Chemical data evaluation: general considerations and approaches for IUPAC projects and the chemistry community (IUPAC Technical Report).

The International Union of Pure and Applied Chemistry (IUPAC) has a long tradition of supporting the compilation of chemical data and their evaluation through direct projects, nomenclature and terminology work, and partnerships with international scientific bodies, government agencies and other organizations. The IUPAC Interdivisional Subcommittee on Critical Evaluation of Data (ISCED) has been established to provide guidance on issues related to the evaluation of chemical data. In this first report we define the general principles of the evaluation of scientific data and describe best practices and approaches to data evaluation in chemistry.

Towards improved FAIRness of the ThermoML Archive.

The ThermoML Archive is a subset of Thermodynamics Research Center (TRC) data holdings corresponding to cooperation between NIST TRC and five journals: Journal of Chemical Engineering and Data (ISSN: 1520-5134), The Journal of Chemical Thermodynamics (ISSN: 1096-3626), Fluid Phase Equilibria (ISSN: 0378-3812), Thermochimica Acta (ISSN: 0040-6031), and International Journal of Thermophysics (ISSN: 1572-9567). Data from initial cooperation (around 2003) through the 2019 calendar year are included. The archive has undergone a major update with the goal of improving the FAIRness and user experience of the data provided by the service. The web application provides comprehensive property browsing and searching capabilities; searching relies on a RESTful API provided by the Cordra software for managing digital objects. JSON files with a schema derived from ThermoML are provided as an additional serialization to lower the barrier to programmatic consumption of the information, for stakeholders who may have a preference of JSON over XML. The ThermoML and JSON files for all available entries can be downloaded from data.nist.gov (https://data.nist.gov/od/id/mds2-2422).

Reference Materials for Phase Equilibrium Studies. 1. Liquid-Liquid Equilibria (IUPAC Technical Report).

This article is the first of three projected IUPAC Technical Reports resulting from IUPAC Project 2011-037-2-100 (Reference Materials for Phase Equilibrium Studies). The goal of that project was to select reference systems with critically evaluated property values for the validation of instruments and techniques used in phase equilibrium studies for mixtures. This Report proposes seven systems for liquid-liquid equilibrium studies, covering the four most common categories of binary mixtures: aqueous systems of moderate solubility, non-aqueous systems, systems with low solubility, and systems with ionic liquids. For each system, the available literature sources, accepted data, smoothing equations, and estimated uncertainties are given.

Liquid Viscosity and Surface Tension of n-Hexane, n-Octane, n-Decane, and n-Hexadecane up to 573 K by Surface Light Scattering (SLS).

In the present study, the simultaneous and accurate determination of liquid viscosity and surface tension of the n-alkanes n-hexane (n-C6H14), n-octane (n-C8H18), n-decane (n-C10H22), and n-hexadecane (n-C16H34) by surface light scattering (SLS) in thermodynamic equilibrium is demonstrated. Measurements have been performed over a wide temperature range from 283.15 K up to 473.15 K for n-C6H14, 523.15 K for n-C8H18, and 573.15 K for n-C10H22 as well as n-C16H34. The liquid dynamic viscosity and surface tension data with average total measurement uncertainties (k = 2) of (2.0 and 1.7) % agree with the available literature and contribute to a new database at high temperatures. Over the entire temperature range, a Vogel-type equation for the dynamic viscosity and a modified van der Waals equation for the surface tension represent the measured data for the four n-alkanes within experimental uncertainties. By also considering our former SLS data for n-dodecane (n-C12H26) and n-octacosane (n-C28H58), empirical models for the liquid viscosity and surface tension of n-alkanes were developed as a function of temperature and carbon number covering values between 6 and 28. Agreement between these models and reference correlations for further selected n-alkanes which were not included in the development procedure was found.

Validation of thermophysical data for scientific and engineering applications.

High quality thermophysical property data are essential to many scientific and engineering applications. These data are produced at a high rate and are affected by a range of experimental and reporting error sources that often exceed stated uncertainties. As a result, critical evaluation is required to establish the limits of reliability in a quantified way. The present work describes reporting recommendations and property data validation methods developed and applied at the Thermodynamics Research Center at NIST through the use of the ThermoData Engine (TDE; SRD 103a/b) software. Examples are provided with an emphasis on various consistency checks, which may include the use of equations of state (EOS).

