Automated mapping of electronic data capture fields to SDTM.

Objective: The goal of this work is to reduce the amount of manual work required to go from data capture to regulatory submission. It will be shown that the use of Siamese networks will allow for the generation of embeddings that can be used by traditional machine learning classifiers to perform the classification at much higher levels of accuracy than standard approaches.

Methods: Siamese networks are a method for training data embeddings such that data within the same class are closer with respect to a given distance metric than they are to data points in another class.

A novel and accurate full-length HTT mouse model for Huntington's disease.

Here, we report the generation and characterization of a novel Huntington's disease (HD) mouse model BAC226Q by using a bacterial artificial chromosome (BAC) system, expressing full-length human HTT with ~226 CAG-CAA repeats and containing endogenous human HTT promoter and regulatory elements. BAC226Q recapitulated a full-spectrum of age-dependent and progressive HD-like phenotypes without unwanted and erroneous phenotypes. BAC226Q mice developed normally, and gradually exhibited HD-like psychiatric and cognitive phenotypes at 2 months.

Discovery and validation of a novel subgroup and therapeutic target in idiopathic multicentric Castleman disease.

Idiopathic multicentric Castleman disease (iMCD) is a poorly understood hematologic disorder involving cytokine-induced polyclonal lymphoproliferation, systemic inflammation, and potentially fatal multiorgan failure. Although the etiology of iMCD is unknown, interleukin-6 (IL-6) is an established disease driver in approximately one-third of patients. Anti-IL-6 therapy, siltuximab, is the only US Food and Drug Administration-approved treatment.

Rapid, Phase-free Detection of Long Identity-by-Descent Segments Enables Effective Relationship Classification.

Identity-by-descent (IBD) segments are a useful tool for applications ranging from demographic inference to relationship classification, but most detection methods rely on phasing information and therefore require substantial computation time. As genetic datasets grow, methods for inferring IBD segments that scale well will be critical. We developed IBIS, an IBD detector that locates long regions of allele sharing between unphased individuals, and benchmarked it with Refined IBD, GERMLINE, and TRUFFLE on 3,000 simulated individuals.

Inferring Identical-by-Descent Sharing of Sample Ancestors Promotes High-Resolution Relative Detection.

As genetic datasets increase in size, the fraction of samples with one or more close relatives grows rapidly, resulting in sets of mutually related individuals. We present DRUID-deep relatedness utilizing identity by descent-a method that works by inferring the identical-by-descent (IBD) sharing profile of an ungenotyped ancestor of a set of close relatives. Using this IBD profile, DRUID infers relatedness between unobserved ancestors and more distant relatives, thereby combining information from multiple samples to remove one or more generations between the deep relationships to be identified.

Ambient Pollution-related Reprogramming of the Human Small Airway Epithelial Transcriptome.

Rationale: Epidemiologic studies have demonstrated that exposure to particulate matter ambient pollution has adverse effects on lung health, exacerbated by cigarette smoking. Particulate matter less than or equal to 2.5 μm in aerodynamic diameter (PM) is among the most harmful urban pollutants and is closely linked to respiratory disease.

Ontogeny and Biology of Human Small Airway Epithelial Club Cells.

Rationale: Little is known about human club cells, dome-shaped cells with dense cytoplasmic granules and microvilli that represent the major secretory cells of the human small airways (at least sixth-generation bronchi).

Objectives: To define the ontogeny and biology of the human small airway epithelium club cell.

Methods: The small airway epithelium was sampled from the normal human lung by bronchoscopy and brushing.

An independent component analysis confounding factor correction framework for identifying broad impact expression quantitative trait loci.

Genome-wide expression Quantitative Trait Loci (eQTL) studies in humans have provided numerous insights into the genetics of both gene expression and complex diseases. While the majority of eQTL identified in genome-wide analyses impact a single gene, eQTL that impact many genes are particularly valuable for network modeling and disease analysis. To enable the identification of such broad impact eQTL, we introduce CONFETI: Confounding Factor Estimation Through Independent component analysis.

Retake the center stage--new development of rat genetics.

The rat is a powerful model for the study of human physiology and diseases, and is preferred by physiologists, neuroscientists and toxicologists. However, the lack of robust genetic modification tools has severely limited the generation of rat genetic models over the last two decades. In the last few years, several gene-targeting strategies have been developed in rats using N-ethyl-N-nitrosourea (ENU), transposons, zinc-finger nucleases (ZFNs), bacterial artificial chromosome (BAC) mediated transgenesis, and recently established rat embryonic stem (ES) cells.

Kinase signaling dysfunction in Parkinson's disease: a reverse genetic approach in Drosophila.

Drosophila genetics is one of the most powerful tools in modern biology. For many years, the "forward genetic" approach using Drosophila has been extraordinarily successful in elucidating the molecular pathways of many physiological processes and behaviors. Recently, the "reverse genetic" approach in Drosophila is increasingly being developed as a major tool for research in biology, especially in the study of human diseases.

Mouse models for LRRK2 Parkinson's disease.

Parkinson's disease (PD) is the second most common neurodegenerative disease. Mutations in Leucine-rich-repeat-kinase 2 (LRRK2), the causative gene for PARK8 type PD with autosomal dominant inheritance, are the most prevalent genetic causes of both familial and sporadic PD. Animal models are critical tools in the attempt to understand the mechanisms of LRRK2-mediated pathogenesis.

Cellular and subcellular localization of estrogen and progestin receptor immunoreactivities in the mouse hippocampus.

Estrogen receptor-alpha (ERalpha), estrogen receptor-beta (ERbeta), and progestin receptor (PR) immunoreactivities are localized to extranuclear sites in the rat hippocampal formation. Because rats and mice respond differently to estradiol treatment at a cellular level, the present study examined the distribution of ovarian hormone receptors in the dorsal hippocampal formation of mice. For this, antibodies to ERalpha, ERbeta, and PR were localized by light and electron immunomicroscopy in male and female mice across the estrous cycle.