julilili42/papers huggingface dataset:
Human Cytomegalovirus-Induced NKG2ChiCD57hiNatural Killer Cells Are Effectors Dependent on Humoral Antiviral Immunity
2013-05-02

ABSTRACT Recent studies indicate that expansion of NKG2C-positive natural killer (NK) cells is associated with human cytomegalovirus (HCMV); however, their activity in response to HCMV-infected cells remains unclear. We show that NKG2C hi CD57 hi NK cells gated on CD3 neg CD56 dim cells can be phenotypically identified as HCMV-induced NK cells that can be activated by HCMV-infected cells. Using HCMV-infected autologous macrophages as targets, we were able to show that these NKG2C hi CD57 hi NK cells are highly responsive to HCMV-infected macrophages only in the presence of HCMV-specific antibodies, whereas they are functionally poor effectors of natural cytotoxicity. We further demonstrate that NKG2C hi CD57 hi NK cells are intrinsically responsive to signaling through CD16 cross-linking. Our findings show that the activity of pathogen-induced innate immune cells can be enhanced by adaptive humoral immunity. Understanding the activity of NKG2C hi CD57 hi NK cells against HCMV-infected cells will be of relevance for the further development of adoptive immunotherapy.
Sexual dimorphism of the bony labyrinth: A new age‐independent method
2013-05-02

ABSTRACT Currently in physical anthropology there is a need for reliable methods of sex estimation for immature individuals and highly fragmented remains. This study develops a sex estimation technique from discriminant function analysis of the bony labyrinth as it matures before puberty and can survive taphonomic conditions that would destroy most other skeletal material. The bony labyrinth contains the organs of hearing and balance. For this reason biologists and paleoanthropologists have undertaken research in this area to understand evolutionary changes in locomotion. Prior studies have found clear differences between species, but within‐species variation has not been satisfactorily investigated. 3D segmentations of the left and right labyrinths of 94 individuals from a Cretan collection were generated and measured. Mean measurements of height, width, size, and shape indices were analyzed for sexual dimorphism, bilateral asymmetry, and measurement error. Significant sexual dimorphism was detected for several measurements. For sex estimation, the single best variable was the radius of curvature of the posterior semicircular canal, which achieved 76% accuracy. Two multivariate functions increased accuracy to 84%. Although these equations are less accurate than equations for complete long bones and crania, they appear to be as accurate as or better than other techniques for sexing immature individuals and temporal bones. Am J Phys Anthropol 151:290–301, 2013. © 2013 Wiley Periodicals, Inc.
Modeling and inverting reactive stream tracers undergoing two-site sorption and decay in the hyporheic zone
2013-05-02

[1] Performing stream-tracer experiments is an accepted technique to assess transport characteristics of streams undergoing hyporheic exchange. Recently, combining conservative and reactive tracers, in which the latter presumably undergoes degradation exclusively within the hyporheic zone, has been suggested to study in-stream transport, hyporheic exchange, and the metabolic activity of the hyporheic zone. The combined quantitative analysis to adequately describe such tests, however, has been missing. In this paper, we present mathematical methods to jointly analyze breakthrough curves of a conservative tracer (fluorescein), a linearly degrading tracer (resazurin), and its daughter compound (resorufin), which are synchronously introduced into the stream as pulses. In-stream transport is described by the one-dimensional advection-dispersion equation, amended with a convolution term to account for transient storage within the hyporheic zone over a distribution of travel times, transformation of the reactive tracer in the hyporheic zone, and two-site sorption of the parent and daughter compounds therein. We use a shape-free approach of describing the hyporheic travel-time distribution, overcoming the difficulty of identifying the best functional parameterization for transient storage. We discuss how this model can be fitted to the breakthrough curves of all three compounds and demonstrate the method by an application to a tracer test in the third-order stream Goldersbach in Southern Germany. The entire river water passes once through the hyporheic zone over a travel distance of about 200 m with mean hyporheic residence times ranging between 16 and 23 min. We also observed a secondary peak in the transfer functions at about 1 h indicating a second hyporheic flow path. We could jointly fit the breakthrough curves of all compounds in three monitoring stations and evaluated the parameter uncertainty of the individual and joint fits by a method based on conditional realizations of the hyporheic travel-time distribution. The approach gives insight into in-stream transport, hyporheic exchange, metabolic activity, and river-bed sorption of the stream under investigation.
Evidence for Kinetically Limited Thickness Dependent Phase Separation in Organic Thin Film Blends
2013-05-02

