Demonstrating the reliability of in vivo metabolomics based chemical grouping: towards best practice.

While grouping/read-across is widely used to fill data gaps, chemical registration dossiers are often rejected due to weak category justifications based on structural similarity only. Metabolomics provides a route to robust chemical categories via evidence of shared molecular effects across source and target substances. To gain international acceptance, this approach must demonstrate high reliability, and best-practice guidance is required. The MetAbolomics ring Trial for CHemical groupING (MATCHING), comprising six industrial, government and academic ring-trial partners, evaluated inter-laboratory reproducibility and worked towards best-practice. An independent team selected eight substances (WY-14643, 4-chloro-3-nitroaniline, 17α-methyl-testosterone, trenbolone, aniline, dichlorprop-p, 2-chloroaniline, fenofibrate); ring-trial partners were blinded to their identities and modes-of-action. Plasma samples were derived from 28-day rat tests (two doses per substance), aliquoted, and distributed to partners. Each partner applied their preferred liquid chromatography-mass spectrometry (LC-MS) metabolomics workflows to acquire, process, quality assess, statistically analyze and report their grouping results to the European Chemicals Agency, to ensure the blinding conditions of the ring trial. Five of six partners, whose metabolomics datasets passed quality control, correctly identified the grouping of eight test substances into three categories, for both male and female rats. Strikingly, this was achieved even though a range of metabolomics approaches were used. Through assessing intrastudy quality-control samples, the sixth partner observed high technical variation and was unable to group the substances. By comparing workflows, we conclude that some heterogeneity in metabolomics methods is not detrimental to consistent grouping, and that assessing data quality prior to grouping is essential. We recommend development of international guidance for quality-control acceptance criteria. This study demonstrates the reliability of metabolomics for chemical grouping and works towards best-practice.

Cellular and Acellular Assays for Measuring Oxidative Stress Induced by Ambient and Laboratory-Generated Aerosols.

