cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6073/pasta/98b14e18d529573f7bca9e05dc0ad76a
title: Total numbers per square meter and taxa of insects taken from the Kuparuk River during the summer of 2001, Arctic LTER 2001.

description: A Surber sampler (25 X 25 cm frame fitted with a 243 um mesh net) was used to sample invertebrates at several different stations. Two replicates were taken from each station. The same sampling procedure was used for all dates. The stations were measured relative to the site of the dripper ("-" = upstream of the dripper). Samples were preserved in 4% formaldehyde and transported to Orono, Maine, where invertebrates were removed by hand under 15X magnification and then identified and counted. All values are converted to individuals per square meter.
DOI: 10.5281/zenodo.5209376
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Sarah Tassell, https://orcid.org/0000-0002-8083-3111. Claims were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
DOI: 10.6073/pasta/d0abe716146004268bb5f876ee42c992
title: Air and soil temperature data from the Reference Stand network at the Andrews Experimental Forest, 1971 to present

description: The current network of temperature measurement sites are designed to represent spatial variability of air and soil temperature in rugged mountain topography, and serve as second-level stations to capture specific microclimate temperatures in conjunction with a network of Benchmark Meteorological Stations (MS001). The air and soil thermograph network has been reduced from the historical network of 37 sites originally established. Currently there are 10 measurement sites with two of these sites measuring relative humidity in addition to air and soil temperature. An original network of 19 sites (RS01-RS19) were established during the International Biome Program in the early 1970's. Emphasis on phenology, plant moisture stress, and leaf nutrient content led to extending this network of air and soil temperature measurement. A plant community classification system (Dyrness et al., 1971) was used as a primary means of stratification, and a set of permanent vegetation plots (Reference Stands) was installed to represent forest communities with distinct vegetation and hypothesized different environments (Dyrness et al., 1974). A thermograph network was installed within the reference stands in the early 1970's (Zobel et al., 1974), and vegetation standing crop, tree growth and mortality, and plant succession were also measured. The majority of these sites were established to monitor micro-meteorological data under the canopy. The purpose of this network was to provide air and soil temperature data for modeling photosynthesis, respiration, phenology, and decomposition, and to measure environmental gradients.
DOI: 10.6069/2w4t-j381
title: Skyline Batch: An Intuitive User Interface for Batch Processing with Skyline

description: Skyline Batch is a newly developed Windows forms application that enables easy and consistent reprocessing of data with Skyline. Skyline has made previous advances in this direction; however, none enable seamless automated reprocessing of local and remote files. Skyline keeps a log of all the steps that were taken in the document; however, reproducing these steps takes time and allows room for human error. Skyline also has a command-line interface, enabling it to be run from a batch script, but using the program in this way requires expertise in editing these scripts. By formalizing the workflow of a highly used set of batch scripts into an intuitive and powerful user interface, Skyline Batch can reprocess data stored in remote repositories just by opening and running a Skyline Batch configuration file. When run, a Skyline Batch configuration downloads all necessary remote files and then runs a four-step Skyline workflow. By condensing the steps needed to reprocess the data into one file, Skyline Batch gives researchers the opportunity to publish their processing along with their data and other analysis files. These easily run configuration files will greatly increase the transparency and reproducibility of published work. Skyline Batch is freely available at https://skyline.ms/batch.url.
DOI: 10.25345/c5zz98
title: MassIVE MSV000088385 - GNPS - 11152021_TRF_NASHandHCC_liver
title: NASH and HCC mouse cohorts were fed normal and high fat diets ad libidum and time-restricted. Livers were harvested after mice were sacrificed.
DOI: 10.6073/pasta/6022898a200f7fac09aa36e79e0e66d7
title: Precipitation measurements from historic and current standard, storage and recording rain gauges at the Andrews Experimental Forest, 1951 to present

description: Andrews Forest precipitation has been measured continuously using various rain gage types since 1951. Most of these rain gages are standard (non-recording) gages with 7.5 or 8 inch orifices or large capacity storage gages intended for sites with limited access collected irregularly over longer intervals. Recording rain gages have also been established to collect higher temporal resolutions (e.g., 5 minute or 15 minute) and also used as a means of parsing (“prorating”) these periodic interval measurements from these standard and storage gages into daily totals. This data set includes an inventory of all rain gages that have operated within the Andrews as well as one site in the nearby Wildcat RNA and one in the town of Blue River. The inventory includes information regarding the date range of operation, gage location, type of gage, the rain network within which it was established, general availability of data and descriptive notes. A second table includes all of the raw measurement data for these non-recording gages over every interval where data were taken, and additionally includes the corresponding recording gage and its measurement total used to prorate data into a daily record. A third table includes the prorated daily data for all of these standard and storage gages as well as the true daily totals for two recording rain gages. A fourth table includes high temporal resolution for one early recording gage at Forks and the Mack Creek recording gage. Note that while precipitation data associated with the 6 benchmark stations are included in this rain gage inventory (Entity 1), the daily and high temporal resolution data for these sites are available through a separate meteorological data set, database code MS001.
DOI: 10.6069/qakc-6n51
title: Skyline Batch: An Intuitive User Interface for Batch Processing with Skyline

