The ToxCast pipeline: updates to curve-fitting approaches and database structure.

Introduction: The US Environmental Protection Agency Toxicity Forecaster (ToxCast) program makes in vitro medium- and high-throughput screening assay data publicly available for prioritization and hazard characterization of thousands of chemicals. The assays employ a variety of technologies to evaluate the effects of chemical exposure on diverse biological targets, from distinct proteins to more complex cellular processes like mitochondrial toxicity, nuclear receptor signaling, immune responses, and developmental toxicity. The ToxCast data pipeline (tcpl) is an open-source R package that stores, manages, curve-fits, and visualizes ToxCast data and populates the linked MySQL Database, invitrodb. Methods: Herein we describe major updates to tcpl and invitrodb to accommodate a new curve-fitting approach. The original tcpl curve-fitting models (constant, Hill, and gain-loss models) have been expanded to include Polynomial 1 (Linear), Polynomial 2 (Quadratic), Power, Exponential 2, Exponential 3, Exponential 4, and Exponential 5 based on BMDExpress and encoded by the R package dependency, tcplfit2. Inclusion of these models impacted invitrodb (beta version v4.0) and tcpl v3 in several ways: (1) long-format storage of generic modeling parameters to permit additional curve-fitting models; (2) updated logic for winning model selection; (3) continuous hit calling logic; and (4) removal of redundant endpoints as a result of bidirectional fitting. Results and discussion: Overall, the hit call and potency estimates were largely consistent between invitrodb v3.5 and 4.0. Tcpl and invitrodb provide a standard for consistent and reproducible curve-fitting and data management for diverse, targeted in vitro assay data with readily available documentation, thus enabling sharing and use of these data in myriad toxicology applications. The software and database updates described herein promote comparability across multiple tiers of data within the US Environmental Protection Agency CompTox Blueprint.

Evaluating structure-based activity in a high-throughput assay for steroid biosynthesis.

Data from a high-throughput human adrenocortical carcinoma assay (HT-H295R) for steroid hormone biosynthesis are available for >2000 chemicals in single concentration and 654 chemicals in multi-concentration (mc). Previously, a metric describing the effect size of a chemical on the biosynthesis of 11 hormones was derived using mc data referred to as the maximum mean Mahalanobis distance (maxmMd). However, mc HT-H295R assay data remain unavailable for many chemicals. This work leverages existing HT-H295R assay data by constructing structure-activity relationships to make predictions for data-poor chemicals, including: (1) identification of individual structural descriptors, known as ToxPrint chemotypes, associated with increased odds of affecting estrogen or androgen synthesis; (2) a random forest (RF) classifier using physicochemical property descriptors to predict HT-H295R maxmMd binary (positive or negative) outcomes; and, (3) a local approach to predict maxmMd binary outcomes using nearest neighbors (NNs) based on two types of chemical fingerprints (chemotype or Morgan). Individual chemotypes demonstrated high specificity (85-98%) for modulators of estrogen and androgen synthesis but with low sensitivity. The best RF model for maxmMd classification included 13 predicted physicochemical descriptors, yielding a balanced accuracy (BA) of 71% with only modest improvement when hundreds of structural features were added. The best two NN models for binary maxmMd prediction demonstrated BAs of 85 and 81% using chemotype and Morgan fingerprints, respectively. Using an external test set of 6302 chemicals (lacking HT-H295R data), 1241 were identified as putative estrogen and androgen modulators. Combined results across the three classification models (global RF model and two local NN models) predict that 1033 of the 6302 chemicals would be more likely to affect HT-H295R bioactivity. Together, these in silico approaches can efficiently prioritize thousands of untested chemicals for screening to further evaluate their effects on steroid biosynthesis.

Measuring nutrition-related outcomes in a cohort of multi-trauma patients following intensive care unit discharge.

