25 papers · ranked by Valyu relevance
Wim Van den Noortgate, Patrick Onghena
The use of multilevel models to combine and compare the results of multiple single-case experimental design (SCED) studies has been proposed about two decades ago. Since then, the number of multilevel meta-analyses of SCED studies steadily increased, together with the complexity of multilevel models used. At the same…
Allison Meisner, Prosenjit Kundu, Nilanjan Chatterjee
Investigations of gene (G)-environment (E) interactions have led to limited findings to date, possibly due to weak effects of individual genetic variants. Polygenic risk scores (PRS), which capture the genetic susceptibility associated with a set of variants, can be a powerful tool for detecting global patterns of…
Davis R. L. Watkins, Dan Myers, Hannah E. Xavier, Michael A. Marciano
'Michael A. Marciano'] Forensic science has yet to take full advantage of single cell analysis. Its greatest benefit is the ability to alleviate the challenges associated with DNA mixture analysis, which remains a significant hurdle in forensic science. Many of the factors that cause complexity in mixture…
Stefan Konigorski, Christopher H. Schmid
1 Hasso Plattner Insitute for Digital Engineering, Potsdam, Germany 2 University of Potsdam, Digital Engineering Faculty, Potsdam, Germany 3 Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, USA 4 Department of Biostatistics, School of Public Health…
František Bartoš, Suzanne Hoogeveen, Alexandra Sarafoglou, Samuel Pawel
Empirical claims often rely on one population, design, and analysis. Many-analysts, multiverse, and robustness studies expose how results can vary across plausible analytic choices. Synthesizing these results, however, is nontrivial as all results are computed from the same dataset. We introduce single-dataset…
Ralph Foorthuis
Anomalies are occurrences in a dataset that are in some way unusual and do not fit the general patterns. The concept of the anomaly is typically ill-defined and perceived as vague and domain-dependent. Moreover, despite some 250 years of publications on the topic, no comprehensive and concrete overviews of the…
Lei Feng, Cheng Xu, Xianhai Zeng, Huaicai Zhang + 5 more
'Wanshui Li' 'Zheng Tu' 'Caixia Li' 'Lan Hu'] Aim To obtain individual Y-short tandem repeat (STR) profiles in a multi-suspect sexual assault case. Methods We used laser cut microdissection to capture the single sperm cell in the multi-contributor semen sample, combined with the low volume polymerase chain reaction…
Kaitlin Huffman, Jack Ballantyne, Fulvio Cruciani
Probabilistic genotyping (PG) and its associated software has greatly aided in forensic DNA mixture analysis, with it primarily being applied to mixed DNA profiles obtained from bulk cellular extracts. However, these software applications do not always result in probative information about the identity of all donors to…
Authors not listed
The analysis of molecular dynamics (MD) simulations is a critical but fragmented process, often requiring researchers to chain together multiple software tools and write bespoke scripts for routine structural and dynamic analyses. This workflow complexity creates a significant barrier to efficiency, standardization…
Susan M. Grimes, Heon Seok Kim, Sharmili Roy, Anuja Sathe + 7 more
In this proof-of-concept study, we developed a single cell method that identifies somatic alterations found in coding regions of mRNAs and integrates these mutation genotypes with their matching cell transcriptomes. We used nanopore adaptive sampling on single cell cDNA libraries, generated long read sequences from…
Andrew Bennett, Bear Braumoeller
This paper analyzes the working or default assumptions researchers in the formal, statistical, and case study traditions typically hold regarding the sources of unexplained variance, the meaning of outliers, parameter values, human motivation, functional forms, time, and external validity. We argue that these working…
Nicola Luchi, Pamela Pinzani, Francesca Salvianti, Irene Mancini + 1 more
Single-cell technology is increasingly used to analyze the basis of molecular regulation and provide insights into different aspects of human diseases. Such technology is a breakthrough approach to study blood cancers by characterizing molecular information on a genome-wide scale at the single-cell level. These methods…
Authors not listed
