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A challenge for underground CO2 storage is the leakage of the buoyant supercritical gas through microcracks in wellbores that cannot be sealed with current oilfield cements that are too viscous and cannot penetrate the cracks. Polymer gels consisting of pH-sensitive hydrogel particles suspended in an aqueous solution offer a potential alternative. The rheology of aqueous solutions of Carbopol 934 as a model pH-sensitive gel is measured to find the compositions and pHs for both ease of injection and to seal cracks against the flow of bulk CO2 and CO2 dissolved in brine. The polymer gels have low viscosity at low pH and can easily flow into the microcracks. In the elevated pH of the microcracks, the particles swell creating a significant yield stress sufficient to seal leakage pathways. The yield stress reaches a maximum at pHs and it increases with increasing concentration. The flow curves of stress versus shear rate for all pHs and concentrations are well-described by the Herschel-Bulkley model with an exponent of about 0.34 except for highly acidic conditions when the gelant solutions show a much lower yield stresses and higher exponents. The flow curves can be collapsed onto a single universal flow curve rescaled with the yield stress, the low frequency shear modulus and the suspending fluid viscosity. The presence of salts, especially high valence salts, reduce the yield stress of the gels considerably. It is shown that the addition of chelating agents mitigates this effect and can restore more than 30% of the yield stress of the gelant.

Understanding fluid flow in porous media is essential with complex and multiphase fluid flow. We demonstrate that high-resolution in-line density measurements are a valuable tool in this regard. An in-line densitometer is used in fluid flow in porous media applications to quantify fluid production and obtain quantitative and qualitative information such as breakthrough times, emulsion/foam generation, and steam condensation. In order to determine the potential applications for in-line densitometry for fluid flow in porous media, a series of sand pack floods were performed with a densitometer placed at the outlet of a sand pack. All fluids passed through the measurement cell at experiential temperatures and pressures. An algorithm was developed and applied to the density data to provide a quantitative determination of oil and water production. The second series of tests were performed at high temperature and pressure, with a densitometer placed at the inlet and outlet of a sand pack, for steam applications. In both series of experiments, data acquisition was collected at 1 hertz and the analyzed density data was compared to results from the conventional effluent analysis, including Dean-Stark, toluene separations, magnetic susceptibility measurement, and flash calculations where applicable. The high-resolution monitoring of effluent from a flow experiment through porous media in a system with two phases of known densities enables two-phase production to be accurately quantified in the case of both light and heavy oil. The frequency of measurements results in a high-resolution history of breakthrough times and fluid behavior. In the case of monitoring steam injection processes, reliable laboratory tests show that in-line density measurements enable the determination of steam quality at the inlet and outlet of a sand pack and qualitative determination of steam condensation monitoring The use of in-line densitometry provides insight on the monitoring of complex fluid flow in porous media, which typical bulk effluent analysis is not able to do. The ability to measure produced fluids at high resolution and extreme temperatures reduces mass balance error associated with the effluent collection and broadens our understanding of complex fluid flow in porous media.

Abstract Background PubChem is a free and publicly available resource containing substance descriptions and their associated biological activity information. PubChem3D is an extension to PubChem containing computationally-derived three-dimensional (3-D) structures of small molecules. All the tools and services that are a part of PubChem3D rely upon the quality of the 3-D conformer models. Construction of the conformer models currently available in PubChem3D involves a clustering stage to sample the conformational space spanned by the molecule. While this stage allows one to downsize the conformer models to more manageable size, it may result in a loss of the ability to reproduce experimentally determined “bioactive” conformations, for example, found for PDB ligands. This study examines the extent of this accuracy loss and considers its effect on the 3-D similarity analysis of molecules. Results The conformer models consisting of up to 100,000 conformers per compound were generated for 47,123 small molecules whose structures were experimentally determined, and the conformers in each conformer model were clustered to reduce the size of the conformer model to a maximum of 500 conformers per molecule. The accuracy of the conformer models before and after clustering was evaluated using five different measures: root-mean-square distance (RMSD), shape-optimized shape-Tanimoto (STST-opt) and combo-Tanimoto (ComboTST-opt), and color-optimized color-Tanimoto (CTCT-opt) and combo-Tanimoto (ComboTCT-opt). On average, the effect of clustering decreased the conformer model accuracy, increasing the conformer ensemble’s RMSD to the bioactive conformer (by 0.18 ± 0.12 Å), and decreasing the STST-opt, ComboTST-opt, CTCT-opt, and ComboTCT-opt scores (by 0.04 ± 0.03, 0.16 ± 0.09, 0.09 ± 0.05, and 0.15 ± 0.09, respectively). Conclusion This study shows the RMSD accuracy performance of the PubChem3D conformer models is operating as designed. In addition, the effect of PubChem3D sampling on 3-D similarity measures shows that there is a linear degradation of average accuracy with respect to molecular size and flexibility. Generally speaking, one can likely expect the worst-case minimum accuracy of 90% or more of the PubChem3D ensembles to be 0.75, 1.09, 0.43, and 1.13, in terms of STST-opt, ComboTST-opt, CTCT-opt, and ComboTCT-opt, respectively. This expected accuracy improves linearly as the molecule becomes smaller or less flexible.

Abstract Background To improve the utility of PubChem, a public repository containing biological activities of small molecules, the PubChem3D project adds computationally-derived three-dimensional (3-D) descriptions to the small-molecule records contained in the PubChem Compound database and provides various search and analysis tools that exploit 3-D molecular similarity. Therefore, the efficient use of PubChem3D resources requires an understanding of the statistical and biological meaning of computed 3-D molecular similarity scores between molecules. Results The present study investigated effects of employing multiple conformers per compound upon the 3-D similarity scores between ten thousand randomly selected biologically-tested compounds (10-K set) and between non-inactive compounds in a given biological assay (156-K set). When the “best-conformer-pair” approach, in which a 3-D similarity score between two compounds is represented by the greatest similarity score among all possible conformer pairs arising from a compound pair, was employed with ten diverse conformers per compound, the average 3-D similarity scores for the 10-K set increased by 0.11, 0.09, 0.15, 0.16, 0.07, and 0.18 for STST-opt, CTST-opt, ComboTST-opt, STCT-opt, CTCT-opt, and ComboTCT-opt, respectively, relative to the corresponding averages computed using a single conformer per compound. Interestingly, the best-conformer-pair approach also increased the average 3-D similarity scores for the non-inactive–non-inactive (NN) pairs for a given assay, by comparable amounts to those for the random compound pairs, although some assays showed a pronounced increase in the per-assay NN-pair 3-D similarity scores, compared to the average increase for the random compound pairs. Conclusion These results suggest that the use of ten diverse conformers per compound in PubChem bioassay data analysis using 3-D molecular similarity is not expected to increase the separation of non-inactive from random and inactive spaces “on average”, although some assays show a noticeable separation between the non-inactive and random spaces when multiple conformers are used for each compound. The present study is a critical next step to understand effects of conformational diversity of the molecules upon the 3-D molecular similarity and its application to biological activity data analysis in PubChem. The results of this study may be helpful to build search and analysis tools that exploit 3-D molecular similarity between compounds archived in PubChem and other molecular libraries in a more efficient way.

