objective is to promote and facilitate dialogue and agreement around public policies on justice, citizen security and coexistence. Through this space, the Plan El Salvador Seguro (PESS) was discussed and approved in 2015, which consists of five axes and hundreds of actions to confront violence and crime, guarantee access to justice and protection for victims of all types of crime. In the framework of the implementation of Axis 4 of the PESS (attention and protection of victims), and given the State's concern to determine the characteristics and impact of internal mobility due to violence in El Salvador, the Ministry of Justice and Public Security (MJSP), in coordination with the Secretariat of Governance and Communications (SEGOB), promoted the realization of a profiling study on the dimension, tendencies and profiles of the people and families forced to diplace internally due to violence in recent years. For this effort, the support of the United Nations High Commissioner for Refugees (UNHCR) was requested. The study shows that in El Salvador internal mobility is a multi-causal phenomenon, with the economic and family reasons being predominant. With a significantly lower incidence, it is confirmed that acts of violence or crimes committed against the population are located as the third cause of internal mobility of the population in recent years. According to the information collected, in 1.1% of resident families at least one of its members was forced to change their usual place of residence within El Salvador as to avoid the effects of facts of violence.

Geographic coverage

National coverage

Analysis unit

Household and individual.

Kind of data

Sample survey data [ssd]

Sampling procedure

The survey's objective was to deliver representative data of households affected by internal displacement at national level. For this survey a stratified sample design was applied to take into account that the distribution of the displaced population is more concentrated in certain geographical areas of the country. The total number of internally displaced persons at the time of the survey was estimated at around 71,500 people. The total sample size was 430 internally displaced households (around 1,650 people).

Mode of data collection

Face-to-face interview

Research instrument

The questionnaire included the following sections: household characteristics, dwelling, livelihoods, incidents and displacement, individual characteristics.

In order to test hypotheses about groundwater flow under and into Chesapeake Bay, geophysical surveys were conducted by U.S. Geological Survey (USGS) scientists on Chesapeake Bay and the Potomac River Estuary in September 2006. Chesapeake Bay resource managers are concerned about nutrients that are entering the estuary via submarine groundwater discharge, which are contributing to eutrophication. The USGS has performed many related studies in recent years to provide managers with information necessary to make informed decisions about this issue. The research carried out as part of the study described here was designed to help refine nutrient budgets for Chesapeake Bay by characterizing submarine groundwater flow and discharge of groundwater beneath part of the mainstem and a major tributary, the Potomac River Estuary.

Bed Surface Profiling (BSP) data

The Bed Surface Profiling (BSP) data scanned by an underwater 3D laser scanner for different flow conditions (Case Nos. 1-12). The sampling rate was 10 Hz. Each line of data corresponds to the xyz point cloud data, where x-direction corresponds to streamwise direction, y-direction to trnasverse dirction, and z-dirction to vertical direction.

Code

A python code is included to process the BSP data for calculating sediment pickup probability for each case. This code analyzes 12 case files (Case1.txt to Case12.txt) containing measurement data, processes them using dynamic denoising filters, and calculates a derived metric (p_value) for each case. The results are saved in an Excel file.

Key Components

1. Dynamic Denoising Filter (dynamic_denoise_filter):

   • Implements two filtering schemes based on parameter d:
     • 3-Window Rule (d=0.00185): Checks immediate neighbors (previous and next columns) to correct 0, 1, or -1 values.
     • 11-Window Rule (d=0.00380): Uses a larger window (11 columns) with different criteria:
       • For zeros: Requires immediate neighbors (columns 4 and 6) to be zero.
       • For ±1: Requires all non-center columns (first 5 and last 5) to match the target value.

2. Case Processing (process_case):

   • Data Loading: Reads CSV-like files, extracts y (2nd column) and z (3rd column) values.
   • Derivative Calculation: Computes dz as the finite difference of z values scaled by d.
   • Marker Matrix: Creates a matrix m marking regions where dz exceeds ±0.
   • Denoising: Applies dynamic_denoise_filter to clean the marker matrix.
   • p-value Calculation:
     • Computes y_diff as half the absolute difference between adjacent y values.
     • Identifies valid transitions (1 → -1) in the denoised matrix.
     • Aggregates weighted counts and normalizes by the total y range.