description: Skyline Batch is a newly developed Windows forms application that enables easy and consistent reprocessing of data with Skyline. Skyline has made previous advances in this direction; however, none enable seamless automated reprocessing of local and remote files. Skyline keeps a log of all the steps that were taken in the document; however, reproducing these steps takes time and allows room for human error. Skyline also has a command-line interface, enabling it to be run from a batch script, but using the program in this way requires expertise in editing these scripts. By formalizing the workflow of a highly used set of batch scripts into an intuitive and powerful user interface, Skyline Batch can reprocess data stored in remote repositories just by opening and running a Skyline Batch configuration file. When run, a Skyline Batch configuration downloads all necessary remote files and then runs a four-step Skyline workflow. By condensing the steps needed to reprocess the data into one file, Skyline Batch gives researchers the opportunity to publish their processing along with their data and other analysis files. These easily run configuration files will greatly increase the transparency and reproducibility of published work. Skyline Batch is freely available at https://skyline.ms/batch.url.
DOI: 10.6069/8ba1-8n77
title: Rapid and Sensitive Detection of SARS-CoV-2 Infection Using Quantitative Peptide Enrichment Analysis

description: Reliable, robust, large-scale molecular testing for SARS-CoV-2 is essential for monitoring the ongoing Covid-19 pandemic. We have developed a scalable analytical approach to detect viral proteins based on peptide immunoaffinity enrichment combined with liquid chromatography - mass spectrometry (LC-MS). This is a multiplexed strategy, based on targeted proteomics analysis and read-out by LC-MS, capable of precisely quantifying and confirming the presence of SARS-CoV-2 in PBS swab media from combined throat/nasopharynx/saliva samples.
The results reveal that the levels of SARS-CoV-2 measured by LC-MS correlate well with their corresponding RT-PCR readout. The analytical workflow shows similar turnaround times as regular RT-PCR instrumentation with quantitative readout of viral proteins corresponding to cycle thresholds (Ct) equivalents ranging from 20 to 35. Using RT-PCR as a reference, we demonstrate that the LC-MS-based method has 100% specificity and 86% sensitivity when analyzing clinical samples collected from asymptomatic patients. These results suggest that a scalable analytical method based on LC-MS has a place in future pandemic preparedness centers to complement current virus detection technologies.
DOI: 10.6069/genq-b368
title: Alzheimer's Disease Isomerization

description: Amino acid isomerization is a spontaneous chemical modification potentially related to the underlying causes of Alzheimer’s disease (AD). We demonstrate that data-independent acquisition mass spectrometry can be used to characterize isomerization in complex protein mixtures. Examination of a large cohort of brain samples revealed a striking relationship between isomerization of tau and AD status. Surprisingly, isomerization was found to be more abundant in both autosomal dominant and sporadic AD samples relative to controls. We hypothesize that lower autophagic flux in AD brains accounts for these results. Additional data strongly support this hypothesis, including quantitative analysis of proteins related to autophagy. For example, isomerization of tau is positively correlated with levels of p62, a recognized indicator of autophagic inhibition. In sum, the data suggest strong ties between isomerization and autophagic flux, which may therefore represent a promising target for future investigations into the therapy and prevention of AD.
DOI: 10.6069/jmvf-zy76
title: Linking post-translational modifications and protein turnover by site-resolved protein turnover (SPOT) profiling

description: Proteome-wide measurements of protein turnover have largely ignored the impact of post-translational modifications (PTMs). To address this gap, we employ stable isotope labelling and mass spectrometry to measure the turnover of >120,000 peptidoforms including >33,000 phosphorylated, acetylated, and ubiquitinated peptides for >9,000 native proteins. This site-resolved protein turnover (SPOT) profiling discloses global and site-specific differences in turnover associated with the presence or absence of PTMs. While causal relationships may not always be immediately apparent, we hypothesize that PTMs with diverging turnover may distinguish states of differential protein stability, structure, localization, enzymatic activity, or protein-protein interactions. We exemplify how the turnover data may facilitate insights into unknown functions of PTMs and provide a web-tool for the scientific community that allows interrogation and visualisation of all turnover data. Since the methodology is applicable to many cell types and modifications, it has substantial potential to prioritize PTMs for functional investigation in the future.
DOI: 10.6069/rzyh-9n48
title: Quantification of Soy-Derived Ingredients in Model Bread and Frankfurter Matrices with an Optimized LC-MS/MS External Standard Calibration Workflow