Abstract Background Electron Transfer Dissociation [ETD] can dissociate multiply charged precursor polypeptides, providing extensive peptide backbone cleavage. ETD spectra contain charge reduced precursor peaks, usually of high intensity, and whose pattern is dependent on its parent precursor charge. These charge reduced precursor peaks and associated neutral loss peaks should be removed before these spectra are searched for peptide identifications. ETD spectra can also contain ion-types other than c and z˙. Modifying search strategies to accommodate these ion-types may aid in increased peptide identifications. Additionally, if the precursor mass is measured using a lower resolution instrument such as a linear ion trap, the charge of the precursor is often not known, reducing sensitivity and increasing search times. We implemented algorithms to remove these precursor peaks, accommodate new ion-types in noise filtering routine in OMSSA and to estimate any unknown precursor charge, using Linear Discriminant Analysis [LDA]. Results Spectral pre-processing to remove precursor peaks and their associated neutral losses prior to protein sequence library searches resulted in a 9.8% increase in peptide identifications at a 1% False Discovery Rate [FDR] compared to previous OMSSA filter. Modifications to the OMSSA noise filter to accommodate various ion-types resulted in a further 4.2% increase in peptide identifications at 1% FDR. Moreover, ETD spectra when searched with charge states obtained from the precursor charge determination algorithm is shown to be up to 3.5 times faster than the general range search method, with a minor 3.8% increase in sensitivity. Conclusion Overall, there is an 18.8% increase in peptide identifications at 1% FDR by incorporating the new precursor filter, noise filter and by using the charge determination algorithm, when compared to previous versions of OMSSA.

Abstract Background A significant portion of the biomedical and chemical literature refers to small molecules. The accurate identification and annotation of compound name that are relevant to the topic of the given literature can establish links between scientific publications and various chemical and life science databases. Manual annotation is the preferred method for these works because well-trained indexers can understand the paper topics as well as recognize key terms. However, considering the hundreds of thousands of new papers published annually, an automatic annotation system with high precision and relevance can be a useful complement to manual annotation. Results An automated chemical name annotation system, MeSH Automated Annotations (MAA), was developed to annotate small molecule names in scientific abstracts with tunable accuracy. This system aims to reproduce the MeSH term annotations on biomedical and chemical literature that would be created by indexers. When comparing automated free text matching to those indexed manually of 26 thousand MEDLINE abstracts, more than 40% of the annotations were false-positive (FP) cases. To reduce the FP rate, MAA incorporated several filters to remove "incorrect" annotations caused by nonspecific, partial, and low relevance chemical names. In part, relevance was measured by the position of the chemical name in the text. Tunable accuracy was obtained by adding or restricting the sections of the text scanned for chemical names. The best precision obtained was 96% with a 28% recall rate. The best performance of MAA, as measured with the F statistic was 66%, which favorably compares to other chemical name annotation systems. Conclusions Accurate chemical name annotation can help researchers not only identify important chemical names in abstracts, but also match unindexed and unstructured abstracts to chemical records. The current work is tested against MEDLINE, but the algorithm is not specific to this corpus and it is possible that the algorithm can be applied to papers from chemical physics, material, polymer and environmental science, as well as patents, biological assay descriptions and other textual data.

Abstract Background PubChem is an open repository for small molecules and their experimental biological activity. PubChem integrates and provides search, retrieval, visualization, analysis, and programmatic access tools in an effort to maximize the utility of contributed information. There are many diverse chemical structures with similar biological efficacies against targets available in PubChem that are difficult to interrelate using traditional 2-D similarity methods. A new layer called PubChem3D is added to PubChem to assist in this analysis. Description PubChem generates a 3-D conformer model description for 92.3% of all records in the PubChem Compound database (when considering the parent compound of salts). Each of these conformer models is sampled to remove redundancy, guaranteeing a minimum (non-hydrogen atom pair-wise) RMSD between conformers. A diverse conformer ordering gives a maximal description of the conformational diversity of a molecule when only a subset of available conformers is used. A pre-computed search per compound record gives immediate access to a set of 3-D similar compounds (called "Similar Conformers") in PubChem and their respective superpositions. Systematic augmentation of PubChem resources to include a 3-D layer provides users with new capabilities to search, subset, visualize, analyze, and download data. A series of retrospective studies help to demonstrate important connections between chemical structures and their biological function that are not obvious using 2-D similarity but are readily apparent by 3-D similarity. Conclusions The addition of PubChem3D to the existing contents of PubChem is a considerable achievement, given the scope, scale, and the fact that the resource is publicly accessible and free. With the ability to uncover latent structure-activity relationships of chemical structures, while complementing 2-D similarity analysis approaches, PubChem3D represents a new resource for scientists to exploit when exploring the biological annotations in PubChem.

Abstract Background The use of 3-D similarity techniques in the analysis of biological data and virtual screening is pervasive, but what is a biologically meaningful 3-D similarity value? Can one find statistically significant separation between "active/active" and "active/inactive" spaces? These questions are explored using 734,486 biologically tested chemical structures, 1,389 biological assay data sets, and six different 3-D similarity types utilized by PubChem analysis tools. Results The similarity value distributions of 269.7 billion unique conformer pairs from 734,486 biologically tested compounds (all-against-all) from PubChem were utilized to help work towards an answer to the question: what is a biologically meaningful 3-D similarity score? The average and standard deviation for the six similarity measures STST-opt, CTST-opt, ComboTST-opt, STCT-opt, CTCT-opt, and ComboTCT-opt were 0.54 ± 0.10, 0.07 ± 0.05, 0.62 ± 0.13, 0.41 ± 0.11, 0.18 ± 0.06, and 0.59 ± 0.14, respectively. Considering that this random distribution of biologically tested compounds was constructed using a single theoretical conformer per compound (the "default" conformer provided by PubChem), further study may be necessary using multiple diverse conformers per compound; however, given the breadth of the compound set, the single conformer per compound results may still apply to the case of multi-conformer per compound 3-D similarity value distributions. As such, this work is a critical step, covering a very wide corpus of chemical structures and biological assays, creating a statistical framework to build upon. The second part of this study explored the question of whether it was possible to realize a statistically meaningful 3-D similarity value separation between reputed biological assay "inactives" and "actives". Using the terminology of noninactive-noninactive (NN) pairs and the noninactive-inactive (NI) pairs to represent comparison of the "active/active" and "active/inactive" spaces, respectively, each of the 1,389 biological assays was examined by their 3-D similarity score differences between the NN and NI pairs and analyzed across all assays and by assay category types. While a consistent trend of separation was observed, this result was not statistically unambiguous after considering the respective standard deviations. While not all "actives" in a biological assay are amenable to this type of analysis, e.g., due to different mechanisms of action or binding configurations, the ambiguous separation may also be due to employing a single conformer per compound in this study. With that said, there were a subset of biological assays where a clear separation between the NN and NI pairs found. In addition, use of combo Tanimoto (ComboT) alone, independent of superposition optimization type, appears to be the most efficient 3-D score type in identifying these cases. Conclusion This study provides a statistical guideline for analyzing biological assay data in terms of 3-D similarity and PubChem structure-activity analysis tools. When using a single conformer per compound, a relatively small number of assays appear to be able to separate "active/active" space from "active/inactive" space.

