HaplotagLR: An efficient and configurable utility for haplotagging long reads.

Understanding the functional effects of sequence variation is crucial in genomics. Individual human genomes contain millions of variants that contribute to phenotypic variability and disease risks at the population level. Because variants rarely act in isolation, we must consider potential interactions of neighboring variants to accurately predict functional effects.

Towards quantifying atmospheric dispersion of pesticide spray drift in Yuma County Arizona.

While pesticide vapor and particles from agricultural spray drift have been reported to pose a risk to public health, limited baseline ambient measurements exist to warrant an accurate assessment of their impacts at community-to-county-wide scale. Here, we present an initial modeling investigation of the transport and deposition of applied pesticides in an agricultural county in Arizona (Yuma County), to provide initial estimates on the corresponding enhancements in ambient levels of these spray drifts downwind of application sites. With a 50 × 50 km domain, we use the dispersion model CALPUFF with meteorology from the Weather Research and Forecasting (WRF) to investigate the spatiotemporal distribution of pesticide abundance due to spray drift from a representative sample of nine application sites.

Challenges in screening for noncoding variants contributing to genetically complex phenotypes.

Understanding the genetic basis for complex, heterogeneous disorders, such as autism spectrum disorder (ASD), is a persistent challenge in human medicine. Owing to their phenotypic complexity, the genetic mechanisms underlying these disorders may be highly variable across individual patients. Furthermore, much of their heritability is unexplained by known regulatory or coding variants.

LRphase: an efficient method for assigning haplotype identity to long reads.

Understanding the functional effects of sequence variation is among the primary goals of contemporary genomics. Individual human genomes contain millions of variants which are thought to contribute to phenotypic variability and differential disease risks at the population level. However, because variants rarely act in isolation, we cannot accurately predict functional effects without first considering the potential effects of other interacting variants on the same chromosome.

Long-run economic and social determinants of the ecological footprint of latin america: a panel causality approach.

As a region rich in natural resources and biodiversity, Latin America is particularly vulnerable to environmental crises. The ecological footprint (EF) of Latin America and the variables that affect it in the long run are examined through a panel data approach and causality, using a sample of 12 countries in the region over the period 1990 to 2014. The study uses human development instead of human capital, because the former considers health and standard of living in addition to schooling.

Enhanced jet stream waviness induced by suppressed tropical Pacific convection during boreal summer.

Consensus on the cause of recent midlatitude circulation changes toward a wavier manner in the Northern Hemisphere has not been reached, albeit a number of studies collectively suggest that this phenomenon is driven by global warming and associated Arctic amplification. Here, through a fingerprint analysis of various global simulations and a tropical heating-imposed experiment, we suggest that the suppression of tropical convection along the Inter Tropical Convergence Zone induced by sea surface temperature (SST) cooling trends over the tropical Eastern Pacific contributed to the increased summertime midlatitude waviness in the past 40 years through the generation of a Rossby-wave-train propagating within the jet waveguide and the reduced north-south temperature gradient. This perspective indicates less of an influence from the Arctic amplification on the observed mid-latitude wave amplification than what was previously estimated.

Cas9 targeted enrichment of mobile elements using nanopore sequencing.

Mobile element insertions (MEIs) are repetitive genomic sequences that contribute to genetic variation and can lead to genetic disorders. Targeted and whole-genome approaches using short-read sequencing have been developed to identify reference and non-reference MEIs; however, the read length hampers detection of these elements in complex genomic regions. Here, we pair Cas9-targeted nanopore sequencing with computational methodologies to capture active MEIs in human genomes.

Comparing potential recharge estimates from three Land Surface Models across the Western US.

Groundwater is a major source of water in the western US. However, there are limited recharge estimates available in this region due to the complexity of recharge processes and the challenge of direct observations. Land surface Models (LSMs) could be a valuable tool for estimating current recharge and projecting changes due to future climate change.

Mechanical insufflation-exsufflation: pressure, volume, and flow relationships and the adequacy of the manufacturer's guidelines.

Objective: Pulmonary complications of neuromuscular disease can be averted by increasing peak cough flows with the use of a forced exsufflation device. The purpose of this study was to examine the pressure, volume, and flow relationships for a range of settings generated by this device, and compare them with clinically efficacious values and the manufacturer's guidelines.

Methods: The In-exsufflator was connected to a standard lung model.