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The ability to detect regularities in sound (i.e., recurring structure) is critical for effective perception, enabling, for example, change detection and prediction. Two seemingly unconnected lines of research concern the neural operations involved in processing regularities: one investigates how neural activity synchronizes with temporal regularities (e.g., frequency modulation; FM) in sounds, whereas the other focuses on increases in sustained activity during stimulation with repeating tone-frequency patterns. In three electroencephalography studies with male and female human participants, we investigated whether neural synchronization and sustained neural activity are dissociable, or whether they are functionally interdependent. Experiment I demonstrated that neural activity synchronizes with temporal regularity (FM) in sounds, and that sustained activity increases concomitantly. In Experiment II, phase coherence of FM in sounds was parametrically varied. Although neural synchronization was more sensitive to changes in FM coherence, such changes led to a systematic modulation of both neural synchronization and sustained activity, with magnitude increasing as coherence increased. In Experiment III, participants either performed a duration categorization task on the sounds, or a visual object tracking task to distract attention. Neural synchronization was observed irrespective of task, whereas the sustained response was observed only when attention was on the auditory task, not under (visual) distraction. The results suggest that neural synchronization and sustained activity levels are functionally linked: both are sensitive to regularities in sounds. However, neural synchronization might reflect a more sensory-driven response to regularity, compared with sustained activity which may be influenced by attentional, contextual, or other experiential factors.Significance statementOptimal perception requires that the auditory system detects regularities in sounds. Synchronized neural activity and increases in sustained neural activity both appear to index the detection of a regularity, but the functional interrelation of these two neural signatures is unknown. In three electroencephalography experiments, we measured both signatures concomitantly while listeners were presented with sounds containing frequency modulations that differed in their regularity. We observed that both neural signatures are sensitive to temporal regularity in sounds, although they functionally decouple when a listener is distracted by a demanding visual task. Our data suggest that neural synchronization reflects a more automatic response to regularity, compared with sustained activity which may be influenced by attentional, contextual, or other experiential factors.

Human brain function draws on predictive mechanisms that exploit higher-level context during lower-level perception. These mechanisms are particularly relevant for situations in which sensory information is compromised or incomplete, as for example in natural speech where speech segments may be omitted due to sluggish articulation. Here, we investigate which brain areas support the processing of incomplete words that were predictable from semantic context, compared with incomplete words that were unpredictable. During functional magnetic resonance imaging (fMRI), participants heard sentences that orthogonally varied in predictability (semantically predictable vs. unpredictable) and completeness (complete vs. incomplete, i.e. missing their final consonant cluster). The effects of predictability and completeness interacted in heteromodal semantic processing areas, including left angular gyrus and left precuneus, where activity did not differ between complete and incomplete words when they were predictable. The same regions showed stronger activity for incomplete than for complete words when they were unpredictable. The interaction pattern suggests that for highly predictable words, the speech signal does not need to be complete for neural processing in semantic processing areas. Hum Brain Mapp 37:704-716, 2016. © 2015 Wiley Periodicals, Inc.

Within the growing order of Chlamydiales, there are a number of pathogens. One is Chlamydia psittaci, a zoonotic pathogen, with birds as natural hosts that may be transmitted to humans and cause severe respiratory disease, psittacosis. The prevalence of this pathogen in Antarctic birds is almost unknown as well as the ramifications of its potential spread in naive bird populations. To investigate the prevalence of chlamydia organisms, cloacal and fecal samples were collected from 264 penguins and 263 seabirds on the Antarctic Peninsula and in Southern Chile. No C. psittaci could be detected by 23S rRNA real-time PCR. However, DNA sequencing of the 16S rRNA 298-bp signature sequence revealed a Chlamydiaceae-like bacterium previously found in seabirds from the subarctic zone, demonstrating that this not yet fully characterized bacterium is widespread. In conclusion, the prevalence of C. psittaci among wild birds on the Antarctic Peninsula seems to be low, but other types of chlamydial organisms are common. Further studies are required to taxonomically define and finally understand the role of these non-classified Chlamydiae.

Stimulus-specific adaptation is the phenomenon whereby neural response magnitude decreases with repeated stimulation. Inconsistencies between recent nonhuman animal recordings and computational modeling suggest dynamic influences on stimulus-specific adaptation. The present human electroencephalography (EEG) study investigates the potential role of statistical context in dynamically modulating stimulus-specific adaptation by examining the auditory cortex-generated N1 and P2 components. As in previous studies of stimulus-specific adaptation, listeners were presented with oddball sequences in which the presentation of a repeated tone was infrequently interrupted by rare spectral changes taking on three different magnitudes. Critically, the statistical context varied with respect to the probability of small versus large spectral changes within oddball sequences (half of the time a small change was most probable; in the other half a large change was most probable). We observed larger N1 and P2 amplitudes (i.e., release from adaptation) for all spectral changes in the small-change compared with the large-change statistical context. The increase in response magnitude also held for responses to tones presented with high probability, indicating that statistical adaptation can overrule stimulus probability per se in its influence on neural responses. Computational modeling showed that the degree of coadaptation in auditory cortex changed depending on the statistical context, which in turn affected stimulus-specific adaptation. Thus the present data demonstrate that stimulus-specific adaptation in human auditory cortex critically depends on statistical context. Finally, the present results challenge the implicit assumption of stationarity of neural response magnitudes that governs the practice of isolating established deviant-detection responses such as the mismatch negativity.

Paper-based biosensors offer a promising technology to be used at the point of care, enabled by good performance, convenience and low-cost. In this article, we describe a colorimetric vertical-flow DNA microarray (DNA-VFM) that takes advantage of the screening capability of DNA microarrays in a paper format together with isothermal amplification by means of Recombinase Polymerase Amplification (RPA). Different assay parameters such as hybridization buffer, flow rate, printing buffer and capture probe concentration were optimized. A limit of detection (LOD) of 4.4 nM was achieved as determined by tabletop scanning. The DNA-VFM was applied as a proof of concept for detection of Neisseria meningitidis, a primary cause of bacterial meningitis. The LOD was determined to be between 38 and 2.1 × 10

Objectives Chlamydia trachomatis ompA genotypes A and B, primarily associated with trachoma, were unexpectedly detected in urogenital samples of patients in Spain, a trachoma-free country. In this study, we aimed to explain this finding using analysis of organotropism-related genes and a multilocus sequence typing (MLST) technique. Methods C. trachomatis genotypes A or B were detected in 8/930 (0.9%) infection episodes between 2006 and 2012. In these strains, organotropism-related genes (polymorphic membrane protein gene H, tryptophan synthase gene A, CTA0934, and cytotoxin) were studied. Further, the strains were analysed by MLST, using a polymerase chain reaction that amplifies five highly variable genomic loci ( hctB , CT058, CT144, CT172, and pbpB ). Amplicons were sequenced and phylogenetic analysis was conducted. Results Seven strains were detected in the eight infection episodes (in one patient, an identical strain being found in two episodes). Analysis of organotropism-related genes showed that these strains shared genetic features characteristic of genitotropic genotypes but not of trachoma strains. Three strains of genotype A showed a unique and new MLST-sequence type (ST551, allele profile 8-8-2-27-69). The four strains of genotype B belonged to ST138. Conclusions C. trachomatis ompA genotypes A and B associated with trachoma, but detected sporadically in urogenital samples in trachoma-free countries, may be the result of recombination between strains adapted to trachoma and strains adapted to sexual transmission.