Abstract Background PubChem provides a 3-D neighboring relationship, which involves finding the maximal shape overlap between two static compound 3-D conformations, a computationally intensive step. It is highly desirable to avoid this overlap computation, especially if it can be determined with certainty that a conformer pair cannot meet the criteria to be a 3-D neighbor. As such, PubChem employs a series of pre-filters, based on the concept of volume, to remove approximately 65% of all conformer neighbor pairs prior to shape overlap optimization. Given that molecular volume, a somewhat vague concept, is rather effective, it leads one to wonder: can the existing PubChem 3-D neighboring relationship, which consists of billions of shape similar conformer pairs from tens of millions of unique small molecules, be used to identify additional shape descriptor relationships? Or, put more specifically, can one place an upper bound on shape similarity using other "fuzzy" shape-like concepts like length, width, and height? Results Using a basis set of 4.18 billion 3-D neighbor pairs identified from single conformer per compound neighboring of 17.1 million molecules, shape descriptors were computed for all conformers. These steric shape descriptors included several forms of molecular volume and shape quadrupoles, which essentially embody the length, width, and height of a conformer. For a given 3-D neighbor conformer pair, the volume and each quadrupole component (Qx, Qy, and Qz) were binned and their frequency of occurrence was examined. Per molecular volume type, this effectively produced three different maps, one per quadrupole component (Qx, Qy, and Qz), of allowed values for the similarity metric, shape Tanimoto (ST) ≥ 0.8. The efficiency of these relationships (in terms of true positive, true negative, false positive and false negative) as a function of ST threshold was determined in a test run of 13.2 billion conformer pairs not previously considered by the 3-D neighbor set. At an ST ≥ 0.8, a filtering efficiency of 40.4% of true negatives was achieved with only 32 false negatives out of 24 million true positives, when applying the separate Qx, Qy, and Qz maps in a series (Qxyz). This efficiency increased linearly as a function of ST threshold in the range 0.8-0.99. The Qx filter was consistently the most efficient followed by Qy and then by Qz. Use of a monopole volume showed the best overall performance, followed by the self-overlap volume and then by the analytic volume. Application of the monopole-based Qxyz filter in a "real world" test of 3-D neighboring of 4,218 chemicals of biomedical interest against 26.1 million molecules in PubChem reduced the total CPU cost of neighboring by between 24-38% and, if used as the initial filter, removed from consideration 48.3% of all conformer pairs at almost negligible computational overhead. Conclusion Basic shape descriptors, such as those embodied by size, length, width, and height, can be highly effective in identifying shape incompatible compound conformer pairs. When performing a 3-D search using a shape similarity cut-off, computation can be avoided by identifying conformer pairs that cannot meet the result criteria. Applying this methodology as a filter for PubChem 3-D neighboring computation, an improvement of 31% was realized, increasing the average conformer pair throughput from 154,000 to 202,000 per second per CPU core.

Abstract Background PubChem is a free and open public resource for the biological activities of small molecules. With many tens of millions of both chemical structures and biological test results, PubChem is a sizeable system with an uneven degree of available information. Some chemical structures in PubChem include a great deal of biological annotation, while others have little to none. To help users, PubChem pre-computes "neighboring" relationships to relate similar chemical structures, which may have similar biological function. In this work, we introduce a "Similar Conformers" neighboring relationship to identify compounds with similar 3-D shape and similar 3-D orientation of functional groups typically used to define pharmacophore features. Results The first two diverse 3-D conformers of 26.1 million PubChem Compound records were compared to each other, using a shape Tanimoto (ST) of 0.8 or greater and a color Tanimoto (CT) of 0.5 or greater, yielding 8.16 billion conformer neighbor pairs and 6.62 billion compound neighbor pairs, with an average of 253 "Similar Conformers" compound neighbors per compound. Comparing the 3-D neighboring relationship to the corresponding 2-D neighboring relationship ("Similar Compounds") for molecules such as caffeine, aspirin, and morphine, one finds unique sets of related chemical structures, providing additional significant biological annotation. The PubChem 3-D neighboring relationship is also shown to be able to group a set of non-steroidal anti-inflammatory drugs (NSAIDs), despite limited PubChem 2-D similarity. In a study of 4,218 chemical structures of biomedical interest, consisting of many known drugs, using more diverse conformers per compound results in more 3-D compound neighbors per compound; however, the overlap of the compound neighbor lists per conformer also increasingly resemble each other, being 38% identical at three conformers and 68% at ten conformers. Perhaps surprising is that the average count of conformer neighbors per conformer increases rather slowly as a function of diverse conformers considered, with only a 70% increase for a ten times growth in conformers per compound (a 68-fold increase in the conformer pairs considered). Neighboring 3-D conformers on the scale performed, if implemented naively, is an intractable problem using a modest sized compute cluster. Methodology developed in this work relies on a series of filters to prevent performing 3-D superposition optimization, when it can be determined that two conformers cannot possibly be a neighbor. Most filters are based on Tanimoto equation volume constraints, avoiding incompatible conformers; however, others consider preliminary superposition between conformers using reference shapes. Conclusion The "Similar Conformers" 3-D neighboring relationship locates similar small molecules of biological interest that may go unnoticed when using traditional 2-D chemical structure graph-based methods, making it complementary to such methodologies. The computational cost of 3-D similarity methodology on a wide scale, such as PubChem contents, is a considerable issue to overcome. Using a series of efficient filters, an effective throughput rate of more than 150,000 conformers per second per processor core was achieved, more than two orders of magnitude faster than without filtering.

Abstract Background The shape diversity of 16.4 million biologically relevant molecules from the PubChem Compound database and their 1.46 billion diverse conformers was explored as a function of molecular volume. Results The diversity of shape space was investigated by determining the shape similarity threshold to achieve a maximum on the count of reference shapes per unit of conformer volume. The rate of growth in shape space, as represented by a decreasing shape similarity threshold, was found to be remarkably smooth as a function of volume. There was no apparent correlation between the count of conformers per unit volume and their diversity, meaning that a single reference shape can describe the shape space of many chemical structures. The ability of a volume to describe the shape space of lesser volumes was also examined. It was shown that a given volume was able to describe 40-70% of the shape diversity of lesser volumes, for the majority of the volume range considered in this study. Conclusion The relative growth of shape diversity as a function of volume and shape similarity is surprisingly uniform. Given the distribution of chemicals in PubChem versus what is theoretically synthetically possible, the results from this analysis should be considered a conservative estimate to the true diversity of shape space.

Abstract Background PubChem, an open archive for the biological activities of small molecules, provides search and analysis tools to assist users in locating desired information. Many of these tools focus on the notion of chemical structure similarity at some level. PubChem3D enables similarity of chemical structure 3-D conformers to augment the existing similarity of 2-D chemical structure graphs. It is also desirable to relate theoretical 3-D descriptions of chemical structures to experimental biological activity. As such, it is important to be assured that the theoretical conformer models can reproduce experimentally determined bioactive conformations. In the present study, we investigate the effects of three primary conformer generation parameters (the fragment sampling rate, the energy window size, and force field variant) upon the accuracy of theoretical conformer models, and determined optimal settings for PubChem3D conformer model generation and conformer sampling. Results Using the software package OMEGA from OpenEye Scientific Software, Inc., theoretical 3-D conformer models were generated for 25,972 small-molecule ligands, whose 3-D structures were experimentally determined. Different values for primary conformer generation parameters were systematically tested to find optimal settings. Employing a greater fragment sampling rate than the default did not improve the accuracy of the theoretical conformer model ensembles. An ever increasing energy window did increase the overall average accuracy, with rapid convergence observed at 10 kcal/mol and 15 kcal/mol for model building and torsion search, respectively; however, subsequent study showed that an energy threshold of 25 kcal/mol for torsion search resulted in slightly improved results for larger and more flexible structures. Exclusion of coulomb terms from the 94s variant of the Merck molecular force field (MMFF94s) in the torsion search stage gave more accurate conformer models at lower energy windows. Overall average accuracy of reproduction of bioactive conformations was remarkably linear with respect to both non-hydrogen atom count ("size") and effective rotor count ("flexibility"). Using these as independent variables, a regression equation was developed to predict the RMSD accuracy of a theoretical ensemble to reproduce bioactive conformations. The equation was modified to give a minimum RMSD conformer sampling value to help ensure that 90% of the sampled theoretical models should contain at least one conformer within the RMSD sampling value to a "bioactive" conformation. Conclusion Optimal parameters for conformer generation using OMEGA were explored and determined. An equation was developed that provides an RMSD sampling value to use that is based on the relative accuracy to reproduce bioactive conformations. The optimal conformer generation parameters and RMSD sampling values determined are used by the PubChem3D project to generate theoretical conformer models.