BACKGROUND: Functional recovery is an important outcome for those who survive critical illness. The present study aimed to assess nutrition provision and nutrition-related outcomes in a multi-trauma cohort following intensive care unit (ICU) discharge. METHODS: The present study investigated a prospective cohort of patients discharged from an ICU, who had been admitted because of major trauma and required mechanical ventilation for at least 48 h. Nutrition-related outcomes, including body weight, quadriceps muscle layer thickness (QMLT), handgrip strength and subjective global assessment, were recorded on ICU discharge, days 5-7 post-ICU discharge and then weekly until hospital discharge. Nutrition intake was recorded for 5 days post-ICU discharge. Unless otherwise stated, data are presented as the mean (SD). RESULTS: Twenty-eight patients [75% males, 55 (22.5) years] were included. Intake met 64% (28%) of estimated energy and 72% (32%) of protein requirements over the 5 days post-ICU discharge, which was similar to over the ICU admission. From ICU admission to hospital discharge, the mean reduction in weight was 4.2 kg (95% confidence interval = 2.2-6.3, P < 0.001) and after ICU discharge, the mean reduction in weight and QMLT was 2.6 kg (95% confidence interval = 1.0-4.2, P = 0.004) and 0.23 cm (95% confidence interval = 0.06-0.4, P = 0.01), respectively. CONCLUSIONS: Patients received less energy and protein than estimated requirements after ICU discharge. Weight loss and reduction in QMLT also occurred during this period.

Major trauma in older persons.

BACKGROUND: Globally, populations are ageing, creating challenges for trauma system design. Despite this, little is known about causes of injury and long-term outcomes in older injured patients. This study aims to describe temporal trends in the incidence, causes and functional outcomes of major trauma in older adults. METHODS: The population-based Victorian State Trauma Registry was used to identify patients with major trauma aged 65 years and older with a date of injury between 1 January 2007 and 31 December 2016. Temporal trends in population-based incidence rates were evaluated. Functional outcome was measured using the Glasgow Outcome Scale - Extended. RESULTS: There were 9250 older adults with major trauma during the study period. Low falls were the most common mechanism of injury (62·5 per cent), followed by transport-related events (22·2 per cent) and high falls (9·5 per cent). The number of patients with major trauma aged 65 years and older more than doubled from 2007 to 2016, and the incidence increased by 4·3 per cent per year (incidence rate ratio 1·043, 95 per cent c.i. 1·035 to 1·050; P < 0·001). At 12 months after injury, 41·8 per cent of older adults with major trauma had died, and 52·2 per cent of those who survived to hospital discharge were not living independently. CONCLUSIONS: The number and proportion of older adults with major trauma are increasing rapidly and this will impact on trauma system design. Given the poor long-term outcomes, there needs to be greater emphasis on ensuring that appropriate interventions are targeted to the right patients and enhanced efforts in primary prevention.

Development of a curated Hershberger database.

A systematic literature review was conducted to identify Hershberger bioassays for ∼3200 chemicals including those used to validate the OECD/US EPA guideline assay, US EPA's chemicals screened for endocrine activity, and the library of chemicals run in US EPA 's ToxCast in vitro assays. For 134 chemicals that met pre-defined criteria, experimental results were extracted into a database used to characterize uncertainty in results and evaluate the concordance of the Hershberger assay with other in vivo rodent studies that measure androgen-responsive endpoints. Of 25 chemicals tested in >1 Hershberger study, 28% had disagreements between studies (i.e. ≥1 positive and ≥1 negative study), and of the 65 chemicals tested in Hershberger studies and other in vivo studies with androgen-responsive endpoints, 43% indicated disagreements, though in some cases these may be explained by differences in study designs or physiology of the animal model. Ultimately, 49 chemicals were identified with reproducible androgen pathway responses confirmed in ≥2 in vivo rodent studies that could be considered reference chemicals useful for validating alternative methods.

Evaluation of androgen assay results using a curated Hershberger database.

A set of 39 reference chemicals with reproducible androgen pathway effects in vivo, identified in the companion manuscript [1], were used to interrogate the performance of the ToxCast/Tox 21 androgen receptor (AR) model based on 11 high throughput assays. Cytotoxicity data and specificity confirmation assays were used to distinguish assay loss-of-function from true antagonistic signaling suppression. Overall agreement was 66% (19/29), with ten additional inconclusive chemicals. Most discrepancies were explained using in vitro to in vivo extrapolation to estimate equivalent administered doses. The AR model had 100% positive predictive value for the in vivo response, i.e. there were no false positives, and chemicals with conclusive AR model results (agonist or antagonist) were consistently positive in vivo. Considering the lack of reproducibility of the in vivo Hershberger assay, the in vitro AR model may better predict specific AR interaction and can rapidly and cost-effectively screen thousands of chemicals without using animals.