3. Parameter Settings:

   • **d Values**:
     • 0.00185 for Cases 1–6
     • 0.00380 for Cases 7–12
   • Critical Value (cr): Set to 0 for thresholding dz.
   • Data Directory: Configured as D:/data_ana_ca.

4. Output:

   • Results are saved in analysis_result_ca_cr.xlsx with columns Case and p_value.

Usage

• Input: 12 text files (Case1.txt to Case12.txt) with comma-separated data.
• Output: Excel file containing calculated p-values.
• Runtime Monitoring: Prints processing time for each case during execution.

The code efficiently handles large datasets using vectorized operations and sliding window techniques, ensuring scalability for similar analytical tasks.

Abstract: This sub-bottom Chirp profiling data set was acquired in eastern Long Island Sound using an EdgeTech Chirp 424 system with a sweep frequency of 4-24kHz. The data set was collected using small boats in April 2018, and lines were run in north-south and east-west directions lines. The sub-bottom surveys were conducted in order to guide subsequent sediment coring. The data files are in standard SEG-Y format. Funding was provided by the Long Island Sound Study and by the Connecticut Department of Energy and Environmental Protection (DEEP).

Bear Lake is a tectonic lake that has existed for at least several hundred thousand years. The lake basin is a relatively simple half graben, a spoon-shaped depression tilted toward the main fault on the east side of the lake. The U.S. Geological Survey, in cooperation with researchers from several universities, has been studying the sediments of Bear Lake since 1996. The general purpose of this effort is to reconstruct past limnological conditions and regional climate on a range of timescales, from hundreds of years to hundreds of thousands of years. This research relates to a variety of human concerns, including water usage in the Bear River basin. Past work has included several coring operations, a seismic-reflection survey, sediment-trap deployments, a barge-mounted drilling operation with the GLAD800 drill rig, and a variety of other studies. The objectives of the September, 2002 operations, preliminarily reported here, were (1) to compile a detailed bathymetric map of the la ...

Seismic data were recorded aboard the R/V Parke Snavely (RVPS; source vessel) during USGS field activity 2021-619-FA. Data were recorded with a broadband spherical reference Reson TC4034 hydrophone positioned directly below the SIG ELP790 or the Applied Acoustics Delta sparker source which were towed from the stern of the vessel. Source data were recorded as the R/V Parke Snavely made several passes along 7 different water depth transects and are presented in SEG-Y format. Shot point navigation are provided in an accompanying comma-delimited text file, as well as in a shapefile for visualization purposes. Navigation data for the source and receiver vessels, as well as seismic data from the receiver vessel, sound velocity, and other survey data, are provided elsewhere in this data release.

Dataset consists of two-dimensional marine seismic reflection profile data from the San Francisco Bay area. These data were acquired in 1997, with the vessel Davidt Johnston. The USGS identifier for these data is J497SF.

For more information on the seismic surveys see http://walrus.wr.usgs.gov/infobank/j/j497sf/html/j-4-97-sf.meta.html

These data are also available via GeoMapApp (http://www.geomapapp.org/) and Virtual Ocean ( http://www.virtualocean.org/) earth science exploration and visualization applications.