Increased memory load is often signified by enhanced neural oscillatory power in the alpha range (8–13 Hz), taken to reflect inhibition of task-irrelevant brain regions. The corresponding neural correlates of memory decay, however, are not yet well-understood. Here, we investigated auditory sensory memory decay using a delayed matching-to-sample task with pure-tone sequences. First, in a behavioral experiment we modeled memory behavior over six different delay-phase durations. Second, in a magnetoencephalography (MEG) experiment, we assessed alpha-power modulations over three different delay-phase durations. In both experiments, the temporal expectation for the to-be-remembered sound was manipulated, so that it was either temporally expected or not. In both studies, memory performance declined over time but this decline was less strong under a more precise temporal expectation. Similarly, patterns of alpha power in and alpha-tuned connectivity between sensory cortices changed parametrically with delay duration (i.e., decrease in occipito-parietal regions, increase in temporal regions). Notably, temporal expectation counteracted alpha-power decline in heteromodal brain areas (i.e., supramarginal gyrus), in line with its memory-decay counteracting effect on performance. Correspondingly, temporal expectation also boosted alpha connectivity within attention networks known to play an active role during memory maintenance. The present data outline how patterns of alpha power orchestrate sensory memory decay, and encourage a refined perspective on alpha power and its inhibitory role across brain space and time.Significance StatementOur sensory memories of the physical world fade quickly. We show here that this decay of sensory memory can be counteracted by so-called temporal expectation, that is, knowledge of when to expect the to-be-remembered sensory event (here, brief sound patterns). We also show that distinct patterns and modulations of neural oscillations in the “alpha” (8–13 Hz) range index both, the degree of memory decay, and any benefit from temporal expectation, both of which affect memory performance. Critically, spatially distributed cortical patterns of alpha power, with opposing effects in auditory vs. visual sensory cortices and alpha-tuned connectivity changes within supramodal attention networks, reflect the allocation of neural resources as sensory memory representations fade.

In absence of direct experimental evidence, it is essential to constrain the parameter space of the Minimal Supersymmetric Standard Model (MSSM) both at the Supersymmetry breaking and the electroweak scale. After a brief introduction to Supersymmetry (SUSY), we present an extensive analysis of electroweak, low energy, and cosmological constraints in minimal supergravity (mSUGRA) and gauge-mediated SUSY-breaking (GMSB) scenarios. We include the possibility of non-minimal flavour violation (NMFV) in the squark sector and define ``collider-friendly'' benchmark points based on detailed scans of the parameter space. We then consider neutralino pair annihilation into quark-antiquark pairs that dominates wide ranges of the mSUGRA parameter space. We present the corresponding full one-loop QCD and SUSY-QCD calculation and show numerically that the loop diagrams have an important impact on the annihilation cross section and, in consequence, in the prediction of the dark matter relic density, resulting in a modification of the preferred regions of the parameter space.We finally present analytical expressions and numerical predictions for squark, gaugino, and gravitino production cross sections at the LHC in GMSB with NMFV. We also discuss the phenomenology of flavour mixing and cosmological implications on the gravitino mass within this context., En l'absence d'évidence expérimentale directe de superpartenaires, il est essentiel de contraindre l'espace des paramètres du Modèle Standard Supersymétrique Minimal (MSSM) aux échelles de la brisure de la Supersymétrie et électrofaible. Après une brève introduction à la Supersymétrie (SUSY), nous présentons une analyse extensive des contraintes électrofaible, de basse énergie et cosmologiques dans des modèles de supergravité minimale (mSUGRA) et de brisure de Supersymétrie par médiation de jauge (GMSB). Nous incluons la possibilité de violation non-minimale de la saveur (NMFV) et définissons des scénarios ``benchmark'' basés sur des ``scans'' détaillés de l'espace des paramètres. Ensuite, nous considérons l'annihilation d'une paire de neutralinos en une paire de quark-antiquark qui domine dans de larges régions de l'espace des paramètres dans les modèles mSUGRA. Nous présentons le calcul complet incluant des corrections à une boucle en QCD et SUSY-QCD de ces processus et montrons numériquement que les diagrammes à une boucle ont un impact non négligeable sur la section efficace d'annihilation. En conséquence, la prédiction de densité relique de matière noire reçoit des corrections importantes, ce qui résulte en une modification de la région cosmologiquement favorisée dans l'espace des paramètres.Finalement, nous présentons des expressions analytiques et des prédictions numériques pour des sections efficaces de production de squarks, jauginos et gravitinos au LHC dans les modèles GMSB avec NMFV. Nous discutons également la phénoménologie du mélange de saveur et les implications cosmologiques sur la masse du gravitino dans ce contexte.

Introduction Lymphogranuloma venereum (LGV) has become prevalent among men who have sex with men (MSM) in Europe since an outbreak in The Netherlands in 2003. The aim of this study was to describe the development of LGV in relation to HIV since 2004, and genotypes of LGV and other Chlamydia trachomatis (Ct) genovars in a MSM population in 2014/15. Methods All testing for LGV in Sweden is referred to Uppsala University Hospital. LGV-specific pmpH-gene PCR was used for detection. High-resolution genotyping based on ompA gene and multilocus sequence typing (MLST) was performed on all Ct-positive cases from an STI clinic for MSM in Stockholm between 1.9. 2014 and 1.7.2015. Results The annual numbers of detected LGV cases in Sweden were 2 in 2004 to 2006, between 5 and 20 in 2007 to 2012, and between 23 and 38 in 2013 to 2016. The number of LGV-tests increased from 68 in 2008 to 268 in 2016. During the study in 2014/15 31 LGV cases were identified in 309 patients with successful PCR-results. In 39% (12/31) LGV was unexpected and had not been detected without extended screening. The HIV-prevalence among LGV-positive patients decreased from 88% 2006–2013% to 68% 2014–2015. Of ompA genotyped LGV cases 69% were L2% and 31% were L2b type. This contrasts to earlier Swedish and European data from 2004–2009 when only L2b was found. Complete genotyping, including ompA and MLST, was obtained for 151 patients with non-LGV Ct and resulted in genovar D, 27%; E, 14%; G, 30% and J 21%. MLST resulted in 27 STs of which 3 predominated and accounted for 51%. Eight STs were new when compared to the database http://mlstdb.bmc.uu.se comprising 540 STs from >3300 specimens. Conclusion In Sweden LGV has gone from sporadic import cases to a probable endemic spread among HIV-negative MSM, which emphasises the need for LGV-testing This emphasises the need for LGV-testing within this high risk group. LGV has developed from being of clonal nature to occur as different strains among MSM.

