The Effects of Living in Segregated vs. Mixed Areas in Northern Ireland: A Simultaneous Analysis of Contact and Threat Effects in the Context of Micro-Level Neighbourhoods

This study examines the consequences of living in segregated and mixed neighbourhoods on ingroup bias and offensive action tendencies, taking into consideration the role of intergroup experiences and perceived threat. Using adult data from a cross-sectional survey in Belfast, Northern Ireland, we tested a model that examined the relationship between living in segregated (N = 396) and mixed (N = 562) neighbourhoods and positive contact, exposure to violence, perceived threat and outgroup orientations. Our results show that living in mixed neighbourhoods was associated with lower ingroup bias and reduced offensive action tendencies. These effects were partially mediated by positive contact. However, our analysis also shows that respondents living in mixed neighbourhoods report higher exposure to political violence and higher perceived threat to physical safety. These findings demonstrate the importance of examining both social experience and threat perceptions when testing the relationship between social environment and prejudice.

Analysis of eye and head coordination in a visual peripheral recognition task

Coordinated eye and head movements simultaneously occur to scan the visual world for relevant targets. However, measuring both eye and head movements in experiments allowing natural head movements may be challenging. This paper provides an approach to study eye-head coordination: First, we demonstra- te the capabilities and limits of the eye-head tracking system used, and compare it to other technologies. Second, a beha- vioral task is introduced to invoke eye-head coordination. Third, a method is introduced to reconstruct signal loss in video- based oculography caused by cornea reflection artifacts in order to extend the tracking range. Finally, parameters of eye- head coordination are identified using EHCA (eye-head co- ordination analyzer), a MATLAB software which was developed to analyze eye-head shifts. To demonstrate the capabilities of the approach, a study with 11 healthy subjects was performed to investigate motion behavior. The approach presented here is discussed as an instrument to explore eye-head coordination, which may lead to further insights into attentional and motor symptoms of certain neurological or psychiatric diseases, e.g., schizophrenia.

Ragu: a free tool for the analysis of EEG and MEG event-related scalp field data using global randomization statistics

We present a program (Ragu; Randomization Graphical User interface) for statistical analyses of multichannel event-related EEG and MEG experiments. Based on measures of scalp field differences including all sensors, and using powerful, assumption-free randomization statistics, the program yields robust, physiologically meaningful conclusions based on the entire, untransformed, and unbiased set of measurements. Ragu accommodates up to two within-subject factors and one between-subject factor with multiple levels each. Significance is computed as function of time and can be controlled for type II errors with overall analyses. Results are displayed in an intuitive visual interface that allows further exploration of the findings. A sample analysis of an ERP experiment illustrates the different possibilities offered by Ragu. The aim of Ragu is to maximize statistical power while minimizing the need for a-priori choices of models and parameters (like inverse models or sensors of interest) that interact with and bias statistics.

OMA and OPA—Software-Supported Mass Spectra Analysis of Native and Modified Nucleic Acids

The platform-independent software package consisting of the oligonucleotide mass assembler (OMA) and the oligonucleotide peak analyzer (OPA) was created to support the analysis of oligonucleotide mass spectra. It calculates all theoretically possible fragments of a given input sequence and annotates it to an experimental spectrum, thus, saving a large amount of manual processing time. The software performs analysis of precursor and product ion spectra of oligonucleotides and their analogues comprising user-defined modifications of the backbone, the nucleobases, or the sugar moiety, as well as adducts with metal ions or drugs. The ability to expand the library of building blocks and to implement individual structural variations makes it extremely useful for supporting the analysis of therapeutically active compounds. The functionality of the software tool is demonstrated on the examples of a platinated doublestranded oligonucleotide and a modified RNA sequence. Experiments also reveal the unique dissociation behavior of platinated higher-order DNA structures.