The RNA-Binding Protein HuR Posttranscriptionally Regulates IL-2 Homeostasis and CD4+ Th2 Differentiation.

Posttranscriptional gene regulation by RNA-binding proteins, such as HuR (elavl1), fine-tune gene expression in T cells, leading to powerful effects on immune responses. HuR can stabilize target mRNAs and/or promote translation by interacting with their 3' untranslated region adenylate and uridylate-rich elements. It was previously demonstrated that HuR facilitates Th2 cytokine expression by mRNA stabilization. However, its effects upon IL-2 homeostasis and CD4+ Th2 differentiation are not as well understood. We found that optimal translation of Il2ra (CD25) required interaction of its mRNA with HuR. Conditional HuR knockout in CD4+ T cells resulted in loss of IL-2 homeostasis and defects in JAK-STAT signaling, Th2 differentiation, and cytokine production. HuR-knockout CD4+ T cells from OVA-immunized mice also failed to proliferate in response to Ag. These results demonstrate that HuR plays a pivotal role in maintaining normal IL-2 homeostasis and initiating CD4+ Th2 differentiation.

Thermodynamic Properties at Saturation Derived from Experimental Two-Phase Isochoric Heat Capacity of 1-Hexyl-3-methylimidazolium Bis[(trifluoromethyl)sulfonyl]imide.

New measurements are reported for the isochoric heat capacity of the ionic liquid substance 1-hexyl-3-methylimidazolium bis[(trifluoromethyl)sulfonyl]imide ([C6mim][NTf2]). These measurements extend the ranges of our earlier study [N.G. Polikhronidi et al., Phys. Chem. Liq. 52, 657 (2014)] by 5 % of the compressed liquid density and by 75 kelvins. An adiabatic calorimeter was used to measure one-phase (CV1) liquid and two-phase (CV2) liquid + vapor isochoric heat capacities, densities (ρS ), and phase-transition temperatures (TS ) of the ionic liquid (IL) substance. The combined expanded uncertainty of the density ρ and isochoric heat capacity CV measurements at the 95 % confidence level with a coverage factor of k = 2 is estimated to be 0.15 % and 3 %, respectively. Measurements are concentrated in the immediate vicinity of the liquid + vapor phase transition curve, in order to closely observe phase transitions. The present measurements and those of our earlier study are analyzed together, and are presented in terms of thermodynamic properties (TS, ρS, CV1 and CV2) evaluated at saturation and in terms of key derived thermodynamic properties Cp, CS, [Formula: see text], and [Formula: see text] on the liquid + vapor phase transition curve. A thermodynamic relation by Yang and Yang is used to confirm the internal consistency of measured two-phase heat capacities CV2, which are observed to fall perfectly on a line as a function of specific volume at a constant temperature. The observed linear behavior is exploited to evaluate contributions to the quantity CV2 = f(V,T) from chemical potential [Formula: see text] and from vapor pressure [Formula: see text]. The physical nature and specific details of the temperature and specific volume dependence of the two-phase isochoric heat capacity and some features of the other derived thermodynamic properties of IL at liquid saturation curve are considered in detail.

Transcriptomic-Wide Discovery of Direct and Indirect HuR RNA Targets in Activated CD4+ T Cells.

Due to poor correlation between steady state mRNA levels and protein product, purely transcriptomic profiling methods may miss genes posttranscriptionally regulated by RNA binding proteins (RBPs) and microRNAs (miRNAs). RNA immunoprecipitation (RIP) methods developed to identify in vivo targets of RBPs have greatly elucidated those mRNAs which may be regulated via transcript stability and translation. The RBP HuR (ELAVL1) and family members are major stabilizers of mRNA. Many labs have identified HuR mRNA targets; however, many of these analyses have been performed in cell lines and oftentimes are not independent biological replicates. Little is known about how HuR target mRNAs behave in conditional knock-out models. In the present work, we performed HuR RIP-Seq and RNA-Seq to investigate HuR direct and indirect targets using a novel conditional knock-out model of HuR genetic ablation during CD4+ T activation and Th2 differentiation. Using independent biological replicates, we generated a high coverage RIP-Seq data set (>160 million reads) that was analyzed using bioinformatics methods specifically designed to find direct mRNA targets in RIP-Seq data. Simultaneously, another set of independent biological replicates were sequenced by RNA-Seq (>425 million reads) to identify indirect HuR targets. These direct and indirect targets were combined to determine canonical pathways in CD4+ T cell activation and differentiation for which HuR plays an important role. We show that HuR may regulate genes in multiple canonical pathways involved in T cell activation especially the CD28 family signaling pathway. These data provide insights into potential HuR-regulated genes during T cell activation and immune mechanisms.

