Pulsecal: A valuable tool, but cautio consilium for use in deuterated organic solvents

Nanoelectrospray ionization (nano-ESI) is a highly efficient and a widely used technique for the ionization of minute amounts of analyte. Offline nano-ESI sources are convenient for the direct infusion of complex mixtures that suffer from high matrix content and are crucial for the native mass spectrometric analysis of proteins. For Bruker instruments, no such source is readily available. Here we close this gap and present a 3D-printable nano-ESI source for Bruker instruments, which can be assembled by anyone with access to 3D printers. The source can be fitted to any Bruker mass spectrometer with an ionBooster ESI source and only requires minor, reversible changes to the original Bruker hardware. The general utility was demonstrated by recording high-resolution MS spectra of small molecules, intact proteins, as well as complex biological samples in negative and positive ion mode on two different Bruker instruments.

We assessed the analytical performance of metagenomic workflows using NIST Reference Material 8376 DNA from bacterial pathogens spiked into two simulated clinical samples: cerebral spinal fluid (CSF) and stool. Sequencing and taxonomic classification were used to generate signals for each sample and taxa of interest, and to estimate the limit of detection (LOD), the response function, and linear dynamic range. We found that the LODs for taxa spiked into CSF ranged from approximately (0.1 to 0.3) copy/μL, with a linearity of 0.96 to 0.99. For stool, the LODs ranged from (10 to 221) copy/μL, with a linearity of 0.99 to 1.01. Further, discriminating differentE. colistrains proved to be workflow-dependent, as only one classifier:database combination of the three tested showed the ability to differentiate the two pathogenic and commensal strains. Surprisingly, when we compared the response functions of the same taxa in the two different sample types, we found those functions to be the same, despite large differences in LODs. This suggests that the “agnostic diagnostic” theory for metagenomics may apply to different target organismsanddifferent sample types. Using RMs, we were able to generate quantitative analytical performance metrics for each workflow and sample set, enabling relatively rapid workflow screening before employing clinical samples. This makes these RMs a useful tool that will generate data needed to support translation of metagenomics into regulated use.ImportanceAssessing the analytical performance of metagenomic workflows, especially when developing clinical diagnostics, is foundational for ensuring that the measurements underlying a diagnosis are supported by rigorous characterization. To facilitate the translation of metagenomics into clinical practice, workflows must be tested using control samples designed to probe the analytical limitations (e.g. limit of detection). Spike-ins allow developers to generate fit-for-purpose control samples for initial workflow assessments and inform decisions about further development. However, clinical sample types include a wide range of compositions and concentrations, each presenting different detection challenges. In this work, we demonstrate how spike-ins elucidate workflow performance in two highly dissimilar sample types (stool and CSF); and we provide evidence that detection of individual organisms is unaffected by background sample composition, making detection sample agnostic within a workflow. These demonstrations and performance insights will facilitate translation of the technology to the clinic.

Saliva as a gold-standard sample for SARS-CoV-2 detection

Current optimizations in the fabrication processes of multilayer dielectric (MLD) high-reflectivity (HR) coatings struggle to meet the demand for picosecond (ps) laser damage resistance in high-energy petawatt laser systems. This study investigates laser conditioning (LC) effects of 250 ps, 500 ps, 800 ps, and 10 nanosecond (ns) laser pulses on the ps laser-induced damage resistance of electron beam (e-beam) HfO2/SiO2 HR coatings. Results demonstrate a 12% enhancement in the laser-induced damage threshold (LIDT) under ∼10 ps laser irradiation for 500 ps conditioned samples compared to unconditioned ones, while negligible LIDT variations are observed for other pulse widths. The defect density and damage types in unconditioned and conditioned samples exhibit no statistical alteration. This indicates that LC does not eliminate nanoscale defects but only increases their LIDTs for 500 ps conditioned samples. To reveal the improvement mechanism of 500 ps LC on the ps laser-induced damage resistance, a simulated model of the interaction between sub-ns laser pulses and localized defect states is proposed, combining ionization rate equations with the two-temperature model (TTM). For 500 ps LC, although the initial electron number density of the defect energy level is increased, the defect energy level gap is also widened due to the appropriate lattice temperature. The effect of this widening gap surpasses that of the aforementioned increased initial electron density, making electron ionization more difficult under ∼10 ps laser irradiation. This work provides new strategies and approaches for enhancing the ps laser-induced damage resistance of MLD HR coatings.

Thin-layer chromatography (TLC) allows the swift analysis of larger sample sets in almost any laboratory. The obtained chromatograms are patterns of coloured zones that are conveniently evaluated and classified by visual inspection. This manual approach reaches its limit when several dozens or a few hundred samples need to be evaluated. Methods to classify TLCs automatically and objectively have been explored but without a definitive conclusion; established methods, such as principal component analysis, suffer from the variability of the data, while contemporary omics methods were constructed for the analysis of large numbers of highly resolved analyses.Self-organizing maps (SOMs) are an algorithm for unsupervised learning that reduces higher dimensional datasets to a two-dimensional map, locating similar samples close to each other. It tolerates small variations between samples of the same type.We investigated the capability of SOMs for the evaluation of TLCs with two sample sets. With the first one (495 analyses of essential oils), it was confirmed that SOMs arrange the same type of sample in a common region. The obtained multi-class maps were used to classify a test set and to explore the causes for the few misclassifications (<3%). With the second test set (50 extracts of experimental wheats), the effects of a greater variability within substance classes was explored. With SOMs, it was possible to single out the exceptional samples that warranted a more detailed investigation.In addition, the SOM quality control index method was tested. It proved to be considerably stricter than the classification with a SOM of all samples. When this method was unable to classify a sample correctly, it would flag the sample for inspection, as it gave either multiple assignments or none at all.The combination of SOMs and TLC — two accessible analytical tools — can be most useful for the unsupervised classification of samples by TLC, and to identify samples that stand out from a set and are therefore worth the investment into additional analyses with more complex or expensive methods.

Non-invasive pre-implantation genetic testing's reliability for aneuploidy using Cell-free DNA in embryo culture media

Carbon blacks are the most widely used reinforcing fillers. The raw material of carbon black manufacture depends on petroleum industry to a great extent. Reclamation of used tires is to be enormously significant as oil will be used up in the near future. Pyrolytic carbon black (PCB) is one of the most important products from the pyrolysis of scrap tires. One of the most essential applications for modified PCB is to reinforce the rubber matrix to obtain extra values. High inorganic ash content and a large amount of carbonaceous deposits on the surface of PCB confirmed by atomic force microscopy (AFM)are the two main barriers for PCB further application. Adsorption layer with an adequately thick could not be formed on the surface of PCB because of the lack of effective active sites. Techniques for PCB modification have been developed. The rubber vulcanization and reinforcement properties of pyrolytic and modified carbon black were investigated and compared with those of commercial carbon black. The crosslink structure, relaxation and self-diffusion properties were investigated by solid-state high resolution nuclear magnetic resonance respectively. Demineralization and modification with NDZ- 105 titan ate coupling agent not only intensify the interactions between carbon black and the neighboring polyisoprene chains, but also increase the chemical cross-link density of the vulcanized rubber with TWPC. TWPC could be used to replace the commercial semi-reinforcing carbon black.

Identification of Lignin and Polysaccharide Modifications in Populus Wood by Chemometric Analysis of 2D NMR Spectra from Dissolved Cell Walls

Rapid pulse length determination in high-resolution NMR

Background: Understanding heterogeneity within individual breast tumors is key to the ability to predict therapeutic outcome. Molecular heterogeneity is commonly evaluated based on genomic features, including mRNA abundance, gene copy number events, and somatic mutations. The expression profile and activation state of key proteins is widely recognized as another key element in defining tumor heterogeneity. We have taken advantage of NanoString 3D Biology™ technology (for research use only) and curated nCounter Vantage 3DTM Solid Tumor Assay to interrogate a survey panel of HER2-positive breast tumors with the ultimate goal of determining key relationships between multiple genomic and proteomic profiles in individual tumors. Methods: We analyzed samples from 24 HER2+ breast cancer patients using NanoString technology to quantify the expression profile for over 25 total and phospho signaling proteins, including PI3K/MAPK/EGFR/HER2, 770 mRNA corresponding to 13 canonical cancer pathways, and 104 somatic mutations and small INDELS that are commonly associated with cancer, including 8 known PIK3CA mutations. These analyses were carried out in a matched fresh frozen and FFPE samples on the nCounter paltform. Data were analyzed by nSolver to identify genotype specific expression profiles across the 24 samples. Results: In our proof-of-concept data set, we successfully demonstrate that NanoString’s 3D biology Technology shows concordance across both FFPE and fresh frozen sample types for DNA, RNA, and protein. NanoString analysis also showed high concordance to gold-standard techniques used to assess genotype and RNA expression profiles. The combination of digital DNA, RNA, and protein data from our HER2+ breast cancer samples yielded potentially actionable data based on mapping of mutational status as the driver of key differences in protein expression and mRNA abundance of the signaling targets profiled. This work sheds new light on HER2+ breast cancer biology and the interplay between genomic and proteomic profiles while setting the stage for future studies that further probe the differences observed in this sample set. Conclusions: Simultaneous analysis of mutational status (SNV) and expression at the level of both mRNA and protein promises to enable a more detailed view of the relationship between genotype and the biological and clinical behavior of key tumor types. The NanoString Vantage 3DTM Solid Tumor platform provides a rapid, reliable, and economic means of assessing these analytes simultaneously. The application of these analytes to models that make clinically actionable predictions will require additional analyses of large sample cohorts, but such analysis is quite feasible using a variety of sample types. Acknowledgements: Supported in part by grants from the Breast Cancer Research Foundation and the 26.2 with Donna Foundation. Citation Format: Sarayna Chumsri, Daniel J. Serie, Brian M. Necela, Jennifer M. Kachergus, Bianca C. Axenfeld, Gokhan Demirkan, Gavin Meredith, P. Martin Ross, Anisha Kharkia, Erin Piazza, Afshin Mashadi-Hossein, Sarah Warren, Sarah A. McLaughlin, Joseph Beechem, Gary Geiss, E. Aubrey Thompson. Simultaneous analysis of the mutational landscape and RNA and protein expression profile of HER2-positive breast cancer using 3D BiologyTM [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3377. doi:10.1158/1538-7445.AM2017-3377

Comparison of Headspace GC and Electronic Sensor Techniques for Classification of Processed Orange Juices

Summary.A series of correlation studies has been carried out between the seed characteristics and early growth data of a number of Record oats samples; many coefficients of correlation obtained gave values of no biological significance. The influence of “outlying” readings had to be carefully considered as the number of readings was limited. For this purpose dot charts were employed as well as mathematical coefficients.The results can be summarised as follows: Generally the total germination figures in a sand test were correlated with field establishment, but within the narrow germination range 85–100 per cent. no correlation with establishment was found. The amount of available food in the seed as measured by the average dry weight of the caryopses influenced the size and weight of the seedlings produced. The moisture content of the grain was negatively correlated with the rate of germination, indicating that samples stored with a high water content did not germinate well. The percentage husk bore no relation to germination. Ten weeks after sowing the mass of the plants obtained from a given sowing depended primarily upon the number of plants established. Although tillering was well advanced plants possessing additional space did not compensate for low establishment figures at this stage by increased growth. When the grain was heated for 15 minutes at 75°C. those samples containing a high moisture content suffered more than well dried samples. Indications were also obtained that the following type of sample was particularly susceptible to such injury—artificial heating—(a) a rapidly germinating sample,(b) a thin‐husked sample,(c) a sample with heavy grain.

P 230. Third generation controllable pulse parameter transcranial magnetic stimulation device

Accurate accelerator mass spectrometry (AMS) measurements rely on standards with well-known isotopic ratios. For radiocarbon measurements, a number of standards with different properties are commercially available, of which the IAEA-C6 sucrose standard with a 14C value of 150.61 pMC is the most active. When analyzing biological samples resulting from studies using 14C-labeled substances, the activity content can be up to 100 times this value. Thus, there is a need for a standard material with higher activity content than IAEA-C6 for making accurate AMS measurements on this type of sample. This paper describes the attempts of producing a standard with an activity content of about 10 times modern carbon. The material chosen has to be chemically inert, preferably non-toxic, commercially available in 14C-labeled form, and the activity must be homogeneously distributed within the material. Two different standard materials were considered: urea and sucrose. Sucrose was chosen for the new standard, since it is non-toxic, inexpensive, and organic and on combustion, forms only carbon dioxide (CO2) and water (H2O). In this paper, we discuss our experience in the production and homogeneity analysis of this material, from the crystallization of the sucrose solution to the graphitization of the samples. When using an online combustion method and a septa-sealed vial reduction method, the AMS measurements indicated that the activity was not homogeneously distributed throughout the material. Contrary to this, measurements of the sucrose solution prior to recrystallization indicated that the activity was more homogeneously distributed before than after the recrystallization. In order to determine whether the inhomogeneity depended on the graphitization method (i.e. the combustion or the reduction method) or on the material itself, 3 different graphitization methods and 2 different methods of recrystallization were tested.

La mayoría de las industrias vitivinícolas enfrentan el desafío de encontrar soluciones que les permitan avanzar en la gestión de la economía circular durante el proceso de producción del vino. Las bodegas buscan reducir, reutilizar o reciclar los desechos producidos durante el proceso de elaboración. La investigación llevada a cabo en este estudio se centra en el desarrollo de una bebida fermentada tipo kombucha, por parte de una colonia simbiótica de bacterias y levaduras (SCOBY, del inglés Symbiotic Culture of Bacteria and Yeast), a partir de subproductos vitivinícolas, con el propósito de desarrollar una bebida saludable y sostenible. Para llevar a cabo esta tarea, se realizaron mediciones fisicoquímicas, incluyendo pH, grados Brix, acidez, concentración de azúcares, etanol y ácido acético. El diseño experimental contempló la evaluación de los siguientes tipos de muestras: una muestra control (sin matriz vegetal), una bebida tipo kombucha de bagazo de uva, y bebidas comerciales de kombucha disponibles en el mercado. Durante el análisis estadístico de los resultados, se encontraron similitudes significativas entre nuestra bebida experimental y las bebidas comerciales, lo que demuestra la calidad fisicoquímica de la bebida fermentada desarrollada en el marco de esta investigación. Es importante destacar que, en el análisis de las kombuchas comerciales, se identificó un contenido de etanol superior al detectado en la bebida de bagazo desarrollada en este estudio. Esto sugiere que las bebidas de bagazo podrían ser más beneficiosas en comparación con las bebidas comerciales debido a su menor contenido de etanol y perfil nutricional optimizado. Los resultados obtenidos en el presente trabajo indican que la bebida experimental tipo kombucha desarrollada a partir de bagazo de uva cumple con los estándares de calidad fisicoquímica. Esta investigación refuerza la viabilidad de incorporar subproductos vitivinícolas en la elaboración de bebidas, ofreciendo una alternativa sostenible y saludable.