DeepCell Kiosk: scaling deep learning-enabled cellular image analysis with Kubernetes.

Deep learning is transforming the analysis of biological images, but applying these models to large datasets remains challenging. Here we describe the DeepCell Kiosk, cloud-native software that dynamically scales deep learning workflows to accommodate large imaging datasets. To demonstrate the scalability and affordability of this software, we identified cell nuclei in 10 1-megapixel images in ~5.

Reduction in lead exposures with lead-free ammunition in an advanced urban assault course.

The training of soldiers for urban conflict involves marksmanship instruction on outdoor flat ranges and the teaching of close-quarter battle techniques in indoor facilities, referred to as shoot houses, where intense firing exercises can generate high air lead levels from small arms ammunition, flash bang grenades, and explosive devices. Levels of lead and copper in air were evaluated during five training activities of a 45-day training course using both stationary general area and breathing zone sampling over a 2-year period. Individual blood lead values were determined prior to and at course completion.

Chemical Speciation, Plant Uptake, and Toxicity of Heavy Metals in Agricultural Soils.

Heavy metals in agricultural soils exist in diverse dissolved (free cations and complexed species of positive, neutral, or negative charges), particulate (sorbed, structural, and coprecipitated), and colloidal (micro- and nanometer-sized particles) species. The fate of different heavy metal species is controlled by the master variables: pH (solubility), ionic strength (activity and charge-shielding), and dissolved organic carbon (complexation). In the rhizosphere, chemical speciation controls toxicokinetics (uptake and transport of metals by plants) while toxicodynamics (interaction between the plant and absorbed species) drives the toxicity outcome.

Gene expression in mouse muscle over time after nickel pellet implantation.

The transition metal nickel is used in a wide variety of alloys and medical devices. Nickel can cause a range of toxicities from allergy in humans to tumors when implanted in animals. Several microarray studies have examined nickel toxicity, but so far none have comprehensively profiled expression over an extended period.

Principles of open source bioinstrumentation applied to the poseidon syringe pump system.

The poseidon syringe pump and microscope system is an open source alternative to commercial systems. It costs less than $400 and can be assembled in under an hour using the instructions and source files available at https://pachterlab.github.

Deep learning for cellular image analysis.

Recent advances in computer vision and machine learning underpin a collection of algorithms with an impressive ability to decipher the content of images. These deep learning algorithms are being applied to biological images and are transforming the analysis and interpretation of imaging data. These advances are positioned to render difficult analyses routine and to enable researchers to carry out new, previously impossible experiments.

Matching target dose to target organ.

assays have become a mainstay of modern approaches to toxicology with the promise of replacing or reducing the number of tests required to establish benchmark doses, as well as increasing mechanistic understanding. However, matching target dose to target organ is an often overlooked aspect of assays, and the calibration of exposure against benchmark doses is often ignored, inadvertently or otherwise.  An example of this was recently published in by Wagner (2016), where neural stems cells were used to model the molecular toxicity of lead.

Toxic and transcriptional responses of PC12 cells to soluble tungsten alloy surrogates.

There is increasing evidence that metals have a role in the etiology of diverse neurological diseases. This study used PC12 cells as an in vitro model to examine the toxicity of tungsten alloys that have important military applications. Initially, the relative concentrations of tungsten (W), nickel (Ni), and cobalt (Co) mobilized from pellets of a weapons-grade tungsten alloy incubated in physiologically relevant solutions were determined.

Toxicokinetic Model Development for the Insensitive Munitions Component 2,4-Dinitroanisole.

The Armed Forces are developing new explosives that are less susceptible to unintentional detonation (insensitive munitions [IMX]). 2,4-Dinitroanisole (DNAN) is a component of IMX. Toxicokinetic data for DNAN are required to support interpretation of toxicology studies and refinement of dose estimates for human risk assessment.

How Relevant Are Imaging Findings in Animal Models of Movement Disorders to Human Disease?

The combination of novel imaging techniques with the use of small animal models of disease is often used in attempt to understand disease mechanisms, design potential clinical biomarkers and therapeutic interventions, and develop novel methods with translatability to human clinical conditions. However, it is clear that most animal models are deficient when compared to the complexity of human diseases: they cannot sufficiently replicate all the features of multisystem disorders. Furthermore, some practical differences may affect the use or interpretation of animal imaging to model human conditions such as the use of anesthesia, various species differences, and limitations of methodological tools.

Toxicokinetic Model Development for the Insensitive Munitions Component 3-Nitro-1,2,4-Triazol-5-One.

3-Nitro-1,2,4-triazol-5-one (NTO) is a component of insensitive munitions that are potential replacements for conventional explosives. Toxicokinetic data can aid in the interpretation of toxicity studies and interspecies extrapolation, but only limited data on the toxicokinetics and metabolism of NTO are available. To supplement these limited data, further in vivo studies of NTO in rats were conducted and blood concentrations were measured, tissue distribution of NTO was estimated using an in silico method, and physiologically based pharmacokinetic models of the disposition of NTO in rats and macaques were developed and extrapolated to humans.