An automated curation procedure for addressing chemical errors and inconsistencies in public datasets used in QSAR modelling.

The increasing availability of large collections of chemical structures and associated experimental data provides an opportunity to build robust QSAR models for applications in different fields. One common concern is the quality of both the chemical structure information and associated experimental data. Here we describe the development of an automated KNIME workflow to curate and correct errors in the structure and identity of chemicals using the publicly available PHYSPROP physicochemical properties and environmental fate datasets. The workflow first assembles structure-identity pairs using up to four provided chemical identifiers, including chemical name, CASRNs, SMILES, and MolBlock. Problems detected included errors and mismatches in chemical structure formats, identifiers and various structure validation issues, including hypervalency and stereochemistry descriptions. Subsequently, a machine learning procedure was applied to evaluate the impact of this curation process. The performance of QSAR models built on only the highest-quality subset of the original dataset was compared with the larger curated and corrected dataset. The latter showed statistically improved predictive performance. The final workflow was used to curate the full list of PHYSPROP datasets, and is being made publicly available for further usage and integration by the scientific community.

Screw Placement Accuracy and Outcomes Following O-Arm-Navigated Atlantoaxial Fusion: A Feasibility Study.

Study Design Case series of seven patients. Objective C2 stabilization can be challenging due to the complex anatomy of the upper cervical vertebrae. We describe seven cases of C1-C2 fusion using intraoperative navigation to aid in the screw placement at the atlantoaxial (C1-C2) junction. Methods Between 2011 and 2014, seven patients underwent posterior atlantoaxial fusion using intraoperative frameless stereotactic O-arm Surgical Imaging and StealthStation Surgical Navigation System (Medtronic, Inc., Minneapolis, Minnesota, United States). Outcome measures included screw accuracy, neurologic status, radiation dosing, and surgical complications. Results Four patients had fusion at C1-C2 only, and in the remaining three, fixation extended down to C3 due to anatomical considerations for screw placement recognized on intraoperative imaging. Out of 30 screws placed, all demonstrated minimal divergence from desired placement in either C1 lateral mass, C2 pedicle, or C3 lateral mass. No neurovascular compromise was seen following the use of intraoperative guided screw placement. The average radiation dosing due to intraoperative imaging was 39.0 mGy. All patients were followed for a minimum of 12 months. All patients went on to solid fusion. Conclusion C1-C2 fusion using computed tomography-guided navigation is a safe and effective way to treat atlantoaxial instability. Intraoperative neuronavigation allows for high accuracy of screw placement, limits complications by sparing injury to the critical structures in the upper cervical spine, and can help surgeons make intraoperative decisions regarding complex pathology.

Improved Accuracy of Minimally Invasive Transpedicular Screw Placement in the Lumbar Spine With 3-Dimensional Stereotactic Image Guidance: A Comparative Meta-Analysis.

STUDY DESIGN: This study compares the accuracy rates of lumbar percutaneous pedicle screw placement (PPSP) using either 2-dimensional (2-D) fluoroscopic guidance or 3-dimensional (3-D) stereotactic navigation in the setting of minimally invasive spine surgery (MISS). This represents the largest single-operator study of its kind and first comprehensive review of 3-D stereotactic navigation in the setting of MISS. OBJECTIVE: To examine differences in accuracy of lumbar pedicle screw placement using 2-D fluoroscopic navigation and 3-D stereotaxis in the setting of MISS. SUMMARY OF BACKGROUND DATA: Surgeons increasingly rely upon advanced image guidance systems to guide minimally invasive PPSP. Three-dimensional stereotactic navigation with intraoperative computed tomography offers well-documented benefit in open surgical approaches. However, the utility of 3-D stereotaxis in the setting of MISS remains incompletely explored by few studies with limited patient numbers. MATERIALS AND METHODS: A total of 599 consecutive patients underwent minimally invasive lumbar PPSP aided by 3-D stereotactic navigation. Postoperative imaging and medical records were analyzed for patient demographics, incidence and degree of pedicle breach, and other surgical complications. A total of 2132 screw were reviewed and compared with a meta-analysis created from published data regarding the placement of 4248 fluoroscopically navigated pedicle screws in the setting of MISS. RESULTS: In the 3-D navigation group, a total of 7 pedicle breaches occurred in 6 patients, corresponding to a per-person breach rate of 1.15% (6/518) and a per-screw breach rate of 0.33% (7/2132). Meta-analysis comprised of data from 10 independent studies showed overall breach risk of 13.1% when 2-D fluoroscopic navigation was utilized in MISS. This translates to a 99% decrease in odds of breach in the 3-D navigation technique versus the traditional 2-D-guided technique, with an odds ratio of 0.01, (95% confidence interval, 0.01-0.03), P<0.001. CONCLUSIONS: Three-dimensional stereotactic navigation based upon intraoperative computed tomography imaging offers markedly improved accuracy of percutaneous lumbar pedicle screw placement when used in the setting of MISS.