Unification of matter fields implies the existence of accidental permutation symmetries, which potentially remain immune to large quantum corrections up to the TeV scale. We investigate the case of a supersymmetric $SU(5)$ grand unified theory, where such a permutation symmetry is present in the up-type squark sector. We present a variety of tests allowing to challenge the $SU(5)$ hypothesis based on the observation of squarks at the LHC. These tests appear as relations among observables involving flavour-violating or chirality-flipping decays of squarks. Moreover, they rely on top-polarimetry and charm-tagging. As an example, we discuss the application to the scenario of Natural Supersymmetry, while more examples can be found in the related journal publications.

Enhanced alpha power compared with a baseline can reflect states of increased cognitive load, for example, when listening to speech in noise. Can knowledge about “when” to listen (temporal expectations) potentially counteract cognitive load and concomitantly reduce alpha? The current magnetoencephalography (MEG) experiment induced cognitive load using an auditory delayed-matching-to-sample task with 2 syllables S1 and S2 presented in speech-shaped noise. Temporal expectation about the occurrence of S1 was manipulated in 3 different cue conditions: “Neutral” (uninformative about foreperiod), “early-cued” (short foreperiod), and “late-cued” (long foreperiod). Alpha power throughout the trial was highest when the cue was uninformative about the onset time of S1 (neutral) and lowest for the late-cued condition. This alpha-reducing effect of late compared with neutral cues was most evident during memory retention in noise and originated primarily in the right insula. Moreover, individual alpha effects during retention accounted best for observed individual performance differences between late-cued and neutral conditions, indicating a tradeoff between allocation of neural resources and the benefits drawn from temporal cues. Overall, the results indicate that temporal expectations can facilitate the encoding of speech in noise, and concomitantly reduce neural markers of cognitive load.

Behaviorally relevant environmental stimuli are often characterized by some degree of temporal regularity. Dynamic attending theory provides a framework for explaining how perception of stimulus events is affected by the temporal context within which they occur. However, the precise neural implementation of dynamic attending remains unclear. Here, we provide a suggestion for a potential neural implementation of dynamic attending by appealing to low-frequency neural oscillations. The current review will familiarize the reader with the basic theoretical tenets of dynamic attending theory, and review empirical work supporting predictions derived from the theory. The potential neural implementation of dynamic attending theory with respect to low-frequency neural oscillations will be outlined, covering stimulus processing in regular and irregular contexts. Finally, we will provide some more speculative connections between dynamic attending and neural oscillations, and suggest further avenues for future research.

Classically, neural adaptation refers to a reduction in response magnitude by sustained stimulation. In human electroencephalography (EEG), neural adaptation has been measured, for example, as frequency-specific response decrease by previous stimulation. Only recently and mainly based on animal studies, it has been suggested that statistical properties in the stimulation lead to adjustments of neural sensitivity and affect neural response adaptation. However, it is thus far unresolved which statistical parameters in the acoustic stimulation spectrum affect frequency-specific neural adaptation, and on which time scales the effects take place. The present human EEG study investigated the potential influence of the overall spectral range as well as the spectral spacing of the acoustic stimulation spectrum on frequency-specific neural adaptation. Tones randomly varying in frequency were presented passively and computational modeling of frequency-specific neural adaptation was used. Frequency-specific adaptation was observed for all presentation conditions. Critically, however, the spread of adaptation (i.e., degree of coadaptation) in tonotopically organized regions of auditory cortex changed with the spectral range of the acoustic stimulation. In contrast, spectral spacing did not affect the spread of frequency-specific adaptation. Therefore, changes in neural sensitivity in auditory cortex are directly coupled to the overall spectral range of the acoustic stimulation, which suggests that neural adjustments to spectral stimulus statistics occur over a time scale of multiple seconds.

Neural oscillatory dynamics are a candidate mechanism to steer perception of time and temporal rate change. While oscillator models of time perception are strongly supported by behavioral evidence, a direct link to neural oscillations and oscillatory entrainment has not yet been provided. In addition, it has thus far remained unaddressed how context-induced illusory percepts of time are coded for in oscillator models of time perception. To investigate these questions, we used magnetoencephalography and examined the neural oscillatory dynamics that underpin pitch-induced illusory percepts of temporal rate change. Human participants listened to frequency-modulated sounds that varied over time in both modulation rate and pitch, and judged the direction of rate change (decrease vs increase). Our results demonstrate distinct neural mechanisms of rate perception: Modulation rate changes directly affected listeners' rate percept as well as the exact frequency of the neural oscillation. However, pitch-induced illusory rate changes were unrelated to the exact frequency of the neural responses. The rate change illusion was instead linked to changes in neural phase patterns, which allowed for single-trial decoding of percepts. That is, illusory underestimations or overestimations of perceived rate change were tightly coupled to increased intertrial phase coherence and changes in cerebro-acoustic phase lag. The results provide insight on how illusory percepts of time are coded for by neural oscillatory dynamics.

Spectral analysis of acoustic stimuli occurs in the auditory periphery (termed frequency selectivity) as well as at the level of auditory cortex (termed frequency specificity). Frequency selectivity is commonly investigated using an auditory filter model, while frequency specificity is often investigated as neural adaptation of the N1 response in electroencephalography (EEG). However, the effects of aging on frequency-specific adaptation, and the link between peripheral frequency selectivity and neural frequency specificity have not received much attention. Here, normal hearing younger (20–31 years) and older participants (49–63 years) underwent a psychophysical notched noise experiment to estimate individual auditory filters, and an EEG experiment to investigate frequency-specific adaptation in auditory cortex. The shape of auditory filters was comparable between age groups, and thus shows intact frequency selectivity in normal aging. In auditory cortex, both groups showed N1 frequency-specific neural adaptation effects that similarly varied with the spectral variance in the stimulation, while N1 responses were overall larger for older than younger participants. Importantly, the overall N1 amplitude, but not frequency-specific neural adaptation was correlated with the pass-band of the auditory filter. Thus, the current findings show a dissociation of peripheral frequency selectivity and neural frequency specificity, but suggest that widened auditory filters are compensated for by a response gain in frequency-specific areas of auditory cortex.

