Standardizing Extracted Data Using Automated Application of Controlled Vocabularies.

BACKGROUND: Extraction of toxicological end points from primary sources is a central component of systematic reviews and human health risk assessments. To ensure optimal use of these data, consistent language should be used for end point descriptions. However, primary source language describing treatment-related end points can vary greatly, resulting in large labor efforts to manually standardize extractions before data are fit for use. OBJECTIVES: To minimize these labor efforts, we applied an augmented intelligence approach and developed automated tools to support standardization of extracted information via application of preexisting controlled vocabularies. METHODS: We created and applied a harmonized controlled vocabulary crosswalk, consisting of Unified Medical Language System (UMLS) codes, German Federal Institute for Risk Assessment (BfR) DevTox harmonized terms, and The Organization for Economic Co-operation and Development (OECD) end point vocabularies, to roughly 34,000 extractions from prenatal developmental toxicology studies conducted by the National Toxicology Program (NTP) and 6,400 extractions from European Chemicals Agency (ECHA) prenatal developmental toxicology studies, all recorded based on the original study report language. RESULTS: We automatically applied standardized controlled vocabulary terms to 75% of the NTP extracted end points and 57% of the ECHA extracted end points. Of all the standardized extracted end points, about half (51%) required manual review for potential extraneous matches or inaccuracies. Extracted end points that were not mapped to standardized terms tended to be too general or required human logic to find a good match. We estimate that this augmented intelligence approach saved >350 hours of manual effort and yielded valuable resources including a controlled vocabulary crosswalk, organized related terms lists, code for implementing an automated mapping workflow, and a computationally accessible dataset. DISCUSSION: Augmenting manual efforts with automation tools increased the efficiency of producing a findable, accessible, interoperable, and reusable (FAIR) dataset of regulatory guideline studies. This open-source approach can be readily applied to other legacy developmental toxicology datasets, and the code design is customizable for other study types. https://doi.org/10.1289/EHP13215.

Computational application of internationally harmonized defined approaches to skin sensitization: DASS App.

BACKGROUND: Chemically induced skin sensitization, or allergic contact dermatitis, is a common occupational and public health issue. Regulatory authorities require an assessment of potential to cause skin sensitization for many chemical products. Defined approaches for skin sensitization (DASS) identify potential chemical skin sensitizers by integrating data from multiple non-animal tests based on human cells, molecular targets, and computational model predictions using standardized data interpretation procedures. While several DASS are internationally accepted by regulatory agencies, the data interpretation procedures vary in logical complexity, and manual application can be time-consuming or prone to error. RESULTS: We developed the DASS App, an open-source web application, to facilitate user application of three regulatory testing strategies for skin sensitization assessment: the Two-out-of-Three (2o3), the Integrated Testing Strategy (ITS), and the Key Event 3/1 Sequential Testing Strategy (KE 3/1 STS) without the need for software downloads or computational expertise. The application supports upload and analysis of user-provided data, includes steps to identify inconsistencies and formatting issues, and provides predictions in a downloadable format. CONCLUSION: This open-access web-based implementation of internationally harmonized regulatory guidelines for an important public health endpoint is designed to support broad user uptake and consistent, reproducible application. The DASS App is freely accessible via https://ntp.niehs.nih.gov/go/952311 and all scripts are available on GitHub ( https://github.com/NIEHS/DASS ).

CATMoS: Collaborative Acute Toxicity Modeling Suite.