Abstract Background In recent years, the number of High Throughput Screening (HTS) assays deposited in PubChem has grown quickly. As a result, the volume of both the structured information (i.e. molecular structure, bioactivities) and the unstructured information (such as descriptions of bioassay experiments), has been increasing exponentially. As a result, it has become even more demanding and challenging to efficiently assemble the bioactivity data by mining the huge amount of information to identify and interpret the relationships among the diversified bioassay experiments. In this work, we propose a text-mining based approach for bioassay neighboring analysis from the unstructured text descriptions contained in the PubChem BioAssay database. Results The neighboring analysis is achieved by evaluating the cosine scores of each bioassay pair and fraction of overlaps among the human-curated neighbors. Our results from the cosine score distribution analysis and assay neighbor clustering analysis on all PubChem bioassays suggest that strong correlations among the bioassays can be identified from their conceptual relevance. A comparison with other existing assay neighboring methods suggests that the text-mining based bioassay neighboring approach provides meaningful linkages among the PubChem bioassays, and complements the existing methods by identifying additional relationships among the bioassay entries. Conclusions The text-mining based bioassay neighboring analysis is efficient for correlating bioassays and studying different aspects of a biological process, which are otherwise difficult to achieve by existing neighboring procedures due to the lack of specific annotations and structured information. It is suggested that the text-mining based bioassay neighboring analysis can be used as a standalone or as a complementary tool for the PubChem bioassay neighboring process to enable efficient integration of assay results and generate hypotheses for the discovery of bioactivities of the tested reagents.

Abstract Background The study of protein-small molecule interactions is vital for understanding protein function and for practical applications in drug discovery. To benefit from the rapidly increasing structural data, it is essential to improve the tools that enable large scale binding site prediction with greater emphasis on their biological validity. Results We have developed a new method for the annotation of protein-small molecule binding sites, using inference by homology, which allows us to extend annotation onto protein sequences without experimental data available. To ensure biological relevance of binding sites, our method clusters similar binding sites found in homologous protein structures based on their sequence and structure conservation. Binding sites which appear evolutionarily conserved among non-redundant sets of homologous proteins are given higher priority. After binding sites are clustered, position specific score matrices (PSSMs) are constructed from the corresponding binding site alignments. Together with other measures, the PSSMs are subsequently used to rank binding sites to assess how well they match the query and to better gauge their biological relevance. The method also facilitates a succinct and informative representation of observed and inferred binding sites from homologs with known three-dimensional structures, thereby providing the means to analyze conservation and diversity of binding modes. Furthermore, the chemical properties of small molecules bound to the inferred binding sites can be used as a starting point in small molecule virtual screening. The method was validated by comparison to other binding site prediction methods and to a collection of manually curated binding site annotations. We show that our method achieves a sensitivity of 72% at predicting biologically relevant binding sites and can accurately discriminate those sites that bind biological small molecules from non-biological ones. Conclusions A new algorithm has been developed to predict binding sites with high accuracy in terms of their biological validity. It also provides a common platform for function prediction, knowledge-based docking and for small molecule virtual screening. The method can be applied even for a query sequence without structure. The method is available at http://www.ncbi.nlm.nih.gov/Structure/ibis/ibis.cgi.

Abstract Correction to Chakrabarti S, Lanczycki CJ, Panchenko AR, Przytycka TM, Thiessen PA and Bryant SH: State of the art: refinement of multiple sequence alignments. BMC Bioinformatics 2006, 7:499.

Abstract PubChem is an important public, Web-based information source for chemical and bioactivity information. In order to provide convenient structure search methods on compounds stored in this database, one mandatory component is a Web-based drawing tool for interactive sketching of chemical query structures. Web-enabled chemical structure sketchers are not new, being in existence for years; however, solutions available rely on complex technology like Java applets or platform-dependent plug-ins. Due to general policy and support incident rate considerations, Java-based or platform-specific sketchers cannot be deployed as a part of public NCBI Web services. Our solution: a chemical structure sketching tool based exclusively on CGI server processing, client-side JavaScript functions, and image sequence streaming. The PubChem structure editor does not require the presence of any specific runtime support libraries or browser configurations on the client. It is completely platform-independent and verified to work on all major Web browsers, including older ones without support for Web2.0 JavaScript objects.

Abstract Background Recent advances in high-throughput screening (HTS) techniques and readily available compound libraries generated using combinatorial chemistry or derived from natural products enable the testing of millions of compounds in a matter of days. Due to the amount of information produced by HTS assays, it is a very challenging task to mine the HTS data for potential interest in drug development research. Computational approaches for the analysis of HTS results face great challenges due to the large quantity of information and significant amounts of erroneous data produced. Results In this study, Decision Trees (DT) based models were developed to discriminate compound bioactivities by using their chemical structure fingerprints provided in the PubChem system http://pubchem.ncbi.nlm.nih.gov. The DT models were examined for filtering biological activity data contained in four assays deposited in the PubChem Bioassay Database including assays tested for 5HT1a agonists, antagonists, and HIV-1 RT-RNase H inhibitors. The 10-fold Cross Validation (CV) sensitivity, specificity and Matthews Correlation Coefficient (MCC) for the models are 57.2~80.5%, 97.3~99.0%, 0.4~0.5 respectively. A further evaluation was also performed for DT models built for two independent bioassays, where inhibitors for the same HIV RNase target were screened using different compound libraries, this experiment yields enrichment factor of 4.4 and 9.7. Conclusion Our results suggest that the designed DT models can be used as a virtual screening technique as well as a complement to traditional approaches for hits selection.

Abstract Background Large chemical databases require fast, efficient, and simple ways of looking for similar structures. Although such tasks are now fairly well resolved for graph-based similarity queries, they remain an issue for 3D approaches, particularly for those based on 3D shape overlays. Inspired by a recent technique developed to compare molecular shapes, we designed a hybrid methodology, alignment-recycling, that enables efficient retrieval and alignment of structures with similar 3D shapes. Results Using a dataset of more than one million PubChem compounds of limited size (< 28 heavy atoms) and flexibility (< 6 rotatable bonds), we obtained a set of a few thousand diverse structures covering entirely the 3D shape space of the conformers of the dataset. Transformation matrices gathered from the overlays between these diverse structures and the 3D conformer dataset allowed us to drastically (100-fold) reduce the CPU time required for shape overlay. The alignment-recycling heuristic produces results consistent with de novo alignment calculation, with better than 80% hit list overlap on average. Conclusion Overlay-based 3D methods are computationally demanding when searching large databases. Alignment-recycling reduces the CPU time to perform shape similarity searches by breaking the alignment problem into three steps: selection of diverse shapes to describe the database shape-space; overlay of the database conformers to the diverse shapes; and non-optimized overlay of query and database conformers using common reference shapes. The precomputation, required by the first two steps, is a significant cost of the method; however, once performed, querying is two orders of magnitude faster. Extensions and variations of this methodology, for example, to handle more flexible and larger small-molecules are discussed.

Abstract Background Accurate multiple sequence alignments of proteins are very important in computational biology today. Despite the numerous efforts made in this field, all alignment strategies have certain shortcomings resulting in alignments that are not always correct. Refinement of existing alignment can prove to be an intelligent choice considering the increasing importance of high quality alignments in large scale high-throughput analysis. Results We provide an extensive comparison of the performance of the alignment refinement algorithms. The accuracy and efficiency of the refinement programs are compared using the 3D structure-based alignments in the BAliBASE benchmark database as well as manually curated high quality alignments from Conserved Domain Database (CDD). Conclusion Comparison of performance for refined alignments revealed that despite the absence of dramatic improvements, our refinement method, REFINER, which uses conserved regions as constraints performs better in improving the alignments generated by different alignment algorithms. In most cases REFINER produces a higher-scoring, modestly improved alignment that does not deteriorate the well-conserved regions of the original alignment.