Historically wildlife conservation was based on habitat protection and exploitation control. Only recently have diseases been considered an important issue. However, pathogens are usually described during or after disease outbreaks, but to determine which pathogens may be emerging, surveys of wildlife health are critical in a given time. This study deals with the health status of gentoo penguins Pygoscelis papua in two localities at the Antarctica Peninsula and one at Ardley Island off the South Shetland Islands. Cloacal swaps, fresh fecal samples, ectoparasites, and blood smears were collected. We examined and dissected 14 penguin corpses found dead. Fecal samples were positive for Campylobacter, Escherichia coli and in the carcasses four endoparasitic species were found: Diphyllobothrium sp. and Parorchites zederi, Corynosoma shackletoni and Stegophorus adeliae. The tick Ixodes uriae occurred in five of the examined penguins, and the louse Austrogoniodes gressitti on six birds. From the colony grounds, we collected 1,184 I. uriae. We recorded antibiotic-resistant bacteria, such as E. coli, in ecosystems where gentoo penguins breed. Cloacal samples (300) were negative for Chlamydia, as well as for Salmonella, Campylobacter, E. coli, Newcastle and Influenza viruses.

In auditory cortex, activation and subsequent adaptation is strongest for regions responding best to a stimulated tone frequency and less for regions responding best to other frequencies. Previous attempts to characterize the spread of neural adaptation in humans investigated the auditory cortex N1 component of the event-related potentials. Importantly, however, more recent studies in animals show that neural response properties are not independent of the stimulation context. To link these findings in animals to human scalp potentials, we investigated whether contextual factors of the acoustic stimulation, namely, spectral variance, affect the spread of neural adaptation. Electroencephalograms were recorded while human participants listened to random tone sequences varying in spectral variance (narrow vs. wide). Spread of adaptation was investigated by modeling single-trial neural adaptation and subsequent recovery based on the spectro-temporal stimulation history. Frequency-specific neural responses were largest on the N1 component, and the modeled neural adaptation indices were strongly predictive of trial-by-trial amplitude variations. Yet the spread of adaption varied depending on the spectral variance in the stimulation, such that adaptation spread was broadened for tone sequences with wide spectral variance. Thus the present findings reveal context-dependent auditory cortex adaptation and point toward a flexibly adjusting auditory system that changes its response properties with the spectral requirements of the acoustic environment.

We present an extensive study of the MSSM parameter space allowing for general generation mixing in the squark sector. Employing an MCMC algorithm, we establish the parameter ranges which are allowed with respect to various experimental and theoretical constraints. Based on this analysis, we propose benchmark scenarios for future studies. Moreover, we discuss aspects of signatures at the LHC., 4 pages, 3 figures. Contribution to the proceedings of the 38th International Conference of High Energy Physics (ICHEP), Chicago, Aug. 3-10, 2016

Extracting temporal periodicities and envelope shapes of sounds is important for listening within complex auditory scenes but declines behaviorally with age. Here we recorded local field potentials (LFPs) and spikes to investigate how aging affects the neural representations of different modulation rates and envelope shapes in the inferior colliculus of rats. We specifically aimed to explore the input-output (LFP-spike) response transformations of inferior colliculus neurons. Our results show that envelope shapes up to 256-Hz modulation rates are represented in the neural synchronization phase lags in younger and older animals. Critically, aging was associated with (1) an enhanced gain in onset response magnitude from LFPs to spikes; (2) an enhanced gain in neural synchronization strength from LFPs to spikes for a low modulation rate (45 Hz); (3) a decrease in LFP synchronization strength for higher modulation rates (128 and 256 Hz); and (4) changes in neural synchronization strength to different envelope shapes. The current age-related changes are discussed in the context of an altered excitation-inhibition balance accompanying aging. This article is protected by copyright. All rights reserved.

This study compared conventional ompA genotyping of Chlamydia trachomatis with multilocus sequence typing (MLST) and multilocus typing (MLT) DNA microarray. DNA extracts of 104 C. trachomatis positive specimens were analyzed by ompA sequencing and MLST and of these 76 by MLT array. Obtained MLST sequence types (STs) were compared to sequences in the database http://mlstdb.uu.se. The resolution obtained for MLST (35 STs) was 2.1 higher than for ompA sequencing (17 variants) and 1.3 higher than MLT array (27 MLT groups). Among the 104 samples the predominant genotype E could be divided into 5 ompA variants and 23 STs of which 16 had not been reported in previous studies. The most common STs, ST3 and ST56, were identified as founders and are common in several countries on a global scale. The MLST and the MLT array provided similar strain discrimination capacity and showed considerably higher resolution than conventional ompA sequencing.

With the latest Planck results the dark matter relic density is determined to an unprecedented precision. In order to reduce current theoretical uncertainties in the dark matter relic density prediction, we have calculated next-to-leading order SUSY-QCD corrections to neutralino (co)annihilation processes including Coulomb enhancement effects. We demonstrate that these corrections can have significant impact on the cosmologically favoured MSSM parameter space and are thus of general interest for parameter studies and global fits., 9 pages, 8 figures, to appear in the proceedings of the European Physical Society Conference on High Energy Physics 2015 (EPS-HEP 2015), Vienna, Austria, 22nd to 29th of July 2015

We present an extensive study of non-minimally flavour violating (NMFV) terms in the Lagrangian of the Minimal Supersymmetric Standard Model (MSSM). We impose a variety of theoretical and experimental constraints and perform a detailed scan of the parameter space by means of a Markov Chain Monte-Carlo (MCMC) setup. This represents the first study of several non-zero flavour-violating elements within the MSSM. We present the results of the MCMC scan with a special focus on the flavour-violating parameters. Based on these results, we define benchmark scenarios for future studies of NMFV effects at the LHC.

A duplex real-time PCR based on the rnpB gene was developed for Mycobacterium spp. The assay was specific for the Mycobacterium tuberculosis complex (MTB) and also detected all 19 tested species of non-tuberculous mycobacteria (NTM). The assay was evaluated on 404 clinical samples: 290 respiratory samples and 114 from tissue and other non-respiratory body sites. M. tuberculosis was detected by culture in 40 samples and in 30 samples by the assay. The MTB assay showed a sensitivity similar to Roche Cobas Amplicor MTB-PCR (Roche Molecular Systems, Pleasanton, CA, USA). There were only nine samples with non-tuberculous mycobacteria detected by culture. Six of them were detected by the PCR assay.