INTRODUCTION: Many studies have established associations between exposure to air pollution, or atmospheric particulate matter (PM), and adverse health effects. An increasing array of studies have suggested oxidative stress as a possible mechanism by which PM-induced health effects arise, and as a result, many chemical and cellular assays have been developed to study PM-induced oxidant production. Although significant progress has been made in recent years, there are still many gaps in this area of research that have not been addressed. Many prior studies have focused on the aerosol of primary origin (e.g., the aerosol emitted from combustion engines) although the aerosol formed from the oxidation of volatile species, secondary organic aerosol (SOA), has been shown to be the predominant type of aerosol even in urban areas. Current SOA health studies are limited in number, and as such, the health effects of SOA are poorly characterized. Also, there is a lack of perspective in terms of the relative toxicities of different SOA systems. Additionally, although chemical assays have identified some SOA constituents associated with adverse health endpoints, the applicability of these results to cellular responses has not been well established. SPECIFIC AIMS: The overall objective of this study was to better understand the oxidative properties of different types and components of PM mixtures (especially SOA) through systematic laboratory chamber experiments and ambient field studies. The study had four specific aims.1 To develop a cellular assay optimized for measuring reactive oxygen and nitrogen species (ROS/RNS) production resulting from PM exposure and to identify a robust parameter that could represent ROS/RNS levels for comparison with different endpoints.2 To identify ambient PM components associated with ROS/RNS production and evaluate whether results from chemical assays represented cellular responses in terms of ROS/RNS production.3 To investigate and provide perspective on the relative toxicities of SOA formed from common biogenic and anthropogenic precursors under different conditions (e.g., humidity, nitrogen oxides [NOx], and redox-active metals) and identify bulk aerosol properties associated with cellular responses.4 To investigate the effects of photochemical aging on aerosol toxicity. METHODS: Ambient PM samples were collected from urban and rural sites in the greater Atlanta area as part of the Southeastern Center for Air Pollution and Epidemiology (SCAPE) study between June 2012 and October 2013. The concentrations of water-soluble species (e.g., water-soluble organic carbon [WSOC], brown carbon [Br C], and metals) were characterized using a variety of instruments. Samples for this study were chosen to span the observed range of dithiothreitol (DTT) activities.Laboratory studies were conducted in the Georgia Tech Environmental Chamber (GTEC) facility in order to generate SOA under well-controlled photooxidation conditions. Precursors of biogenic origin (isoprene, α-pinene, and ß-caryophyllene) and anthropogenic origin (pentadecane, m-xylene, and naphthalene) were oxidized under various formation conditions (dry vs. humid, NOx, and ammonium sulfate vs. iron sulfate seed particles) to produce SOA of differing chemical composition and mass loading. For the naphthalene system, a series of experiments were conducted with different initial hydrocarbon concentrations to produce aerosols with various degree of oxidation. A suite of instruments was utilized to monitor gas- and particle-phase species. Bulk aerosol properties (e.g., O:C, H:C, and N:C ratios) were measured using a high-resolution time-of-flight aerosol mass spectrometer. Filter samples were collected for chemical oxidative potential and cellular measurements. For the naphthalene system, multiple filter samples were collected over the course of a single experiment to collect aerosols of different photochemical aging.For all filter samples, chemical oxidative potentials were determined for water-soluble extracts using a semiautomated DTT assay system. Murine alveolar macrophages and neonatal rat ventricular myocytes were also exposed to PM samples extracted in cell culture medium to investigate cellular responses. ROS/RNS production was detected using the intracellular ROS/RNS probe, carboxy-2',7'-dichlorodihydrofluorescein diacetate (carboxy-H2DCFA), whereas cellular metabolic activity was assessed using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT). Finally, cytokine production, that is, secreted levels of tumor necrosis factor-α (TNF-α) and interleukin-6 (IL-6), were measured post-exposure using an enzyme-linked immunosorbent assay (ELISA). To identify PM constituents associated with oxidative properties, linear regressions between oxidative properties (cellular responses or DTT activity) and aerosol composition (metals, elemental ratios, etc.) were evaluated using Pearson's correlation coefficient, where the significance was determined using multiple imputation and evaluated using a 95% confidence interval. RESULTS: We optimized several parameters for the ROS/RNS assay, including cell density (2 × 104 cells/well for macrophages and 3.33 × 104 cells/well for cardiomyocytes), probe concentration (10 µM), and sample incubation time (24 hours). Results from both ambient and laboratory-generated aerosols demonstrate that ROS/RNS production was highly dose-dependent and nonlinear with respect to PM dose. Of the dose-response metrics investigated in this study (maximum response, dose at which the response is 10% above the baseline [threshold], dose at which 50% of the response is attained [EC50], rate at which the maximum response is attained [Hill slope], and area under the dose-response curve [AUC]), we found that the AUC was the most robust parameter whose informativeness did not depend on dose range.A positive, significant correlation was observed between ROS/RNS production as represented by AUC and chemical oxidative potential as measured by DTT for ambient samples collected in summer. Conversely, a relatively constant AUC was observed for ambient samples collected in winter regardless of the corresponding DTT activity. We also identified several PM constituents (WSOC, BrC, iron, and titanium) that were significantly correlated with AUC for summer samples. The strong correlation between organic species and ROS/RNS production highlights a need to understand the contribution of organic aerosols to PM-induced health effects. No significant correlations were observed for other ROS/RNS metrics or PM constituents, and no spatial trends were observed.For laboratory-generated aerosol, precursor identity influenced oxidative potentials significantly, with isoprene and naphthalene SOA having the lowest and highest DTT activities, respectively. Both precursor identity and formation condition significantly influenced inflammatory responses induced by SOA exposure, and several response patterns were identified for SOA precursors whose photooxidation products share similar carbon-chain length and functionalities. The presence of iron sulfate seed particles did not have an apparent effect on oxidative potentials; however, a higher level of ROS/RNS production was observed for all SOA formed in the presence of iron sulfate compared with ammonium sulfate. We also identified a significant positive correlation between ROS/RNS production and average carbon oxidation state, a bulk aerosol property. It may therefore be possible to roughly estimate ROS/RNS production using this property, which is readily obtainable. This correlation may have significant implications as aerosols have an atmospheric lifetime of a week, during which average carbon oxidation state increases because of atmospheric photochemical aging. Our results suggest that aerosols might become more toxic as they age in the atmosphere. Finally, in the context of ambient samples, laboratory-generated SOA induced comparable or higher levels of ROS/RNS. Oxidative potentials for all laboratory SOA systems, with the exception of naphthalene (which was higher), were all comparable with oxidative potentials observed in ambient samples.

Predictive value of abdominal CT in evaluating internal herniation after bariatric laparoscopic Roux-en-Y gastric bypass.