BACKGROUND: Humans are exposed to tens of thousands of chemical substances that need to be assessed for their potential toxicity. Acute systemic toxicity testing serves as the basis for regulatory hazard classification, labeling, and risk management. However, it is cost- and time-prohibitive to evaluate all new and existing chemicals using traditional rodent acute toxicity tests. In silico models built using existing data facilitate rapid acute toxicity predictions without using animals. OBJECTIVES: The U.S. Interagency Coordinating Committee on the Validation of Alternative Methods (ICCVAM) Acute Toxicity Workgroup organized an international collaboration to develop in silico models for predicting acute oral toxicity based on five different end points: Lethal Dose 50 (LD50 value, U.S. Environmental Protection Agency hazard (four) categories, Globally Harmonized System for Classification and Labeling hazard (five) categories, very toxic chemicals [LD50 (LD50≤50mg/kg)], and nontoxic chemicals (LD50>2,000mg/kg). METHODS: An acute oral toxicity data inventory for 11,992 chemicals was compiled, split into training and evaluation sets, and made available to 35 participating international research groups that submitted a total of 139 predictive models. Predictions that fell within the applicability domains of the submitted models were evaluated using external validation sets. These were then combined into consensus models to leverage strengths of individual approaches. RESULTS: The resulting consensus predictions, which leverage the collective strengths of each individual model, form the Collaborative Acute Toxicity Modeling Suite (CATMoS). CATMoS demonstrated high performance in terms of accuracy and robustness when compared with in vivo results. DISCUSSION: CATMoS is being evaluated by regulatory agencies for its utility and applicability as a potential replacement for in vivo rat acute oral toxicity studies. CATMoS predictions for more than 800,000 chemicals have been made available via the National Toxicology Program's Integrated Chemical Environment tools and data sets (ice.ntp.niehs.nih.gov). The models are also implemented in a free, standalone, open-source tool, OPERA, which allows predictions of new and untested chemicals to be made. https://doi.org/10.1289/EHP8495.

Passive, continuous monitoring of carbon dioxide geostorage using muon tomography.

Carbon capture and storage is a transition technology from a past and present fuelled by coal, oil and gas and a planned future dominated by renewable energy sources. The technology involves the capture of carbon dioxide emissions from fossil fuel power stations and other point sources, compression of the CO2 into a fluid, transporting it and injecting it deep beneath the Earth's surface into depleted petroleum reservoirs and other porous formations. Once injected, the CO2 must be monitored to ensure that it is emplaced and assimilated as planned and that none leaks back to surface. A variety of methods have been deployed to monitor the CO2 storage site and many such methods have been adapted from oilfield practice. However, such methods are commonly indirect, episodic, require active signal generation and remain expensive throughout the monitoring period that may last for hundreds of years. A modelling framework was developed to concurrently simulate CO2 geostorage conditions and background cosmic-ray muon tomography, in which the potential was assessed for using variations in muon attenuation, due to changes in CO2 abundance, as a means of CO2 detection. From this, we developed a passive, continuous monitoring method for CO2 storage sites using muon tomography, the tools for which can be deployed during the active drilling phase (development) of the storage site. To do this, it was necessary to develop a muon detector that could be used in the hostile environment (saline, high temperature) of the well bore. A prototype detector has been built and tested at the 1.1 km deep Boulby potash mine on the northeast coast of England, supported by the existing STFC Boulby Underground Laboratory on the site. The detector is now ready to be commercialized.This article is part of the Theo Murphy meeting issue 'Cosmic-ray muography'.

Good Cell Culture Practice for stem cells and stem-cell-derived models.

The first guidance on Good Cell Culture Practice (GCCP) dates back to 2005. This document expands this to include aspects of quality assurance for in vitro cell culture focusing on the increasingly diverse cell types and culture formats used in research, product development, testing and manufacture of biotechnology products and cell-based medicines. It provides a set of basic principles of best practice that can be used in training new personnel, reviewing and improving local procedures, and helping to assure standard practices and conditions for the comparison of data between laboratories and experimentation performed at different times. This includes recommendations for the documentation and reporting of culture conditions. It is intended as guidance to facilitate the generation of reliable data from cell culture systems, and is not intended to conflict with local or higher level legislation or regulatory requirements. It may not be possible to meet all recommendations in this guidance for practical, legal or other reasons. However, when it is necessary to divert from the principles of GCCP, the risk of decreasing the quality of work and the safety of laboratory staff should be addressed and any conclusions or alternative approaches justified. This workshop report is considered a first step toward a revised GCCP 2.0.

The Allelic Landscape of Human Blood Cell Trait Variation and Links to Common Complex Disease.