Conditional knockout of the RNA-binding protein HuR in CD4⁺ T cells reveals a gene dosage effect on cytokine production.

The posttranscriptional mechanisms by which RNA binding proteins (RBPs) regulate T-cell differentiation and cytokine production in vivo remain unclear. The RBP HuR binds to labile mRNAs, usually leading to increases in mRNA stability and/or translation. Previous work demonstrated that HuR binds to the mRNAs encoding the Th2 transcription factor trans-acting T-cell-specific transcription factor (GATA-3) and Th2 cytokines interleukin (IL)-4 and IL-13, thereby regulating their expression. By using a novel conditional HuR knockout (KO) mouse in which HuR is deleted in activated T cells, we show that Th2-polarized cells from heterozygous HuR conditional (OX40-Cre HuR(fl/+)) KO mice had decreased steady-state levels of Gata3, Il4 and Il13 mRNAs with little changes at the protein level. Surprisingly, Th2-polarized cells from homozygous HuR conditional (OX40-Cre HuR(fl/fl)) KO mice showed increased Il2, Il4 and Il13 mRNA and protein via different mechanisms. Specifically, Il4 was transcriptionally upregulated in HuR KO T cells, whereas Il2 and Il13 mRNA stabilities increased. Additionally, when using the standard ovalbumin model of allergic airway inflammation, HuR conditional KO mice mounted a robust inflammatory response similar to mice with wild-type HuR levels. These results reveal a complex differential posttranscriptional regulation of cytokines by HuR in which gene dosage plays an important role. These findings may have significant implications in allergies and asthma, as well as autoimmune diseases and infection.

ThermoData Engine (TDE): software implementation of the dynamic data evaluation concept. 9. Extensible thermodynamic constraints for pure compounds and new model developments.

ThermoData Engine (TDE) is the first full-scale software implementation of the dynamic data evaluation concept, as reported in this journal. The present article describes the background and implementation for new additions in latest release of TDE. Advances are in the areas of program architecture and quality improvement for automatic property evaluations, particularly for pure compounds. It is shown that selection of appropriate program architecture supports improvement of the quality of the on-demand property evaluations through application of a readily extensible collection of constraints. The basis and implementation for other enhancements to TDE are described briefly. Other enhancements include the following: (1) implementation of model-validity enforcement for specific equations that can provide unphysical results if unconstrained, (2) newly refined group-contribution parameters for estimation of enthalpies of formation for pure compounds containing carbon, hydrogen, and oxygen, (3) implementation of an enhanced group-contribution method (NIST-Modified UNIFAC) in TDE for improved estimation of phase-equilibrium properties for binary mixtures, (4) tools for mutual validation of ideal-gas properties derived through statistical calculations and those derived independently through combination of experimental thermodynamic results, (5) improvements in program reliability and function that stem directly from the recent redesign of the TRC-SOURCE Data Archival System for experimental property values, and (6) implementation of the Peng-Robinson equation of state for binary mixtures, which allows for critical evaluation of mixtures involving supercritical components. Planned future developments are summarized.

Posttranscriptional gene regulation of IL-17 by the RNA-binding protein HuR is required for initiation of experimental autoimmune encephalomyelitis.

