Abstract Innovations in machine learning and cloud‐based computing were merged with historical remote sensing field data to provide the first moderate resolution, annual, percent cover maps of plant functional types across rangeland ecosystems effectively efficiently respond pressing challenges facing conservation biodiversity ecosystem services. We utilized Landsat satellite record, gridded meteorology, abiotic land surface data, over 30,000 plots within a Random Forests model predict...

For decades, mass spectrometry data has been analyzed to investigate a wide array of research interests, including disease diagnostics, biological and chemical theory, genomics, drug development. Progress towards solving any these disparate problems depends upon overcoming the common challenge interpreting large sets generated. Despite interim successes, many interpretation in are still challenging. Further, though challenges inherently interdisciplinary nature, significant domain-specific...

INTRODUCTION: Liver cirrhosis and its complication — hepatocellular carcinoma (HCC) have been associated with increased exhaled limonene. It is currently unclear whether this increase more strongly the presence of HCC or severity liver dysfunction. METHODS: We compared breath 40 controls, 32 cirrhotic patients, 12 patients using Breath Biopsy platform. samples were analyzed by thermal desorption–gas chromatography–mass spectrometry. Limonene levels between groups correlated to bilirubin,...

Abstract Motivation: Isotope trace (IT) detection is a fundamental step for liquid or gas chromatography mass spectrometry (XC-MS) data analysis that faces multitude of technical challenges on complex samples. The Kalman filter (KF) application to IT addresses some these challenges; it discriminates closely eluting ITs in the m/z dimension, flexibly handles heteroscedastic variances and does not bin axis. Yet, behavior this KF has been fully characterized, as no cost-free open-source...

Background and AimsThe prevalence of chronic liver disease in adults exceeds 30% some countries there is significant interest developing tests treatments to help control progression reduce healthcare burden. Breath a rich sampling matrix that offers non-invasive solutions suitable for early-stage detection monitoring. Having previously investigated targeted analysis single biomarker, here we multiparametric approach breath testing would provide more robust reliable results clinical use.

Aspects of the ecology and behaviour Ocypode cursor were studied on beaches Northern Cyprus.The crabs widely distributed around north coast island, occurring 68 77 sandy investigated.At main study beach at Alagadi, occupied a band approximately 12 m wide; starting 3 horizontally from edge sea (tidal fluctuation was minimal).Most small burrows occurred near to sea, with larger predominating higher up beach.Burrow numbers varied during summer which mainly attributable variations in...

The most important step in any quantitative proteomic pipeline is feature detection (aka peak picking). However, generating quality hand-annotated data sets to validate the algorithms, especially for lower abundance peaks, nearly impossible. An alternative creating gold standard simulate it with features closely mimicking real data. We present Mspire-Simulator, a free, open-source shotgun simulator that goes beyond previous simulation attempts by LC-MS realistic m/z and intensity variance...

Abstract Summary: Countless proteomics data processing algorithms have been proposed, yet few critically evaluated due to lack of labeled (data with known identities and quantities). Although labeling techniques exist, they are limited in terms confidence accuracy. In silico simulators recently used create complex quantities. We propose Java Mass Spectrometry Simulator (JAMSS): a fast, self-contained simulator capable generating simulated MS LC-MS runs while providing meta information on the...

Extracted ion chromatograms (XIC) are the fundamental signal unit in mass spectrometry. There many algorithms for analyzing raw spectrometry data tasked with distinguishing real isotopic signals from noise. While one or more of available typically chained together end-to-end analysis, analysis each algorithm isolation provides a specific measurement strengths and weaknesses approach. Though qualitative opinions on extraction performance abound, quantitative has never been publicly...

Mass spectrometry (MS) uses mass-to-charge ratios of measured particles to decode the identities and quantities molecules in a sample. Interpretation raw MS depends upon data processing algorithms that render it human-interpretable. Quantitative workflows are complex experimental chains is crucial know performance bias each method as they impact accuracy, coverage, statistical significance result. Creation ground truth necessary for quantitatively evaluating MS1-aware difficult tedious task,...

The comparison of analyte mass spectrometry precursor (MS1) signal is central to many proteomic (and other -omic) workflows. Standard vocabularies for exist and provide good coverage most experimental applications yet are insufficient concise unambiguous description data concepts spanning the range provenance from a molecular perspective (e.g. charged peptides down fine isotopes). Without standard nomenclature, literature searches, algorithm reproducibility evaluation MS-omics processing...