Many common variants have been associated with hematological traits, but identification of causal genes and pathways has proven challenging. We performed a genome-wide association analysis in the UK Biobank and INTERVAL studies, testing 29.5 million genetic variants for association with 36 red cell, white cell, and platelet properties in 173,480 European-ancestry participants. This effort yielded hundreds of low frequency (<5%) and rare (<1%) variants with a strong impact on blood cell phenotypes. Our data highlight general properties of the allelic architecture of complex traits, including the proportion of the heritable component of each blood trait explained by the polygenic signal across different genome regulatory domains. Finally, through Mendelian randomization, we provide evidence of shared genetic pathways linking blood cell indices with complex pathologies, including autoimmune diseases, schizophrenia, and coronary heart disease and evidence suggesting previously reported population associations between blood cell indices and cardiovascular disease may be non-causal.

Dead shrimp blues: a global assessment of extinction risk in freshwater shrimps (Crustacea: Decapoda: Caridea).

We present the first global assessment of extinction risk for a major group of freshwater invertebrates, caridean shrimps. The risk of extinction for all 763 species was assessed using the IUCN Red List criteria that include geographic ranges, habitats, ecology and past and present threats. The Indo-Malayan region holds over half of global species diversity, with a peak in Indo-China and southern China. Shrimps primarily inhabit flowing water; however, a significant subterranean component is present, which is more threatened than the surface fauna. Two species are extinct with a further 10 possibly extinct, and almost one third of species are either threatened or Near Threatened (NT). Threats to freshwater shrimps include agricultural and urban pollution impact over two-thirds of threatened and NT species. Invasive species and climate change have the greatest overall impact of all threats (based on combined timing, scope and severity of threats).

Comparison of radiographic osteoarthritis scores in dogs less than 24 months or greater than 24 months following tibial plateau leveling osteotomy.

Radiographic osteoarthritis scores were determined in 60 dogs up to 3 years following tibial plateau leveling osteotomy. Radiographs taken immediately following surgery and at long-term follow-up 1 to 3 years later were evaluated by 2 certified radiologists using a modified 32-point osteoarthritis scale. Changes in osteoarthritis scores were evaluated by paired t-tests and regression analysis. Sub-groups of dogs were formed to evaluate if osteoarthritis scores changed differently for follow-up periods of < 24 months compared with those > 24 months. There was a significant increase in osteoarthritis score from post-operative to follow-up evaluations for all dogs studied. Regression analysis of the relationship of months after surgery to change in osteoarthritis score was not significant. These results indicate that osteoarthritis did progress following tibial plateau leveling osteotomy, but not in a linear fashion over time.

Comparaison des cotes radiographiques pour l'ostéoarthrite chez les chiens âgés de moins de 24 mois ou de plus de 24 mois après une ostéotomie de stabilisation du plateau tibial. Les cotes radiographiques d'ostéoarthrite ont été déterminées chez 60 chiens jusqu'à 3 ans après une ostéotomie de stabilisation du plateau tibial. Les radiographies prises immédiatement après la chirurgie et au suivi à long terme, de 1 à 3 ans plus tard, ont été évaluées par 2 radiologistes certifiés à l'aide d'une échelle d'ostéoarthrite modifiée de 32 points. Les changements des cotes d'ostéoarthrite ont été évalués à l'aide de tests de t pairés et d'analyses de régression. Des sous-groupes de chiens ont été formés afin d'évaluer si les cotes d'ostéoarthrite avaient évolué différemment pour les périodes de suivi de < 24 mois comparativement à celles de > 24 mois. Il y a eu une hausse importante de la cote d'ostéoarthrite entre les évaluations postopératoires et les évaluations de suivi pour tous les chiens examinés. L'analyse de régression de la relation entre le nombre de mois après la chirurgie et le changement de la cote d'ostéoarthrite n'était pas significative. Les résultats indiquent que l'ostéoarthrite a progressé après l'ostéotomie de stabilisation du plateau tibial, mais non d'une manière linéaire au fil du temps.(Traduit par Isabelle Vallières).

The incidence and outcomes of fetomaternal alloimmune thrombocytopenia: a UK national study using three data sources.

