cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.48370/ofd/42lzgt
title: Sorex araneus - 146288, Zoological collection of the Mammal Research Institute, PAS

description: Sorex araneus (Common shrew) from Zoological collection of the Mammal Research Institute, PAS. Collected 1983-05-10, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/w7cyi2
title: Sorex araneus - 86336, Zoological collection of the Mammal Research Institute, PAS

description: Sorex araneus (Common shrew) from Zoological collection of the Mammal Research Institute, PAS. Collected 1969-07-16, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/idyerp
title: Sorex araneus - 7774, Zoological collection of the Mammal Research Institute, PAS

description: Sorex araneus (Common shrew) from Zoological collection of the Mammal Research Institute, PAS. Collected 1955-03-27, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/qsuxej
title: Sorex araneus - 4113, Zoological collection of the Mammal Research Institute, PAS

description: Sorex araneus (Common shrew) from Zoological collection of the Mammal Research Institute, PAS. Collected 1954-03-13, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/y4gi83
title: Sorex araneus - 98048, Zoological collection of the Mammal Research Institute, PAS

description: Sorex araneus (Common shrew) from Zoological collection of the Mammal Research Institute, PAS. Collected 1971-07-03, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/dwcr0v
title: Sorex araneus - 328, Zoological collection of the Mammal Research Institute, PAS

description: Sorex araneus (Common shrew) from Zoological collection of the Mammal Research Institute, PAS. Collected 1952-09-07, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/htacj5
title: Sorex araneus - 154727, Zoological collection of the Mammal Research Institute, PAS

description: Sorex araneus (Common shrew) from Zoological collection of the Mammal Research Institute, PAS. Collected 1987-02-19, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/psksee
title: Sorex araneus - 380, Zoological collection of the Mammal Research Institute, PAS

description: Sorex araneus (Common shrew) from Zoological collection of the Mammal Research Institute, PAS. Collected 1952-09-20, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/kclgth
title: Sorex araneus - 91025, Zoological collection of the Mammal Research Institute, PAS

description: Sorex araneus (Common shrew) from Zoological collection of the Mammal Research Institute, PAS. Collected 1970-06-15, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/i7gxaa
title: Sorex araneus - 31934, Zoological collection of the Mammal Research Institute, PAS

description: Sorex araneus (Common shrew) from Zoological collection of the Mammal Research Institute, PAS. Collected 1963-06-18, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/j1eqxa
title: Sorex araneus - 4017, Zoological collection of the Mammal Research Institute, PAS

description: Sorex araneus (Common shrew) from Zoological collection of the Mammal Research Institute, PAS. Collected 1954-02-05, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/jm1ibg
title: Sorex araneus - 235, Zoological collection of the Mammal Research Institute, PAS

description: Sorex araneus (Common shrew) from Zoological collection of the Mammal Research Institute, PAS. Collected 1952-08-21, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/pmj9o7
title: Sorex araneus - 291, Zoological collection of the Mammal Research Institute, PAS

description: Sorex araneus (Common shrew) from Zoological collection of the Mammal Research Institute, PAS. Collected 1952-08-29, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/z59kzx
title: Sorex araneus - 4298, Zoological collection of the Mammal Research Institute, PAS

description: Sorex araneus (Common shrew) from Zoological collection of the Mammal Research Institute, PAS. Collected 1954-04-16, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/bdwbex
title: Sorex araneus - 307, Zoological collection of the Mammal Research Institute, PAS

description: Sorex araneus (Common shrew) from Zoological collection of the Mammal Research Institute, PAS. Collected 1952-09-02, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/vioiiz
title: Sorex araneus - 154743, Zoological collection of the Mammal Research Institute, PAS

description: Sorex araneus (Common shrew) from Zoological collection of the Mammal Research Institute, PAS. Collected 1987-02-20, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/qbwdnc
title: Sorex araneus - 143, Zoological collection of the Mammal Research Institute, PAS

description: Sorex araneus (Common shrew) from Zoological collection of the Mammal Research Institute, PAS. Collected 1952-07-31, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/v3vert
title: Sorex araneus - 3582, Zoological collection of the Mammal Research Institute, PAS