IL-17 is a proinflammatory cytokine produced by activated Th17 cells and other immune cells. IL-17-producing Th17 cells are major contributors to chronic inflammatory and autoimmune diseases, such as multiple sclerosis, rheumatoid arthritis, and inflammatory bowel disease. Although the transcriptional regulation of Th17 cells is well understood, the posttranscriptional regulation of IL-17 gene expression remains unknown. The RNA-binding protein HuR positively regulates the stability of many target mRNAs via binding the AU-rich elements present in the 3' untranslated region of many inflammatory cytokines including IL-4, IL-13, and TNF-α. However, the regulation of IL-17 expression by HuR has not been established. CD4(+) Th17 cells from HuR knockout mice had decreased IL-17 steady-state mRNA and protein levels compared with wild-type Th17 cells, as well as decreases in frequency of IL-17(+) cells. Moreover, we demonstrated that HuR directly binds to the IL-17 mRNA 3' untranslated region by using RNA immunoprecipitation and biotin pulldown assays. In addition, the knockout of HuR decreased cellular proliferation of CD4(+) T cells. Mice with adoptively transferred HuR KO Th17 cells had delayed initiation and reduced disease severity in the onset of experimental autoimmune encephalomyelitis compared with wild-type Th17 cells. Our results reveal a HuR-induced posttranscriptional regulatory mechanism of Th17 differentiation that influences IL-17 expression. These findings may provide novel therapeutic targets for the treatment of Th17-mediated autoimmune neuroinflammation.

ThermoData Engine (TDE): software implementation of the dynamic data evaluation concept. 8. Properties of material streams and solvent design.

ThermoData Engine (TDE) is the first full-scale software implementation of the dynamic data evaluation concept, as reported in this journal. The present paper describes the first application of this concept to the evaluation of thermophysical properties for material streams involving any number of chemical components with assessment of uncertainties. The method involves construction of Redlich-Kister type equations for individual properties (excess volume, thermal conductivity, viscosity, surface tension, and excess enthalpy) and activity-coefficient models for phase equilibrium properties (vapor-liquid equilibrium). Multicomponent models are based on those for the pure-components and all binary subsystems evaluated on demand through the TDE software algorithms. Models are described in detail, and extensions to the class structure of the program are provided. Novel program features, such as ready identification of key measurements for subsystems that can reduce the combined uncertainty for a particular stream property, are described. In addition, new product-design features are described for selection of solvents for optimized crystal dissolution, separation of binary crystal mixtures, and solute extraction from a single-component solvent. Planned future developments are summarized.

Method for the isolation and identification of mRNAs, microRNAs and protein components of ribonucleoprotein complexes from cell extracts using RIP-Chip.

As a result of the development of high-throughput sequencing and efficient microarray analysis, global gene expression analysis has become an easy and readily available form of data collection. In many research and disease models however, steady state levels of target gene mRNA does not always directly correlate with steady state protein levels. Post-transcriptional gene regulation is a likely explanation of the divergence between the two. Driven by the binding of RNA Binding Proteins (RBP), post-transcriptional regulation affects mRNA localization, stability and translation by forming a Ribonucleoprotein (RNP) complex with target mRNAs. Identifying these unknown de novo mRNA targets from cellular extracts in the RNP complex is pivotal to understanding mechanisms and functions of the RBP and their resulting effect on protein output. This protocol outlines a method termed RNP immunoprecipitation-microarray (RIP-Chip), which allows for the identification of specific mRNAs associated in the ribonucleoprotein complex, under changing experimental conditions, along with options to further optimize an experiment for the individual researcher. With this important experimental tool, researchers can explore the intricate mechanisms associated with post-transcriptional gene regulation as well as other ribonucleoprotein interactions.

ThermoData Engine (TDE) software implementation of the dynamic data evaluation concept. 7. Ternary mixtures.

ThermoData Engine (TDE) is the first full-scale software implementation of the dynamic data evaluation concept, as reported in this journal. The present paper describes the first application of this concept to the evaluation of thermophysical properties for ternary chemical systems. The method involves construction of Redlich-Kister type equations for individual properties (excess volume, thermal conductivity, viscosity, surface tension, and excess enthalpy) and activity coefficient models for phase equilibrium properties (vapor-liquid and liquid-liquid equilibrium). Constructed ternary models are based on those for the three pure component and three binary subsystems evaluated on demand through the TDE software algorithms. All models are described in detail, and extensions to the class structure of the program are provided. Reliable evaluation of properties for the binary subsystems is essential for successful property evaluations for ternary systems, and algorithms are described to aid appropriate parameter selection and fitting for the implemented activity coefficient models (NRTL, Wilson, Van Laar, Redlich-Kister, and UNIQUAC). Two activity coefficient models based on group contributions (original UNIFAC and NIST-KT-UNIFAC) are also implemented. Novel features of the user interface are shown, and directions for future enhancements are outlined.

