Publications

BACKGROUND

Very rapidly progressive "acute silicosis" was observed prior to the 1930 International Labour Office Conference on silicosis, but its clinical significance and pathologic relationship to classic silica caused pneumoconiosis were not settled.

METHODS

Textual analysis of the 1930 Conference proceedings identified data relevant to rapidly progressive silicosis. Standard bibliographic searches identified relevant biomedical literature dating from before and after the Conference.

RESULTS

The 1930 Johannesburg Conference contained descriptions of acute silicosis, especially in the abrasive powders industry, but acute silica-related lung disease did not conform to a three-stage disease model in which tuberculosis supra-infection caused advanced disease, a model accepted at the Conference. Over following decades, additional reports appeared of rapidly progressive silicosis, unrelated to tuberculosis. Pulmonary alveolar proteinosis was identified only in 1958.

CONCLUSIONS

Adoption by the 1930 Johannesburg Conference of a classification scheme into which acute rapidly progressive disease unrelated to tuberculosis fitted poorly may have impeded the understanding of acute silicosis and its importance.

Corneal injury can produce photophobia, an aversive sensitivity to light. Using topical application of lidocaine, a local anesthetic, and tetrodotoxin (TTX), a selective voltage-sensitive sodium channel blocker, we assessed whether enhanced aversiveness to light induced by corneal injury in rats was caused by enhanced activity in corneal afferents. Eye closure induced by 30 seconds of exposure to bright light (460-485 nm) was increased 24 hours after corneal injury induced by de-epithelialization. Although the topical application of lidocaine did not affect the baseline eye closure response to bright light in control rats, it eliminated the enhancement of the response to the light stimulus after corneal injury (photophobia). Similarly, topical application of TTX had no effect on the eye closure response to bright light in rats with intact corneas, but it markedly attenuated photophobia in rats with corneal injury. Given the well-established corneal toxicity of local anesthetics, we suggest TTX as a therapeutic option to treat photophobia and possibly other symptoms that occur in clinical diseases that involve corneal nociceptor sensitization. Perspective: We show that lidocaine and TTX attenuate photophobia induced by corneal injury. Although corneal toxicity limits use of local anesthetics, TTX may be a safer therapeutic option to reduce the symptom of photophobia associated with corneal injury.

MOTIVATION

A basic problem of broad public and scientific interest is to use the DNA of an individual to infer the genomic ancestries of the parents. In particular, we are often interested in the fraction of each parent's genome that comes from specific ancestries (e.g. European, African, Native American, etc). This has many applications ranging from understanding the inheritance of ancestry-related risks and traits to quantifying human assortative mating patterns.

RESULTS

We model the problem of parental genomic ancestry inference as a pooled semi-Markov process. We develop a general mathematical framework for pooled semi-Markov processes and construct efficient inference algorithms for these models. Applying our inference algorithm to genotype data from 231 Mexican trios and 258 Puerto Rican trios where we have the true genomic ancestry of each parent, we demonstrate that our method accurately infers parameters of the semi-Markov processes and parents' genomic ancestries. We additionally validated the method on simulations. Our model of pooled semi-Markov process and inference algorithms may be of independent interest in other settings in genomics and machine learning.

MOTIVATION

Approaches to identifying new risk loci, training risk prediction models, imputing untyped variants and fine-mapping causal variants from summary statistics of genome-wide association studies are playing an increasingly important role in the human genetics community. Current summary statistics-based methods rely on global 'best guess' reference panels to model the genetic correlation structure of the dataset being studied. This approach, especially in admixed populations, has the potential to produce misleading results, ignores variation in local structure and is not feasible when appropriate reference panels are missing or small. Here, we develop a method, Adapt-Mix, that combines information across all available reference panels to produce estimates of local genetic correlation structure for summary statistics-based methods in arbitrary populations.

RESULTS

We applied Adapt-Mix to estimate the genetic correlation structure of both admixed and non-admixed individuals using simulated and real data. We evaluated our method by measuring the performance of two summary statistics-based methods: imputation and joint-testing. When using our method as opposed to the current standard of 'best guess' reference panels, we observed a 28% decrease in mean-squared error for imputation and a 73.7% decrease in mean-squared error for joint-testing.

AVAILABILITY AND IMPLEMENTATION

Our method is publicly available in a software package called ADAPT-Mix available at https://github.com/dpark27/adapt_mix.