Strain imaging of nanoscale semiconductor heterostructures with x-ray Bragg projection ptychography.

We report the imaging of nanoscale distributions of lattice strain and rotation in complementary components of lithographically engineered epitaxial thin film semiconductor heterostructures using synchrotron x-ray Bragg projection ptychography (BPP). We introduce a new analysis method that enables lattice rotation and out-of-plane strain to be determined independently from a single BPP phase reconstruction, and we apply it to two laterally adjacent, multiaxially stressed materials in a prototype channel device. These results quantitatively agree with mechanical modeling and demonstrate the ability of BPP to map out-of-plane lattice dilatation, a parameter critical to the performance of electronic materials.

Discovery of sialyl Lewis A and Lewis X modified protein cancer biomarkers using high density antibody arrays.

We report on a high-dimensional method to globally profile glycoproteins that are modified with sialyl Lewis A or Lewis X glycans. Specifically, glycoproteins in serum or plasma are fractionated on a high-density antibody microarray (i.e., each are localized to their specific antibody spot) and are specifically detected via fluorescently labeled anti-sialyl Lewis A or anti-Lewis X antibodies with quantification in a microarray scanner. Non-glycosylated proteins or glycoproteins with other glycan motifs do not interfere with this assay. The whole process is very rapid and applicable for high-throughput screening without the need for purification of glycoproteins from the samples. Using these methods, sialyl Lewis A or Lewis X moieties were found to be expressed on many previously unreported secreted or membrane associated proteins. Furthermore, the combination of sialyl Lewis A or Lewis X content with protein level increased the ability of certain glycoproteins to distinguish 30 patients with stage III and IV colon cancer from 60 control samples. Thus, this highly sensitive method is capable of discovering novel specific glycan modifications on proteins, many of which will likely be useful for disease detection and monitoring. BIOLOGICAL SIGNIFICANCE: In this paper, we show that we can detect cancer-specific glycan modifications on thousands of proteins using a high-density antibody array paired with a glycan specific antibody to probe the bound glycoproteins. To our knowledge, our array is by far the largest and densest that has ever been used for global profiling of specific glycan modification on proteins. Analysis of colon cancer patient plasma for sialyl Lewis A and Lewis X modifications revealed previously unknown protein carriers of these modifications and significant increases in these specific glycans on some proteins in people with cancer versus healthy controls, suggesting this method could be used to discover novel biomarkers.

Development of a consumer product ingredient database for chemical exposure screening and prioritization.

Consumer products are a primary source of chemical exposures, yet little structured information is available on the chemical ingredients of these products and the concentrations at which ingredients are present. To address this data gap, we created a database of chemicals in consumer products using product Material Safety Data Sheets (MSDSs) publicly provided by a large retailer. The resulting database represents 1797 unique chemicals mapped to 8921 consumer products and a hierarchy of 353 consumer product "use categories" within a total of 15 top-level categories. We examine the utility of this database and discuss ways in which it will support (i) exposure screening and prioritization, (ii) generic or framework formulations for several indoor/consumer product exposure modeling initiatives, (iii) candidate chemical selection for monitoring near field exposure from proximal sources, and (iv) as activity tracers or ubiquitous exposure sources using "chemical space" map analyses. Chemicals present at high concentrations and across multiple consumer products and use categories that hold high exposure potential are identified. Our database is publicly available to serve regulators, retailers, manufacturers, and the public for predictive screening of chemicals in new and existing consumer products on the basis of exposure and risk.