description: The detection and quantification of soy protein is important for food allergen management and identifying the presence of undeclared soy proteins. Heat processing and matrix interactions can affect the accuracy of allergen detection methods. The sensitivity of ELISA methods can be compromised if protein epitopes are modified during processing. Therefore, an MS-based method was evaluated for the recovery of total soy protein in incurred matrices. MS-based quantification of total soy protein was assessed using a combination of external and internal standards. The reproducibility of the standard curves was investigated by comparing within-day and among among-day variation. Incurred samples were prepared using bread and frankfurters as model food matrices. Several soy-derived ingredients were used to prepare the matrices with varying levels of soy protein (1, 10, 50, or 100 ppm total soy protein). A pooled standard curve was used to estimate the total soy protein concentration of the incurred food matrices and the percent total protein recovery. The variation of replicate standard curves between days and among all days was not significant. The differences in slopes obtained from replicate standards run on different days were minimal. The most influential factor on the quantitative protein recovery in incurred samples was the effect of the physical matrix structure on protein extraction. The lowest percent protein recoveries, less than 50%, were calculated for uncooked matrices. The cooked matrices had percent recoveries between 50-150% for all total soy protein levels. Other factors, such as type of ingredient, were determined to be not as impactful on recovery. The MS method described in this study was able to provide sensitive detection and accurate quantification of total soy protein from various soy-derived ingredients present in processed food matrices.
DOI: 10.6073/pasta/3e34534da2a008d84269356442f772b8
title: Rainfall at El Verde Field Station, Rio Grande, Puerto Rico since 1975

description: Rainfall has been measured at the El Verde Field Station since 1964. McDowell and Estrada-Pinto, 1988 presents a description of the collection procedures, raw data from 1964 to 1986, and some summary statistics for this period of record. Precipitation for this period showed some seasonality in monthly means, with a peak in May. Monthly averages for the period of 1975 to current chart can be found at this site. The highest values for the monthly averages for the period of 1975 to 2000 are from August to December with a low in October and November the highest. In this period the highest amount of total annual rainfall was in 1998 with 5293.61 mm and the minimum in 1994 with 1402.87 mm.
DOI: 10.6073/pasta/44835db7c9f0d16602131aad9370ba1f
title: Chemistry of soil solution collected from zero tension lysimeters in the Canopy Trimming Experiment (CTE) plots

description: Soil solution chemistry: Soil solution was collected monthly from zero tension lysimeters installed in the CTE plots. Sampling began prior to cutting the canopy and continue to the present.
DOI: 10.6073/pasta/8a6c85713bf55573c457d92076385bee
title: Chemistry of rainfall and throughfall from El Verde and Bisley

description: Rain, throughfall, and stream water are collected weekly at the LEF sites listed below. These data sets begin as early as 1983; LTER sampling began in 1988. Rain and throughfall samples are the total catch for the week, and are exposed to field conditions for that time. No event sampling is conducted on a routine basis. Rain samples from WDEV are wet only from an automatically-closing collector that prevents any dry deposition (Aerochem Metrics NADP collector). RCEV and RCB are bulk or always-open collectors that receive dry deposition by sedimentation. All samples are measured for pH and conductivity, and then filtered (pre-combusted Whatman GF/F glass fiber filter) prior to further analysis. From 1983-1994 samples were cooled and returned to the San Juan chemistry laboratory for analysis. During those years, samples for NH4 and NO3 analyses were refrigerated continuously until analysis. Subsamples for NH4 analysis were also preserved with 1 molar H2SO4. From 1994 on, samples for NH4 and NO3 were frozen until analysis, were not acidified, and all analyses were conducted at the University of New Hampshire. Rain and Throughfall Sampling SitesDescriptions of LTER LUQ rain and throughfall weekly sample chemistry data from 1988 onwards. Chemical concentrations are recorded as mg/L or mg/L as appropriate. Values below detection limits are recorded as 1/2 the detection limit. Site Abbreviation Description Comments Rain collector BisleyÂ . RCB Bulk collector. Â Rain collector El VerdeÂ RCEVÂ Bulk collector. Â Wet/dry El VerdeÂ . WDEV. Wet only collector. Â Throughfall Bisley. TFB=TCB TF bulk 10-collector composite Â Bisley gapÂ . BGAPÂ . TF bulk 10-collector composite Â
DOI: 10.6073/pasta/8d2ee3d7d5e3e8655063e738ae3700e2
title: Meteorological data from several climate stations in the northeast section of the Luquillo Experimental Forest