Assessment of 3-nitro-1,2,4-triazol-5-one as a potential endocrine disrupting chemical in rats using the Hershberger and uterotrophic bioassays.

The explosive 3-nitro-1,2,4-triazol-5-one (NTO) is an insensitive formulation developed to replace high energetics that are susceptible to accidental detonation from heat, shock, and impact. Although studies have shown NTO to be nontoxic at acute exposures, recent subacute and subchronic tests have demonstrated effects on testes and subsequent sperm production in rats. This study assessed endocrine disruption as a potential mechanism for these reproductive effects via the Hershberger and uterotrophic bioassays.

A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages.

The rat has been used extensively as a model for evaluating chemical toxicities and for understanding drug mechanisms. However, its transcriptome across multiple organs, or developmental stages, has not yet been reported. Here we show, as part of the SEQC consortium efforts, a comprehensive rat transcriptomic BodyMap created by performing RNA-Seq on 320 samples from 11 organs of both sexes of juvenile, adolescent, adult and aged Fischer 344 rats.

Biomarkers of oral exposure to 3-nitro-1,2,4-triazol-5-one (NTO) and 2,4-dinitroanisole (DNAN) in blood and urine of rhesus macaques (Macaca mulatta).

The U.S. Department of Defense is using the chemicals 2,4-dinitroanisole (DNAN) and 3-nitro-1, 2,4-triazol-5-one (NTO) in new munitions development.

Solubility of lead and copper in biochar-amended small arms range soils: influence of soil organic carbon and pH.

Biochar is often considered a strong heavy metal stabilizing agent. However, biochar in some cases had no effects on, or increased the soluble concentrations of, heavy metals in soil. The objective of this study was to determine the factors causing some biochars to stabilize and others to dissolve heavy metals in soil.

In vivo corrosion, tumor outcome, and microarray gene expression for two types of muscle-implanted tungsten alloys.

Tungsten alloys are composed of tungsten microparticles embedded in a solid matrix of transition metals such as nickel, cobalt, or iron. To understand the toxicology of these alloys, male F344 rats were intramuscularly implanted with pellets of tungsten/nickel/cobalt, tungsten/nickel/iron, or pure tungsten, with tantalum pellets as a negative control. Between 6 and 12 months, aggressive rhabdomyosarcomas formed around tungsten/nickel/cobalt pellets, while those of tungsten/nickel/iron or pure tungsten did not cause cancers.

Lead retention by broiler litter biochars in small arms range soil: impact of pyrolysis temperature.

Phosphorus-rich manure biochar has a potential for stabilizing Pb and other heavy metal contaminants, as well as serving as a sterile fertilizer. In this study, broiler litter biochars produced at 350 and 650 °C were employed to understand how biochar's elemental composition (P, K, Ca, Mg, Na, Cu, Pb, Sb, and Zn) affects the extent of heavy metal stabilization. Soil incubation experiments were conducted using a sandy, slightly acidic (pH 6.

Retention of heavy metals by carboxyl functional groups of biochars in small arms range soil.

Long-term effectiveness of biochar for heavy metal stabilization depends upon biochar's sorptive property and recalcitrance in soil. To understand the role of carboxyl functional groups on heavy metal stabilization, cottonseed hull biochar and flax shive steam-activated biochar having a low O/C ratio (0.04-0.

Feasibility of self-sampling and human papillomavirus testing for cervical cancer screening in First Nation women from Northwest Ontario, Canada: a pilot study.

Background The incidence of cervical cancer is up to sixfold higher among First Nation women in Canada than in the general population. This is probably due to lower participation rates in cervical cancer prevention programmes. Objective To raise screening participation in this underserved population by launching an alternative approach to (Pap)anicolaou testing in a clinic-namely, vaginal self-sampling followed by human papillomavirus (HPV) diagnostics.

RDX binds to the GABA(A) receptor-convulsant site and blocks GABA(A) receptor-mediated currents in the amygdala: a mechanism for RDX-induced seizures.

Background: Hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) is a high-energy, trinitrated cyclic compound that has been used worldwide since World War II as an explosive in both military and civilian applications. RDX can be released in the environment by way of waste streams generated during the manufacture, use, and disposal of RDX-containing munitions and can leach into groundwater from unexploded munitions found on training ranges. For > 60 years, it has been known that exposure to high doses of RDX causes generalized seizures, but the mechanism has remained unknown.

Lead and copper in pigeons (Columbia livia) exposed to a small arms-range soil.

Small arms-range (SAR) soils can be contaminated with metals from spent copper (Cu)-jacketed bullets. Avian species are particularly at risk because they are exposed to lead (Pb) through ingestion of grit, soil intake from preening, or ingestion of contaminated food near ranges. Examination of the effects of Pb on birds at ranges have mainly focused on intake and toxicity of Pb shot pellets or fragments; however, Pb in soils may be an important pathway of exposure.