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Human beings must often perform multiple tasks concurrently or in rapid succession. Laboratory research has revealed striking limitations in the ability to dual task by asking participants to identify two target objects that are inserted into a rapid stream of irrelevant items. Under a variety of conditions, identification of the second target (T2) is impaired for a short period of time following presentation of the first target (T1). Several theories have been developed to account for this “attentional blink” (AB), but none makes a specific prediction about how processing of T1 might impact an observer’s ability to ignore a salient distractor that accompanies T2. Using event-related potentials (ERPs) to track target and distractor processing, we show that healthy young adults are capable of suppressing a salient visual-search distractor (D2) while dual tasking (as measured by the PD component, which has been associated with suppression) but struggle to do so shortly after the appearance of T1. In fact, the impairment was more severe for distractor processing than it was for target processing (as measured by the N2pc component). Whereas, the T2-elicited N2pc was merely delayed during the AB, the distractor PD was reduced in magnitude and was found to be statistically absent. We conclude that the inhibitory control processes that are typically engaged to prevent distraction are unavailable while an observer is busy processing a target that appeared earlier.

Extremely rare circulating tumor cell (CTC) clusters are both increasingly appreciated as highly metastatic precursors and virtually unexplored. Technologies are primarily designed to detect single CTCs and often fail to account for the fragility of clusters or to leverage cluster-specific markers for higher sensitivity. Meanwhile, the few technologies targeting CTC clusters lack scalability. Here, we introduce the Cluster-Wells, which combines the speed and practicality of membrane filtration with the sensitive and deterministic screening afforded by microfluidic chips. The >100,000 microwells in the Cluster-Wells physically arrest CTC clusters in unprocessed whole blood, gently isolating virtually all clusters at a throughput of >25 mL/h, and allow viable clusters to be retrieved from the device. Using the Cluster-Wells, we isolated CTC clusters ranging from 2 to 100+ cells from prostate and ovarian cancer patients and analyzed a subset using RNA sequencing. Routine isolation of CTC clusters will democratize research on their utility in managing cancer.

Recent evidence has implicated microRNAs (miRNAs) as potentially significant players in the acquisition of cancer-drug resistance in pancreatic and other cancers. To evaluate the potential contribution of miRNAs in acquired resistance to cisplatin in pancreatic cancer, we compared levels of more than 2000 human miRNAs in a cisplatin-resistant cell line (BxPC3-R) derived from parental (BxPC3) cells by step-wise exposure to increasing concentrations of the drug over more than 20 passages. The acquired drug resistance was accompanied by significant changes in the expression of 57 miRNAs, of which 23 were downregulated and 34 were upregulated. Employing a hidden Markov model (HMM) algorithm, we identified downregulation of miR-374b as likely being directly involved in acquisition of the drug-resistant phenotype. Consistent with this prediction, ectopic overexpression of miR-374b in the resistant BxPC3-R cells restored cisplatin sensitivity to levels approaching those displayed by the BxPC3 parental cells. The results are consistent with a growing body of evidence implicating miRNAs in acquired cancer-drug resistance and with the potential therapeutic value of these small regulatory RNAs in blocking and/or reversing the process.

Semi-sessile Mytilus mussels are used as indicators of climate changes, but their geographic distribution is not sufficiently known in the Arctic. The aim of this study was to investigate the taxonomic status and genetic differentiation of Mytilus populations in a Northwest Greenlandic fjord at Maarmorilik, impacted by contaminations from a former mine. In this study, mussels were collected at three sites differing in exposure to environmental factors. A total of 54 polymorphic SNPs found in the Mytilus EST and DNA sequences analyzed were successfully applied to 256 individuals. The results provided the first evidence for the existence of M. trossulus in Greenland. The mussel from M. trossulus and M. edulis taxa are shown to coexist and hybridize in the fjord. The three studied sites were found to differ significantly in the distribution of taxa with a higher prevalence of M. trossulus in the inner fjord. The identified M. edulis × M. trossulus hybrids mostly had a hybrid index score of about 0.5, indicating a similar number of alleles characteristic for M. trossulus and M. edulis. There was a low number of backcrosses between ‘pure’ taxa and hybrids. This newly discovered hybrid zone between the two taxa is unique in comparison with the Canadian populations. As Mytilus mussels in Greenland hitherto have been regarded as the one taxon M. edulis, the results have importance for biogeography and future monitoring and environmental studies.

Generating sentences from a library of signs implemented through a sparse set of key frames derived from the segmental structure of a phonetic model of ASL has the advantage of flexibility and efficiency, but lacks the lifelike detail of motion capture. These difficulties are compounded when faced with real-time generation and display. This paper describes a technique for automatically adding realism without the expense of manually animating the requisite detail. The new technique layers transparently over and modifies the primary motions dictated by the segmental model and does so with very little computational cost, enabling real-time production and display. The paper also discusses avatar optimizations that can lower the rendering overhead in real-time displays.