description: Sorex araneus (Common shrew) from Zoological collection of the Mammal Research Institute, PAS. Collected 1953-09-07, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/9a7oix
title: Sorex araneus - 18, Zoological collection of the Mammal Research Institute, PAS

description: Sorex araneus (Common shrew) from Zoological collection of the Mammal Research Institute, PAS. Collected 1952-07-11, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/3b2a0o
title: Sorex araneus - 32472, Zoological collection of the Mammal Research Institute, PAS

description: Sorex araneus (Common shrew) from Zoological collection of the Mammal Research Institute, PAS. Collected 1963-07-24, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/0xhtbp
title: Sorex araneus - 154778, Zoological collection of the Mammal Research Institute, PAS

description: Sorex araneus (Common shrew) from Zoological collection of the Mammal Research Institute, PAS. Collected 1987-02-23, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/ybnpcf
title: Sorex araneus - 275, Zoological collection of the Mammal Research Institute, PAS

description: Sorex araneus (Common shrew) from Zoological collection of the Mammal Research Institute, PAS. Collected 1952-08-27, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/zudedo
title: Sorex araneus - 4018, Zoological collection of the Mammal Research Institute, PAS

description: Sorex araneus (Common shrew) from Zoological collection of the Mammal Research Institute, PAS. Collected 1954-02-05, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/s250ym
title: Sorex araneus - 7786, Zoological collection of the Mammal Research Institute, PAS

description: Sorex araneus (Common shrew) from Zoological collection of the Mammal Research Institute, PAS. Collected 1955-03-28, in: Białowieża National Park, Poland. Material type:
DOI: 10.17632/jtdvbm2tzx.1
title: Case Study: Host and Pathogen Response to Bacteriophage Engineered Against Mycobacterium abscessus Lung Infection. Nick et al.

description: Summary: Two engineered mycobacteriophages were administered intravenously with antibiotics to a male with treatment-refractory M. abscessus pulmonary infection and severe cystic fibrosis lung disease. Evidence of phage-induced lysis was observed using molecular and metabolic assays within days of phage treatment initiation, computerized tomography (CT) assessment, and airway cultures. Anti-phage neutralizing antibody titers to one phage increased with time. The subject received lung transplantation on day 379, and systematic cultures of the explanted lung did not detect M. abscessus. This study describes the course and associated markers of successful phage treatment of M. abscessus in the context of advanced lung disease.

CT scans: Video files incorporating a complete set of axial, coronal and sagittal reconstructions of high-resolution CT scans pre- and post-phage. Scans demonstrate severe diffuse varicose upper-lobe cystic bronchiectasis with a left apical cavity. Multifocal mucoid impaction, widespread mosaic attenuation, and scattered poorly defined nodules were present. Focal tree-in-bud pattern was most marked in the right lower lobe. Areas of improvement were seen post-phage day 81 that were further improved by day 229.

H& E: Gross and microscopic pathological photographs of the explanted lungs at time of lung transplant (day 379 of phage). The left and right lungs showed similar changes and are described together. 
Gross appearance of the pleural surface was tan-purple, wrinkled and dull displaying moderate cobblestoning and induration, with no grossly discernable masses or lesions. 
H&E-stained sections showed extensive bronchiectasis with dilation of both bronchi and bronchioles frequently associated with acute bronchopneumonia consisting of neutrophils, mucin and cellular debris within the airway lumens.  

Master data: Raw data from Figures 1A, 1F, 4A, 4B, 4C, 4D, 6A and Supplemental Table 1. Airway culture results (Figures 1A, 1F and 4A) from day -3519 days pre- phage, through day 469. CF cultures are tabulated as positive or negative for P. aeruginosa and/or MRSA. NTM cultures are tabulated as positive or negative for either M. abscessus or M. avium. Cultures prior to transplant (day 379) were obtained from expectorated sputum, and post-transplant from BAL. 
 qPCR analysis of M. abscessus DNA over time (Figure 4B). M. abscessus DNA concentrations (pg/ul) were extrapolated from a standard curve (Sup. Fig. 2). The participant was unable to produce sputum post-transplant (day 379).
Urine LAM components D-ara and TBSA (ng/ml) over time (Figure 4C). Levels of both peaked 47 days after initiation of phage, and by day 152 were both below LOD, continuing post-transplant.
Serum anti-M. abscessus IgA and IgG over time (Figure 4D). 
Half maximal titers of IgG antibodies over various time points pre- and post-phage for phages BPs∆33HTH_HRM10 and D29_HRMGD40 (depicted in Figure 6A).
DOI: 10.15482/usda.adc/1526433
title: Standard Quality Controlled Research Weather Data – USDA-ARS, Bushland, Texas