High-resolution genotyping of Chlamydia trachomatis improves the characterization of strains infecting different patient groups and sexual networks. In this study, multilocus sequence typing (MLST) and ompA sequence determination were used for an analysis of C. trachomatis strains from 203 men who have sex with men (MSM) from Sweden, the Netherlands, and the United States. The results obtained were compared with data from 153 heterosexual women from Sweden and the Netherlands. The overlap in MLST/ ompA profiles between MSM from Sweden and the Netherlands was 68%, while the overlap between heterosexual populations from these countries was only 18%. The distribution of genotypes in MSM from the United States was less similar to that in MSM from the European countries, with 45% and 46% overlaps for MSM in Sweden and the Netherlands, respectively. Minimum-spanning-tree analysis of MLST/ ompA sequence types identified two large clusters that contained almost exclusively samples from MSM and comprised 74% of all MSM samples. Three other clusters were predominated by samples from women but also contained MSM specimens. Of 19 detected variants of the MLST target CT144, three variants were highly associated with MSM. Our study supports the hypotheses of both tissue tropism as well as epidemiological network structures as explanations for the linkage between specific genetic variants and sexual orientation.

The present magnetoencephalography study investigated whether the brain states of early syntactic and auditory-perceptual processes can be decoded from single-trial recordings with a multivariate pattern classification approach. In particular, it was investigated whether the early neural activation patterns in response to rule violations in basic auditory perception and in high cognitive processes (syntax) reflect a functional organization that largely generalizes across individuals or is subject-specific. On this account, subjects were auditorily presented with correct sentences, syntactically incorrect sentences, correct sentences including an interaural time difference change, and sentences containing both violations. For the analysis, brain state decoding was carried out within and across subjects with three pairwise classifications. Neural patterns elicited by each of the violation sentences were separately classified with the patterns elicited by the correct sentences. The results revealed the highest decoding accuracies over temporal cortex areas for all three classification types. Importantly, both the magnitude and the spatial distribution of decoding accuracies for the early neural patterns were very similar for within-subject and across-subject decoding. At the same time, across-subject decoding suggested a hemispheric bias, with the most consistent patterns in the left hemisphere. Thus, the present data show that not only auditory-perceptual processing brain states but also cognitive brain states of syntactic rule processing can be decoded from single-trial brain activations. Moreover, the findings indicate that the neural patterns in response to syntactic cognition and auditory perception reflect a functional organization that is highly consistent across individuals.

A nucleic acid amplification test (NAAT) may enable the laboratory to detect Chlamydia trachomatis and Neisseria gonorrhoeae with high sensitivity and specificity in traditional urogenital swabs and in different types of samples obtained noninvasively by patients at home or in other settings. This chapter provides guidance in selecting the most appropriate NAATs for C. trachomatis and N. gonorrhoeae among available commercial and in-house assays. The selection of targets for detection of C. trachomatis and N. gonorrhoeae is a major point in determining which assay to use for routine diagnostics. Sequence variation in the target region may lead to false-negative results, whereas the presence of the target gene in other species may lead to false-positive results. Routine diagnostics of C. trachomatis infections is predominantly performed with commercial NAAT high-volume test systems, but there are still applications where in-house-developed methods are useful. The number of samples in a pool depends on the prevalence, and it is calculated from the number of samples, which needs to be tested individually from positive pools. Samples from a negative pool should be reported as negative. The rapid spread of a mutant variant of C. trachomatis in Sweden escaping detection by some NAATs has been a warning that vigilance for drug-resistant mutants should be enforced.

We study the effect of squark generation mixing on squark production and decays at the LHC in the Minimal Supersymmetric Standard Model (MSSM). We show that the effect can be very large despite the very strong constraints on quark flavour violation (QFV) from experimental data on B mesons. We find that the two lightest up-type squarks can have large branching ratios for the decays into and at the same time, leading to QFV signals ‘ + missing-ET + X′ with a significant rate. The observation of this remarkable signature would provide a powerful test of supersymmetric QFV at LHC. This could have a significant impact on the search for squarks and the determination of the underlying MSSM parameters.

In language processing, the relative contribution of early sensory and higher cognitive brain areas is still an open issue. A recent controversial hypothesis proposes that sensory cortices show sensitivity to syntactic processes, whereas other studies suggest a wider neural network outside sensory regions. The goal of the current event‐related fMRI study is to clarify the contribution of sensory cortices in auditory syntactic processing in a 2 × 2 design. Two‐word utterances were presented auditorily and varied both in perceptual markedness (presence or absence of an overt word category marking “‐t”), and in grammaticality (syntactically correct or incorrect). A multivariate pattern classification approach was applied to the data, flanked by conventional cognitive subtraction analyses. The combination of methods and the 2 × 2 design revealed a clear picture: The cognitive subtraction analysis found initial syntactic processing signatures in a neural network including the left IFG, the left aSTG, the left superior temporal sulcus (STS), as well as the right STS/STG. Classification of local multivariate patterns indicated the left‐hemispheric regions in IFG, aSTG, and STS to be more syntax‐specific than the right‐hemispheric regions. Importantly, auditory sensory cortices were only sensitive to the overt perceptual marking, but not to the grammaticality, speaking against syntax‐inflicted sensory cortex modulations. Instead, our data provide clear evidence for a distinction between regions involved in pure perceptual processes and regions involved in initial syntactic processes. Hum Brain Mapp, 2012. © 2011 Wiley Periodicals, Inc.

Background: In the past, contradictory results have been obtained linking Chlamydia trachomatis serovars (ompA gene) to different clinical courses of infection. Methods: A high resolution multilocus sequence typing (MLST) system was used to genotype 6 genetic regions, including ompA, in 70 Dutch urogenital C. trachomatis strains from patients with different degrees of defined clinical symptoms (asymptomatic, symptomatic, and lower abdominal pain), to determine if MLST genotypes correlated with clinical manifestations of infection. Results and conclusions: We identified 46 MLST types, with only a small overlap to Swedish MLST types. This study found no correlation between MLST profiles and symptomatology. To understand the clinical course of infection, future studies should not only consider bacterial factors but also look on the immunogenetics of the host

We aimed to compare conventional ompA typing of Chlamydia trachomatis with multilocus sequence typing (MLST) and multilocus variable-number tandem-repeat (VNTR) analysis (MLVA). Previously used MLST and MLVA systems were compared to modified versions that used shorter target regions and nested PCR. Heterosexual couples were selected from among persons with urogenital C. trachomatis infections visiting the sexually transmitted infection outpatient clinic in Amsterdam, The Netherlands. We identified 30 couples with a total of 65 C. trachomatis -positive samples on which MLST and MLVA for eight target regions were performed. All regions were successfully sequenced in 52 samples, resulting in a complete profile for 18 couples and 12 individuals. Nine ompA genovars from D to K, with two variants of genovar G, were found. The numbers of sequence type and MLVA type profiles were 20 for MLST and 21 for MLVA, and a combination of MLST and MLVA yielded 28 profiles, with discriminatory indexes ( D ) ranging from 0.95 to 0.99. Partners in 17 couples shared identical profiles, while partners in 1 couple had completely different profiles. Three persons had infections at multiple anatomical locations, and within each of these three individuals, all profiles were identical. The discriminatory capacity of all MLST and MLVA methods is much higher than that of ompA genotyping ( D = 0.78). No genotype variation was found within the samples of the same person or from heterosexual couples with a putative single transmission. This shows that the chlamydial genome in clinical specimens has an appropriate polymorphism to enable epidemiological cluster analysis using MLST and MLVA.