BACKGROUND: Internal herniation, a serious complication after bariatric surgery, is challenging to diagnose. The aim of this study was to determine the accuracy of abdominal CT in diagnosing internal herniation. METHODS: The study included consecutive patients who had undergone laparoscopic gastric bypass surgery between 1 January 2011 and 1 January 2015 at a bariatric centre of excellence. To select patients suspected of having internal herniation, reports of abdominal CT and reoperations up to 1 January 2017 were screened. CT was presumed negative for internal herniation if no follow-up CT or reoperation was performed within 90 days after the initial CT, or no internal herniation was found during reoperation. The accuracy of abdominal CT in diagnosing internal herniation was calculated using two-way contingency tables. RESULTS: A total of 1475 patients were included (84·7 per cent women, mean age 46·5 years, median initial BMI 41·8 kg/m2 ). CT and/or reoperation was performed in 192 patients (13·0 per cent) in whom internal herniation was suspected. Internal herniation was proven laparoscopically in 37 of these patients. The incidence of internal herniation was 2·5 per cent. An analysis by complaint included a total of 265 episodes, for which 247 CT scans were undertaken. CT was not used to investigate 18 episodes, but internal herniation was encountered in one-third of these during reoperation. Combining the follow-up and intraoperative findings, the accuracy of CT for internal herniation had a sensitivity of 83·8 (95 per cent c.i. 67·3 to 93·2) per cent, a specificity of 87·1 (81·7 to 91·2) per cent, a positive predictive value of 53·4 (40·0 to 66·5) per cent and a negative predictive value of 96·8 (92·9 to 98·7) per cent. CONCLUSION: Abdominal CT is an important tool in diagnosing internal herniation, with a high specificity and a high negative predictive value.

Developing Multipollutant Exposure Indicators of Traffic Pollution: The Dorm Room Inhalation to Vehicle Emissions (DRIVE) Study.