Coronaviruses represent a diverse family of enveloped positive-sense single stranded RNA viruses. COVID-19, caused by Severe Acute Respiratory Syndrome Coronavirus-2, is a highly contagious respiratory disease transmissible mainly via close contact and respiratory droplets which can result in severe, life-threatening respiratory pathologies. It is understood that glutathione, a naturally occurring antioxidant known for its role in immune response and cellular detoxification, is the target of various proinflammatory cytokines and transcription factors resulting in the infection, replication, and production of reactive oxygen species. This leads to more severe symptoms of COVID-19 and increased susceptibility to other illnesses such as tuberculosis. The emergence of vaccines against COVID-19, usage of monoclonal antibodies as treatments for infection, and implementation of pharmaceutical drugs have been effective methods for preventing and treating symptoms. However, with the mutating nature of the virus, other treatment modalities have been in research. With its role in antiviral defense and immune response, glutathione has been heavily explored in regard to COVID-19. Glutathione has demonstrated protective effects on inflammation and downregulation of reactive oxygen species, thereby resulting in less severe symptoms of COVID-19 infection and warranting the discussion of glutathione as a treatment mechanism.

One critical yet understudied concept associated with cancer information is cancer fatalism, i.e. deterministic thoughts about the cause of cancer, the inability to prevent it and the unavoidability of death upon diagnosis. The aim of this study is to understand how information seeking about cancer online influences cancer fatalism and whether and to what extent education and eHealth literacy moderate the relationship between them. Findings from an online survey of a nationally representative sample in the United States (N = 578) showed differential impacts of using the internet to search for information about cancer among the more and the less educated. For the less educated, more exposure to information about cancer via medical and health websites led to an increased level of cancer fatalism, whereas among the more educated, greater exposure lowered cancer fatalism. These differences were explained by the fact that the more educated were equipped with a higher level of eHealth literacy skills than the less educated. Findings show that only when one has necessary skills to apply digital resources can those resources help mitigate cancer fatalism. We suggest the need to enhance eHealth literacy skills among the less educated to reduce cancer fatalism., (� The Author(s) 2019. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

Background: There is no effective way to predict cystic fibrosis (CF) pulmonary exacerbations (CFPE) before they become symptomatic or to assess satisfactory treatment responses., Methods: RNA sequencing of peripheral blood neutrophils from CF patients before and after therapy for CFPE was used to create transcriptome profiles. Transcripts with an average transcripts per million (TPM) level > 1.0 and a false discovery rate (FDR) < 0.05 were used in a cosine K-nearest neighbor (KNN) model. Real time PCR was used to corroborate RNA sequencing expression differences in both neutrophils and whole blood samples from an independent cohort of CF patients. Furthermore, sandwich ELISA was conducted to assess plasma levels of MRP8/14 complexes in CF patients before and after therapy., Results: We found differential expression of 136 transcripts and 83 isoforms when we compared neutrophils from CF patients before and after therapy (>1.5 fold change, FDR-adjusted P < 0.05). The model was able to successfully separate CF flare samples from those taken from the same patients in convalescence with an accuracy of 0.75 in both the training and testing cohorts. Six differently expressed genes were confirmed by real time PCR using both isolated neutrophils and whole blood from an independent cohort of CF patients before and after therapy, even though levels of myeloid related protein MRP8/14 dimers in plasma of CF patients were essentially unchanged by therapy., Conclusions: Our findings demonstrate the potential of machine learning approaches for classifying disease states and thus developing sensitive biomarkers that can be used to monitor pulmonary disease activity in CF., (Copyright © 2018 European Cystic Fibrosis Society. Published by Elsevier B.V. All rights reserved.)

Neonates suffering from pulmonary hypertension of the newborn (PPHN) continue to represent an important proportion of patients requiring intensive neonatal care, and have an increased risk of morbidity and mortality. The human fetus has evolved to maintain a high pulmonary vascular resistance (PVR) in utero to allow the majority of the fetal circulation to bypass the lungs, which do not participate in gas exchange, towards the low resistance placenta. At birth, oxygen plays a major role in decreasing PVR to enhance pulmonary blood flow and establish the lungs as the organ of gas exchange. The failure of PVR to fall following birth results in PPHN, and oxygen remains the mainstay therapeutic intervention in the management of PPHN. Knowledge gaps on what constitutes the optimal oxygenation target leads to a wide variation in practices, and often leads to excessive oxygen use. Owing to the risk of oxygen toxicity, avoiding hyperoxemia is as important as avoiding hypoxemia in the management of PPHN. Current evidence supports maintaining arterial oxygen tension in the range of 50-80 mm Hg, and oxygen saturation between 90-97% in term infants with hypoxemic respiratory failure. Clinical studies evaluating the optimal oxygenation in the treatment of PPHN will be enthusiastically awaited., Competing Interests: The authors declare no conflict of interest.

Mammalian cells are amenable to the study of regulatory mechanisms dictating cell cycle progression in vitro by shifting them into the same phase of the cycle. Procedures to arrest cultured cells in specific phases of the cell cycle may be termed in vitro synchronization. The procedure described here was developed for the study of primary astrocytes and a glioma cell line, but is broadly applicable to other mammalian cells. Its application allows astrocytes to re-enter the cell cycle from a state of quiescence (G 0 ) under carefully defined experimental conditions to move together into subsequent phases such as the G 1 and S phases. A number of methods have been established to synchronize mammalian cell cultures, which include counterflow centrifugal elutriation, mitotic shake off, chemically induced cell cycle arrest, and newer live cell methods, such as cell permeable dyes. Yet, there are intrinsic limitations associated with these methods. In the present protocol, we describe a simple, reliable, and reversible procedure to synchronize astrocyte and glioma cultures from newborn rat brain by serum deprivation. The procedure is similar, and generally applicable, to other mammalian cells. This protocol consists essentially of two parts: (1) proliferation of astrocytes under optimal conditions in vitro until reaching desired confluence; and (2) synchronization and G 0 phase arrest of cultures by serum down-shift. This procedure has been utilized to examine cell cycle control in astroglioma cells and astrocytes from injured adult brain. It has also been employed in precursor cloning studies in developmental biology, suggesting wide applicability.

Background: Airway obstruction due to enlargement of tonsils and adenoids is a common pediatric problem resulting in sleep disordered breathing. The cause for the relatively abnormal growth of tonsils and adenoids is poorly understood., Methods: Non-acutely ill children undergoing tonsillectomy and adenoidectomy (T&A) for various reasons were enrolled prospectively in a study to determine the frequency of asymptomatic respiratory viral infections in each lymphoid tissue and to relate the number and types of virus to the degree of airway obstruction. Molecular techniques were used to detect 9 respiratory viruses while Brodsky scores and measurements of percentages airway obstruction were used to estimate the degree of airway compromise due to the tonsil and adenoid, respectively., Results: Viruses were detected in 70.9% of tonsils and 94.7% of adenoids, p < 0.001. Adenovirus was the most common virus detected at 71.1%. Adenoids had an average of 2.4 viruses compared to 0.92 for tonsils, p < 0.001. Higher Brodsky scores were only associated with EBV in tonsils, p = 0.03, while greater percentages of airway obstruction in the adenoids were associated with adenovirus, EBV, corona virus, parainfluenza virus and rhinovirus, p ≤ 0.005., Conclusions: Asymptomatic viral infections are common and directly related to the degree of airway obstruction significantly more often in adenoids than tonsils., (Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.)