Fetomaternal alloimmune thrombocytopenia (FMAIT) is the most common cause of severe neonatal thrombocytopenia in otherwise well, term infants. First pregnancies are often severely affected. This descriptive, population-based national study was undertaken in order to inform the case for antenatal screening. Cases were identified using three sources and capture-recapture techniques used to generate a robust incidence estimate. One hundred and seventy three cases were identified between October 2006 and September 2008. An extra 20 cases were estimated from capture-recapture analysis, giving an estimated incidence of clinically detected FMAIT of 12·4 cases per 100 000 total births (95%confidence interval: 10·7, 14·3). Fifty-two cases (30%) were known at the start of pregnancy; 120 (70%) were unknown (n=115) or unrecognized (n=5). Unknown cases were more likely to experience a haemorrhagic complication (67% vs. 5%) (P<0·001) and more likely to have an intracranial haemorrhage (20% vs. 4%) (P=0·014) than known cases receiving antenatal management. In view of the incidence of severe disease identified, further assessment of the case for antenatal screening is important. There were a number of cases in which the significance of a history of FMAIT in a previous sibling was not recognized and there is a need to raise awareness of the importance of this diagnosis.

Recipient-derived HPA-1a antibodies: a cause of prolonged thrombocytopenia after unrelated donor stem cell transplantation.

BACKGROUND: Patients with human platelet antigen (HPA) specific antibodies in cases of neonatal alloimmune thrombocytopenia and platelet (PLT) refractoriness derive clinical benefit from the use of HPA-selected PLTs. STUDY DESIGN AND METHODS: This study describes three patients with underlying diagnoses of acute myeloid leukemia, chronic lymphocytic leukemia, and myelodysplasia, respectively, who underwent allogeneic bone marrow transplantation (BMT) with unrelated donors matched at the HLA-A, B, C, Dr, and DQ loci but who failed to achieve an adequate PLT count. Investigation using PLT immunofluorescence test, monoclonal antibody immobilization of PLT antigens assay, and genotyping revealed the presence of recipient-derived HPA-1a antibodies. RESULTS: In two patients, anti-HPA-1a was detected post-BMT and in the third patient, anti-HPA-1a was detected during pre-BMT chemotherapy. Despite apparent 100% engraftment of donor cells, the patients' PLT counts failed to recover 9-10 months posttransplant. The patients remained PLT-transfusion dependent and failed to achieve satisfactory increments following random donor or HLA-matched PLT transfusions. After the identification of HPA-1a antibodies, the patients were supported by HPA-1a(-) PLTs and satisfactory posttransfusion PLT increments were obtained. These cases illustrate that HPA-1a antibodies may remain detectable for 10 months following apparently successful donor engraftment and the disappearance of recipient-derived HLA antibodies. The prolonged persistence of recipient-derived PLT-specific antibodies following BMT has to our knowledge not been described previously. CONCLUSION: HPA-1a antibodies were associated with protracted PLT-transfusion dependence and significant hemorrhagic complications. Appropriate and timely laboratory investigation for HPA-specific antibodies followed by transfusion support with HPA-selected PLTs provided the cornerstone of the hemostatic management in these cases.

Evidence for the specificity for platelet HPA-1a alloepitope and the presenting HLA-DR52a of diverse antigen-specific helper T cell clones from alloimmunized mothers.

Maternal alloantibodies against the human platelet Ag (HPA)-1a allotype of the platelet beta(3) integrin GpIIb/IIIa can cause severe fetal or neonatal hemorrhage. Almost all anti-HPA-1a-immune mothers are homozygous for HPA-1b and carry HLA-DR52a (DRB3*0101). The single Pro(33) -->Leu substitution (HPA-1b-->HPA-1a) was previously predicted to create a binding motif for HLA-DR52a that can lead to alloimmunization. We have isolated six CD4(+) T cell clones from three such mothers, which all respond to intact HPA-1a(+), but not HPA-1b(+), platelets. We used them to define the "core" and "anchor" residues of this natural T cell epitope. Molecular modeling based on a recently published crystal structure can explain the preferential presentation of the Leu(33) (but not Pro(33) variant) by HLA-DR52a rather than the linked HLA-DR3 or the allelic DR52b. The modeling also predicts efficient anchoring at position 33 by several alternative hydrophobic alpha-amino acids; indeed, a recently identified variant with Val(33) is presented well to two clones, and is therefore potentially alloimmunogenic. Finally, these HPA-1a-specific T cell clones use a variety of T cell receptors, but all have a "Th1" (IFN-gamma-producing) profile and are suitable for testing selective immunotherapies that might be applicable in vivo.