description: Electronic sensors are placed at the field location to support other activities. Data set includes measurementes from several climate stations in the northeast section of the Luquillo Experimental Forest. These stations are surround the Bisley Experimental watersheds and the Sabana Field Station that are operated by the USFS and the USGS. The collection of data in the Sabana Field Station ended in 9/10/2009.
DOI: 10.6073/pasta/b14b442a87fff9dc22b68bc462be756b
title: Sonadora elevational plots: long-term monitoring of air temperature

description: This is a long-term monitoring of air temperature at each elevation plot along the Sonadora gradient. At each plot a HOBO sensor is located close to the middle of the plot: at 1m above ground: and placed inside a radiation shield (a plastic cup). Sensors are programmed to sample and store air temperature every hour. A daily average is computed from hourly readings. Sensors are downloaded twice a year: thus blanks represent sensor malfunction: loss of battery: or memory full. Initial blanks were due to lack of enough sensors to cover the gradient
DOI: 10.6073/pasta/bc3c46b7ebc4f53c3cef1d9c052169df
title: Prieta stream - Discharge and water level at pool 0

description: This is a long-term monitoring of water discharge and water level at Prieta Stream. The monitoring point is located at Pool 0: which is the same location where we sample stream chemistry. Measurements are taken automatically with a pressure transducer: every 15 minutes. Measure are originally of pressure: which are translated to water level using the reference gauge. Using an equation provided by Dr. Fred Scatena: water level is converted into discharge. Stage height to discharge equation created by Fred N Scatena used from 2006 to 3-26-2013 10 AM: discharge (m3/sec) = 1.095 - 1.585 * stage + 0.578 * stage * stage Stage height to discharge equation created by William H McDowell and Jody Potter used from 3-26-2013 10:15 to present: discharge (m3/sec) = 0.0005*((stage)^8.8846)*35.314666
DOI: 10.6073/pasta/e73e96da124481de01486a0dab0178dc
title: Meteorological data from El Verde Field Station: NADP Tower

description: Meteorological sensors are located at the top of a 20 m tower, the NADP Tower, behind the main buildings of El Verde Field Station, 350 masl. No large trees are present near the tower. Sensors are connected to a Campbell 1000X data logger, with a storage module, and downloaded every two weeks using a wireless radio connection from the laboratory to the tower. Data are compiled at the station before it is made available. The station was initiated in 2000. Complementary manual measurements of rainfall and maximum and minimum air temperatures are taken on a daily basis at a separate physical location.
DOI: 10.6073/pasta/f9df56348f510da0113b1e6012fa2967
title: Chemistry of stream water from the Luquillo Mountains

description: Stream water is collected weekly at theÂ LuquilloÂ Mountain sites listed below. These data sets begin as early as 1983; LTER sampling began in 1988. Stream water samples are grab samples taken from the water/air interface at stream channel center on the sampling day (usually Tuesdays). A continuous record of stream stage (height) is recorded by aÂ dataloggerÂ at all ongoing stream sampling sites. Average dailyÂ streamflowsÂ are available from the USGS and at other locations (Hydrology and Meteorology) on this site. All samples are measured for pH and conductivity, and then filtered (pre-combustedÂ WhatmanÂ GF/F glass fiber filter) prior to further analysis. From 1983-1994 samples were cooled and returned to the San Juan chemistry laboratory for analysis. During those years, samples for NH4Â and NO3Â analyses were refrigerated continuously until analysis. Subsamples for NH4Â analysis were also preserved with 1 molarÂ H2SO4. From 1994 on, samples for NH4Â and NO3were frozen until analysis, were not acidified, and all analyses were conducted at the University of New Hampshire. Stream water Sampling SitesDescriptions of LTER LUQ stream water weekly sample chemistry data from 1988 onwards.Â Chemical concentrations are recorded as mg/L orÂ mg/L as appropriate. Values below detection limits are recorded as 1/2 the detection limit.Â Site Abbreviation Description Comments Quebrada Sonadora QS El Verde stream. Â Quebrada Toronja QT = QT1 El Verde stream. Â Rio Espiritu Santo RES4 LEF North Stream LEF= Luquillo Experimental Forest Quebrada Prieta A QPA El Verde stream Â Quebrada Prieta B QPB El Verde stream Â Quebrada Prieta QP El Verde stream Â Puente Roto Mameyes MPR Bisley stream Previously "PRM" Quebrada uno-Bisley Q1Â . Bisley stream Â Quebrada dos-Bisley Q2Â Bisley stream Â Quebrada tres-Bisley Q3Â . Bisley stream Â Rio Mameyes GageÂ MG Bisley stream Â Rio Icacos RI LEF South stream Â Rio Sabana RS LEF West stream Â Quebrada Guaba QG Icacois stream Â