The Single-probe is a multifunctional device that can be coupled to mass spectrometry (MS) for molecular analysis of microscale samples, such as single cells, tissue slices, and multicellular spheroids, under ambient conditions. In Single-probe single cell MS (SCMS) studies, this technique leverages direct sampling and…
H. Robert Frost
Single cell RNA sequencing (scRNA-seq) is a powerful tool for analyzing complex tissues with recent advances enabling the transcriptomic profiling of thousands to tens-of-thousands of individual cells. Although scRNA-seq provides unprecedented insights into the biology of heterogeneous cell populations, analyzing such…
Suzette N. Palmer, Andrew Y. Koh, Xiaowei Zhan
Single-cell proteomics provide unprecedented resolution to examine biological processes. Customized data analysis and facile data visualization are crucial for scientific discovery. Further, userfriendly data analysis and visualization software that is easily accessible for the general scientific community is…
Marta Diepenbroek, Birgit Bayer, Katja Anslinger, Yutaka Suzuki
Single-cell sequencing is a fast developing and very promising field; however, it is not commonly used in forensics. The main motivation behind introducing this technology into forensics is to improve mixture deconvolution, especially when a trace consists of the same cell type. Successful studies demonstrate the…
Ahmed Warshanna, Benjamin C. Orsburn
Single cell proteomics (SCP) requires the analysis of dozens to thousands of single human cells to draw biological conclusions. However, assessing of the abundance of single proteins in output data presents a considerable challenge, and no simple universal solutions currently exist. To address this, we developed SCP…
Juerg Straubhaar, Alexandria D’Souza, Zachary Niziolek, Bogdan Budnik
Single-cell analysis has clearly established itself in biology and biomedical fields as an invaluable tool that allows one to comprehensively understand the relationship between cells, including their types, states, transitions, trajectories, and spatial position. Scientific methods such as fluorescence labeling…
Helland, Eric, Yun, Minjae
Case management by judges is increasingly determining the outcome of litigation, particularly in the multidistrict litigation (MDL) process. One concern is that the MDL process pressures defendants to settle, regardless of the merits, and provides insufficient information on the value of individual cases within the…
Joao M Alves, Laura Tomás, David Posada
Single-cell RNA sequencing (scRNA-seq) has transformed our understanding of phenotypic heterogeneity. Although the predominant focus of scRNA-seq analyses has been assessing gene expression changes, several approaches have been proposed in recent years to identify changes at the DNA level from scRNA-seq data. In this…
Dylan S. Small
For learning about the causal effect of a treatment, a randomized controlled trial (RCT) is considered the gold standard. However, randomizing treatment is sometimes unethical or infeasible, and instead an observational study may be conducted. While some aspects of a well designed RCT cannot be replicated in an…
Authors not listed
Quantitative analysis of small extracellular vesicles (sEVs) at single-particle resolution remains challenging due to their nanoscale dimensions and compositional heterogeneity. Existing methods often rely on specialized and costly instrumentation, limiting accessibility for many researchers and necessitates extensive…
José Camacho, Michael Armstrong, Luz García, Caridad Díaz + 1 more
'Carolina Gómez‐Llorente'] Over the past few years, technological advances have allowed for measurement of omics data at the cell level, creating a new type of data generally referred to as single-cell (sc) omics. On the other hand, the so-called spatial omics are a family of techniques that generate biological…
Justin Eilertsen, Santiago Schnell
As a case study, we consider a coupled (or auxiliary) enzyme assay of two reactions obeying the Michaelis-Menten mechanism. The coupled reaction consists of a single-substrate, single-enzyme non-observable reaction followed by another single-substrate, single-enzyme observable reaction (indicator reaction). In this…
Dylan Smith, Kristin Lauro, Dymond Kelly, Joel Fish + 6 more
A physical chemistry lab for undergraduate students described in this report is about applying kinetic models to analyze the spread of COVID-19 in the United States and obtain the reproduction numbers. The susceptible-infectious-recovery (SIR) model and the SIR-vaccinated (SIRV) model are explained to the students and…