Introduction: The Dorm Room Inhalation to Vehicle Emissions (DRIVE2) study was conducted to measure traditional single-pollutant and novel multipollutant traffic indicators along a complete emission-to-exposure pathway. The overarching goal of the study was to evaluate the suitability of these indicators for use as primary traffic exposure metrics in panel-based and small-cohort epidemiological studies. Methods: Intensive field sampling was conducted on the campus of the Georgia Institute of Technology (GIT) between September 2014 and January 2015 at 8 monitoring sites (2 indoors and 6 outdoors) ranging from 5 m to 2.3 km from the busiest and most congested highway artery in Atlanta. In addition, 54 GIT students living in one of two dormitories either near (20 m) or far (1.4 km) from the highway were recruited to conduct personal exposure sampling and weekly biomonitoring. The pollutants measured were selected to provide information about the heterogeneous particulate and gaseous composition of primary traffic emissions, including the traditional traffic-related species (e.g., carbon monoxide [CO], nitrogen dioxide [NO2], nitric oxide [NO], fine particulate matter [PM2.5], and black carbon [BC]), and of secondary species (e.g., ozone [O3] and sulfate as well as organic carbon [OC], which is both primary and secondary) from traffic and other sources. Along with these pollutants, we also measured two multipollutant traffic indicators: integrated mobile source indicators (IMSIs) and fine particulate matter oxidative potential (FPMOP). IMSIs are derived from elemental carbon (EC), CO, and nitrogen oxide (NOx) concentrations, along with the fractions of these species emitted by gasoline and diesel vehicles, to construct integrated estimates of gasoline and diesel vehicle impacts. Our FPMOP indicator was based on an acellular assay involving the depletion of dithiothreitol (DTT), considering both water-soluble and insoluble components (referred to as FPMOPtotal-DTT). In addition, a limited assessment of 18 low-cost sensors was added to the study to supplement the four original aims. Results: Pollutant levels measured during the study showed a low impact by this highway hotspot source on its surrounding vicinity. These findings are broadly consistent with results from other studies throughout North America showing decreased relative contributions to urban air pollution from primary traffic emissions. We view these reductions as an indication of a changing near-road environment, facilitated by the effectiveness of mobile source emission controls. Many of the primary pollutant species, including NO, CO, and BC, decreased to near background levels by 20 to 30 m from the highway source. Patterns of correlation among the sites also varied by pollutant and time of day. NO2 exhibited spatial trends that differed from those of the other single-pollutant primary traffic indicators. We believe this was caused by kinetic limitations in the photochemical chemistry, associated with primary emission reductions, required to convert the NO-dominant primary NOx, emitted from automobiles, to NO2. This finding provides some indication of limitations in the use of NO2 as a primary traffic exposure indicator in panel-based health effect studies. Roadside monitoring of NO, CO, and BC tended to be more strongly correlated with sites, both near and far from the road, during morning rush hour periods and often weakly to moderately correlated during other time periods of the day. This pattern was likely associated with diurnal changes in mixing and chemistry and their impact on spatial heterogeneity across the campus. Among our candidate multipollutant primary traffic indicators, we report several key findings related to the use of oxidative potential (OP)-based indicators. Although earlier studies have reported elevated levels of FPMOP in direct exhaust emissions, we found that atmospheric processing further enhanced FPMOPtotal-DTT, likely associated with the oxidation of primary polycyclic aromatic hydrocarbons (PAHs) to quinones and hydroxyquinones and with the oxidization and water solubility of metals. This has important implications in terms both of the utility of FPMOPtotal-DTT as a marker for exhaust emissions and of the importance of atmospheric processing of particulate matter (PM) being tied to potential health outcomes. The results from the personal exposure monitoring also point to the complexity and diversity of the spatiotemporal variability patterns among the study monitoring sites and the importance of accounting for location and spatial mobility when estimating exposures in panel-based and small-cohort studies. This was most clearly demonstrated with the personal BC measurements, where ambient roadside monitoring was shown to be a poor surrogate for exposures to BC. Alternative surrogates, including ambient and indoor BC at the participants' respective dorms, were more strongly associated with personal BC, and knowledge of the participants' mean proximity to the highway was also shown to explain a substantial level of the variability in corresponding personal exposures to both BC and NO2. In addition, untargeted metabolomic indicators measured in plasma and saliva, which represent emerging methods for measuring exposure, were used to extract approximately 20,000 and 30,000 features from plasma and saliva, respectively. Using hydrophilic interaction liquid chromatography (HILIC) in the positive ion mode, we identified 221 plasma features that differed significantly between the two dorm cohorts. The bimodal distribution of these features in the HILIC column was highly idiosyncratic; one peak consisted of features with elevated intensities for participants living in the near dorm; the other consisted of features with elevated intensities for participants in the far dorm. Both peaks were characterized by relatively short retention times, indicative of the hydrophobicity of the identified features. The results from the metabolomics analyses provide a strong basis for continuing this work toward specific chemical validation of putative biomarkers of traffic-related pollution. Finally, the study had a supplemental aim of examining the performance of 18 low-cost CO, NO, NO2, O3, and PM2.5 pollutant sensors. These were colocated alongside the other study monitors and assessed for their ability to capture temporal trends observed by the reference monitoring instrumentation. Generally, we found the performance of the low-cost gas-phase sensors to be promising after extensive calibration; the uncalibrated measurements alone, however, would likely not have led to reliable results. The low-cost PM sensors we evaluated had poor accuracy, although PM sensor technology is evolving quickly and warrants future attention. Conclusions: An immediate implication of the changing near-road environment is that future studies aimed at characterizing hotspots related to mobile sources and their impacts on health will need to consider multiple approaches for characterizing spatial gradients and exposures. Specifically and most directly, the mobile source contributions to ambient concentrations of single-pollutant indicators of traffic exposure are not as distinguishable to the degree that they have been in the past. Collectively, the study suggests that characterizing exposures to traffic-related pollutants, which is already difficult, will become more difficult because of the reduction in traffic-related emissions. Additional multi-tiered approaches should be considered along with traditional measurements, including the use of alternative OP measures beyond those based on DTT assays, metabolomics, low-cost sensors, and air quality modeling.

Iron solubility related to particle sulfur content in source emission and ambient fine particles.

The chemical factors influencing iron solubility (soluble iron/total iron) were investigated in source emission (e.g., biomass burning, coal fly ash, mineral dust, and mobile exhaust) and ambient (Atlanta, GA) fine particles (PM2.5). Chemical properties (speciation and mixing state) of iron-containing particles were characterized using X-ray absorption near edge structure (XANES) spectroscopy and micro-X-ray fluorescence measurements. Bulk iron solubility (soluble iron/total iron) of the samples was quantified by leaching experiments. Major differences were observed in iron solubility in source emission samples, ranging from low solubility (<1%, mineral dust and coal fly ash) up to 75% (mobile exhaust and biomass burning emissions). Differences in iron solubility did not correspond to silicon content or Fe(II) content. However, source emission and ambient samples with high iron solubility corresponded to the sulfur content observed in single particles. A similar correspondence between bulk iron solubility and bulk sulfate content in a series of Atlanta PM2.5 fine particle samples (N = 358) further supported this trend. In addition, results of linear combination fitting experiments show the presence of iron sulfates in several high iron solubility source emission and ambient PM2.5 samples. These results suggest that the sulfate content (related to the presence of iron sulfates and/or acid-processing mechanisms by H(2)SO(4)) of iron-containing particles is an important proxy for iron solubility.