Background: Extracellular matrix is used in various applications. We present our preliminary experience using a new device that consists of a porcine extracellular matrix with an epithelial basement membrane (MatriStem(®), ACell, Inc. Columbia, MD, USA) for adolescent pilonidal disease., Methods: A retrospective review of four patients with pilonidal disease was undertaken. Three occurred in the gluteal cleft, and the fourth in the umbilicus. In the first patient, the wound deficit was filled with lyophilized MicroMatrix powder and a sheet of Multilayer Wound Matrix was placed to cover the wound. In the second patient, two sinus tracts were debrided, packed with MicroMatrix, and a sheet of fenestrated Burn Matrix was applied. In the third patient, MicroMatrix and Surgical Matrix PSMX (six-layer) was applied as a roll filling the dead space. In the last patient, an umbilical sinus 3 cm deep was packed with MicroMatrix powder followed by a rolled sheet of 2-ply Surgical Matrix RS. Patients were evaluated weekly post-operatively, and more MicroMatrix and sheet material was added if a wound deficit was still present. Measurements were taken in two dimensions, diameter and depth, to characterize wounds., Results: Resolution of wound deficit was graphed versus time. Pain was assessed by scoring 0-10. Rapid wound closure was achieved. Two of the patients had failed wound healing with saline dressing changes prior to MatriStem application. These two patients in particular were highly satisfied with the comfort of the MatriStem approach relative to their time with saline dressings. Most had no pain after 1 week when bolster sutures were removed., Conclusion: In the treatment of open pilonidal wounds in adolescents, porcine urinary bladder matrix wound care devices offer closure times and cost similar to well-established methods while offering a substantial advantage in terms of patient comfort and convenience. This preliminary experience supports a prospective study.

Purpose: We sought to develop a temperature-based respiratory instrument to measure respiration noninvasively outside critical care settings., Method: Respiratory temperature profiles were recorded using a temperature-based noninvasive instrument comprised of three rapid responding medical-grade thermistors-two in close proximity to the mouth/nose (sensors) and one remote to the airway (reference). The effect of the gas flow rate on the amplitude of the tracings was determined. The temperature-based instrument, the Linshom Respiratory Monitoring Device (LRMD) was mounted to a face mask and positioned on a mannequin face. Respiratory rates of 5-40 breaths·min(-1) were then delivered to the mannequin face in random order using artificial bellows (IngMar Lung Model). Data from the sensors were collected and compared with the bellows rates using least squares linear regression and coefficient of determination. The investigators breathed at fixed rates of 0-60 breaths·min(-1) in synchrony with a metronome as their respiratory temperature profiles were recorded from sensors mounted to either a face mask or nasal prongs. The recordings were compared with a contemporaneously recorded sidestream capnogram from a CARESCAPE GEB450 Monitor. The extracted respiratory rates from the LRMD tracings and capnograms were compared using linear regression with a coefficient of determination and a Bland-Altman plot., Results: The amplitude of the sensor tracings was independent of the oxygen flow rate. Respiratory rates from the new temperature-based sensor were synchronous and correlated identically with both the artificial bellows (r(2) = 0.9997) and the capnometer mounted to both the face mask and nasal prongs (r(2) = 0.99; bias = -0.17; 95% confidence interval, -2.15 to 1.8)., Conclusions: Respiratory rates using the LRMD, a novel temperature-based respiratory instrument, were consistent with those using capnometry.

Study Objective: This study aimed to characterize the current practice patterns with cuffed tracheal tubes (CTT) in neonates, infants, and children among members of the Society of Pediatric Anesthesia (SPA)., Design and Setting: An electronic mail survey was distributed using Survey Monkey to members of SPA between December 2013 and February 2014. Each member was permitted one response., Patients/intervention/measurements: Not applicable as this is a practice survey study., Main Results: A total of 805 (28%) of the 2901 members of the SPA responded. Of the respondents, 88% were from the US, 83% were fellowship trained, 82% practiced pediatric anesthesia >50% of the time, and 65% practiced in academic centers. Eighty-five percent used CTT >50% of the time in children >2 years and 60% used CTT in full-term neonates >50% of the time. Twenty-nine percent reported always using CTT whereas 5% reported never using CTT. Those in practice <5 years, who were fellowship trained or in academic practice used CTT more often in neonates compared with those in practice >20 years, not fellowship trained or in private practice (P< .0001, P= .0003 and P= .0005, respectively). The most common reason for avoiding CTT was concern about post-extubation stridor (39%). Almost 70% of respondents accept the TT if it passes the subglottis without resistance and has a leak at 15 to 20 cmH2O. More than 60% of respondents do not monitor cuff pressures in CTT., Conclusion: A majority of SPA members routinely use CTT in neonates, infants and children., (Copyright © 2016 Elsevier Inc. All rights reserved.)

Biliary disease in children has changed over the past few decades, with a marked rise in incidence-perhaps most related to the parallel rise in pediatric obesity-as well as a rise in cholecystectomy rates. In addition to stone disease (cholelithiasis), acalculous causes of gallbladder pain such as biliary dyskinesia, also appear to be on the rise and present diagnostic and treatment conundrums to surgeons., (Copyright © 2016 Elsevier Inc. All rights reserved.)

Kidney disease disparately affects those of African descent. Age trends have generally been established for kidney function in the overall US population, but the contribution of age at the time of immigration for African immigrants is unknown. To examine the independent and joint effects of age and age at the time of immigration, and kidney function. Estimated glomerular filtration rate (eGFR) was calculated for 93 African immigrants (60 % male; mean age = 33.5). Hierarchical regression and post hoc analyses revealed a significant age × age at the time of immigration interaction after accounting for traditional risk factors among those who immigrated at age ≤21. Younger age at the time of immigration to the US may exacerbate an inverse relationship between age and kidney function in a self-identified healthy African immigrant sample. Investigation of biopsychosocial factors associated with kidney health among African immigrants is warranted.

Comprehensive care of patients in conflict and disaster requires coordination of medical, social, and public health agencies. Pediatric patients in these settings comprise a particularly vulnerable group subject to disruption of social networks and separation from family, inadequate surgical care due to lack of surgeon, anesthetist, and nursing specialization, and a general lack of advocacy within the global public health agenda. In the recent upswell of attention to the global surgical burden of disease and deficiencies in necessary infrastructure, the needs of pediatric surgical patients remain underappreciated and underemphasized amid calls for improvement in global surgical health. Experience in recent natural and man-made disasters has demonstrated that pediatric patients makeup a significant proportion of those injured, and has perhaps refocused our need to better characterize the surgical needs of children in conflict and disaster. In addition to treat such patients, we recognize the unmet challenges of improving pediatric emergency and surgical infrastructures in the low- and middle-income country settings where conflict and disaster occur most often, and continuing to advocate for vulnerable children worldwide and keep them out of harm's way., (Copyright © 2016 Elsevier Inc. All rights reserved.)

Aim: This article aims to gain understanding into the perception of undergraduate dental students in terms of their confidence and competence at performing root canal treatment and their perception of the quality of endodontic education., Methods: An online questionnaire was distributed to all 3rd, 4th and 5th year dental students at Cardiff University via their academic e-mail addresses. The questionnaire utilised both scaled response and open questions to gain an insight into undergraduate opinion., Results: Out of a possible 208 students, 98 responses were obtained (response rate = 47%). Perception of competence and confidence were significantly greater amongst the more senior year groups (P < 0.01). However, 49% (n = 38) of participants did not feel competent performing root canal treatment on anterior, single-rooted teeth, whilst 74% (n = 70) did not feel competent performing root canal treatment on posterior, multirooted teeth. Free comments from participants indicated that this was due to a lack of clinical experience. Approximately, 80% of participants ranked education in endodontics at Cardiff University as ≤5 on a Likert scale (1 = inadequate to 10 = good), indicating that improvement was required. Improvements that were suggested by the students included the provision of further information within lectures, a broader range of lecturers, an increased number of shorter, more organised practical sessions, additional training equipment, greater supervision and online reference guides to root canal treatment., Conclusion: Enhancing undergraduate education in endodontics is necessary to increase students' perception of their confidence and competence when performing root canal treatment., (© 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)

Persistent pulmonary hypertension of the newborn (PPHN) is characterized by elevated pulmonary vascular resistance resulting in right-to-left shunting of blood and hypoxemia. PPHN is often secondary to parenchymal lung disease (such as meconium aspiration syndrome, pneumonia or respiratory distress syndrome) or lung hypoplasia (with congenital diaphragmatic hernia or oligohydramnios) but can also be idiopathic. The diagnosis of PPHN is based on clinical evidence of labile hypoxemia often associated with differential cyanosis. The diagnosis is confirmed by the echocardiographic demonstration of - (a) right-to-left or bidirectional shunt at the ductus or foramen ovale and/or, (b) flattening or leftward deviation of the interventricular septum and/or, (c) tricuspid regurgitation, and finally (d) absence of structural heart disease. Management strategies include optimal oxygenation, avoiding respiratory and metabolic acidosis, blood pressure stabilization, sedation and pulmonary vasodilator therapy. Failure of these measures would lead to consideration of extracorporeal membrane oxygenation (ECMO); however decreased need for this rescue therapy has been documented with advances in medical management. While trends also note improved survival, long-term neurodevelopmental disabilities such as deafness and learning disabilities remain a concern in many infants with severe PPHN. Funded by: 1R01HD072929-0 (SL).