Abstract Motivation: Quantification of lipids is a primary goal in lipidomics. In direct infusion/injection (or shotgun) lipidomics, accurate downstream identification and quantitation requires summarization repetitive peak measurements. Imprecise multiplies error by propagating into species intensity estimation. To our knowledge, this the first analysis infusion literature. Results: We present two novel algorithms for samples compare them with an off-machine ad hoc algorithm as well...

Mass spectrometry is an important tool used by many scientists throughout the world. Nonetheless, feedback on strengths and limitations of current software often restricted to anecdote rather than formal inquiry. Over course 100 interviews over state mass software, surprising patterns coalesced several topics: perception frontier, quality, differences between commercial nonprofit environments. Most notably, suggested a substantial schism user satisfaction with developer perceptions quality....

The number and diversity of wrappers for chemoinformatic toolkits suggests the diverse needs community. While existing chemoinformatics libraries provide a broad range utilities, many chemoinformaticians find compiled language intimidating, time-consuming, arcane, verbose. Although high-level have been implemented, more can be done to leverage intuitiveness object-orientation, paradigms languages, extensibility languages such as Ruby. We introduce Rubabel, an intuitive, object-oriented suite...

Mass spectrometry, a popular technique for elucidating the molecular contents of experimental samples, creates data sets comprised millions three-dimensional (m/z, retention time, intensity) points that correspond to types and quantities analyzed molecules. Open commercial MS formats are arranged by creating latency when accessing across multiple m/z. Existing storage retrieval methods have been developed overcome limitations time-based formats, but do not provide certain features such as...

Abstract While expandable tubular technology significantly increased traction within the oil&gas industry in last few years, materials behavior knowledge for casing has not progress sufficiently. This is due to lack of a diffused definition most appropriate procedures verify post-expansion material performance and difficulties performing investigation activity. These investigations rely on post-expanded material, which costly time-consuming obtain, especially range very large plastic...

Modern label-free quantitative mass spectrometry workflows are complex experimental chains for devising the composition of biological samples. With benchtop and in silico steps that each have a significant effect on accuracy, coverage, statistical significance study result, it is crucial to understand efficacy biases protocol decision. Although many studies been conducted wet lab protocols, postacquisition data processing methods not adequately evaluated large part due lack available ground...

Nuclear reactor fuel pellets of PuO2 and UO2 are fabricated within safety enclosures at Hanford Engineering Development Laboratory, Richland, Washington. Samples the aerosols coincidentally formed during a plutonium oxide uranium powder mixing operation centerless grinding mixed were taken from enclosures. A small seven-stage cascade impactor was used to determine aerodynamic size distribution concentration spiral-duct aerosol centrifuge, Lovelace Aerosol Particle Separator (LAPS) study...

Abstract While the introduction on market of expandable casing has undoubtedly been successful, full potentiality this technology seems not yet accomplished. Uncertainties related to reliability applications prevent exploitation tubular reduce well construction costs and improve productivity. One key limiting factor is incomplete knowledge mechanical performance after expansion materials used for casing. This partially due lack industry consensus most appropriate methods measure...

Despite the ubiquity of mass spectrometry (MS), data processing tools can be surprisingly limited. To date, there is no stand-alone, cross-platform 3-D visualizer for MS data. Available visualization toolkits require large libraries with multiple dependencies and are not well suited custom modules, such as storage systems or algorithms.We present JS-MS, a 3-D, modular JavaScript client application viewing JS-MS provides several advantages over existing viewers, dependency-free,...

Liquid chromatography mass spectrometry is a popular technique for high throughput analysis of biological samples. Identification and quantification molecular species via output requires postexperimental computational the raw instrument output. While tandem remains primary method identification quantification, species-resolved precursor data provides rich source unexploited information. Several algorithms have been proposed to resolve signals into isotopic envelopes. Many methods are...

Liquid chromatography-mass spectrometry is a popular technique for high-throughput protein, lipid, and metabolite comparative analysis. Such statistical comparison of millions data points requires the generation an inter-run correspondence. Though many techniques generating this correspondence exist, few if any, address certain well-known run-to-run LC-MS behaviors such as elution order swaps, unbounded retention time missing data, significant differences in abundance. Moreover, not all...

Shotgun differential mass spectrometry, the untargeted discovery of statistically significant differences between two or more samples, is a popular application with potential to advance biomarker detection, disease diagnostics, and other health objectives. Although many methods have been proposed, few quantitatively evaluated. The lack ground truth data for shotgun difference detection limits quantitative evaluation algorithmic advancement. While public mass-spectrometry sets single samples...