A geophysical survey to delineate the fresh-saline groundwater interface and associated sub-bottom sedimentary structures beneath Indian River Bay, Delaware, was carried out in April 2010. This included surveying at higher spatial resolution in the vicinity of a study site at Holts Landing, where intensive onshore and offshore studies were subsequently completed. The total length of continuous resistivity profiling (CRP) survey lines was 145 kilometers (km), with 36 km of chirp seismic lines surveyed around the perimeter of the bay. Medium-resolution CRP surveying was performed using a 50-meter streamer in a bay-wide grid. Results of the surveying and data inversion showed the presence of many buried paleochannels beneath Indian River Bay that generally extended perpendicular from the shoreline in areas of modern tributaries, tidal creeks, and marshes. An especially wide and deep paleochannel system was imaged in the southeastern part of the bay near White Creek. Many paleochannels also had high-resistivity anomalies corresponding to low-salinity groundwater plumes associated with them, likely due to the presence of fine-grained estuarine mud and peats in the channel fills that act as submarine confining units. Where present, these units allow plumes of low-salinity groundwater that was recharged onshore to move beyond the shoreline, creating a complex fresh-saline groundwater interface in the subsurface. The properties of this interface are important considerations in construction of accurate coastal groundwater flow models. These models are required to help predict how nutrient-rich groundwater, recharged in agricultural watersheds such as this one, makes its way into coastal bays and impacts surface water quality and estuarine ecosystems. For more information on the survey conducted for this project, see https://cmgds.marine.usgs.gov/fan_info.php?fan=2010-006-FA.

In spring and summer 2017, the U.S. Geological Survey’s Gas Hydrates Project conducted two cruises aboard the research vessel Hugh R. Sharp to explore the geology, chemistry, ecology, physics, and oceanography of sea-floor methane seeps and water column gas plumes on the northern U.S. Atlantic margin between the Baltimore and Keller Canyons. Split-beam and multibeam echo sounders and a chirp subbottom profiler were deployed during the cruises to map water column backscatter, sea-floor bathymetry and backscatter, and subsurface stratigraphy associated with known and undiscovered sea-floor methane seeps. The first cruise, known as the Interagency Mission for Methane Research on Seafloor Seeps and designated as field activity 2017-001-FA, was conducted from May 4 to May 11, 2017, and acquired geophysical data to support remotely operated vehicle exploration of seep sites using the Global Explorer, which is operated by Oceaneering International, Inc. Geophysical operations during cruise 2017-002-FA from August 25 to September 6, 2017, were also focused on mapping water column methane plumes, sea-floor seep sites, and subseafloor strata, but primarily supported conductivity, temperature, and depth instrument deployment, surface-water methane-concentration mapping, and water-sampling operations as part of a collaborative study with the University of Rochester of the effect of methane seepage on ocean water biogeochemistry. The National Oceanic and Atmospheric Administration’s Office of Ocean Exploration and Research partially sponsored cruise 2017-001-FA, and the U.S. Department of Energy partially sponsored both cruises.

RNase Y of Bacillus subtilis is a key member of the degradosome and important for bulk mRNA turnover. In contrast to B. subtilis, the RNase Y homologue (rny/cvfA) of Staphylococcus aureus is not essential for growth. Here we found that RNase Y plays a major role in virulence gene regulation. Accordingly, rny deletion mutants demonstrated impaired virulence in a murine bacteraemia model. RNase Y is important for the processing and stabilisation of the immature transcript of the global virulence regulator system SaePQRS. Moreover, RNase Y is involved in the activation of virulence gene expression at the promoter level. This control is independent of both the virulence regulator agr and the saePQRS processing and may be mediated by small RNAs some of which were shown to be degraded by RNase Y. Besides this regulatory effect, mRNA levels of several operons were significantly increased in the rny mutant and the half-life of one of these operons was shown to be extremely extended. However, the half-life of many mRNA species was not significantly altered. Thus, RNase Y in S. aureus influences mRNA expression in a tightly controlled regulatory manner and is essential for coordinated activation of virulence genes. Three biological replicates of both wild type and rny (cvfA) mutant bacteria were grown in complex medium until the late exponential phase at which point RNA was prepared for microarray analysis on GeneChip S. aureus Genome Array (Affymetrix). Preliminary results indicated that during the late exponential growth phase, the most prominent differences between wild type and rny mutants were observed when selected gene expression was analysed by Northern hybridisation.

This dataset supports the development of CLIPⁿ, a contrastive-learning framework designed to align heterogeneous high-content screening (HCS) profile datasets.