Aim: To assess the deformation of HyFlex CM instruments (Coltene Whaledent) when used in two instrumentation sequences and to assess their shape recovery after heat sterilization., Methodology: Simulated root canals with four different shapes were prepared with HyFlex CM instruments using a single-length technique (n = 40) or a crown down technique (n = 40). Pre-preparation, post-preparation and post-sterilization standardized images of each instrument were recorded. Assessment of instrument deformation and their subsequent shape recovery was carried out visually and by comparing the digitised images. Data analysis was carried out using chi-square tests., Results: None of the 400 instruments fractured. Visual assessment of instruments post-preparation revealed that 30.5% had unwound and 0.5% had reverse winding. Following sterilization 8.5% remained unwound and 0.5% remained with reverse winding. When assessing instrument shape using digital images, 35.25% were unwound post-preparation, which reduced to 11% post-sterilization. Nine size 25, 0.08 instruments deformed, but none fully regained their original shape after sterilization; however, other sizes of deformed instruments did regain their shape (P < 0.001)., Conclusion: Approximately one third of instruments became deformed as a result of use. However, two thirds of these fully recovered their shape following sterilization. The number of deformed instruments was underestimated when no magnification was used for assessment. Instrument size was related to incidence of deformation and shape recovery., (© 2014 International Endodontic Journal. Published by John Wiley & Sons Ltd.)

The relatively young specialty field of pediatric neurosurgery addresses a number of surgical diseases that, while first encountered in children, may involve long-term post-operative sequelae that persist into adulthood. These diagnoses present a challenge for care providers as patients transition from pediatric to adult age groups. Brain tumors, shunted hydrocephalus, and myelomeningocele are three of the most common examples of this interesting category. The provision of coordinated transitional care to affected pediatric neurosurgical patients is made all the more difficult by the common comorbidity of developmental delay, affecting not only personal and social growth but also the character and composition of the care team. This article seeks to provide a background for some of the common pediatric neurosurgical diseases requiring a transitional care framework for survivors entering young adulthood, a summary of the adult surgical care challenges faced by these patients, and a rationale for different approaches to optimize care., (Copyright © 2015 Elsevier Inc. All rights reserved.)

Birth asphyxia accounts for about 23% of the approximately 4 million neonatal deaths each year worldwide (Black et al, Lancet, 2010, 375(9730):1969-87). The majority of newborn infants require little assistance to undergo physiologic transition at birth and adapt to extrauterine life. Approximately 10% of infants require some assistance to establish regular respirations at birth. Less than 1% need extensive resuscitative measures such as chest compressions and approximately 0.06% require epinephrine (Wyllie et al, Resuscitation, 2010, 81 Suppl 1:e260-e287). Transition at birth is mediated by significant changes in circulatory and respiratory physiology. Ongoing research in the field of neonatal resuscitation has expanded our understanding of neonatal physiology enabling the implementation of improved recommendations and guidelines on how to best approach newborns in need for intervention at birth. Many of these recommendations are extrapolated from animal models and clinical trials in adults. There are many outstanding controversial issues in neonatal resuscitation that need to be addressed. This article provides a comprehensive and critical literature review on the most relevant and current research pertaining to evolving new strategies in neonatal resuscitation. The key elements to a successful neonatal resuscitation include ventilation of the lungs while minimizing injury, the judicious use of oxygen to improve pulmonary blood flow, circulatory support with chest compressions, and vasopressors and volume that would hasten return of spontaneous circulation. Several exciting new avenues in neonatal resuscitation such as delayed cord clamping, sustained inflation breaths, and alternate vasopressor agents are briefly discussed. Finally, efforts to improve resuscitative efforts in developing countries through education of basic steps of neonatal resuscitation are likely to decrease birth asphyxia and neonatal mortality.

Background: Miller laryngoscope blades are preferred for laryngoscopy in infants and children <2 yr of age. Despite their long history, the laryngeal view with the Miller blade size 1 has never been compared with that with the Macintosh (MAC) blade in children. This prospective, single-blinded, randomized study was designed to compare the laryngeal views with the size 1 Miller and MAC blades in children <2 yr., Methods: With IRB approval, 50 ASA I and II children <2 yr undergoing elective surgery were enrolled. After an inhalation induction and neuromuscular block with i.v. rocuronium 0.5 mg kg(-1), two laryngeal views were obtained with a single blade (Miller or MAC) in each child: one lifting the epiglottis and another lifting the tongue base. The best laryngeal views in each blade position were photographed with a SONY(®) Cyber-shot camera and rated by a blinded anaesthesiologist using the percentage of glottic opening scale., Results: The scores with the Miller blade lifting the epiglottis and the MAC blade lifting the tongue base were similar. The scores with the Miller blade lifting the epiglottis and the tongue base were similar. The scores for the MAC blade lifting the tongue base were greater than those lifting the epiglottis (95% confidence interval: 7.6-26.8) (P=0.0004)., Conclusions: In infants and children <2 yr of age, optimal laryngeal views may be obtained with either the Miller size 1 blade lifting the epiglottis or with the Miller or MAC blades lifting the tongue base., Clinical Trial Registration: NCT01717872 at Clinical Trials.gov., (© The Author 2014. Published by Oxford University Press on behalf of the British Journal of Anaesthesia. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)

Purpose: We investigated the effects of tidal volume (VT), fresh gas flow (FGF), and a charcoal filter in the inspiratory limb on the washout of sevoflurane from the following Datex Ohmeda (GE) Anesthesia Workstations (AWSs): Aisys, Aestiva/5, and Excel 210SE., Methods: After equilibrating the AWSs with 2% sevoflurane, the anesthetic was discontinued, and the absorbent anesthesia breathing circuit (ABC), reservoir bag, and test lung were changed. The lung was ventilated with 350 or 200 mL·breath(-1), 15 breaths·min(-1), and a FGF of 10 L·min(-1) while the washout of sevoflurane was performed in triplicate using a calibrated Datex Ohmeda Capnomac Ultima™ and a calibrated MIRAN SapphIRe XL ambient air analyzer until the concentration was ≤ 10 parts per million (ppm). The effects of decreasing the FGF to 5 and 2 L·min(-1) after the initial washout and of a charcoal filter in the ABC were recorded separately., Results: The median washout times with the Aisys AWS (14 min, P < 0.01) and the Aestiva/5 (17 min, P < 0.001) with VT 350 mL·breath(-1) were significantly less than that with the Excel 210SE (32 min). The mean (95% confidence interval) washout time with the Aisys increased to 23.5 (21.5 to 25.5) min with VT 200 mL·breath(-1) (P < 0.01). Decreasing the FGF from 10 to 5 and 2 L·min(-1) with the Aisys caused a rebound in sevoflurane concentration to ≥ 50 ppm. Placement of a charcoal filter in the inspiratory limb reduced the sevoflurane concentration to < 2 ppm in the Aisys and Aestiva/5 AWSs within two minutes., Conclusion: The GE AWSs should be purged with large FGFs and VTs ~350 mL·breath(-1) for ~25 min to achieve 10 ppm sevoflurane. The FGF should be maintained to avoid a rebound in anesthetic concentration. Charcoal filters rapidly decrease the anesthetic concentration to < 2 ppm.