Coordinate regulation of GATA-3 and Th2 cytokine gene expression by the RNA-binding protein HuR.

The posttranscriptional mechanisms whereby RNA-binding proteins (RBPs) regulate T cell differentiation remain unclear. RBPs can coordinately regulate the expression of functionally related genes via binding to shared regulatory sequences, such as the adenylate-uridylate-rich elements (AREs) present in the 3' untranslated region (UTR) of mRNA. The RBP HuR posttranscriptionally regulates IL-4, IL-13, and other Th2 cell-restricted transcripts. We hypothesized that the ARE-bearing GATA-3 gene, a critical regulator of Th2 polarization, is under HuR control as part of its coordinate posttranscriptional regulation of the Th2 program. We report that in parallel with stimulus-induced increase in GATA-3 mRNA and protein levels, GATA-3 mRNA half-life is increased after restimulation in the human T cell line Jurkat, in human memory and Th2 cells, and in murine Th2-skewed cells. We demonstrate by immunoprecipitation of ribonucleoprotein complexes that HuR associates with the GATA-3 endogenous transcript in human T cells and found, using biotin pulldown assay, that HuR specifically interacts with its 3'UTR. Using both loss-of-function and gain-of-function approaches in vitro and in animal models, we show that HuR is a critical mediator of stimulus-induced increase in GATA-3 mRNA and protein expression and that it positively influences GATA-3 mRNA turnover, in parallel with selective promotion of Th2 cytokine overexpression. These results suggest that HuR-driven posttranscriptional control plays a significant role in T cell development and effector function in both murine and human systems. A better understanding of HuR-mediated control of Th2 polarization may have utility in altering allergic airway inflammation in human asthmatic patients.

ThermoData Engine (TDE): software implementation of the dynamic data evaluation concept. 6. Dynamic web-based data dissemination through the NIST Web Thermo Tables.

ThermoData Engine (TDE) is the first full-scale software implementation of the dynamic data evaluation concept, as reported recently in this journal. In the present paper, we describe the development of a World Wide Web-based interface to TDE evaluations of pure compound properties, including critical properties, phase boundary equilibria (vapor pressures, sublimation pressures, and crystal-liquid boundary pressures), densities, energetic properties, and transport properties. This includes development of a system for caching evaluation results to maintain high availability and an advanced window-in-window interface that leverages modern Web-browser technologies. Challenges associated with bringing the principal advantages of the TDE technology to the Web are described, as are compromises to maintain general access and speed of interaction while remaining true to the tenets of dynamic data evaluation. Future extensions of the interface and associated Web-services are outlined.

ThermoData Engine (TDE): software implementation of the dynamic data evaluation concept. 5. Experiment planning and product design.

ThermoData Engine (TDE) is the first full-scale software implementation of the dynamic data evaluation concept, as reported recently in this journal. In the present paper, we describe development of an algorithmic approach to assist experiment planning through assessment of the existing body of knowledge, including availability of experimental thermophysical property data, variable ranges studied, associated uncertainties, state of prediction methods, and parameters for deployment of prediction methods and how these parameters can be obtained using targeted measurements, etc., and, indeed, how the intended measurement may address the underlying scientific or engineering problem under consideration. A second new feature described here is the application of the software capabilities for aid in the design of chemical products through identification of chemical systems possessing desired values of thermophysical properties within defined ranges of tolerance. The algorithms and their software implementation to achieve this are described. Finally, implementation of a new data validation and weighting system is described for vapor-liquid equilibrium (VLE) data, and directions for future enhancements are outlined.

Overexpression of the RNA binding protein HuR impairs tumor growth in triple negative breast cancer associated with deficient angiogenesis.

