Resolution Enhancement of Metabolomic J-Res NMR Spectra Using Deep Learning.

J-Resolved (J-Res) nuclear magnetic resonance (NMR) spectroscopy is pivotal in NMR-based metabolomics, but practitioners face a choice between time-consuming high-resolution (HR) experiments or shorter low-resolution (LR) experiments which exhibit significant peak overlap. Deep learning neural networks have been successfully used in many fields to enhance quality of natural images, especially with regard to resolution, and therefore offer the prospect of improving two-dimensional (2D) NMR data. Here, we introduce the J-RESRGAN, an adapted and modified generative adversarial network (GAN) for image super-resolution (SR), which we trained specifically for metabolomic J-Res spectra to enhance peak resolution.

Efficacy and Toxicity of Robotic Stereotactic Body Radiotherapy of Lung Metastases in Patients With Oligometastatic Disease.

Background: Stereotactic body radiotherapy is a locally effective treatment for lung metastases in patients with oligometastatic disease, a modern variant of which is robotic (rSBRT). Since it is unclear which factors determine the success of rSBRT, we investigated a cohort of patients with lung metastases treated with rSBRT.

Patients And Methods: In our retrospective single-center analysis, we included patients with oligometastatic disease of different cancer types who underwent SBRT of lung metastases using an Accuray Cyberknife device between 2012 and 2019.

Intertidal habitat complexity influences the density of the non-native crab .

Habitat structural complexity can provide protection from predators, potentially affecting population density of native and non-native prey. The invasive Asian shore crab, , occurs in variable densities in the rocky intertidal zone of eastern North America and northern Europe, often in densities greater than in its native range. The present study examined the influence of habitat complexity on the density of .

Use of dose-area product to assess plan quality in robotic radiosurgery.

Purpose: In robotic stereotactic radiosurgery (SRS), optimal selection of collimators from a set of fixed cones must be determined manually by trial and error. A unique and uniformly scaled metric to characterize plan quality could help identify Pareto-efficient treatment plans.

Methods: The concept of dose-area product (DAP) was used to define a measure (DAP) of the targeting efficiency of a set of beams by relating the integral DAP of the beams to the mean dose achieved in the target volume.

Problems, principles and progress in computational annotation of NMR metabolomics data.

Background: Compound identification remains a critical bottleneck in the process of exploiting Nuclear Magnetic Resonance (NMR) metabolomics data, especially for H 1-dimensional (H 1D) data. As databases of reference compound spectra have grown, workflows have evolved to rely heavily on their search functions to facilitate this process by generating lists of potential metabolites found in complex mixture data, facilitating annotation and identification. However, approaches for validating and communicating annotations are most often guided by expert knowledge, and therefore are highly variable despite repeated efforts to align practices and define community standards.

Uncovering in vivo biochemical patterns from time-series metabolic dynamics.

System biology relies on holistic biomolecule measurements, and untangling biochemical networks requires time-series metabolomics profiling. With current metabolomic approaches, time-series measurements can be taken for hundreds of metabolic features, which decode underlying metabolic regulation. Such a metabolomic dataset is untargeted with most features unannotated and inaccessible to statistical analysis and computational modeling.

Impact of prescription isodose level and collimator selection on dose homogeneity and plan quality in robotic radiosurgery.

Purpose: In stereotactic radiosurgery (SRS), prescription isodoses and resulting dose homogeneities vary widely across different platforms and clinical entities. Our goal was to investigate the physical limitations of generating dose distributions with an intended level of homogeneity in robotic SRS.

Methods: Treatment plans for non-isocentric irradiation of 4 spherical phantom targets (volume 0.

The Human Side of COVID-19.

The COVID-19 pandemic has had, and continues to have, a broad, deep, and pervasive impact on our lives, our work, and how our justice system functions. While it is easy to contemplate the "system" as a massive behemoth that is impervious, impersonal, and impenetrable, the truth is that the "system" is made up of people. The men and women whose work is the building blocks of the justice system are individuals, each with their own narrative, experience, perspective, and role in the administration of justice.

RTExtract: time-series NMR spectra quantification based on 3D surface ridge tracking.

Motivation: Time-series nuclear magnetic resonance (NMR) has advanced our knowledge about metabolic dynamics. Before analyzing compounds through modeling or statistical methods, chemical features need to be tracked and quantified. However, because of peak overlap and peak shifting, the available protocols are time consuming at best or even impossible for some regions in NMR spectra.

Chronic arsenate exposure affects amphipod size distribution and reproduction.

Arsenate (As V) is the predominant inorganic species of arsenic in oxic aquatic environments. Chronic water quality criteria for arsenate have not been established due to the scarcity of relevant studies on its impact on aquatic biota. We examined the acute and chronic effects of arsenate on the benthic amphipod , an important test organism for ecotoxicological studies.

Correlations Between LC-MS/MS-Detected Glycomics and NMR-Detected Metabolomics in Development.

This study examined the relationship between glycans, metabolites, and development in . Samples of N2 animals were synchronized and grown to five different time points ranging from L1 to a mixed population of adults, gravid adults, and offspring. Each time point was replicated seven times.

Continuous Metabolism by NMR.

Dense time-series metabolomics data are essential for unraveling the underlying dynamic properties of metabolism. Here we extend high-resolution-magic angle spinning (HR-MAS) to enable continuous monitoring of metabolism by NMR (CIVM-NMR) and provide analysis tools for these data. First, we reproduced a result in human chronic lymphoid leukemia cells by using isotope-edited CIVM-NMR to rapidly and unambiguously demonstrate unidirectional flux in branched-chain amino acid metabolism.

Abundance of non-native crabs in intertidal habitats of New England with natural and artificial structure.

Marine habitats containing complex physical structure (e.g., crevices) can provide shelter from predation for benthic invertebrates.

The application of near-infrared spectroscopy for the quality control analysis of rocket propellant fuel pre-mixes.

The viability of near-infrared (NIR) spectroscopy as a technique for the quality control analysis of ingredient concentrations in a rocket propellant fuel liquid pre-mix was investigated. The pre-mix analyzed consisted of a polybutadiene pre-polymer, a plasticizer and two antioxidants. It was determined that NIR spectroscopy offered a fast and convenient method of verifying the percentage level of all four ingredients while requiring no sample preparation.