Comparative analyses of multi-species sequences from targeted genomic regions.

The systematic comparison of genomic sequences from different organisms represents a central focus of contemporary genome analysis. Comparative analyses of vertebrate sequences can identify coding and conserved non-coding regions, including regulatory elements, and provide insight into the forces that have rendered modern-day genomes. As a complement to whole-genome sequencing efforts, we are sequencing and comparing targeted genomic regions in multiple, evolutionarily diverse vertebrates. Here we report the generation and analysis of over 12 megabases (Mb) of sequence from 12 species, all derived from the genomic region orthologous to a segment of about 1.8 Mb on human chromosome 7 containing ten genes, including the gene mutated in cystic fibrosis. These sequences show conservation reflecting both functional constraints and the neutral mutational events that shaped this genomic region. In particular, we identify substantial numbers of conserved non-coding segments beyond those previously identified experimentally, most of which are not detectable by pair-wise sequence comparisons alone. Analysis of transposable element insertions highlights the variation in genome dynamics among these species and confirms the placement of rodents as a sister group to the primates.

Drying stress and damage processes in human stratum corneum.

SYNOPSIS: The drying stresses that develop in stratum corneum (SC) are crucial for its mechanical and biophysical function, its cosmetic feel and appearance, and play a central role in processes of dry skin damage. However, quantitative methods to characterize these stresses are lacking and little understanding exists regarding the effects of drying environment, chemical exposures and moisturizing treatments. We describe the application of a substrate curvature technique adapted for biological tissue to accurately characterize SC drying stresses as a function of time following environmental pre-conditioning and chemical treatment in a range of drying environments. SC stresses were observed to increase to stress levels of up to approximately 3 MPa over periods of 8 h depending on pretreatment and drying environment. A unique relationship between the SC stress and water in the drying environment was established. The effect of glycerol on lowering SC stresses and damaging surfactants on elevating SC stresses were quantified. Extensions of the method to continuous monitoring of SC stresses in response to changes in environmental moisture content and temperature are reported. Finally, a biomechanics framework to account for the SC drying stress as a mechanical driving force for dry skin damage is presented.

Neuronal adaptations, neuroendocrine and immune correlates of heroin self-administration.

Opioid receptor-mediated action in the central nervous system (CNS) has been consistently shown to trigger changes in the hypothalamic-pituitary-adrenal (HPA) axis and the sympathetic nervous system (SNS) and suppress a variety of parameters of immune function in investigator-delivered paradigms. Overwhelming evidence supports the concept that the CNS undergoes numerous and complex neuronal adaptive changes in addicts, and in animal models of heroin addiction as a result of the training of drug stimuli to serve as reinforcers, altering the function of individual neurons and the larger neural circuits within which the neurons operate. Taken together, these advances suggest that since plastic neuronal changes occur in drug addiction and related animal model paradigms, profiles of neuroendocrine and immune function would differ in a rat model of heroin self-administration compared to passive infusion of drug. Self-administration of heroin induces neuronal circuitry adaptations in specific brain regions that may be related to alterations in neuroendocrine and T lymphocyte function also observed. Animals self-administering (SA) heroin exhibit increased mu-opioid receptor agonist ([D-Ala2, N-Me-Phe4, Gly5-ol]-enkephalin (DAMGO))-stimulated guanosine-5'-O-(gamma-thio)-triphosphate ([(35)S]GTPgammaS) binding in the anterior hypothalamus (50% and 33%) and rostral medial thalamus (33% and 36%) compared with control animals receiving identical non-contingent injections of yoked-heroin (YH) or yoked-saline (YS), respectively. No changes in agonist-stimulated G-protein sensitization were observed in 14 other brain regions studied. No changes in mu-opioid receptor density, ((3)H-DAMGO binding) were seen in all brain regions examined. The neuronal changes in SA animals were correlated with elevated adrenocorticotrophic hormone (ACTH) (64% and 104%) and glucocorticoid production (198% and 79%) compared with YH and YS groups, respectively. Neuroendocrine adaptive changes in SA animals were associated with thymic hypoplasia. Splenic T lymphocytes from animals that had self-administered heroin showed a profoundly reduced ability to proliferate in response to concanavalin A (50% and 48% compared with YH and YS controls, respectively; Fig. 1A), or a monoclonal antibody (R73) to the CD3/T-cell receptor complex (anti-TCR) plus IL-2 (55% and 59% compared with YH and YS controls, respectively; Fig. 1B). Self-administration of heroin selectively alters T lymphocyte function, as no effects on natural killer cell activity or macrophage functions were observed. These findings may have relevance to the acquisition and documented increased incidence of infectious diseases, including HIV, in heroin addicts, due to a pre-existing T-cell immunodeficient state.