Interactions between RNA binding proteins (RBPs) and genes are not well understood, especially in regulation of angiogenesis. The RBP HuR binds to the AU-rich (ARE) regions of labile mRNAs, facilitating their translation into protein and has been hypothesized to be a tumor-maintenance gene. Elevated levels of cytoplasmic HuR directly correlate with increased invasiveness and poor prognosis for many cancers, including those of the breast. HuR controls the expression of multiple genes involved in angiogenesis including VEGFα, HIF1α and thrombospondin 1 (TSP1). We investigated the role of HuR in estrogen receptor negative (ER(-)) breast cancer. MDA-MB-231 cells with higher levels of HuR have alterations in cell cycle kinetics and faster growth. Unexpectedly, HuR overexpression significantly interfered with tumor growth in orthotopic mouse models. The putative mechanism seems to be an anti-angiogenetic effect by increasing expression of TSP1 but also surprisingly, downregulating VEGF, a target which HuR normally increases. Our findings reveal that HuR may be regulating a cluster of genes involved in blood vessel formation which controls tumor angiogenesis. An approach of modulating HuR levels may overcome limitations associated with monotherapies targeting tumor vessel formation.

The RNA binding protein HuR differentially regulates unique subsets of mRNAs in estrogen receptor negative and estrogen receptor positive breast cancer.

BACKGROUND: The discordance between steady-state levels of mRNAs and protein has been attributed to posttranscriptional control mechanisms affecting mRNA stability and translation. Traditional methods of genome wide microarray analysis, profiling steady-state levels of mRNA, may miss important mRNA targets owing to significant posttranscriptional gene regulation by RNA binding proteins (RBPs). METHODS: The ribonomic approach, utilizing RNA immunoprecipitation hybridized to microarray (RIP-Chip), provides global identification of putative endogenous mRNA targets of different RBPs. HuR is an RBP that binds to the AU-rich elements (ARE) of labile mRNAs, such as proto-oncogenes, facilitating their translation into protein. HuR has been shown to play a role in cancer progression and elevated levels of cytoplasmic HuR directly correlate with increased invasiveness and poor prognosis for many cancers, including those of the breast. HuR has been described to control genes in several of the acquired capabilities of cancer and has been hypothesized to be a tumor-maintenance gene, allowing for cancers to proliferate once they are established. RESULTS: We used HuR RIP-Chip as a comprehensive and systematic method to survey breast cancer target genes in both MCF-7 (estrogen receptor positive, ER+) and MDA-MB-231 (estrogen receptor negative, ER-) breast cancer cell lines. We identified unique subsets of HuR-associated mRNAs found individually or in both cell types. Two novel HuR targets, CD9 and CALM2 mRNAs, were identified and validated by quantitative RT-PCR and biotin pull-down analysis. CONCLUSION: This is the first report of a side-by-side genome-wide comparison of HuR-associated targets in wild type ER+ and ER- breast cancer. We found distinct, differentially expressed subsets of cancer related genes in ER+ and ER- breast cancer cell lines, and noted that the differential regulation of two cancer-related genes by HuR was contingent upon the cellular environment.

Relative volatilities of ionic liquids by vacuum distillation of mixtures.

The relative volatilities of a variety of common ionic liquids have been determined for the first time. Equimolar mixtures of ionic liquids were vacuum-distilled in a glass sublimation apparatus at approximately 473 K. The composition of the initial distillate, determined by NMR spectroscopy, was used to establish the relative volatility of each ionic liquid in the mixture. The effect of alkyl chain length was studied by distilling mixtures of 1-alkyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ionic liquids, or mixtures of N-alkyl-N-methylpyrrolidinium bis(trifluoromethylsulfonyl)imide ionic liquids, with different alkyl chain lengths. For both classes of salts, the volatility is highest when the alkyl side chain is a butyl group. The effect of cation structure on volatility has been determined by distilling mixtures containing different types of cations. Generally speaking, ionic liquids based on imidazolium and pyridinium cations are more volatile than ionic liquids based on ammonium and pyrrolidinium cations, regardless of the types of counterions present. Similarly, ionic liquids based on the anions [(C2F5SO2)2N](-), [(C4F9SO2)(CF3SO2)N](-) , and [(CF3SO2)2N](-) are more volatile than ionic liquids based on [(CF3SO2)3C](-) and [CF3SO3](-), and are much more volatile than ionic liquids based on [PF6](-).