Beyond the tree of texts: Building an empirical model of scribal variation through graph analysis of texts and stemmata

Stemmatology, or the reconstruction of the transmission history of texts, is a field that stands particularly to gain from digital methods. Many scholars already take stemmatic approaches that rely heavily on computational analysis of the collated text (e.g. Robinson and O’Hara 1996; Salemans 2000; Heikkilä 2005; Windram et al. 2008 among many others). Although there is great value in computationally assisted stemmatology, providing as it does a reproducible result and allowing access to the relevant methodological process in related fields such as evolutionary biology, computational stemmatics is not without its critics. The current state-of-the-art effectively forces scholars to choose between a preconceived judgment of the significance of textual differences (the Lachmannian or neo-Lachmannian approach, and the weighted phylogenetic approach) or to make no judgment at all (the unweighted phylogenetic approach). Some basis for judgment of the significance of variation is sorely needed for medieval text criticism in particular. By this, we mean that there is a need for a statistical empirical profile of the text-genealogical significance of the different sorts of variation in different sorts of medieval texts. The rules that apply to copies of Greek and Latin classics may not apply to copies of medieval Dutch story collections; the practices of copying authoritative texts such as the Bible will most likely have been different from the practices of copying the Lives of local saints and other commonly adapted texts. It is nevertheless imperative that we have a consistent, flexible, and analytically tractable model for capturing these phenomena of transmission. In this article, we present a computational model that captures most of the phenomena of text variation, and a method for analysis of one or more stemma hypotheses against the variation model. We apply this method to three ‘artificial traditions’ (i.e. texts copied under laboratory conditions by scholars to study the properties of text variation) and four genuine medieval traditions whose transmission history is known or deduced in varying degrees. Although our findings are necessarily limited by the small number of texts at our disposal, we demonstrate here some of the wide variety of calculations that can be made using our model. Certain of our results call sharply into question the utility of excluding ‘trivial’ variation such as orthographic and spelling changes from stemmatic analysis.

A Near-Real-Time Automatic Orbit Determination System for COSMIC and Its Follow-On Satellite Mission: Analysis of Orbit and Clock Errors on Radio Occultation

The COSMIC-2 mission is a follow-on mission of the Constellation Observing System for Meteorology, Ionosphere, and Climate (COSMIC) with an upgraded payload for improved radio occultation (RO) applications. The objective of this paper is to develop a near-real-time (NRT) orbit determination system, called NRT National Chiao Tung University (NCTU) system, to support COSMIC-2 in atmospheric applications and verify the orbit product of COSMIC. The system is capable of automatic determinations of the NRT GPS clocks and LEO orbit and clock. To assess the NRT (NCTU) system, we use eight days of COSMIC data (March 24-31, 2011), which contain a total of 331 GPS observation sessions and 12 393 RO observable files. The parallel scheduling for independent GPS and LEO estimations and automatic time matching improves the computational efficiency by 64% compared to the sequential scheduling. Orbit difference analyses suggest a 10-cm accuracy for the COSMIC orbits from the NRT (NCTU) system, and it is consistent as the NRT University Corporation for Atmospheric Research (URCA) system. The mean velocity accuracy from the NRT orbits of COSMIC is 0.168 mm/s, corresponding to an error of about 0.051 μrad in the bending angle. The rms differences in the NRT COSMIC clock and in GPS clocks between the NRT (NCTU) and the postprocessing products are 3.742 and 1.427 ns. The GPS clocks determined from a partial ground GPS network [from NRT (NCTU)] and a full one [from NRT (UCAR)] result in mean rms frequency stabilities of 6.1E-12 and 2.7E-12, respectively, corresponding to range fluctuations of 5.5 and 2.4 cm and bending angle errors of 3.75 and 1.66 μrad .