description: [ NOTE – 2022/05/06: this dataset supersedes the earlier version https://doi.org/10.15482/USDA.ADC/1482548 ].
This dataset contains 15-minute mean weather data from the USDA-ARS Conservation and Production Laboratory (CPRL), Soil and Water Management Research Unit (SWMRU) research weather station, Bushland, Texas (Lat. 35.186714°, Long. -102.094189°, elevation 1170 m above MSL) for all days in each year. The data are from sensors placed at 2-m height over a level, grass surface mowed to not exceed 12 cm height and irrigated and fertilized to maintain reference conditions as promulgated by Allen et al. (2005, 1998). Irrigation was by surface flood in 1989 through 1994, and by subsurface drip irrigation after 1994. Sensors were replicated and intercompared between replicates and with data from nearby weather stations, which were sometimes used for gap filling. Quality control and assurance methods are described by Evett et al. (2018). Data from a duplicate sensor were used to fill gaps in data from the primary sensor using appropriate regression relationships. Gap filling was also accomplished using sensors deployed at one of the four large weighing lysimeters immediately west of the weather station, or using sensors at other nearby stations when reliable regression relationships could be developed. The primary paper describes details of the sensors used and methods of testing, calibration, inter-comparison, and use. The weather data include air temperature (C) and relative humidity (%), wind speed (m/s), solar irradiance (W m-2), barometric pressure (kPa), and precipitation (rain and snow in mm). Because the large (3 m by 3 m surface area) weighing lysimeters are better rain gages than are tipping bucket gages, the 15-minute precipitation data are derived for each lysimeter from changes in lysimeter mass. The land slope is &lt;0.3% and flat. The mean annual precipitation is ~470 mm, the 20-year pan evaporation record indicates ~2,600 mm Class A pan evaporation per year, and winds are typically from the South and Southwest. The climate is semi-arid with ~70% (350 mm) of the annual precipitation occurring from May to September, during which period the pan evaporation averages ~1520 mm.
These datasets originate from research aimed at determining crop water use (ET), crop coefficients for use in ET-based irrigation scheduling based on a reference ET, crop growth, yield, harvest index, and crop water productivity as affected by irrigation method, timing, amount (full or some degree of deficit), agronomic practices, cultivar, and weather. The data have utility for testing simulation models of crop ET, growth, and yield and have been used by the Agricultural Model Intercomparison and Improvement Project (AgMIP), by OPENET, and by many others for testing, and calibrating models of ET that use satellite and/or weather data.
DOI: 10.5281/zenodo.6539485
title: REIP: a Reconfigurable Environmental Intelligence Platform and Software Framework for Fast Sensor Network Prototyping - use case dataset

description: Sensor networks have dynamically expanded our ability to monitor and study the world. Their presence and need keep increasing, and new hardware configurations expand the range of physical stimuli that can be accurately recorded. Sensors are also no longer simply recording the data, they process it and transform into something useful before uploading to the cloud. However, building sensor networks is costly and very time consuming. It is difficult to build upon other people’s work and there are only a few open-source solutions for integrating different devices and sensing modalities. We introduce REIP, a Reconfigurable Environmental Intelligence Platform for fast sensor network prototyping. REIP’s first and most central tool, implemented in this work, is an open-source software framework, an SDK, with a flexible modular API for data collection and analysis using multiple sensing modalities. REIP is developed with the aim of being user-friendly, device-agnostic, and easily extensible, allowing for fast prototyping of heterogeneous sensor networks. Furthermore, our software framework is implemented in Python to reduce the entrance barrier for future contributions. We show the potential and versatility of REIP in real world applications, along with performance studies and benchmark REIP SDK against similar systems. This dataset was created for the case study in Section 5 of the paper.
DOI: 10.5281/zenodo.6539484
title: REIP: a Reconfigurable Environmental Intelligence Platform and Software Framework for Fast Sensor Network Prototyping - use case dataset