The family Chlamydiaceae contains several bacterial pathogens of important human and veterinary medical concern, such as Chlamydia trachomatis and Chlamydophila psittaci. Within the order Chlamydia ...

A new concept for multiplex detection and quantification of microbes is here demonstrated on a range of infectious fungal species. Padlock probe methodology in conjunction with qPCR and Luminex technology was used for simultaneous detection of ten fungal species in one single experiment. By combining the multiplexing properties of padlock probes and Luminex detection with the well established quantitative characteristics of qPCR, quantitative microbe detection was done in 10-plex mode. A padlock probe is an oligonucleotide that via a ligation reaction forms circular DNA when hybridizing to specific target DNA. The region of the padlock probe that does not participate in target DNA hybridization contains generic primer sequences for amplification and a tag sequence for Luminex detection. This was the fundament for well performing multiplexing. Circularized padlock probes were initially amplified by rolling circle amplification (RCA), followed by a SybrGreen real time PCR which allowed an additive quantitative assessment of target DNA in the sample. Detection and quantification of amplified padlock probes were then done on color coded Luminex microspheres carrying anti-tag sequences. A novel technique, using labeled oligonucleotides to prevent reannealing of amplimers by covering the flanks of the address sequence, improved the signal to noise ratio in the detection step considerably. The method correctly detected fungi in a variety of clinical samples and offered quantitative information on fungal nucleic acid.

A quantitative real-time polymerase chain reaction (PCR) based on the omp P6 gene was developed to detect Haemophilus influenzae. Its specificity was determined by analysis of 29 strains of 11 different Haemophilus spp. and was compared with PCR assays having other target genes: rnpB, 16S rRNA, and bexA. The method was evaluated on nasopharyngeal aspirates from 166 adult patients with community-acquired pneumonia. When 10(4) DNA copies/mL was used as cutoff limit for the method, P6 PCR had a sensitivity of 97.5% and a specificity of 96.0% compared with the culture. Of 20 culture-negative but P6 PCR-positive cases, 18 were confirmed by fucK PCR as H. influenzae. Five (5.9%) of 84 nasopharyngeal aspirates from adult controls tested PCR positive. We conclude that the P6 real-time PCR is both sensitive and specific for identification of H. influenzae in respiratory secretions. Quantification facilitates discrimination between disease-causing H. influenzae strains and commensal colonization.

Background: Genital chlamydia infection (chlamydia) is the most commonly reported sexually transmitted infection (STI) in Sweden. To guide prevention needs, we aimed to investigate factors associated with chlamydia. Methods: A cohort of visitors aged 20-40 years at an urban STI clinic in Sweden was recruited. Behavioural data were collected using a self-administered questionnaire. Self-sampled specimens were tested for chlamydia by a DNA amplification assay. Statistically significant (p

The dark matter relic density being a powerful observable to constrain models of new physics, the recent experimental progress calls for more precise theoretical predictions. On the particle physics side, improvements are to be made in the calculation of the (co)annihilation cross-section of the dark matter particle. We present the project DM@NLO which aims at calculating the neutralino (co)annihilation cross-section in the MSSM including radiative corrections in QCD. In the present document, we briefly review selected results for different (co)annihilation processes. We then discuss the estimation of the associated theory uncertainty obtained by varying the renormalization scale. Finally, perspectives are discussed., Comment: 7 pages. Contribution to the proceedings of the 38th International Conference of High Energy Physics (ICHEP), Chicago, Aug. 3-10, 2016

Objectives: The so-called small-world effect can have a great impact on efforts to control the incidence and prevalence of sexually transmitted infections. This is because a small number of so-called spatial bridgers (individuals who, through sexual contacts, interconnect geographically distant areas) can drastically lower the average path length in the sexual network and, as a result, make locally based intervention programs much less effective. The objectives of this study were to analyze the sociodemographic characteristics of these bridgers and to compare the result with the remaining study population. The purpose was to determine whether it is possible to identify them for targeted intervention programs. Study Design: During 2001, contact tracing was performed in approximately 98% of all cases with positive test results in Varmland County. The sexual networks obtained constituted a study population of 851 individuals. Statistical analysis was used to characterize individuals engaged in spatial bridging behavior. Results: Approximately 8% of the study population was characterized as spatial bridgers. Using multivariate analysis, we found almost no significant differences between these individuals and the rest of the study population when it came to sociodemographic variables, including education, economy, and ethnicity. Conclusion: The number of spatial bridgers is high enough to create a small-world network with links that can fuel the endemic chlamydia in Varmland County. Sociodemographic information could not be used to characterize spatial bridgers. In interventions against chlamydia, spatial bridgers shall be considered as potentially important for sustaining the disease.

The latest Planck data allow one to determine the dark matter relic density with previously unparalleled precision. In order to achieve a comparable precision on the theory side, we have calculated the full $\mathcal{O}(\alpha_s)$ corrections to the most relevant annihilation and coannihilation processes for relic density calculations within the Minimal Supersymmetric Standard Model (MSSM). The interplay of these processes is discussed. The impact of the radiative corrections on the resulting relic density is found to be larger than the experimental uncertainty of the Planck data., Comment: 7 pages, 2 figures, 18th International Conference From the Planck Scale to the Electroweak Scale, 25-29 May 2015. Ioannina, Greece

Autoimmune polyendocrine syndrome type I (APS I) is an inherited recessive disorder with a progressive immunological destruction of many tissues including the adrenal cortex, the parathyroid glands, and the gonads. APS I is caused by mutations in the AIRE gene (autoimmune regulator), expressed in cells of the thymus and spleen, suggesting a role in central and peripheral tolerance. Aire(-/-) mice replicate the autoimmune features of APS I patients with the presence of multiple autoantibodies and lymphocytic infiltrates in various tissues, but young mice appear clinically healthy. We here report the investigation of 15- to 24-month-old Aire(-/-) mice. We did not observe any endocrinological abnormalities, nor did sera from these mice recognize known APS I autoantigens. Interestingly, however, there was a high frequency of marginal zone B-cell lymphoma in Aire(-/-) mice and liver infiltrates of B cells, suggesting chronic antigen exposure and exaggerated activation. Furthermore, increased numbers of monocytes in blood were identified as well as augmented numbers of metallophilic macrophages in the spleen. We propose that Aire, in addition to its function in the thymus, also has a peripheral regulatory role by controlling the development of antigen-presenting cells (APCs) and marginal zone B-cell activation.