The periaqueductal gray matter mediates opiate-induced immunosuppression.

The periaqueductal gray matter of the mesencephalon (PAG) subserves a variety of diverse autonomic functions and also appears to be a site for opiate action in the induction of immunosuppression. Microinjections of morphine into the PAG, but not into other opiate receptor-containing neuroanatomical sites, result in a rapid suppression of natural killer (NK) cell activity. The NK cell suppression can be blocked by prior peripheral administration of the opiate antagonist naltrexone. These findings demonstrate that certain central actions of opiates that produce changes in NK cell function are mediated through opiate receptors in the PAG and identify a brain region involved in opiate regulation of immune function.

Direct evidence that endogenous GM1 ganglioside can mediate thymocyte proliferation.

The B subunit of cholera toxin, which is multivalent and binds exclusively to a specific ganglioside, GM1, was mitogenic for rat thymocytes. When exposed to the B subunit, the cells proliferated, as measured by 3H-labeled thymidine incorporation. Mitogenesis depended on the direct interaction of the B subunit with GM1 on the surface of the cells. This demonstrates that endogenous plasma membrane gangliosides can mediate proliferation in lymphocytes.

Benzodiazepine receptor-mediated chemotaxis of human monocytes.

Benzodiazepines, which are widely prescribed for their antianxiety effects, are shown to be potent stimulators of human monocyte chemotaxis. The chemotactic effects of benzodiazepine receptor agonists were blocked by the peripheral benzodiazepine receptor antagonist PK-11195, suggesting that these effects are mediated by the peripheral-type benzodiazepine receptor. Diazepam was also active in inducing chemotaxis. Binding studies on purified monocytes revealed high-affinity peripheral benzodiazepine receptors, and the displacement potencies of various benzodiazepines correlated with their relative potencies in mediating chemotaxis. The demonstration of functional benzodiazepine receptors on human monocytes, together with recent evidence of receptor-mediated monocyte chemotaxis by other psychoactive peptides (such as opiate peptides), suggests a biochemical substrate for psychosomatic communication.

The UCSC Genome Browser Database: update 2006.

The University of California Santa Cruz Genome Browser Database (GBD) contains sequence and annotation data for the genomes of about a dozen vertebrate species and several major model organisms. Genome annotations typically include assembly data, sequence composition, genes and gene predictions, mRNA and expressed sequence tag evidence, comparative genomics, regulation, expression and variation data. The database is optimized to support fast interactive performance with web tools that provide powerful visualization and querying capabilities for mining the data. The Genome Browser displays a wide variety of annotations at all scales from single nucleotide level up to a full chromosome. The Table Browser provides direct access to the database tables and sequence data, enabling complex queries on genome-wide datasets. The Proteome Browser graphically displays protein properties. The Gene Sorter allows filtering and comparison of genes by several metrics including expression data and several gene properties. BLAT and In Silico PCR search for sequences in entire genomes in seconds. These tools are highly integrated and provide many hyperlinks to other databases and websites. The GBD, browsing tools, downloadable data files and links to documentation and other information can be found at http://genome.ucsc.edu/.

[A boy with a white striped knee on a radiograph]. / Witte strepen op een röntgenfoto van de knie.

A 10-year-old boy presented at the radiology department with pain in the right knee. Radiographs of the knee revealed dens metaphyseal bands and subchondral epiphyseal sclerosis as a result of periodic bisphosphonate administration for the treatment of Legg-Calvé-Perthes disease three years ago.

The UCSC Genome Browser Database.

The University of California Santa Cruz (UCSC) Genome Browser Database is an up to date source for genome sequence data integrated with a large collection of related annotations. The database is optimized to support fast interactive performance with the web-based UCSC Genome Browser, a tool built on top of the database for rapid visualization and querying of the data at many levels. The annotations for a given genome are displayed in the browser as a series of tracks aligned with the genomic sequence. Sequence data and annotations may also be viewed in a text-based tabular format or downloaded as tab-delimited flat files. The Genome Browser Database, browsing tools and downloadable data files can all be found on the UCSC Genome Bioinformatics website (http://genome.ucsc.edu), which also contains links to documentation and related technical information.

Morphology of interleukin-2-stimulated human peripheral blood mononuclear effector cells killing glioma-derived tumor cells in vitro.