Showered calcific emboli to the brain, the 'salted pretzel' sign, originating from the ipsilateral internal carotid artery causing acute cerebral infarction.

BACKGROUND AND PURPOSE: Unenhanced head CT has become the first line imaging study in the evaluation of suspected acute cerebral ischemia. It is important to identify subtle findings of acute ischemia on this exam to direct appropriate patient management. Summary of Case- We report the first case of multiple pial surface distal internal carotid artery territory calcified emboli causing multifocal cerebral infarctions, likely from a carotid bifurcation source. CONCLUSIONS: Visualization of multiple pial surface calcifications on unenhanced head CT, the 'salted pretzel sign', should raise suspicion for acute infarction from showered calcific emboli.

Endovascular repair of cervical aortic arch aneurysm.

Cervical aortic arch (CAA) is a rare congenital anomaly of the aortic arch. Rarely, CAA is associated with aneurysm of the arch and great vessels. A 32-year-old male patient, previously in good health, presented with 2 weeks of severe chest pain. Radiographic evaluation revealed a CAA with aneurysmal dilation of the distal aortic arch. The aneurysm extended into the left subclavian artery. There was also marked angulation just distal to the aneurysmal portion. The aneurysmal arch and subclavian artery were repaired using a thoracic aortic endograft. An open axillary-to-axillary bypass was performed, and the left axillary artery was ligated proximally. This restored perfusion to the left upper extremity and effectively excluded the aneurysm sac. Immediately postoperatively, the patient's chest pain resolved, and he has remained symptom free. To the authors' knowledge, this is the first reported repair of a cervical arch aneurysm by endovascular technique.

Haplotypes of the cholesteryl ester transfer protein gene predict lipid-modifying response to statin therapy.

Cholesteryl ester transfer protein (CETP) plays a central role in high-density lipoprotein (HDL) metabolism. Single nucleotide polymorphisms (SNPs) and haplotypes in the CETP gene were determined in 98 patients with untreated dyslipidemias and analyzed for associations with plasma CETP and plasma lipids before and during statin treatment. Individual CETP SNPs and haplotypes were both significantly associated with CETP enzyme mass and activity. However, only certain CETP haplotypes, but not individual SNPs, significantly predicted the magnitude of change in HDL cholesterol (HDL-C) and triglycerides. After adjusting for covariates and multiple testing, the TTCAAA haplotype showed a gene-dose effect in predicting the HDL-C increase (P=0.03), while the TTCAAAGGG and AAAGGG haplotypes predicted a decrease in triglycerides (P=0.04 both). This is the first study to demonstrate that SNP haplotypes derived from allelic SNP combinations in the CETP gene were more informative than single SNPs in predicting the response to lipid-modifying therapy with statins.

Treatment of the exposed Achilles tendon using negative pressure wound therapy: a case report.

Exposed tendons after burn injury create a surgical challenge for the treating physician. This is particularly true with regard to the exposed Achilles tendon. This case report reviews the nature of this challenge and traditional solutions, and describes the use of negative pressure wound therapy to facilitate coverage of the Achilles tendon. This therapy may provide a more appropriate therapeutic option for dealing with tendon exposure after severe burns.

Haplotype variation and linkage disequilibrium in 313 human genes.

Variation within genes has important implications for all biological traits. We identified 3899 single nucleotide polymorphisms (SNPs) that were present within 313 genes from 82 unrelated individuals of diverse ancestry, and we organized the SNPs into 4304 different haplotypes. Each gene had several variable SNPs and haplotypes that were present in all populations, as well as a number that were population-specific. Pairs of SNPs exhibited variability in the degree of linkage disequilibrium that was a function of their location within a gene, distance from each other, population distribution, and population frequency. Haplotypes generally had more information content (heterozygosity) than did individual SNPs. Our analysis of the pattern of variation strongly supports the recent expansion of the human population.

Notes from the SNP vs. haplotype front.

Single nucleotide polymorphisms (SNPs) and haplotypes are commonly used genetic markers in clinical studies. We provide some broad guidelines for deciding which of the two is most appropriate in particular circumstances. Molecular haplotyping techniques are also briefly reviewed and contrasted with electronic approaches.