Pyrosequencing technology was evaluated for identification of species within the Streptococcus genus. Two variable regions in the rnpB gene, which encodes the RNA subunit of endonuclease P, were sequenced in two reactions. Of 43 species, all could be identified to the species level except strains of the species pairs Streptococcus anginosus / S. constellatus and S. infantis / S. peroris . A total of 113 blood culture isolates were identified by pyrosequencing analysis of partial rnpB sequences. All but eight isolates could be unambiguously assigned to a specific species when the first 30 nucleotides of the two regions were compared to an rnpB database comprising 107 streptococcal strains. Principal coordinate analysis of sequence variation of strains from viridans group streptococci resulted in species-specific clusters for the mitis and the salivarius groups but not for the anginosus group. The identification capacity of pyrosequencing was compared to the biochemical test systems VITEK 2 and Rapid ID 32 Strep. The concordance between pyrosequencing and VITEK 2 was 75%, and for Rapid ID 32 Strep the corresponding figure was 77%. Isolates with discrepant identifications in the three methods were subjected to entire rnpB DNA sequence analysis that confirmed the identifications by pyrosequencing. In conclusion, pyrosequencing analysis of the rnpB gene can reliably identify Streptococcus species with high resolution.

Pharmacodynamic knowledge about Chlamydia trachomatis exposed to antibiotics is hampered due to methodological limitations. We have developed a quantitative real-time PCR method (qRT-PCR) for determination of viable C. trachomatis. The method measures specific RNA transcripts of omp2 (omcB) as an expression of viable C. trachomatis. Two clinical isolates (one strain derived from a patient with recurrent symptoms despite doxycycline treatment) were cultured in McCoy cells and exposed to doxycycline at concentrations of 0.0078-64 mg/L. MIC values were evaluated microscopically by immunofluorescence (IF) and by qRT-PCR performed on cDNA prepared from the total RNA. The MIC for two C. trachomatis strains were determined to 0.016 and 0.031 mg/L by both qRT-PCR and IF. The qRT-PCR assay enabled MIC determinations without subjective evaluation, which is a problem when visually evaluating inclusions. The presented qRT-PCR is a suitable method for MIC determination of C. trachomatis. It has the advantage of giving quantitative measurements of chlamydial RNA levels and the method is useful in pharmacodynamic studies of C. trachomatis.

The vast majority of genital Chlamydia trachomatis infections are non-symptomatic or mildly symptomatic. Efficient contact tracing and screening programmes are the most effective means to reveal these infections. We conducted a prospective study on the effects of contact tracing performed by specially trained midwives in a centralized municipality-based organization during one year. In order to improve the efficiency of the contact tracing, all C. trachomatis-positive isolates in the county during one year were typed by sequencing the ompA gene. Contact tracing in two municipalities the year prior to the study revealed 1.6 partners for each index case ( n = 110). The corresponding figure for the whole county during the study period was 2.1 partners per index case ( n = 2065). Genotyping added valuable information in mapping individual sexual networks, but was not essential for achieving satisfactory contact tracing results.

A duplex quantitative real-time PCR (qPCR) assay was designed to detect both the polymerase gene ( pol ) and the glycoprotein gene ( gB ) of cytomegalovirus (CMV). The detection limit of the qPCR was determined to be 1 to 3 copies/reaction and the linear measure interval was 10 3 to 10 8 copies/ml. The qPCR system was compared to the COBAS Amplicor CMV Monitor test (COBAS) by an analysis of 138 plasma samples. Both systems detected CMV in 71 cases and had negative results for 33 samples. In addition, 34 samples were positive by qPCR and negative by the COBAS assay, but in no case was the COBAS result positive and the qPCR result negative. Thus, qPCR detected 48% more positive cases than the COBAS method. For samples with ≥10 5 copies/ml by qPCR, a saturation effect was seen in the COBAS assay and quantification required dilution. Copy numbers for pol and gB by qPCR generally agreed. However, the reproducibility of qPCR assays and the need for an international standard are discussed. Discrepant copy numbers for pol and gB by qPCR were found for samples from two patients, and sequence analysis revealed that the corresponding CMV strains were mismatched at four nucleotide positions compared with the gB fragment primer sequences. In conclusion, a duplex qPCR assay in a real-time format facilitates quantitative measurements and minimizes the risk of false-negative results.

Pathological and serological evidence and DNA-DNA reassociation data indicate that Chlamydophila psittaci and Chlamydophila abortus are separate species. C. psittaci causes avian systemic disease and C. abortus causes abortion. Both previously belonged to Chlamydia psittaci are associated with zoonotic and enzootic outbreaks. Genetic studies suggest that they are closely related and because of the recent availability of diverse C. psittaci strains and comparative data for several genes, it was possible to explore this relationship. The parrot C. psittaci strain 84/2334 was found to have DNA sequences that were identical to an extrachromosomal plasmid in duck C. psittaci strain N352, to rnpB in strain R54 from a brown skua and to the rrn intergenic spacer in parakeet strain Prk/Daruma (from Germany, Antarctica and Japan, respectively). Analysis of ompA and the rrn spacer revealed progressive diversification of the strains, with 84/2334 resembling what might have been a recent ancestor of C. abortus. Another C. psittaci strain (VS225) showed evidence of having undergone convergent evolution towards the C. abortus-like genotype, whereas strain R54 diverged independently. For the first time, these studies link C. abortus in an evolutionary context to the C. psittaci lineage. It has been concluded that C. abortus diverged from C. psittaci, and so strain R54 was designated a C. psittaci strain. It is recommended that characterization of C. psittaci and C. abortus strains should utilize more than a single method and more than a single gene.

Oscillatory activity in sensory cortices reflects changes in local excitation–inhibition balance, and recent work suggests that phase signatures of ongoing oscillations predict the perceptual detection of subsequent stimuli. Low-frequency oscillations are also entrained by dynamic natural scenes, suggesting that the chance of detecting a brief target depends on the relative timing of this to the entrained rhythm. We tested this hypothesis in humans by implementing a cocktail-party-like scenario requiring subjects to detect a target embedded in a cacophony of background sounds. Using EEG to measure auditory cortical oscillations, we find that the chance of target detection systematically depends on both power and phase of theta-band (2–6 Hz) but not alpha-band (8–12 Hz) oscillations before target. Detection rates were higher and responses faster when oscillatory power was low and both detection rate and response speed were modulated by phase. Intriguingly, the phase dependency was stronger for miss than for hit trials, suggesting that phase has a inhibiting but not ensuring role for detection. Entrainment of theta range oscillations prominently occurs during the processing of attended complex stimuli, such as vocalizations and speech. Our results demonstrate that this entrainment to attended sensory environments may have negative effects on the detection of individual tokens within the environment, and they support the notion that specific phase ranges of cortical oscillations act as gatekeepers for perception.

