Sampling precision

Precision oncology involves analysis of individual cancer samples to understand the genes and pathways involved in the development and progression of a cancer. To improve patient care, knowledge of diagnostic, prognostic, predisposing, and drug response markers is essential.

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Accurate identification of real somatic variants is a primary part of cancer genome studies and precision oncology. However, artifacts introduced in various steps of sequencing obfuscate confidence in variant calling. Current computational approaches to variant filtering involve intensive interrogation of Binary Alignment Map (BAM) files and require massive computing power, data storage, and manual labor.

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Patient stratification based on molecular subtypes is an important strategy for cancer precision medicine. Deriving clinically informative cancer molecular subtypes from transcriptomic data generated on whole tumor tissue samples is a non-trivial task, especially given the various non-cancer cellular elements intertwined with cancer cells in the tumor microenvironment.

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Populations of closely related microbial strains can be simultaneously present in bacterial communities such as the human gut microbiome. We recently developed a de novo genome assembly approach that uses read cloud sequencing to provide more complete microbial genome drafts, enabling precise differentiation and tracking of strain-level dynamics across metagenomic samples.

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Ebook "Development of an effusive molecular beam apparatus" presents the development of an effusive molecular beam apparatus, which allows the dosing of gases, liquids, and solids in ultra-high vacuum. The apparatus is designed to adsorb precise and reproducible doses to a defined area on metal oxide samples, which is required in Temperature Programmed Desorption and other surface chemistry experiments. The design and the construction of the apparatus is described.

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Many mutations in cancer are of unknown functional significance. Standard methods use statistically significant recurrence of mutations in tumor samples as an indicator of functional impact. We extend such analyses into the long tail of rare mutations by considering recurrence of mutations in clusters of spatially close residues in protein structures.

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The benefit of precision medicine based on relatively limited gene sets and often-archived samples remains unproven. PERMED-01 (NCT02342158) was a prospective monocentric clinical trial assessing, in adults with advanced solid cancer, the feasibility and impact of extensive molecular profiling applied to newly biopsied tumor sample and based on targeted NGS (t-NGS) of the largest gene panel to date and whole-genome arraycomparative genomic hybridization (aCGH) with assessment of single-gene alterations and clinically relevant genomic scores.

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Epigenetic clocks can track both chronological age (cAge) and biological age (bAge). The latter is typically defined by physiological biomarkers and risk of adverse health outcomes, including all-cause mortality. As cohort sample sizes increase, estimates of cAge and bAge become more precise. Here, we aim to develop accurate epigenetic predictors of cAge and bAge, whilst improving our understanding of their epigenomic architecture.

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Part 1 book "A guide to sample size for animal-based studies" includes content: The sample size problem in animal‐based research, sample size basics, ten strategies to increase information (and reduce sample size), why pilot studies, operational pilot studies - Can it work, empirical and translational pilots, feasibility calculations - arithmetic, feasibility - counting subjects, descriptions and summaries, confidence intervals and precision.

138p muasambanhan01 11-12-2023 5 3   Download

Lecture Business research methods (12/e) - Appendix 14A: Determining sample size. This chapter presents the following content: Random samples, increasing precision, confidence levels & the normal curve, standard errors, central limit theorem, estimates of dining visits, calculating sample size for questions involving means,...

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Lecture Business research methods (12/e) - Chapter 14: Sampling. After studying this chapter you will be able to understand: The two premises on which sampling theory is based, the accuracy and precision for measuring sample validity, the five questions that must be answered to develop a sampling plan,...

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The representation of cotton color is a key element in deciding the cotton grade. The color of cotton fibre is measured with instruments as well as visual assessment. But, these two methods always represent disagreement in the measurements. The main reason for disagreement is the trash particles on the cotton surface. The threshold segregation technique is used for the segmentation of trash and cotton fibres from the image of cotton sample. It is used in this research for the trash segmentation and precise color measurement.

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Weed identification helps ensure crop yield and realize precision agriculture. Although the deep learning-based methods have achieved high performance, their needed large-scale annotated data is difficult to obtain, and the massive parameters lead to difficulties in model deployment in embedded applications. To develop efficient crop weeds classification system, we propose a dissimilarity-based method to select few but representative samples and consider data diversity.

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The beta-particle emission from a sediment or rock sample can be measured very precisely using beta-counting instruments. The observed count rate is largely a function of the radionuclide concentration in the sample, so has the potential to provide a precise estimate of the natural radiation dose rate.

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Electronic Health Record (EHR) data are increasingly being used to monitor population health on account of their timeliness, granularity, and large sample sizes. While EHR data are often sufficient to estimate disease prevalence and trends for large geographic areas, the same accuracy and precision may not carry over for smaller areas that are sparsely represented by non-random samples.

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This study, conducted with a sample of Vietnam non-financial listed firms during the period from 2008 to 2015, investigates the impact of accruals quality in the access to bank debt. The result illustrate a positive association between accruals quality and bank debt, even when controlling for other determinants of bank debt and for possible endogeneity between bank debt and accruals quality, which suggests that higher precision of earnings reduces information asymmetries with banks and favors the access of firms to bank loans.

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A fast and easy method was validated for simultaneous determination of ciprofloxacin hydrochloride monohydrate (CP), levofloxacin hemihydrate (LV), and N-acetylcysteine (NAC) in samples. The analysis was performed on a C18 column (250 × 4.6mm, 5µm) (Inertsil ODS-3V) using an isocratic elution method with a mobile phase composed of 25mM KH2PO4 (pH 3.0) and methanol (72:28, v/v) at a flow rate of 1mL/min. UV detection was performed at 214nm for NAC and 293nm for CP and LV.

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In this study, silver nanoclusters as prooxidant biosensor were eco‒friendly synthesized using chicken egg white protein without any chemical reducing agents for measuring copper(II)-induced prooxidant activities of catechin, epicatechin, epigallocatechin gallate, resveratrol, gallic acid, chlorogenic acid, and rutin. The prooxidant activities were evaluated via measuring the absorption at 450 nm wavelength of the Cu(I)‒neocuproine chelate formed by extraction of protein-bound Cu(I) with neocuproine reagent.

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The research aims to identify factors influencing retail investors’ trading behavior or contrarian style in the Vietnam stock market. To be precise, the study is conducted by using a structured questionnaire from a sample of 239 prospective retail equity investors in Vietnam.

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In recent years several different fields, such as ecology, medicine and microbiology, have experienced an unprecedented development due to the possibility of direct sequencing of microbioimic samples. Among problems that researchers in the field have to deal with, taxonomic classification of metagenomic reads is one of the most challenging. State of the art methods classify single reads with almost 100% precision. However, very often, the performance in terms of recall falls at about 50%.

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