GitHub link: https://github.com/AltschulerWu-Lab/CLIPn

Directory Structure

Data Files

• HCS_datasets.pkl: Contains 13 high-content screening (HCS) datasets from multiple studies across 20 years.
• Hypoxia.pkl: Contains 8 profile datasets using different assays and treated under diverse hypoxia durations.
• Expression.pkl: Contains 2 transcriptional profile datasets and 6 image profile datasets for multimodal analysis.

Folders

raw_profiles:
HCS13/
- Contains raw data from 13 high-content screening (HCS) datasets. Each dataset includes meta and feature files.

L1000/
- CDRP_feature_exp.csv: Raw L1000 expression data from the CDRP dataset.
- CDRP_meta_exp.csv: Metadata associated with the CDRP expression data.
- LINCS_feature_exp.csv: Raw L1000 expression data from the LINCS dataset.
- LINCS_meta_exp.csv: Metadata associated with the LINCS expression data.

RxRx3/
- RxRx3_feature_final.csv: Profile data from the RxRx3 dataset.
- RxRx3_meta_final.csv: Metadata from the RxRx3 dataset.

Uncharacterized_compounds/
- NCI_cpnData.csv: Feature data for uncharacterized compounds from the NCI dataset.
- NCI_cpnInfo.csv: Information about uncharacterized compounds in the NCI dataset.
- Prestwick_UTSW_cpnData.csv: Feature data for uncharacterized compounds from the Prestwick UTSW dataset.
- Prestwick_UTSW_cpnInfo.csv: Information about uncharacterized compounds from the Prestwick UTSW dataset.

Usage

import pickle
with open('data.pkl', 'rb') as f:
data = pickle.load(f)

X = data['X']
y = data['y']

Data Reference

For raw datasets from 13 HCS database, data and analysis pipeline for dataset 1 was obtained from https://www.science.org/doi/suppl/10.1126/science.1100709/suppl_file/perlman.som.zip; for datasets 2-3, data were shared by authors; For datasets 4-5, analysis code was downloaded from https://static-content.springer.com/esm/art%3A10.1038%2Fnbt.3419/MediaObjects/41587_2016_BFnbt3419_MOESM21_ESM.zip and data were shared by authors; For datasets 6-7, processed dataset was downloaded from AWS following instructions from https://github.com/carpenter-singh-lab/2022_Haghighi_NatureMethods, and replicate_level_cp_normalized.csv.gz features were used. For project datasets 8-13, datasets and analysis results were downloaded from https://zenodo.org/records/7352487. For RxRx3, dataset was obtained from https://www.rxrx.ai/rxrx3. L1000 transcript datasets were downloaded using the same link as datasets 6-7 and the processed transcript data files (named “replicate_level_l1k.csv”) were used.

This processed, envelope sub-bottom data set was collected with an EdgeTech SB-512i sub-bottom towfish system in May 2018 as part of the Trinity River Paleovalley Project (TRiPP). The envelope information is captured in the "env" data channel during acquisition. Here, the envelope data has been extacted and processed and is stored in SEG-Y format. Funding for the project was provided by the U.S. Department of the Interior, Bureau of Ocean Energy Management, under Agreement Number M16AC00020.

Recent exploitation of the avian immune system has highlighted its suitability for the generation of high-quality, high-affinity antibodies to a wide range of antigens for a number of therapeutic and biotechnological applications. The glycosylation profile of potential immunoglobulin therapeutics is species specific and is heavily influenced by the cell-line/culture conditions used for production. Hence, knowledge of the carbohydrate moieties present on immunoglobulins is essential as certain glycan structures can adversely impact their physicochemical and biological properties. This study describes the detailed N-glycan profile of IgY polyclonal antibodies from the serum of leghorn chickens using a fully quantitative high-throughput N-glycan analysis approach, based on ultra-performance liquid chromatography (UPLC) separation of released glycans. Structural assignments revealed serum IgY to contain complex bi-, tri- and tetra-antennary glycans with or without core fucose and bisects, hybrid and high mannose glycans. High sialic acid content was also observed, with the presence of rare sialic acid structures, likely polysialic acids. It is concluded that IgY is heavily decorated with complex glycans; however, no known non-human or immunogenic glycans were identified. Thus, IgY is a potentially promising candidate for immunoglobulin-based therapies for the treatment of various infectious diseases.