description: Sensor networks have dynamically expanded our ability to monitor and study the world. Their presence and need keep increasing, and new hardware configurations expand the range of physical stimuli that can be accurately recorded. Sensors are also no longer simply recording the data, they process it and transform into something useful before uploading to the cloud. However, building sensor networks is costly and very time consuming. It is difficult to build upon other people’s work and there are only a few open-source solutions for integrating different devices and sensing modalities. We introduce REIP, a Reconfigurable Environmental Intelligence Platform for fast sensor network prototyping. REIP’s first and most central tool, implemented in this work, is an open-source software framework, an SDK, with a flexible modular API for data collection and analysis using multiple sensing modalities. REIP is developed with the aim of being user-friendly, device-agnostic, and easily extensible, allowing for fast prototyping of heterogeneous sensor networks. Furthermore, our software framework is implemented in Python to reduce the entrance barrier for future contributions. We show the potential and versatility of REIP in real world applications, along with performance studies and benchmark REIP SDK against similar systems. This dataset was created for the case study in Section 5 of the paper.
DOI: 10.6073/pasta/30a3232084be9c936c976fbb6b31c5a2
title: Interagency Ecological Program: Over four decades of juvenile fish monitoring data from the San Francisco Estuary, collected by the Delta Juvenile Fish Monitoring Program, 1976-2021

description: The United States Fish and Wildlife Service Delta Juvenile Fish Monitoring Program (DJFMP) has monitored juvenile Chinook Salmon Oncorhynchus tshawytscha and other fish species within the San Francisco Estuary (Estuary) since 1976 using a combination of surface trawls and beach seines. Since 2000, three trawl sites and 58 beach seine sites have been sampled weekly or biweekly within the Estuary and lower Sacramento and San Joaquin Rivers. As part of the Interagency Ecological Program (IEP) that manages the Estuary, the DJFMP has tracked the relative abundance and distribution of naturally and hatchery produced juvenile Chinook Salmon of all races as they outmigrate through the Sacramento-San Joaquin Delta for over four decades. The data that DJFMP collected has been used not only to help inform the management of Chinook Salmon, but also to monitor the status of native species of interest such as the previously listed Sacramento Splittail Pogonichthys macrolepidotus and invasive species such as Mississippi Silverside Menidia audens and Largemouth Bass Micropterus salmoides. DATA CORRECTION/UPDATE: Previous data versions 244.6, 244.7, and 244.8 contained an error and resulted in duplicated records of hatchery Chinook Salmon in the datasets. These datasets were removed from the data repository and the error was corrected in version 244.9 and after. DNA Data: Full more details of the DNA methods and results for juvenile Chinook salmon included in this dataset, please check out Blankenship, S.M., J. Israel, E. Buttermore, and K. Reece. 2021. Knights Landing, California Department of Fish and Wildlife, Genetic Determination of Population of Origin 2017 through 2019 ver 1. Environmental Data Initiative. https://doi.org/10.6073/pasta/85fbc988c0b1362e84c318e69c7a939e. For more information on the Delta Juvenile Fish Monitoring Program: https://www.fws.gov/project/delta-juvenile-fish-monitoring-program
DOI: 10.48370/ofd/kyn6gr
title: Sorex araneus - 106998, Zoological collection of the Mammal Research Institute, PAS

description: Sorex araneus (Common shrew) from Zoological collection of the Mammal Research Institute, PAS. Collected 1972-07-31, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/o81nno
title: Sorex araneus - 115532, Zoological collection of the Mammal Research Institute, PAS

description: Sorex araneus (Common shrew) from Zoological collection of the Mammal Research Institute, PAS. Collected 1974-10-19, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/1opj2r
title: Sorex araneus - 18354, Zoological collection of the Mammal Research Institute, PAS