Background Gene-fusion or chimeric transcripts have been implicated in the onset and progression of a variety of cancers. Massively parallel RNA sequencing (RNA-Seq) of the cellular transcriptome is a promising approach for the identification of chimeric transcripts of potential functional significance. We report here the development and use of an integrated computational pipeline for the de novo assembly and characterization of chimeric transcripts in 55 primary breast cancer and normal tissue samples. Methods An integrated computational pipeline was employed to screen the transcriptome of breast cancer and control tissues for high-quality RNA-sequencing reads. Reads were de novo assembled into contigs followed by reference genome mapping. Chimeric transcripts were detected, filtered and characterized using our R-SAP algorithm. The relative abundance of reads was used to estimate levels of gene expression. Results De novo assembly allowed for the accurate detection of 1959 chimeric transcripts to nucleotide level resolution and facilitated detailed molecular characterization and quantitative analysis. A number of the chimeric transcripts are of potential functional significance including 79 novel fusion-protein transcripts and many chimeric transcripts with alterations in their un-translated leader regions. A number of chimeric transcripts in the cancer samples mapped to genomic regions devoid of any known genes. Several ‘pro-neoplastic’ fusions comprised of genes previously implicated in cancer are expressed at low levels in normal tissues but at high levels in cancer tissues. Conclusions Collectively, our results underscore the utility of deep sequencing technologies and improved bioinformatics workflows to uncover novel and potentially significant chimeric transcripts in cancer and normal somatic tissues. Electronic supplementary material The online version of this article (doi:10.1186/s12920-017-0289-7) contains supplementary material, which is available to authorized users.

Previous studies report professional athletes return to play following arthroscopic microfracture of the hip for chondral defects. Our hypothesis is that professional hockey players undergoing arthroscopic microfracture for chondral defects of the hip achieve the same performance they had pre-injury and compared to matched controls. Seventeen professional hockey players underwent arthroscopic microfracture for an Outerbridge grade IV chondral lesion. Concomitant procedures for labral pathology or FAI were included. Performance data for the full season preceding and following index procedure were analysed, in addition to two matched control players per subject. Data were collected at two points, 2 years apart. Eighty-two per cent (14/17) of players who underwent arthroscopic microfracture returned to play. The year prior to injury for the 14 players who returned was compared to the average of their individual controls. There was no statistical difference between the groups for age, number of seasons in the league, games played, time on ice, points, save percentage, and shots against goal. Post-operatively, there was no statistical difference between the treatment and control groups regarding performance measures. There was a trend towards a decrease in games played and points post-operatively compared with controls. The treatment group decreased 11 games played, while the controls decreased five games. The treatment group also decreased 14 points, while the controls decreased three points for the season. Professional hockey players with a discrete, full-thickness chondral defect of the hip are able to return to elite performance level following an arthroscopic microfracture procedure when compared to pre-injury outcomes and controls. III.

Axon demyelination contributes to the loss of sensory and motor function following injury or disease in the central nervous system. Numerous reports have demonstrated that myelination can be achieved in neuron/oligodendrocyte co-cultures. However, the ability to selectively treat neuron or oligodendrocyte (OL) cell bodies in co-cultures improves the value of these systems when designing mechanism-based therapeutics. We have developed a microfluidic-based compartmentalized culture system to achieve segregation of neuron and OL cell bodies while simultaneously allowing the formation of myelin sheaths. Our microfluidic platform allows for a high replicate number, minimal leakage, and high flexibility. Using a custom built lid, fit with platinum electrodes for electrical stimulation (10-Hz pulses at a constant 3 V with ~190 kΩ impedance), we employed the microfluidic platform to achieve activity-dependent myelin segment formation. Electrical stimulation of dorsal root ganglia resulted in a fivefold increase in the number of myelinated segments/mm² when compared to unstimulated controls (19.6 ± 3.0 vs. 3.6 ± 2.3 MBP+ segments/mm²). This work describes the modification of a microfluidic, multi-chamber system so that electrical stimulation can be used to achieve increased levels of myelination while maintaining control of the cell culture microenvironment.

The causes of the housing bubble are investigated using Granger causality analysis and VAR modeling methods. The study employs the S&P/Case-Shiller aggregate 10 city monthly housing price index, available in the period 1987–2010/8, the 20 city monthly housing price index for 2000–2010/8, and the federal funds rate data for the period 1987–2010/8. The findings are consistent with the view that the interest rate policy of the Federal Reserve in the period 2001–2004 that pushed down the federal funds rate and kept it artificially low was a cause of the housing price bubble.

This study investigates the patterns of recording birth weight data in retrospective surveys and their influence on birth weight estimates in less developed countries. We hypothesise that the method of reporting birth weight in surveys influences the classification of infants in the low birth weight category. Population-level data from Demographic and Health Surveys conducted in six selected countries representing different regions of the world were used. Birth weight data were reported in the survey from either an official health card or from mother's memory. Birth weight distributions were examined in detail and revised low birth weight estimates were calculated accounting for potential heaping and data inconsistencies. There were substantial differences in the distribution of birth weights by method of reporting. The percentage of infants with low birth weight was higher in all six countries for birth weight recalled from memory than when reported from a health card. Health cards displayed less clustering on certain digits than memory recalled weights, but were still highly heaped in certain countries. Heaping of birth weight data on multiples of 500 g was also observed irrespective of any differences in method of reporting. The study concludes that the method of recording birth weight data can affect birth weight estimates in developing countries. Health systems in poor countries should initiate efforts to systematically monitor the recording of birth weight data ensuring for both quality and comparability at the international levels.