Seismic data were recorded from the R/V San Lorenzo (RVSL; receive vessel) of a two-vessel marine sparker seismic survey conducted by the U.S. Geological Survey (USGS) in April of 2021 off the coast of Santa Cruz, California (USGS field activity 2021-619-FA). The R/V Parke Snavely (RVPS; source vessel) towed a marine sparker sound source along seven depth site transects ranging between 25 and 600 meters. The RVSL maintained a nearly stationary position at the midpoint of each transect and recorded sound data with a broadband omnidirectional Cetacean Research CR3 hydrophone positioned between 10- and 20-meters water depth below the RVSL. RVSL receive seismic data are presented in SEG-Y format. Shot point navigation are provided in an accompanying comma-delimited text file, as well as in a shapefile for visualization purposes. Navigation data for the source and receiver vessels, as well as seismic data from the source vessel, sound velocity, and other survey data, are provided elsew ...

Associated with Rappe et al. (2024) Longitudinal autophagy profiling of the mammalian brain reveals sustained mitophagy throughout healthy aging. EMBO Journal https://www.embopress.org/doi/full/10.1038/s44318-024-00241-y Raw data image files and source data spreadsheets.

Knudsen Chirp 320BR subbottom profiler - Knudsen subbottom profile data were collected in Raw Knudsen SEG-Y Datagram format.

In 2008, the U.S. Geological Survey (USGS), Woods Hole Coastal and Marine Science Center (WHCMSC), in cooperation with the U.S. Army Corps of Engineers conducted a geophysical and sampling survey of the riverbed of the Upper St. Clair River between Port Huron, MI, and Sarnia, Ontario, Canada. The objectives were to define the Quaternary geologic framework of the St. Clair River to evaluate the relationship between morphologic change of the riverbed and underlying stratigraphy. This report presents the geophysical and sample data collected from the St. Clair River, May 29-June 6, 2008 as part of the International Upper Great Lakes Study, a 5-year project funded by the International Joint Commission of the United States and Canada to examine whether physical changes in the St. Clair River are affecting water levels within the upper Great Lakes, to assess regulation plans for outflows from Lake Superior, and to examine the potential effect of climate change on the Great Lakes water l ...

In 2008, the U.S. Geological Survey (USGS), Woods Hole Coastal and Marine Science Center (WHCMSC), in cooperation with the U.S. Army Corps of Engineers conducted a geophysical and sampling survey of the riverbed of the Upper St. Clair River between Port Huron, MI, and Sarnia, Ontario, Canada. The objectives were to define the Quaternary geologic framework of the St. Clair River to evaluate the relationship between morphologic change of the riverbed and underlying stratigraphy. This report presents the geophysical and sample data collected from the St. Clair River, May 29-June 6, 2008 as part of the International Upper Great Lakes Study, a 5-year project funded by the International Joint Commission of the United States and Canada to examine whether physical changes in the St. Clair River are affecting water levels within the upper Great Lakes, to assess regulation plans for outflows from Lake Superior, and to examine the potential effect of climate change on the Great Lakes water l ...

In June 2022, the U.S. Geological Survey, in collaboration with the Massachusetts Office of Coastal Zone Management, collected high-resolution geophysical data, in Nantucket Sound to understand the regional geology in the vicinity of Horseshoe Shoal. This effort is part of a long-term collaboration between the USGS and the Commonwealth of Massachusetts to map the State’s waters, support research on the Quaternary evolution of coastal Massachusetts, resolve the influence of sea-level change and sediment supply on coastal evolution, and strengthen efforts to understand the type, distribution, and quality of subtidal marine habitats. This collaboration produces high-resolution geologic data that serve the needs of research, management and the public. Data collected as part of this mapping cooperative continue to be released in a series of USGS Open-File Reports and Data Releases https://www.usgs.gov/centers/whcmsc/science/geologic-mapping-massachusetts-seafloor.