In some clinical trials, treatment allocation on a patient level is not feasible, and whole groups or clusters of patients are allocated to the same treatment. If, for example, a clinical trial is investigating the efficacy of various patient coaching methods and randomization is done on a patient level, then patients who are receiving different methods may come into contact with each other and influence each other. This would create contamination of the treatment effects. Such bias might be prevented by randomization on the coaches level. The patients of a coach constitute a cluster and all the subjects in that cluster receive the same treatment. Disadvantages of this approach may be reduced statistical efficiency and recruitment bias, as the treatment that a subject will receive is known in advance. Pseudo cluster randomization avoids this, because in pseudo cluster randomization, not everybody in a certain cluster receives the same treatment, just the majority. There are two groups of clusters: in one group the majority of subjects receive treatment A, while a limited number receive treatment B. In the other group of clusters the proportions are reversed. The statistical properties of this method are described. When contamination is present, the method appears to be more efficient than randomization on a patient level or on a cluster level.
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http://dx.doi.org/10.1002/sim.2200 | DOI Listing |
Copy number variants (CNVs) are prevalent in both diploid and haploid genomes, with the latter containing a single copy of each gene. Studying CNVs in genomes from single or few cells is significantly advancing our knowledge in human disorders and disease susceptibility. Low-input including low-cell and single-cell sequencing data for haploid and diploid organisms generally displays shallow and highly non-uniform read counts resulting from the whole genome amplification steps that introduce amplification biases.
View Article and Find Full Text PDFAdv Mater
January 2025
Department of Chemistry, University of California, Berkeley, CA, 94720, USA.
Nanoconfinements are utilized to program how polymers entangle and disentangle as chain clusters to engineer pseudo bonds with tunable strength, multivalency, and directionality. When amorphous polymers are grafted to nanoparticles that are one magnitude larger in size than individual polymers, programming grafted chain conformations can "synthesize" high-performance nanocomposites with moduli of ≈25GPa and a circular lifecycle without forming and/or breaking chemical bonds. These nanocomposites dissipate external stresses by disentangling and stretching grafted polymers up to ≈98% of their contour length, analogous to that of folded proteins; use both polymers and nanoparticles for load bearing; and exhibit a non-linear dependence on composition throughout the microscopic, nanoscopic, and single-particle levels.
View Article and Find Full Text PDFFront Immunol
January 2025
Department of Pathology, Honghui Hospital, Xi'an Jiaotong University College of Medicine, Xi'an, Shaanxi, China.
Introduction: Osteosarcoma (OS) is a malignancy of the bone that mainly afflicts younger individuals. Despite existing treatment approaches, patients with metastatic or recurrent disease generally face poor prognoses. A greater understanding of the tumor microenvironment (TME) is critical for enhancing outcomes in OS patients.
View Article and Find Full Text PDFBMC Genomics
December 2024
Department of Biological Sciences, University of Bergen, Bergen, N-5020, Norway.
Background: Fervidobacterium is a genus of thermophilic anaerobic Gram-negative rod-shaped bacteria belonging to the phylum Thermotogota. They can grow through fermentation on a wide range of sugars and protein-rich substrates. Some can also break down feather keratin, which has significant biotechnological potential.
View Article and Find Full Text PDFbioRxiv
December 2024
Bioinformatics and Cellular Genomics, St Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia.
Single-cell Assay for Transposase Accessible Chromatin with sequencing (scATAC-seq) has become a widely used method for investigating chromatin accessibility at single-cell resolution. However, the resulting data is highly sparse with most data entries being zeros. As such, currently available computational methods for scATAC-seq feature a range of transformation procedures to extract meaningful information from the sparse data.
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