This is the first morphological study of interleukin-2-stimulated human peripheral blood mononuclear (PBM) cells resulting in lymphokine-activated killer (LAK) cell activity against human glioma-derived tumor cells in vitro, in which high-resolution differential interference video light microscopy, scanning electron microscopy, and transmission electron microscopy were used. A subset of cells within the LAK cell population are the effector cells and have an asymmetric cellular architecture characteristic of cytotoxic T lymphocytes (CTLs) and natural killer (NK) cells. Upon binding to target cells, the LAK effector cell nucleus is positioned away from the target cell, whereas the granules, Golgi apparatus, and microtubules orient toward the target cell. These LAK-glioma cell conjugates form very tight plasma membrane bonds with numerous interdigitations, and vesicles were found in the small extracellular spaces between the cells. This morphology was not observed in unstimulated PBM-glioma cell co-cultures. Glioma-derived cells react to LAK effector cells by blebbing, becoming round, and rapidly detaching from the substrate. The injured glioma-derived cells had a highly condensed cytoplasm and chromatin, lobular nucleus, and severe plasma membrane blebs, which are consistent with an apoptotic rather than an osmotic lysis mechanism of cell death. This study provides morphological evidence that supports a common cytotoxic mechanism for CTLs, NK cells, and LAK effector cells. The cytotoxic mechanism is based on the local exocytosis of vesicles by the effector cell into the small extracellular space between the effector-target cell conjugate. Granules found in CTLs, NK cells, and LAK cells contain a pore-forming protein that inserts holes in the target cell's plasma membrane through which a lethal substance(s) not yet identified is thought to enter the cell.

The molecular mechanism of cryoimmunoglobulin precipitation--II. Thermodynamic basis for self-association as determined by fluorescence polarization.

Protein MAT is a homogeneous human IgM (lambda) cryoprecipitating cold agglutinin wherein the Fabmu and Fcmu5 fragment interaction is facilitated at low temps. Thermal dependence of the association of 2,5 DNS labeled Fab MAT with unlabeled Fcmu5 MAT was examined by fluorescence depolarization. The association data, treated by the method of van't Hoff, showed a nonlinear increase in binding with decreased temp, suggestive of certain dynamic changes in the system. Temperature effects on the rotational diffusion of five different 1,5 DNS labeled Fabmu fragments (including two derived from cryoglobulins) were also examined by fluorescence polarization. The linear nature of the Perrin plots derived from the data failed to reveal temp-induced hydrodynamic changes in any of the Fabmu fragments studied. Involvement of carbohydrates in the low-temp self-association of protein MAT was established by the finding that glycopeptides isolated from another IgM molecule (BAZ) could inhibit (as judged by depolarization of fluorescence) the interaction of 2,5 DNS labeled Fabmu MAT and unlabeled Fcmu5 BAZ fragments. These findings indicate that, although cryoprecipitation of protein MAT seemingly involves an antigen-antibody-like reaction between a site on the Fab region and carbohydrate moieties on the Fcmu5 region, no direct evidence for a low-temp-induced conformational change in the Fab region was obtained.

Arbitration of discrepant BI-RADS 0 recalls by a third reader at screening mammography lowers recall rate but not the cancer detection rate and sensitivity at blinded and non-blinded double reading.

PURPOSE: To evaluate the characteristics of low suspicion lesions (BI-RADS 0) at blinded and non-blinded double reading of screening mammograms and to determine the potential effect of arbitration of discrepant BI-RADS 0 recalls by a third reader on screening outcome. METHODS: We included a series of 84,927 consecutive digital screening mammograms, double read in a blinded (43,184 screens) or non-blinded (41,743 screens) fashion, between July 2009 and July 2011. Discrepant readings were routinely recalled for further evaluation. During 2 years of follow-up, radiology, surgical and pathology reports were collected of all recalled women. Arbitration of discrepant BI-RADS 0 recalls (only one radiologist assigning a BI-RADS 0 score) was retrospectively performed by a third screening radiologist. RESULTS: At blinded and non-blinded double reading, 32.0% and 32.5% of recalls were assigned BI-RADS 0 with a positive predictive value (PPV) of 7.2% and 6.8%, respectively. Compared to non-blinded double reading, BI-RADS 0 recalls at blinded double reading showed a higher discrepancy rate (9.0 versus 4.3 per 1000 screens, p < 0.001) and false positive recall rate (10.1 versus 8.4 per 1000 screens, p = 0.012). Arbitration of discrepant BI-RADS 0 recalls would have significantly lowered recall rate (from 3.4% to 2.8% at blinded double reading, p < 0.001, and from 2.8% to 2.5% at non-blinded double reading, p = 0.008), without a decrease in cancer detection rate (from 7.5‰ to 7.3‰, p = 0.751, and from 6.6‰ to 6.5‰, p = 0.832, respectively) and program sensitivity (from 83.2% to 81.2%, p = 0.453, and from 76.0% to 74.6%, p = 0.667, respectively). Arbitration would have significantly increased the PPV at blinded double reading (from 22.3% to 26.3%, p = 0.015). CONCLUSION: We advise arbitration of discrepant BI-RADS 0 recalls, at (non-)blinded double reading of screening mammograms, to reduce recall rates and improve the PPV of recall at blinded double reading.

Inhibition of interleukin-2 production and downregulation of IL-2 and transferrin receptors on rat splenic lymphocytes following PAG morphine administration: a role in natural killer and T cell suppression.

We investigated the effects of acute injection of morphine into the rat mesencephalon periaqueductal gray (PAG), on splenic natural killer (NK) cell and lymphocyte functions, interleukin-2 (IL-2) production, expression of T cell (CD3), T helper cell (CD4), T suppressor cell (CD8), and NK cell (NKR-P1) surface markers, and expression of IL-2 (CD25) and transferrin (CD71) receptors. Bilateral microinjection of 10 nmol of morphine in the PAG significantly (p < 0.001) inhibited IL-2 (31%) production by activated splenic lymphocytes compared with that of PAG saline-injected control rats. In addition, morphine significantly (p < 0.01) suppressed splenic NK cell activity (14-33%) and T lymphocyte proliferative responses (25-48%) to various mitogens compared with controls. Furthermore, morphine did not alter the expression of CD3, CD4, CD8, and NKR-P1 surface markers, but significantly (p < 0.001) downregulated the expression of CD25 and CD71 receptors following in vitro activation. These results suggested that injection of morphine in the PAG suppresses NK and T cell functions by reducing the ability of T cells to produce IL-2 and downregulating the expression of CD25 and CD71 surface activation markers.

Electromyographic abnormalities following myelography.

Electromyographic (EMG) abnormalities were found in 13 of 32 patients with previously normal studies following myelography. These abnormalities usually developed by the first day after myelography and resolved by the fourth day. The changes were evenly divided between those restricted to a single paraspinal muscle level, thus mimicking the frequent findings in radioculopathy, and those present bilaterally and at multiple levels. We were unable to correlate these EMG changes with the clinical status of the patient or with events occurring at myelography. Thus, the performance of EMG within four days following myelography can lead to false-positive results if paraspinal muscle EMG abnormalities are used as the diagnostic criteria.

(+)-cis-3-methylfentanyl and its analogs bind pseudoirreversibly to the mu opioid binding site: evidence for pseudoallosteric modulation.

Previous studies demonstrated that preincubation of membranes from the brain of the rat with 1 microM (+)-cis-3-methylfentanyl produced a wash-resistant inhibition of mu receptor binding. The present study was designed to: (1) determine the mechanism by which (+)-cis-3-methylfentanyl produced a wash-resistant inhibition of mu receptor binding, and (2) to generate a structure-activity study, using wash-resistant inhibition as the end-point. Pretreatment of membranes with 500 nM (+)-cis-3-methylfentanyl increased the Kd of binding sites for [3H]ohmefentanyl, without altering the Bmax. The increase in the Kd was only partially due to the presence of residual drug and was accompanied by an increase in the dissociation rate of the binding of [3H]ohmefentanyl. Therefore, pretreatment of membranes with (+)-cis-3-methylfentanyl resulted in a lower affinity interaction of [3H]ohmefentanyl with the mu binding site, consistent with a model postulating pseudoallosteric modulation of mu binding sites by (+)-cis-3-methylfentanyl and its analogs. The rank order of potencies for wash-resistant inhibition of the binding of [3H]6 beta-fluoro-6-desoxyoxymorphone or [3H]ohmefentanyl, was lofentanil greater than (+)-cis-3-methylfentanyl greater than ohmefentanyl greater than sufentanil. All other opioids tested (1 microM morphine, 1 microM naloxone, 1 microM fentanyl, 1 microM (+)-cyclazocine, 1 microM (-)-cis-3-methylfentanyl) did not act as wash-resistant inhibitors of mu binding sites. Although the pseudoirreversible IC50 of these agents did not correlate with their ED50 values for producing antinociception, after intravenous administration, the authors speculate that this property, termed "pseudoirreversible inhibition", might contribute to the extraordinary potency of (+)-cis-3-methylfentanyl and its analogs as antinociceptive agents.