This paper is an empirical study of the capitalization rates for 132 office building sales in downtown Chicago from 1996 to 2007. The capitalization rate is hypothesized to be a function of the classic capital asset pricing model variable and variables intended to capture the expectation that the real market value of the building will change. The results show that the capitalization rate for office buildings incorporates a very low value for “beta.” A lower capitalization rate was associated with a smaller risk-free rate, a lower borrowing rate, class A buildings, newer buildings, buildings that had been renovated, a reduction in the vacancy rate in the downtown Chicago office market, and an increase in employment in the financial sector of the metropolitan area.

Members of the public are increasingly consulted over health care and research priorities. Patient involvement in determining cancer research priorities, however, has remained underdeveloped. This paper presents the findings of the first consultation to be conducted\ud with UK cancer patients concerning research priorities. The study adopted a participatory approach using a collaborative model that sought joint ownership of the study with people affected by cancer. An exploratory, qualitative approach was used. Consultation groups were the main method, combining focus group and nominal group techniques. Seventeen groups were held with a total of 105 patients broadly representative of the UK cancer population. Fifteen areas for research were identified. Top priority areas included the impact cancer has on life, how to live with cancer and related support issues; risk factors and causes of cancer; early detection and prevention. Although biological and treatment related aspects of science were identified as important, patients rated the management of practical, social and emotional issues as a higher priority. There is a mismatch between the research priorities identified by participants and the current UK research portfolio. Current research activity should be broadened to reflect the priorities of people affected by the disease.

High performance mass spectrometry was employed to interrogate the serum metabolome of early-stage ovarian cancer (OC) patients and age-matched control women. The resulting spectral features were used to establish a linear support vector machine (SVM) model of sixteen diagnostic metabolites that are able to identify early-stage OC with 100% accuracy in our patient cohort. The results provide evidence for the importance of lipid and fatty acid metabolism in OC and serve as the foundation of a clinically significant diagnostic test.

Background Genomic rearrangements or structural variants (SVs) are one of the most common classes of mutations in cancer. Methods An integrated DNA sequencing and transcriptional profiling (RNA sequence and microarray gene expression data) analysis was performed on six ovarian cancer patient samples. Matched sets of control (whole blood) samples from these same patients were used to distinguish cancer SVs of germline origin from those arising somatically in the cancer cell lineage. Results We detected 10,034 ovarian cancer SVs (5518 germline derived; 4516 somatically derived) at base-pair level resolution. Only 11 % of these variants were shown to have the potential to form gene fusions and, of these, less than 20 % were detected at the transcriptional level. Conclusions Collectively our results are consistent with the view that gene fusions and other SVs can be significant factors in the onset and progression of ovarian cancer. The results further indicate that it may not only be the occurrence of these variants in cancer but their regulation that contributes to their biological and clinical significance. Electronic supplementary material The online version of this article (doi:10.1186/s12920-015-0118-9) contains supplementary material, which is available to authorized users.

Human endogenous retroviruses (HERVs) represent vestiges of ancient infections that resulted in stable integration of the viral genome. These insertional elements of viral origin are in fact molecular fossils and, as such, a source of evolutionary information. A family of HERV insertions designated HERV-K includes members that are still polymorphic for the original insertional event. The goal of this report is to describe a novel genetic marker system based on polymorphic retroviral insertions (PRVIs) and to assess its potential usefulness in human population genetic analyses. The allelic frequencies of four insertionally polymorphic HERV-K loci were analyzed in nine geographically targeted, worldwide populations. A polymerase chain reaction assay was employed to examine the frequencies of the provirus and/or solo long terminal repeat insertions at these four loci. Several statistical and phylogenetic analyses were performed based on the frequency data. The phylogenetic relationships observed among the nine populations based on the four retroviral HERV-K loci are consistent not only with prior genetic analyses with other traditional marker systems but also with reported historical and biogeographical data. These polymorphic endogenous retroviral sequences display features that make them excellent tools for forensic and population genetic studies.

The neural systems that mediate voluntary shifts of attention to visual and auditory stimuli were investigated by examining the patterns of human brain electricity elicited by attention-directing cues in auditory and visual tasks. Several lateralized event-related potential (ERP) components were observed when participants shifted attention in expectation of visual targets (experiment 1). One component was focused over frontal cortex and a second was focused primarily over the occipital-temporal cortex but also spread to parietal regions of the scalp. Previous work has indicated that the frontal component reflects supramodal processes involved in the executive control of attention and that the posterior component reflects either spatial attentional control processes in the posterior parietal lobe or modulation of processes in visual cortex. Here, the posterior component was observed when participants shifted attention in expectation of auditory targets (experiments 2-4), but the frontal component was found only in the visual task. The posterior component seemed to be generated in parietal and occipital areas even when there was no visual information about the to-be-attended locations. These results are consistent with the view that voluntary shifts of attention are mediated by supramodal processes in the parietal lobe and that the spatial coordinates of the to-be-attended location are based on visual representations of space.

Attended objects are perceived to occur before unattended objects even when the two objects are presented simultaneously. This finding has led to the widespread view that attention modulates the speed of neural transmission in the various perceptual pathways. We recorded event-related potentials during a time-order judgment task to determine whether a reflexive shift of attention to a sudden sound modulates the speed of sensory processing in the human visual system. Attentional cueing influenced the perceived order of lateralized visual events but not the timing of event-related potentials in visual cortex. Attentional cueing did, however, enhance the amplitude of neural activity in visual cortex, which shows that attention-induced shifts in visual time-order perception can arise from modulations of signal strength rather than processing speed in the early visual-cortical pathways.

The fluorine stability of two parylenes, aliphatic-fluorinated AF-4 (α, α, α′, α′ poly(p-tetrafluoroxylylene) and aromatic-fluorinated VT-4 (2, 3, 5, 6 poly(p-tetrafluoroxylylene), were investigated underneath Al, Al2O3, and TaNX overlayers with and without exposure to oxygen reactive-ion etching (RIE). No fluorine diffusion was observed for Al films deposited onto the as-received parylenes. However, after oxygen RIE, x-ray photoelectron spectroscopy (XPS) depth profiling detected fluorine diffusion throughout Al and to a lesser extent Al2O3 but in contrast to Ta2.67N. Metal-fluoride bonding was evident at the metal/parylene interface for all the overlayers after the parylene was exposed to oxygen RIE and annealed.

We develop Metropolis-Hastings algorithms for exact conditional inference, including goodness-of-fit tests, confidence intervals and residual analysis, for binomial and multinomial logistic regression models. We present examples where the exact results, obtained by enumeration, are available for comparison. We also present examples where Monte Carlo methods provide the only feasible approach for exact inference.

Objective: In this study we evaluated the contribution of major histocompatibility complex (MHC) genes to soluble histocompatibility antigen class II (sHLA-II) secretion in African American patients with rheumatoid arthritis (RA).¶Methods: A sensitive enzyme-linked immunoassay was used to quantitate sHLA-II in the serum of 7 patients with RA, as well as 28 of their kinships and 49 HLA typed normal African American individuals.¶Results: Mean sHLA-II values were higher in patients with RA than those in healthy African American individuals (p < 0.05). There were variations in concentrations in individual patients but these were unrelated to any apparent clinical event. The proportion of unaffected family members with detectable levels of sHLA-II was not significantly different than those in normal controls. Neither specific HLA-haplotype, or HLA-allele(s) correlated with high or low sHLA-II secretion.¶Conclusions: Our data suggest that sHLA-II molecules are not regulated by MHC linked genes but may be regulated by non-MHC linked genes and racial background may reflect genetic heterogeneity of the expression of this soluble HLA material. These observations contrast with previous observations concerning soluble HLA class I (sHLA-I) molecules in a described population sample which were almost the precise reverse.

Objectives:The limited number of studies addressing the presence of soluble human leukocyte antigen (HLA) in body fluids such as tears, urine, sweat, and saliva are restricted to healthy subjects. In this study, we applied solid-phase enzyme-linked immunoassay to quantify soluble HLA class I (sHLA-I) and class II (sHLA-II) molecules in saliva and in selected serum samples obtained from patients with systemic lupus erythematosus (SLE), rheumatoid arthritis (RA), and Sjogren's syndrome (SS). Results: While saliva from normal subjects (n=35) contained levels of sHLA-I that were undetectable (n=7) or ranged from 9 ng/ml to 70 ng/ml (30±3.7 ng/ml, n=28), sHLA-I among 38 patients with moderately active RA (n=24) or SLE (n=14) were significantly elevated (222±81.4 ng/ml and 120±27.3 ng/ml, respectively, P

It is appropriate that this review should appear in a volume dedicated to Mert Bernfield. Much of my interest in the cell biology of the extracellular matrix, particularly during development, echoes Mert's pioneering studies. His kind but provocative questioning during meetings is especially missed. The glycosaminoglycan hyaluronan is ubiquitous, and is especially abundant during embryogenesis. Hydrated matrices rich in hyaluronan expand the extracellular space, facilitating cell migration. The viscoelastic properties of hyaluronan are also essential for proper function of cartilage and joints. Recent understanding of hyaluronan biology has benefited from the identification of genes encoding hyaluronan synthases and hyaluronidases, genetic analysis of the roles of hyaluronan during development, elucidation of the biochemical mechanisms of hyaluronan synthesis, and by studies of human genetics and tumors. This review focuses on recent studies utilizing hyaluronan-deficient, gene targeted mice with null alleles for the principal source of hyaluronan during mid-gestation, hyaluronan synthase-2 (has-2).

Introduction: Three-dimensional (3D) echocardiography has been shown to offer highly accurate measurements of left ventricular (LV) volume and mass. The present study evaluated the accuracy of 3D surface reconstruction by the piecewise smooth subdivision method in measuring volume and mass not only in the LV but also in the more complexly shaped right ventricle (RV). Methods: 3D echo scans were obtained of in vitro LV's (n = 15) and RVs (n = 10). From digitized images, ventricular borders were traced and used in surface reconstructions. Mass and volume determined from the reconstructions were compared to true volume and mass determined prior to imaging. Additionally casts of two RVs were made and laser-scanned. Distances between the laser-identified points on the RV surface and the corresponding 3D echo reconstructions were measured. Results: 3D LV volume agreed well with the true volume (y = 0.99x + 1.73, r = 0.99, SEE = 3.35 ml, p < 0.0001), as did 3D LV mass (y = 0.99x − 4.71, r = 0.99, SEE = 9.85 g, p < 0.0001). 3D RV volume overestimated true volume (y = 1.11x + 1.77, r = 0.99, SEE = 3.36 ml, p < 0.001) by 6.23 ± 3.70 ml (p < 0.0001). 3D mass agreed well with RV mass (y = 0.78x + 17.32, r2 = 0.93, SEE = 3.54 g, p < 0.0001). 3D echo reconstructions matched the laser-scanned RV closely with residual distances of 1.1 ± 0.9 and 1.4 ± 1.2 mm, respectively. Conclusions: 3D echo using freehand scanning combined with surface reconstruction by the piecewise smooth subdivision surface method enables accurate determination of LV mass and volume, of RV mass and volume, and of the RV's complex shape.

Tetracycline regulated gene expression in transgenic animals is potentially a very powerful technique (Furth et al., 1994; Gossen & Bujard 1992). We have utilized this system in an attempt to overcome the perinatal lethality resulting from constitutive transgenic expression in the heart (Valencik & McDonald, Am J Physiol Heart Circ Physiol 280: H361–H367). We found that compound hemizygous animals created by mating selected reverse tetracycline transactivator (rtTA) and transresponder (TR) lines display tightly regulated TR expression in the heart. However, we identified two fundamental problems. First, codon usage bias appeared to severely limit the expression of the rtTA driven by the cardiac α-myosin heavy chain promoter. Second, co-injection of rtTA and TR transgenes led to compound hemizygous animals that exhibited unregulated TR gene expression. Codon optimization of the rtTA construct leads to marked improvement (increasing the average induction from 20-fold to 832-fold) in cardiac myocyte expression. The resulting opt-rtTA lines can be bred to homozygosity, facilitating rapid screening of F0 TR animals for doxycycline regulated transgene expression.

In a previous study, Ward (1994) reported that spatially uninformative visual cues orient auditory attention but that spatially uninformative auditory cues fail to orient visual attention. This cross-modal asymmetry is consistent with other intersensory perceptual phenomena that are dominated by the visual modality (e.g., ventriloquism). However, Spence and Driver (1997) found exactly the opposite asymmetry under different experimental conditions and with a different task. In spite of the several differences between the two studies, Spence and Driver (see also Driver & Spence, 1998) argued that Ward’s findings might have arisen from response-priming effects, and that the cross-modal asymmetry they themselves reported, in which auditory cues affect responses to visual targets but not vice versa, is in fact the correct result. The present study investigated cross-modal interactions in stimulus-driven spatial attention orienting under Ward’s complex cue environment conditions using an experimental procedure that eliminates response-priming artifacts. The results demonstrate that the cross-modal asymmetry reported by Ward (1994) does occur when the cue environment is complex. We argue that strategic effects in cross-modal stimulus-driven orienting of attention are responsible for the opposite asymmetries found by Ward and by Spence and Driver (1997).

This article is a theoretical examination of optimal financial leverage for real estate investment in the presence of uncertainty. The main result shows that uncertainty creates the possibility that a borrower will default on a real estate loan and that this possibility is the underlying factor in optimal leverage calculations for both borrower and lender.

Event-related brain potentials (ERPs) were recorded during two spatial-cuing experiments using nonpredictive cues. Our primary goal was to determine the electrophysiological consequences of inhibition of return (IOR). At long (500 msec) cue-target intervals, subjects responded more slowly to targets that appeared at or near the cued location, relative to targets that appeared on the opposite side of fixation from the cue. This behavioral IOR effect was associated with cue-validity effects on several components of the target-elicited ERP waveforms. The earliest such effect was a smaller occipital P1 on valid-cue trials, which we interpret as a P1 reduction. The P2 component was also smaller on valid-cue trials, indicating that nonpredictive spatial cues influence multiple stages of information processing at long cue-target intervals. Both of these effects were observed when sensory interactions between cue and target were likely to be negligible, indicating that they were not caused by sensory refractoriness. A different effect of cue validity, the posterior negative difference, was found when sensory interactions were likely to be greatest, indicating that it could arise from sensory refractoriness.

We report the results of an analysis of natu- rally occurring cis-regulatory variation within and be- tween two families of the copia Drosophila long termi- nal repeat (LTR) retrotransposon. The copia 58 LTR and adjacent untranslated leader region (ULR) consists of a number of well-characterized sequence motifs which play a role in regulating expression of the element. In order to understand the evolutionary forces which may be responsible for generating and maintaining copia regulatory sequence variation, we have quantified levels of naturally occurring copia LTR-ULR nucleotide varia- tion and subjected the data to a series of tests of neutral- ity. Our analysis indicates that the copia LTR-ULR has been subject to negative purifying selection within fami- lies and positive adaptive selection between families. We discuss these findings with respect to the regulatory evo- lution of retrotransposons and the phenomenon of inter- element selection.

Objective. To install and successfully use early commercial automatic anesthesia recordkeepers, the Diatek Arkive “Organizer” units, in the operating rooms at a major university medical center. Methods. Because of the history of previous academic attempts at automatic anesthesia recordkeeping, the units were installed on a “surprise” basis, with hardly any discussion of the devices beforehand. Results. The devices themselves had a number of minor difficulties at the start, most of which were promptly corrected. Eventually the units were in use in all non-cardiac general operating rooms. At one point, usage reached over 90% of possible cases. Continued opposition to the device on the part of certain individuals, coupled with the obsolescence of the present devices in light of new technology, led to the eventual abandonment of the system and removal of the devices from service. Discussion. Total resistance to the new devices on the part of a few vocal faculty members was a major factor in the ultimate downfall of the system. The method of introduction, and especially the lack of involvement of faculty, residents, surgeons, operating room personnel, hospital computer personnel, and the hospital administration in the installation also played a role in the failure of the system. Lack of a workable training mechanism for new residents prevented that user group from rapidly gaining comfort with the systems.

This article examines whether the pattern of urban land use should have been regulated by local government in the 1920s, the decade in which many cities adopted their first zoning ordinances. The study is based on the assumption that land values are influenced by the mix of land use on the block. Conditions for land-value maximization are derived, and the circumstances under which land-use zoning can increase land values are discussed. Empirical land-value and land-use functions are estimated for Chicago in 1921, two years before the first Chicago zoning ordinance was adopted. The empirical results for land values imply that the land-use zoning system adopted in 1923 could not have brought about a general increase in land values. The empirical results for land use document the regularities in the use of land prior to the introduction of zoning.

A library of potential agonists and antagonists for adrenergic receptors was prepared using high-throughput solution-phase parallel synthesis. Traditional solution-phase reductive amination reactions followed by rapid purification by ion exchange chromatography yielded products with near-analytical purity. An array of ketones and amines, arranged in an 8 × 12 matrix, were combined to form 96 individual compounds.

A two-way contingency table in which both variables have the same categories is termed a symmetric table. In many applications, because of the social processes involved, most of the observations lie on the main diagonal and the off-diagonal counts are small. For these tables, the model of independence is implausible and interest is then focussed on the off-diagonal cells and the models of quasi-independence and quasi-symmetry. For ordinal variables, a linear-by-linear association model can be used to model the interaction structure. For sparse tables, large-sample goodness-of-fit tests are often unreliable and one should use an exact test. In this paper, we review exact tests and the computing problems involved. We propose new recursive algorithms for exact goodness-of-fit tests of quasi-independence, quasi-symmetry, linear-by-linear association and some related models. We propose that all computations be carried out using symbolic computation and rational arithmetic in order to calculate the exact p-values accurately and describe how we implemented our proposals. Two examples are presented.

Prostaglandin (PGE(2)) is an inflammatory mediator that plays a critical role in the pathogenesis of periodontal disease. Prostaglandin H synthase (PGHS) a rate-limiting enzyme in PGE(2) biosynthesis exists as two separate isoforms (PGHS-1 and PGHS-2). We have previously demonstrated that both isoforms are generally present in the gingival tissue of periodontitis patients. This study explores in greater detail the variable distribution of each isoenzyme in both inflamed and non-inflamed gingival tissues of patients with periodontitis, and the relationship to adjacent bacteria. Although the positive staining for PGHS-1 was never as intense as for PGHS-2 in the same tissue specimen, either in inflamed or non-inflamed tissues, there was strong staining for both isoenzymes in the epithelium. The keratin layer did not stain. Non-keratinizing crevicular and junctional epithelium contained both isoenzymes through their full thickness in both inflamed and non-inflamed tissues. Pronounced staining of PGHS-2 was evident in the epithelia adjacent to Gram-positively stained organisms. In non-inflamed tissue, PGHS-1 and PGHS-2 were particularly evident in the spinous cell layer; however, fewer of the fibroblasts, endothelial cells, and resident mononuclear inflammatory cells stained positively for PGHS-1 as compared to PGHS-2, but this was less apparent in the inflamed tissues. The immunohistochemical staining patterns indicate that both crevicular and gingival epithelium are important sources of prostaglandin production in the gingival tissue of patients with periodontitis and that bacteria entrapped near to these sites may be important in promoting expression of inducible PGHS-2.

Transposable elements are ubiquitous in all organisms and represent a dynamic component of their genomes, causing mutations and thereby genetic variation. Because of their independent and expansive replication strategy, these elements are called selfish and were thought to have no impact on the adaptive evolution of their host organisms. Although most TE-induced mutations seem to exert only negative effects on the fitness of their carrier, recent evidence indicates that in the course of evolution at least some TE-mediated changes have become established features of the host genome. For example, the insertion of TEs may provide novel cis-regulatory regions to preexisting host genes or TE-derived trans-acting factors may undergo a molecular transition into novel host genes through a process described as molecular domestication. The stationary P element related gene clusters of D. guanche, D. madeirensis and D. subobscura provide an excellent model system to study the evolutionary impact of TEs on genome evolution. Each cluster unit consists of a cis-regulating section composed of different insertion sequences followed by the first three exons of a P element that are coding for a 66 kDa ‘repressor-like’ protein.

Since LTR retrotransposons and retroviruses are especially prone to regional duplications and recombination events, these viral-like systems may be especially conducive to the evolution of closely spaced combinatorial regulatory motifs. Using the Drosophila copia LTR retrotransposon as a model, we show that a regulatory region contained within the element's untranslated leader region (ULR) consists of multiple copies of an 8 bp motif (TTGTGAAA) with similarity to the core sequence of the SV40 enhancer. Naturally occurring variation in the number of these motifs is correlated with the enhancer strength of the ULR. Our results indicate that inter-element selection may favor the evolution of more active enhancers within permissive genetic backgrounds. We propose that LTR retroelements and perhaps other retrotransposons constitute drive mechanisms for the evolution of eukaryotic enhancers which can be subsequently distributed throughout host genomes to play a role in regulatory evolution.

FOR life to be sustained, mistakes in DNA repair must be tolerated when damage obscures the genetic information. In bacteria such as Escherichia coli, DNA damage elicits the well regulated 'SOS response' (reviewed in ref. 1). For the extreme case of damage that cannot be repaired by conventional enzymes, there are proteins that allow the replication of DNA through such lesions, but with a reduction in the fidelity of replication2. Essential proteins in this mutagenic process are RecA, DNA polymerase III, UmuD, UmuD′ and UmuC (umu: UV mutagen-esis)1–3. Regulation of this response involves a RecA-mediated self-cleavage of UmuD to produce UmuD′ To understand this system in more detail, we have determined the crystal structure of the E. coli UmuD′ mutagenesis protein at 2.5 A resolution. Globular heads folded in an unusual β-structure associate to form molecular dimers, and extended ammo-terminal tails associate to produce crystallized filaments. The structure provides insight into the mechanism of the self-cleavage reaction that UmuD-like proteins undergo as part of the global SOS response4–8.

This study investigated the expression of the N-ras oncogene in routinely processed tissue sections from 133 patients with squamous cell carcinoma of the head and neck (SCCHN) by immunohistochemistry using anti-N-ras monoclonal antibody. N-ras expression was present in 67 of 133 (49.6%) cases. There was a highly significant correlation between N-ras expression and clinical stage of disease (P=0.003). This study confirmed that overexpression of the N-ras oncogene is common in SCCHN and that it may be an important event in the late stage of disease.

This article examines urban highway congestion pricing in the instance in which it is not possible to levy a congestion toll on a major portion of the urban road system. This case is pertinent because of technical and/or political constraints. The article uses economic theory and numerical examples to show that the optimum second-best toll can vary appreciably from the optimal tolls in a regime in which efficient tolls can be imposed on all routes.

A Monte Carlo exact conditional test of quasi-independence in two-way incomplete contingency tables is proposed. The null distribution of a random table under quasiindependence is derived. This distribution depends only on the counts in the cells of interest and not on the counts in the remaining cells. This result is used to improve the efficiency of a proposed simulate-and-reject Monte Carlo procedure for estimating the attained significance level.

Prostaglandins are inflammatory mediators that are believed to play an important role in the pathophysiology of periodontal disease. Prostaglandin H synthase (PGHS, EC 1.14.99.1) is the rate-limiting enzyme in prostaglandin biosynthesis. The enzyme exists as two separately encoded isoforms. PGHS-1 which is constitutively expressed and PGHS-2 which is induced by inflammatory stimuli. This is the first report describing the expression of the isoenzymes in gingival tissue from patients diagnosed with adult periodontitis. Tissue was fixed in an alcohol-based fixative and embedded in paraffin. Methods were developed using immunohistochemical controls, such that embedded sections could be processed and stained using isoform-specific antibodies and a peroxidase-antiperoxidase immunohistochemistry technique. Along with populations of mononuclear inflammatory cells, endothelial cells and fibroblasts, the gingival epithelial cell layer appears to be a rich and important source of prostaglandin production within the periodontium of patients with periodontitis as detected by this newly developed immunohistochemical staining technique for PGHS-1 and PGHS-2.

Peptidyl-glycine alpha-amidating monooxygenase (PAM; EC 1.14.17.3) is an enzyme that catalyzes conversion of glycine-extended peptides to alpha-amidated bioactive peptides. Two peptides that are processed at their carboxyl-termini by this enzyme are neuropeptide Y and anglerfish peptide Y, both of which possess a C-terminal glycine that is used as a substrate for amidation. Results from previous reports have demonstrated that neuropeptide Y-like and anglerfish peptide Y-like immunoreactivities are present in the brain of anglerfish (Lophius americanus). Furthermore, neuropeptide Y-like peptides, namely anglerfish peptide Y and anglerfish peptide YG (the homologues of pancreatic polypeptide) are present in the islet organ of this species. Neuropeptide Y has also been localized in the anterior, intermediate and posterior lobes of the pituitary gland in a variety of species. In order to learn more about the distribution of the enzyme responsible for alpha amidation of these peptides in the brain and pituitary and to specifically investigate the relationship of this enzyme to peptide synthesizing endocrine cells of the anglerfish islet, we performed an immunohistochemical study using several antisera generated against different peptide sequences of the enzyme. PAM antisera labeled cells in the islet organ, pituitary and brain, and fibers in the brain and pituitary gland. The PAM staining pattern in the brain was remarkably similar to the distribution of neuropeptide Y immunoreactivity reported previously. Clusters of cells adjacent to vessels in the anterior pituitary displayed punctate PAM immunoreactivity while varicose fibers were observed in the pituitary stalk and neurohypophysis. Endocrine cells of the islet organ were differentially labeled with different PAM antisera. Comparison of the staining patterns of insulin, glucagon, and anglerfish peptide Y in the islet organ to PAM immunoreactivity suggests a distribution of forms of PAM enzyme in insulin and anglerfish peptide Y-containing cells, but no overlap with glucagon-producing cells. The results also indicate that PAM immunoreactivity is widely distributed in the brain, pituitary and islet organ of anglerfish in cells, that contain peptides that require presence of a C-terminal glycine for amidation.