HPA-1a antibody potency and bioactivity do not predict severity of fetomaternal alloimmune thrombocytopenia.

BACKGROUND: The antenatal management of fetomaternal alloimmune thrombocytopenia (FMAIT) due to HPA-1a antibodies remains controversial, and a test identifying pregnancies that do not require therapy would be of clinical value. STUDY DESIGN AND METHODS: The statistical correlation was analyzed between clinical outcome and 1) anti-HPA-1a potency in maternal serum samples determined by a monoclonal antibody immobilization of platelet (PLT) antigen assay with an international anti-HPA-1a potency standard and 2) anti-HPA-1a biological activity measured by a monocyte chemiluminescence (CL) assay. RESULTS: A total of 133 pregnancies with FMAIT due to anti-HPA-1a were analyzed. In 97 newly diagnosed cases, there was no difference in antibody potency or CL signal between cases with intracranial hemorrhage (ICH; n = 15), those with no ICH but a PLT count of less than 20 x 10(9) per L (n = 52), and those with a PLT count of at least 20 x 10(9) per L (n = 30). In 22 previously known pregnancies, the positive predictive value of maternal anti-HPA-1a of greater than 30 IU per mL for a PLT count of less than 20 x 10(9) per L was 90 percent, but the negative predictive value was only 66 percent. Antibody potency tended to stay stable throughout pregnancy (n = 16) and from one pregnancy to the next (n = 16). CONCLUSION: Neither severe thrombocytopenia nor ICH in HPA-1a-alloimmunized pregnancies can be predicted with sufficient sensitivity and specificity for clinical application from maternal anti-HPA-1a potency or bioactivity.

Management and outcome of 200 cases of fetomaternal alloimmune thrombocytopenia.

BACKGROUND: Fetomaternal alloimmune thrombocytopenia (FMAIT) is the commonest cause of severe thrombocytopenia in term neonates but its management remains controversial. STUDY DESIGN AND METHODS: A 7-year prospective observational study of 200 cases of FMAIT evaluated the relationship between human platelet antigen (HPA) antibody specificity, clinical presentation, morbidity, mortality, and therapeutic interventions in the antenatal and postnatal period, with long-term follow-up of neonates with intracranial hemorrhage (ICH). RESULTS: In 1148 referrals for FMAIT, HPA antibodies were confirmed in 200 (17%). The commonest specificities were anti-HPA-1a, 150 (75%); anti-HPA-5b, 31 (15.5%); and anti-HPA-15b, 8 (4%). Of 123 (62%) cases (two sets of twins) with no previous history of FMAIT, intrauterine deaths occurred in 5: anti-HPA-1a alone, 3; in combination with anti-HPA-5b, 1; and anti-HPA-15b, 1. Of the 120 live neonates, 103 had severe thrombocytopenia and 17 (14%) developed ICH (anti-HPA-1a, 13; anti-HPA-5b, 3; anti-HPA-15b, 1). Postnatal care varied widely with 37 percent of neonates receiving random rather than HPA-1a and -5b-negative platelets. Of the remaining 77 cases with a history of FMAIT, 40 received intrauterine transfusions. Six (15%) of these fetuses died in utero and an additional 2 developed ICH postnatally. Of the 19 children with ICH, 1 (anti-HPA-15b) died on Day +1, and neurologic sequelae persist in 13 (mean follow-up, 2.5 years). CONCLUSION: HPA-1a antibodies are most commonly implicated in severe thrombocytopenia but HPA-5b and HPA-15b antibodies can also result in poor outcome. Postnatal transfusion management is extremely variable, and fetal transfusions are associated with significant morbidity and mortality.