Repeatability analysis of global and local metrics of brain structural networks

Computational network analysis provides new methods to analyze the human connectome. Brain structural networks can be characterized by global and local metrics that recently gave promising insights for diagnosis and further understanding of neurological, psychiatric and neurodegenerative disorders. In order to ensure the validity of results in clinical settings the precision and repeatability of the networks and the associated metrics must be evaluated. In the present study, nineteen healthy subjects underwent two consecutive measurements enabling us to test reproducibility of the brain network and its global and local metrics. As it is known that the network topology depends on the network density, the effects of setting a common density threshold for all networks were also assessed. Results showed good to excellent repeatability for global metrics, while for local metrics it was more variable and some metrics were found to have locally poor repeatability. Moreover, between subjects differences were slightly inflated when the density was not fixed. At the global level, these findings confirm previous results on the validity of global network metrics as clinical biomarkers. However, the new results in our work indicate that the remaining variability at the local level as well as the effect of methodological characteristics on the network topology should be considered in the analysis of brain structural networks and especially in networks comparisons.

Analysis of clonality and antibiotic resistance among early clinical isolates of Enterococcus faecium in the United States.

BACKGROUND: The Enterococcus faecium genogroup, referred to as clonal complex 17 (CC17), seems to possess multiple determinants that increase its ability to survive and cause disease in nosocomial environments. METHODS: Using 53 clinical and geographically diverse US E. faecium isolates dating from 1971 to 1994, we determined the multilocus sequence type; the presence of 16 putative virulence genes (hyl(Efm), esp(Efm), and fms genes); resistance to ampicillin (AMP) and vancomycin (VAN); and high-level resistance to gentamicin and streptomycin. RESULTS: Overall, 16 different sequence types (STs), mostly CC17 isolates, were identified in 9 different regions of the United States. The earliest CC17 isolates were part of an outbreak that occurred in 1982 in Richmond, Virginia. The characteristics of CC17 isolates included increases in resistance to AMP, the presence of hyl(Efm) and esp(Efm), emergence of resistance to VAN, and the presence of at least 13 of 14 fms genes. Eight of 41 of the early isolates with resistance to AMP, however, were not in CC17. CONCLUSIONS: Although not all early US AMP isolates were clonally related, E. faecium CC17 isolates have been circulating in the United States since at least 1982 and appear to have progressively acquired additional virulence and antibiotic resistance determinants, perhaps explaining the recent success of this species in the hospital environment.

Isolation and analysis of regulatory and structural mutations in the {\it recA\/} gene of {\it Escherichia coli}

The recA gene is essential for homologous recombination and for inducible DNA repair in Escherichia coli. The level of recA expression is important for these functions. The growth defect of a lambda phage carrying a recA-lacZ fusion was used to select mutations that reduced recA expression. Nine of these mutations were single base changes in the recA promoter; each reduced both induced and basal (repressed) levels of expression, indicating that only one promoter is used under both circumstances. Deletion analysis of the promoter region and S1 mapping of transcripts confirmed that there is only one promoter responsible for both basal and induced expression. Some of the mutants, however, displayed a ratio of induced to repressed expression that was much lower than wild-type. For one of these mutants (recA1270) LexA binding studies showed that this was not due to a change in the affinity of LexA repressor for the operator site. The extent of binding of RNA polymerase to this mutant promoter, however, was much reduced, and the complexes formed were qualitatively different. Further binding experiments provided some evidence that LexA does not block RNA polymerase binding to the recA promoter, but inhibits a later step in initiation. Behavior of the mutants with altered induction ratios could be explained if LexA binding to the operator actually increases RNA polymerase binding to the promoter in a closed complex compensating for defects in polymerase binding caused by the mutations.^ In a study of mutations in the recA structural gene, site-directed mutagenesis was used to replace cysteine codons at positions 90, 116, and 129 with a number of different codons. In vivo analysis of the replacements showed that none of the cysteines is absolutely essential and that they do not have a direct role as catalysts in ATP hydrolysis. Some amino acid substitutions abolished all RecA functions, while a few resulted in partial or altered function. Amino acids at positions 90 and 129 tended to affect all functions equally, while the amino acid at position 116 appeared to have a particular effect on the protease activity of the protein. ^

"When we like what we know – A parametric fMRI analysis of beauty and familiarity"