description: Sorex araneus (Common shrew) from Zoological collection of the Mammal Research Institute, PAS. Collected 1957-06-29, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/2v0df6
title: Sorex araneus - 113264, Zoological collection of the Mammal Research Institute, PAS

description: Sorex araneus (Common shrew) from Zoological collection of the Mammal Research Institute, PAS. Collected 1974-05-12, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/fscvhk
title: Sorex araneus - 11901, Zoological collection of the Mammal Research Institute, PAS

description: Sorex araneus (Common shrew) from Zoological collection of the Mammal Research Institute, PAS. Collected 1955-07-29, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/hgmek6
title: Sorex araneus - 82744, Zoological collection of the Mammal Research Institute, PAS

description: Sorex araneus (Common shrew) from Zoological collection of the Mammal Research Institute, PAS. Collected 1968-10-23, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/5agouh
title: Sorex araneus - 62244, Zoological collection of the Mammal Research Institute, PAS

description: Sorex araneus (Common shrew) from Zoological collection of the Mammal Research Institute, PAS. Collected 1967-03-12, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/n9ny0k
title: Sorex araneus - 28482, Zoological collection of the Mammal Research Institute, PAS

description: Sorex araneus (Common shrew) from Zoological collection of the Mammal Research Institute, PAS. Collected 1962-07-28, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/ks3j5a
title: Sorex araneus - 116937, Zoological collection of the Mammal Research Institute, PAS

description: Sorex araneus (Common shrew) from Zoological collection of the Mammal Research Institute, PAS. Collected 1975-07-30, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/edvbdx
title: Sorex araneus - 167979, Zoological collection of the Mammal Research Institute, PAS

description: Sorex araneus (Common shrew) from Zoological collection of the Mammal Research Institute, PAS. Collected 2001-07-06, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/psy8tp
title: Sorex araneus - 99170, Zoological collection of the Mammal Research Institute, PAS

description: Sorex araneus (Common shrew) from Zoological collection of the Mammal Research Institute, PAS. Collected 1971-09-18, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/vwgh0m
title: Sorex araneus - 162132, Zoological collection of the Mammal Research Institute, PAS

description: Sorex araneus (Common shrew) from Zoological collection of the Mammal Research Institute, PAS. Collected 1992-07-08, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/hknrm8
title: Sorex araneus - 53962, Zoological collection of the Mammal Research Institute, PAS

description: Sorex araneus (Common shrew) from Zoological collection of the Mammal Research Institute, PAS. Collected 1966-08-03, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/qadgie
title: Sorex araneus - 99884, Zoological collection of the Mammal Research Institute, PAS

description: Sorex araneus (Common shrew) from Zoological collection of the Mammal Research Institute, PAS. Collected 1971-10-27, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/gyba40
title: Sorex araneus - 114276, Zoological collection of the Mammal Research Institute, PAS

description: Sorex araneus (Common shrew) from Zoological collection of the Mammal Research Institute, PAS. Collected 1974-08-22, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/lstytc
title: Sorex araneus - 11821, Zoological collection of the Mammal Research Institute, PAS

description: Sorex araneus (Common shrew) from Zoological collection of the Mammal Research Institute, PAS. Collected 1955-07-28, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/vixu7m
title: Sorex araneus - 2928, Zoological collection of the Mammal Research Institute, PAS

description: Sorex araneus (Common shrew) from Zoological collection of the Mammal Research Institute, PAS. Collected 1953-08-06, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/c7zoem
title: Sorex araneus - 52297, Zoological collection of the Mammal Research Institute, PAS

description: Sorex araneus (Common shrew) from Zoological collection of the Mammal Research Institute, PAS. Collected 1966-07-03, in: Białowieża National Park, Poland. Material type:
DOI: 10.48370/ofd/rx6xxg
title: Sorex araneus - 18505, Zoological collection of the Mammal Research Institute, PAS

description: Sorex araneus (Common shrew) from Zoological collection of the Mammal Research Institute, PAS. Collected 1957-07-13, in: Białowieża National Park, Poland. Material type: