Effects Of Sampling Parameters Research Articles

Abstract A051: Identifying patterns of cell-free DNA associated with elevated risk of diffuse large B-cell lymphoma in adult dogs

Abstract Background: Nonrandom patterns of cell-free DNA (cfDNA) are closely associated with malignancy. We hypothesize that they are also found in the systemic microenvironment that gives rise to cancer, and that such signatures can inform a risk stratification test. To achieve this, we have initiated the Lymphoma Risk Assessment (LyRA) study, using machine learning on a training set of dogs with known health status and a test set of otherwise healthy adult pet dogs to identify cfDNA signatures that are associated with elevated risk of developing diffuse large B- cell lymphoma (DLBCL). We will validate the predictive accuracy of these signatures, including the persistence of the risk environment and the interval between risk detection and development of clinical disease. Since cfDNA is the primary input of the LyRA test, we first performed a pilot study to assess how sample characteristics affect cfDNA quality and subsequent low-pass whole genome sequencing (WGS) data. Methods: Blood samples were collected from pet dogs with the owner’s informed consent. Paired samples were collected into potassium (K3)EDTA tubes and additive-free red top tubes (n = 5 dogs) or K3EDTA tubes and Cell-free DNA BCT® Streck Tubes (n = 6 dogs). Additional serum samples (n=3) were generously provided by the Morris Animal Foundation Golden Retriever Lifetime Study. cfDNA was isolated using the QIAamp® Circulating Nucleic Acid kit. Total cfDNA concentration was measured by PicoGreen™ and fragment distribution by Agilent High Sensitivity D500 ScreenTape® Assay, with comparisons made by starting material (plasma vs. serum) and collection tubes. Results: Serum had both higher total concentrations of cfDNA (PicoGreen™) and calibrated concentrations of long fragment cfDNA (515-658 bp Agilent traces) compared to plasma. In addition, total cfDNA concentrations increased with malignancy, following the pattern: no cancer < cancer < hematological cancer. Median fragment lengths of Agilent peaks also increased with malignancy for short (125-181 bp) and medium (340-425 bp) fragments, in both serum and plasma, but decreased for long fragments. In these pilot data the trends seen were consistent with our hypothesis and with prior studies, although due to sample size, no statistical testing was performed. Conclusions: The pilot study demonstrated that the effects of sample parameters on cfDNA quality are consistent with existing literature, validating our methods and supporting the rationale for the LyRA study. These features may prove valuable when integrated with genomic data to identify high-risk microenvironments. Recent research has shown that a majority of cfDNA in tumor patients originates from non-malignant cells and current methods often overlook potentially important patterns in this so-called 'discard cfDNA.' By focusing on these overlooked patterns, with an emphasis on risk stratification, the LyRA test could shift clinical management to a prevention-focused approach, serving as a model of testing and interception for DLBCL and other cancers in dogs, and potentially in humans. Citation Format: Lauren E Burt, Amy E Treeful, Mitzi Lewellen, Kimberly Demos-Davies, Andrea Chehadeh, Sara Pracht, Ashley J Schulte, Caitlin Feiock, Julia Medland, Davis Seelig, Kelly M Makielski, Ali Khammanivong, Antonella Borgatti, Michael S Henson, Michael Linden, Daniel Vallera, Gary R Cutter, Aaron L Sarver, Jaime F Modiano. Identifying patterns of cell-free DNA associated with elevated risk of diffuse large B-cell lymphoma in adult dogs [abstract]. In: Proceedings of the AACR Special Conference: Liquid Biopsy: From Discovery to Clinical Implementation; 2024 Nov 13-16; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(21_Suppl):Abstract nr A051.

UIO-66-NH2 Packed Needle Trap for Accurate and Reliable Sampling and Analysis of the Halogenated Volatile Organic Compounds in Air

ABSTRACT This paper introduces a novel inside needle adsorption trap device based on UiO-66-NH2 adsorbent for the sampling and analysis of halogenated volatile organic compounds (HVOCs), including chloroform, carbon tetrachloride, and perchloroethylene in air. In this study, the UiO-66-NH2 adsorbent was first synthesized and then packed into spinal needles (22 Gauge). This study was conducted both in the laboratory and in the field. Scanning Electron Microscope (SEM), Fourier Transform Infrared Spectroscopy (FT-IR) and X-Ray Diffraction (XRD) were used to investigate the sorbent characteristics. In this study, Response Surface Methodology (RSM) and Central Composite Design (CCD) were utilized to optimize the effects of sampling parameters and desorption parameters on needle trap device (NTD) performance. In this regard, a constant concentration of the compounds of interest was injected into a standard chamber, and then the packed NTD was used for the sampling of HVOCs under a given condition. According to the results, the maximum peak area response was obtained at 280 ˚C of desorption temperature and 4 min of desorption time. The results showed that increased sampling humidity and temperature interfered with the NTD performance and decreased the peak area responses of the analytes. The proposed NTD had a high sensitivity for the sampling and analysis of the desired compounds. Limit of Detection (LOD) and the Limit of Quantitation (LOQ) of the NTD for the analytes were in the range 0.01-0.03 and 0.02-0.05 ng.mL-1, respectively. Moreover, the repeatability of the proposed NTD was obtained to be in the range of 2.3-9.1%. Therefore, the NTD packed with UiO-66-NH2 adsorbent can be used as a suitable and robust method for the active sampling and analysis of occupational/environmental pollutants in the air.

Dynamics of magnetic nanoparticle suspensions

We study the dynamical response of suspensions of single-domain magnetic nanoparticles. The effect of sample parameters on Néel and Brownian relaxation times which characterize the response is studied. Their effect on the ac susceptibility is also investigated. As the relaxation times are strongly size dependent we study the effect of polydispersity on the response functions next. A procedure to extract particle-size distribution in polydisperse samples from Cole–Cole plots is provided. Further, the presence of attractive and repulsive interactions amongst MNP yields a distribution of clusters of varying sizes. We propose a model incorporating the phenomena of aggregation and fragmentation to understand the formation of clusters and their distributions. Finally, we compare our numerical results with the experimental data. These comparisons are satisfactory.

Effect of Contact Time and Contact Pressure on the Transfer of Oil to Surface Sample Media

Abstract Wipe sampling is common practice for the assessment of surface contamination; however, several different wipe sampling methods are currently being used. When the results of one study are compared with those of other studies, it is important to understand the effect of sampling parameters on the collection of contaminants from surfaces. A review of the literature addressing the subject of wipe sampling revealed that while several authors were concerned with parameters such as the contact time and contact pressure, no information was provided on the effect of these parameters on the collection of wipe samples. This study examines the effect of contact time, contact pressure, and surface concentration on the transfer (collection) of oil from contaminated surfaces to wipe sample media. An exposure jig was designed and built that allowed contact time, contact pressure, and surface concentration to be varied individually. This jig was used to test the effect of these parameters on the mass of oil trans...