Background Ovarian cancer stem cells are characterized by self-renewal capacity, ability to differentiate into distinct lineages, as well as higher invasiveness and resistance to many anticancer agents. Since they may be responsible for the recurrence of ovarian cancer after initial response to chemotherapy, development of new therapies targeting this special cellular subpopulation embedded within bulk ovarian cancers is warranted. Methods A high-throughput screening (HTS) campaign was performed with 825 compounds from the Mechanistic Set chemical library [Developmental Therapeutics Program (DTP)/National Cancer Institute (NCI)] against ovarian cancer stem-like cells (CSC) using a resazurin-based cell cytotoxicity assay. Identified sets of active compounds were projected onto self-organizing maps to identify their putative cellular response groups. Results From 793 screening compounds with evaluable data, 158 were found to have significant inhibitory effects on ovarian CSC. Computational analysis indicates that the majority of these compounds are associated with mitotic cellular responses. Conclusions Our HTS has uncovered a number of candidate compounds that may, after further testing, prove effective in targeting both ovarian CSC and their more differentiated progeny.

BackgroundAccumulating evidence suggests that somatic stem cells undergo mutagenic transformation into cancer initiating cells. The serous subtype of ovarian adenocarcinoma in humans has been hypothesized to arise from at least two possible classes of progenitor cells: the ovarian surface epithelia (OSE) and/or an as yet undefined class of progenitor cells residing in the distal end of the fallopian tube.MethodsComparative gene expression profiling analyses were carried out on OSE removed from the surface of normal human ovaries and ovarian cancer epithelial cells (CEPI) isolated by laser capture micro-dissection (LCM) from human serous papillary ovarian adenocarcinomas. The results of the gene expression analyses were randomly confirmed in paraffin embedded tissues from ovarian adenocarcinoma of serous subtype and non-neoplastic ovarian tissues using immunohistochemistry. Differentially expressed genes were analyzed using gene ontology, molecular pathway, and gene set enrichment analysis algorithms.ResultsConsistent with multipotent capacity, genes in pathways previously associated with adult stem cell maintenance are highly expressed in ovarian surface epithelia and are not expressed or expressed at very low levels in serous ovarian adenocarcinoma. Among the over 2000 genes that are significantly differentially expressed, a number of pathways and novel pathway interactions are identified that may contribute to ovarian adenocarcinoma development.ConclusionsOur results are consistent with the hypothesis that human ovarian surface epithelia are multipotent and capable of serving as the origin of ovarian adenocarcinoma. While our findings do not rule out the possibility that ovarian cancers may also arise from other sources, they areinconsistentwith claims that ovarian surface epithelia cannot serve as the origin of ovarian cancer initiating cells.

BackgroundThe majority of ovarian cancer biomarker discovery efforts focus on the identification of proteins that can improve the predictive power of presently available diagnostic tests. We here show that metabolomics, the study of metabolic changes in biological systems, can also provide characteristic small molecule fingerprints related to this disease.ResultsIn this work, new approaches to automatic classification of metabolomic data produced from sera of ovarian cancer patients and benign controls are investigated. The performance of support vector machines (SVM) for the classification of liquid chromatography/time-of-flight mass spectrometry (LC/TOF MS) metabolomic data focusing on recognizing combinations or "panels" of potential metabolic diagnostic biomarkers was evaluated. Utilizing LC/TOF MS, sera from 37 ovarian cancer patients and 35 benign controls were studied. Optimum panels of spectral features observed in positive or/and negative ion mode electrospray (ESI) MS with the ability to distinguish between control and ovarian cancer samples were selected using state-of-the-art feature selection methods such as recursive feature elimination and L1-norm SVM.ConclusionThree evaluation processes (leave-one-out-cross-validation, 12-fold-cross-validation, 52-20-split-validation) were used to examine the SVM models based on the selected panels in terms of their ability for differentiating control vs. disease serum samples. The statistical significance for these feature selection results were comprehensively investigated. Classification of the serum sample test set was over 90% accurate indicating promise that the above approach may lead to the development of an accurate and reliable metabolomic-based approach for detecting ovarian cancer.

Contrasting amounts of geographical variation as evidence for direct selection: the Mpi and Pgm loci in eight crustacean species