This paper presents a neuroscientific study of aesthetic judgments on written texts. In an fMRI experiment participants read a number of proverbs without explicitly evaluating them. In a post-scan rating they rated each item for familiarity and beauty. These individual ratings were correlated with the functional data to investigate the neural correlates of implicit aesthetic judgments. We identified clusters in which BOLD activity was correlated with individual post-scan beauty ratings. This indicates that some spontaneous aesthetic evaluation takes place during reading, even if not required by the task. Positive correlations were found in the ventral striatum and in medial prefrontal cortex, likely reflecting the rewarding nature of sentences that are aesthetically pleasing. On the contrary, negative correlations were observed in the classic left frontotemporal reading network. Midline structures and bilateral temporo-parietal regions correlated positively with familiarity, suggesting a shift from the task-network towards the default network with increasing familiarity.

Patterns of alcohol and illicit substance use in the United States and Mexico. Substantive and methodologic issues in the cross-national analysis of alcohol and drug use data

This research examines prevalence of alcohol and illicit substance use in the United States and Mexico and associated socio-demographic characteristics. The sources of data for this study are public domain data from the U.S. National Household Survey of Drug Abuse, 1988 (n = 8814), and the Mexican National Survey of Addictions, 1988 (n = 12,579). In addition, this study discusses methodologic issues in cross-cultural and cross-national comparison of behavioral and epidemiologic data from population-based samples. The extent to which patterns of substance abuse vary among subgroups of the U.S. and Mexican populations is assessed, as well as the comparability and equivalence of measures of alcohol and drug use in these national samples.^ The prevalence of alcohol use was somewhat similar in the two countries for all three measures of use: lifetime, past year and past year heavy use, (85.0%, 68.1%, 39.6% and 72.6%, 47.7% and 45.8% for the U.S. and Mexico respectively). The use of illegal substances varied widely between countries, with U.S. respondents reporting significantly higher levels of use than their Mexican counterparts. For example, reported use of any illicit substance in lifetime and past year was 34.2%, 11.6 for the U.S., and 3.3% and 0.6% for Mexico. Despite these differences in prevalence, two demographic characteristics, gender and age, were important correlates of use in both countries. Men in both countries were more likely to report use of alcohol and illicit substances than women. Generally speaking, a greater proportion of respondents in both countries 18 years of age or older reported use of alcohol for all three measures than younger respondents; and a greater proportion of respondents between the ages of 18 and 34 years reported use of illicit substances during lifetime and past year than any other age group.^ Additional substantive research investigating population-based samples and at-risk subgroups is needed to understand the underlying mechanisms of these associations. Further development of cross-culturally meaningful survey methods is warranted to validate comparisons of substance use across countries and societies. ^

Genome-wide analysis of genetic and epigenetic control of programmed DNA deletion

During the development of the somatic genome from the Paramecium germline genome the bulk of the copies of ∼45 000 unique, internal eliminated sequences (IESs) are deleted. IES targeting is facilitated by two small RNA (sRNA) classes: scnRNAs, which relay epigenetic information from the parental nucleus to the developing nucleus, and iesRNAs, which are produced and used in the developing nucleus. Why only certain IESs require sRNAs for their removal has been enigmatic. By analyzing the silencing effects of three genes: PGM (responsible for DNA excision), DCL2/3 (scnRNA production) and DCL5 (iesRNA production), we identify key properties required for IES elimination. Based on these results, we propose that, depending on the exact combination of their lengths and end bases, some IESs are less efficiently recognized or excised and have a greater requirement for targeting by scnRNAs and iesRNAs. We suggest that the variation in IES retention following silencing of DCL2/3 is not primarily due to scnRNA density, which is comparatively uniform relative to IES retention, but rather the genetic properties of IESs. Taken together, our analyses demonstrate that in Paramecium the underlying genetic properties of developmentally deleted DNA sequences are essential in determining the sensitivity of these sequences to epigenetic control.