Persistent pulmonary hypertension of the newborn (PPHN) is a syndrome of failed circulatory adaptation at birth, seen in about 2/1000 live born infants. While it is mostly seen in term and near-term infants, it can be recognized in some premature infants with respiratory distress or bronchopulmonary dysplasia. Most commonly, PPHN is secondary to delayed or impaired relaxation of the pulmonary vasculature associated with diverse neonatal pulmonary pathologies, such as meconium aspiration syndrome, congenital diaphragmatic hernia, and respiratory distress syndrome. Gentle ventilation strategies, lung recruitment, inhaled nitric oxide, and surfactant therapy have improved outcome and reduced the need for extracorporeal membrane oxygenation (ECMO) in PPHN. Newer modalities of treatment discussed in this article include systemic and inhaled vasodilators like sildenafil, prostaglandin E1, prostacyclin, and endothelin antagonists. With prompt recognition/treatment and early referral to ECMO centers, the mortality rate for PPHN has significantly decreased. However, the risk of potential neurodevelopmental impairment warrants close follow-up after discharge for infants with PPHN., (© 2013 Published by Elsevier Inc.)

Evidence for the role of oxidative stress in the pathophysiology of mycotoxin-related illness is increasing. The glutathione antioxidant and detoxification systems play a major role in the antioxidant function of cells. Exposure to mycotoxins in humans requires the production of glutathione on an "as needed" basis. Research suggests that mycotoxins can decrease the formation of glutathione due to decreased gene expression of the enzymes needed to form glutathione. Mycotoxin-related compromise of glutathione production can result in an excess of oxidative stress that leads to tissue damage and systemic illness. The review discusses the mechanisms by which mycotoxin-related deficiency of glutathione may lead to both acute and chronic illnesses.

Although pharmacological interventions have been successful in reducing prevention of maternal to child transmission (PMTCT) of HIV, there is concern that complete elimination through this mode of transmission will require other measures. Immunotherapies in infants or pregnant mothers may be able to eradicate this form of transmission. A recent vaccine trial in adults showed encouraging results, but as in most HIV safety and efficacy vaccine trials, the question of MTCT was not addressed. Concentrating transmission studies and vaccine studies in the setting of MTCT offers several advantages. MTCT has a generally reproducible known transmission rate and has been successfully used to assess pharmacological interventions on decreasing transmission. Even in resource poor settings, the infrastructure for neonatal vaccination is already in place. Although rare, both passive and active vaccination trials have been successfully completed in pediatric populations. Unfortunately, little success in affecting MTCT has been shown. Largely, a correlate of protection in any type of transmission, including MTCT, is unknown. Data supports a role for antibodies in effecting strain and transmission during MTCT. The role of antibodies in MTCT is reviewed with a focus on recent passive immunization and considerations for future studies.

A majority of T cells from chronic inflammatory tissues derived from patients with nasal polyposis were found to express an effector memory phenotype. We report here that these memory T cells failed to activate NF-κB in response to TCR stimulation but responded normally when the proximal TCR signaling molecules were bypassed with PMA and ionomycin. The dysfunction of these cells was associated with a decrease in the phosphorylation of several TCR proximal signaling molecules including ZAP70, Lck and SLP-76. In addition to the disruption in the TCR signaling pathway, the nasal polyp-associated T cells were shown to have a defect in their ability to translocate LAMP-1 to the cell surface. The results presented here establish that the phenotype and anergy of the T cells in the nasal polyp are similar to those which is seen in memory T cells derived from human tumors and other sites of chronic inflammation.

A 38-year-old woman with a 2-year history of chronic neck pain radiating down her right arm underwent radiological and neurological evaluations, which revealed no anatomical cause for her pain. She sought alternative therapies including intramuscular heparin injections. Following a right occipital injection of heparin, cyanocobalamin, and lidocaine, she had a sudden cardiorespiratory arrest and was successfully resuscitated, but did not regain consciousness.Computed tomography of the head and neck and subsequent autopsy revealed a right vertebral artery dissection, but at autopsy, no significant subarachnoid hemorrhage was noted at the base of the brain. This is the first case report where heparin (a potent anticoagulant) used in an occipital injection was documented to cause a vertebral artery dissection. It is also the first reported case where radiographically and histologically documented vertebral artery dissection did not present with overwhelming subarachnoid hemorrhage at the base of the brain. The subtle gross anatomical findings in this case highlight the importance of evaluating the cervical spinal cord in any case of sudden cardiorespiratory arrest following even apparently minor neck injury.

Opinion Statement: Therapies for relapsing-remitting pediatric multiple sclerosis (MS) are aimed at preventing relapses (disease modifying therapies), treating acute attacks, and managing disabling cognitive and physical symptoms. Initial disease modifying therapy to prevent relapses should use one of four first-line injectable therapies that are approved for adult relapsing-remitting MS: interferon beta 1a IM, interferon beta 1a SC, interferon beta 1b SC, or glatiramer acetate. If breakthrough disease occurs or the medication is poorly tolerated, the next step should be to try one of the other first-line therapies. If the first-line therapies have been exhausted, second-line therapies such as natalizumab, cyclophosphamide, or mitoxantrone may be considered. One must use caution when choosing these potent therapies, as secondary effects may include serious infection or malignancy. Phase III studies in adult MS have been published on two oral agents, fingolimod and cladribine, and fingolimod has received FDA approval for use in relapsing-remitting MS in adults. These drugs have not been evaluated in the pediatric MS population, nor have any of three other oral agents now in phase III development: laquinimod, BG-12, and teriflunomide. Acute relapses can be treated with pulse methylprednisolone at a dosage of 20 to 30 mg/kg per day (maximum 1 g per day) for 3 to 5 days. If this is ineffective, intravenous immunoglobulin (2 g/kg divided over 2-5 days) or plasmapheresis may be considered. Neuropsychological, physical therapy, and occupational therapy screening should be performed on patients with pediatric MS. Interventions focusing on visual motor integration may be particularly useful in this group Spasticity may be treated with symptomatic therapies, but one must be aware of potential adverse effects of agents such as baclofen and diazepam. Headache, fatigue, anxiety, and depression are frequently seen, and patients may need a psychiatry consultation and counseling.

Children with neuromuscular diseases present a wide range of clinical manifestations and clinical implications for the anaesthesiologist. Neuromuscular diseases in children affect muscle strength by either directly weakening the muscle fibrils or indirectly by a degenerative nerve supply and weak neuromuscular junction. Of the more than 200 neuromuscular disorders known, the vast majority are genetic in origin. This review focuses on four of the more common neuromuscular disorders with emphasis on their pathophysiology and clinical implications for anaesthesiologists: malignant hyperthermia, the muscular dystrophies (Duchenne's, Becker's, and Emery-Dreifuss), mitochondrial disorders, and cerebral palsy.

Intravenous immunoglobulin (IgIV) has immune modulating effects on the differentiation and function of dendritic cells (DC). Peripheral blood CD14+ monocytes were induced to differentiate into immature DC with IL-4/GM-CSF. DC maturation was analyzed by flow cytometry, and function assessed for antigen uptake and antigen processing. IgIV added during the differentiation process induced immature DC to differentiate into a mature DC with increased expression of CD83 and CCR7. A "priming" step with low concentrations of LPS or other TLR agonists that utilize the myD88 signaling pathway was necessary to observe these changes. These modulated DCs had reduced antigen uptake, but exhibited increased antigen presentation. Treatment of the IgIV with pepsin to generate F(ab')2 fragments abrogated these effects on DC maturation and function. The enhanced differentiation of PBM into DC required two signals: an initial exposure to low concentrations of LPS followed by IVIG. The second signal with IVIG was Fc dependent., (Copyright © 2010 Elsevier Inc. All rights reserved.)