A new variant of Chlamydia trachomatis (nvCT) was discovered in Sweden in 2006, and it could not be detected by diagnostic systems from Abbott and Roche, whereas the third system used, from Becton Dickinson (BD), detects nvCT. We analyzed 3648 samples from 2 counties that used Roche and 2 counties that used BD methods from 2007 to 2011. After implementation of a Roche method that detects nvCT, its proportion has decreased and converged in the 4 counties but are still at different levels in Roche and BD counties. Future studies are needed to see if nvCT will decline further.

We elaborate on a recently found SU(5) relation confined to the up-(s)quark flavour space, that remains immune to large quantum corrections up to the TeV scale. We investigate the possibilities opened by this new window on the GUT scale in order to find TeV-scale SU(5) tests realizable at the LHC. These SU(5) tests appear as relations among observables involving either flavour violation or chirality flip in the up-(s)quark sector. The power of these tests is systematically evaluated using a frequentist, p-value based criterion. SU(5) tests in the Heavy supersymmetry (SUSY), Natural supersymmetry and Top-charm supersymmetry spectra are investigated. The latter scenario features light stops and scharms and is well-motivated from various five-dimensional constructions. A variety of SU(5) tests is obtained, involving techniques of top polarimetry, charm-tagging, or Higgs detection from SUSY cascade decays. We find that O(10) to O(100) events are needed to obtain 50% of relative precision at 3-sigma significance for all of these tests. In addition, we propose a set of precision measurements in ultraperipheral collisions in order to search for the flavour-changing dipole operators of Heavy supersymmetry., 46 pages, 10 figures, v3: final version to appear in JHEP

The Uppsala University Chlamydia trachomatis multilocus sequence type (MLST) database ( http://mlstdb.bmc.uu.se ) is based on five target regions (non-housekeeping genes) and the ompA gene. Each target has various numbers of alleles— hctB , 89; CT058, 51; CT144, 30; CT172, 38; and pbpB , 35—derived from 13 studies. Our aims were to perform an overall analysis of all C. trachomatis MLST sequence types (STs) in the database, examine STs with global spread, and evaluate the phylogenetic capability by using the five targets. A total of 415 STs were recognized from 2,089 specimens. The addition of 49 ompA gene variants created 459 profiles. ST variation and their geographical distribution were characterized using eBURST and minimum spanning tree analyses. There were 609 samples from men having sex with men (MSM), with 4 predominating STs detected in this group, comprising 63% of MSM cases. Four other STs predominated among 1,383 heterosexual cases comprising, 31% of this group. The diversity index in ocular trachoma cases was significantly lower than in sexually transmitted chlamydia infections. Predominating STs were identified in 12 available C. trachomatis whole genomes which were compared to 22 C. trachomatis full genomes without predominating STs. No specific gene in the 12 genomes with predominating STs could be linked to successful spread of certain STs. Phylogenetic analysis showed that MLST targets provide a tree similar to trees based on whole-genome analysis. The presented MLST scheme identified C. trachomatis strains with global spread. It provides a tool for epidemiological investigations and is useful for phylogenetic analyses.

Background We aimed to study if certain clinical and/or microbiological factors are associated with a high nasopharyngeal (NP) density of Streptococcus pneumoniae in pneumococcal pneumonia. In addition, we aimed to study if a high NP pneumococcal density could be useful to detect severe pneumococcal pneumonia. Methods Adult patients hospitalized for radiologically confirmed community-acquired pneumonia were included in a prospective study. NP aspirates were collected at admission and were subjected to quantitative PCR for pneumococcal DNA (Spn9802 DNA). Patients were considered to have pneumococcal etiology if S. pneumoniae was detected in blood culture and/ or culture of respiratory secretions and/or urinary antigen test. Results Of 166 included patients, 68 patients had pneumococcal DNA detected in NP aspirate. Pneumococcal etiology was noted in 57 patients (84%) with positive and 8 patients (8.2%) with negative test for pneumococcal DNA (p= 2 days prior to admission, and a medium/high serum immunoglobulin titer against the patient's own pneumococcal serotype. NP pneumococcal density was not associated with sex, age, smoking, co-morbidity, viral co-infection, pneumococcal serotype, or bacteremia. Severe pneumococcal pneumonia was noted in 28 study patients. When we studied the performance of PCR with different DNA cut-off levels for detection of severe pneumococcal pneumonia, we found sensitivities of 54-82% and positive predictive values of 37-56%, indicating suboptimal performance. Conclusions Pneumonia severity, symptom duration similar to 2 days, and a medium/high serum immunoglobulin titer against the patient's own serotype were independently associated with a high NP pneumococcal density. NP pneumococcal density has limited value for detection of severe pneumococcal pneumonia.

We studied the immunoglobulin (Ig) response to causative serotype-specific capsular polysaccharides in adult pneumococcal pneumonia patients. The serotypes were grouped according to their degree of encapsulation and invasive potential. Seventy patients with pneumococcal pneumonia, 20 of whom were bacteremic, were prospectively studied. All pneumococcal isolates from the patients were serotyped, and the Ig titers to the homologous serotype were determined in acute- and convalescent-phase sera using a serotype-specific enzyme-linked immunosorbent assay. The Ig titers were lower in bacteremic cases than in nonbacteremic cases (P< 0.042). The Ig titer ratio (convalescent/acute titer) was ≥2 in 33 patients, 1 to 1.99 in 20 patients, and P< 0.031). The patients with serotypes with a thin capsule (1, 4, 7F, 9N, 9V, and 14) and medium/high invasive potential (1, 4, 7F, 9N, 9V, 14, and 18C) had higher Ig titer ratios than did patients with serotypes with a thick capsule (3, 6B, 11A, 18C, 19A, 19F, and 23F) and low invasive potential (3, 6B, 19A, 19F, and 23F) (P< 0.05 for both comparisons after adjustment for age). Ig titer ratios of

Temporal expectations enhance neural encoding precision, reflected in optimized alignment of slow neural oscillatory phase, and facilitate subsequent stimulus processing. If an event's exact occurrence time is unknown, temporal expectations arise solely from the passage of time. Here, we show that this specific type of temporal expectation is also reflected in neural phase organization. While undergoing magnetoencephalography, participants performed an auditory-delayed matching-to-sample task with two syllables (S1, S2). Critically, S1-onset time varied in the 0.6-1.8-s (i.e., 0.6-1.7 Hz) range. Increasing S1-onset times led to increased slow-delta (0.6-0.9 Hz) phase coherence over right frontotemporal sensors during S1 encoding. Moreover, individuals with higher slow-delta coherence showed decreased alpha power (8-13 Hz) during subsequent memory retention. In sum, temporal expectations based on the passage of time optimize the precise alignment of neural oscillatory phase with an expected stimulus.