We present depth-resolved grazing incidence x-ray diffraction, grazing incidence small angle scattering and x-ray reflectivity studies on the structure of mixed C<sub>60</sub> and diindinoperylene (DIP) films as a function of the mixing ratio. We observe enhanced out-of-plane order and smoothing of the mixed films compared to pure films upon coevaporation of DIP:C<sub>60</sub> thin films (in different mixing ratio) which otherwise phase separate. The mixing ratio of molecules can be tuned to alter the in-plane crystallite size as well as the interisland distances of the mixing molecules. Real-time <em>in situ</em> grazing incidence x-ray diffraction measurements show the kinetics and thickness dependence of phase separation, which appears to proceed only after a certain thickness. The crystallite grain size of the individual phase separated components is significantly larger at the top of the film than at the bottom with implications for the understanding of devices.
Ferromagnetic planar Josephson junction with transparent interfaces: a φ junction proposal
2013-05-02

We calculate the current-phase relation of a planar Josephson junction with a ferromagnetic weak link located on top of a thin normal metal film. Following experimental observations we assume transparent superconductor-ferromagnet interfaces. This provides the best interlayer coupling and a low suppression of the superconducting correlations penetrating from the superconducting electrodes into the ferromagnetic layer. We show that this Josephson junction is a promising candidate for experimental φ junction realization.
Direct Activation of Human Dendritic Cells by Particle-Bound but Not Soluble MHC Class II Ligand
2013-05-02

Dendritic cells (DCs) are key activators of cellular immune responses through their capacity to induce naïve T cells and sustained effector T cell responses. This capacity is a function of their superior efficiency of antigen presentation via MHC class I and class II molecules, and the expression of co-stimulatory cell surface molecules and cytokines. Maturation of DCs is induced by microbial factors via pattern recognition receptors such as Toll-like receptors, pro-inflammatory cytokines or cognate interaction with CD4(+) T cells. Here we show that, unexpectedly, the PanDR helper T cell epitope PADRE, a generic T helper cell antigen presented by a large fraction of HLA-DR alleles, when delivered in particle-bound form induced maturation of human DCs. The DCs that received the particle-bound PADRE displayed all features of fully mature DCs, such as high expression of the co-stimulatory molecules CD80, CD86, CD83, the MHC-II molecule HLA-DR, secretion of high levels of the biologically active IL-12 (IL-12p70) and induction of vigorous proliferation of naïve CD4(+) T cells. Furthermore, the maturation of DCs induced by particle-bound PADRE was shown to involve sphingosine kinase, calcium signaling from internal sources and downstream signaling through the MAP kinase and the p72syk pathways, and finally activation of the transcription factor NF-κB. Based on our findings, we propose that particle-bound PADRE may be used as a DC activator in DC-based vaccines.
Sleep for Preserving and Transforming Episodic Memory
2013-05-03

Sleep is known to support memory consolidation. Here we review evidence for an active system consolidation occurring during sleep. At the beginning of this process is sleep's ability to preserve episodic experiences preferentially encoded in hippocampal networks. Repeated neuronal reactivation of these representations during slow-wave sleep transforms episodic representations into long-term memories, redistributes them toward extrahippocampal networks, and qualitatively changes them to decontextualized schema-like representations. Electroencephalographic (EEG) oscillations regulate the underlying communication: Hippocampal sharp-wave ripples coalescing with thalamic spindles mediate the bottom-up transfer of reactivated memory information to extrahippocampal regions. Neocortical slow oscillations exert a supraordinate top-down control to synchronize hippocampal reactivations of specific memories to their excitable up-phase, thus allowing plastic changes in extrahippocampal regions. We propose that reactivations during sleep are a general mechanism underlying the abstraction of temporally stable invariants from a flow of input that is solely structured in time, thus representing a basic mechanism of memory formation.
High burden of extended-spectrum β-lactamase-producing Enterobacteriaceae in Gabon
2013-05-03

ESBL colonization in hospitalized children in Gabon is high. The risk of nosocomial transmission of ESBL-E is a challenge in rural Africa and underlines the need for sentinel surveillance in the absence of a broad decentralized microbiology laboratory.
Genetic Variation in NR1H4 Encoding the Bile Acid Receptor FXR Determines Fasting Glucose and Free Fatty Acid Levels in Humans
2013-05-03

We conclude that FXR contributes to fasting glucose and FFA levels in humans independent of unhealthy body fat accumulation. The receptor represents an interesting target to influence lipid and glucose metabolism.
Migrating the Mach-Zehnder chemical and bio-sensor to the mid-infrared region
2013-05-03

The properties of integrated optical phase-modulated Mach-Zehnder interferometers (IO-MZI) are used to set up a new generation of chemical and biochemical sensors working in the mid-infrared. First applications of the MZI principle were introduced in the beginning 1990s. They range from a gas sensor to monitor organic solvent concentrations<sup>1</sup> to setting up an immunoassay for the detection of the herbicide simazine<sup>2</sup>. Most if not all sensors of MZI type operate at wavelengths of the visible or near infrared spectrum. There are several reasons to change this strategy and move into the mid-infrared spectral range (MIR): higher manufacturing tolerances, increased evanescent field penetration depth, signal amplification by surface enhanced infrared absorption effect (SEIRA), species identification by MIR fingerprints. The basis of the planned MIR-MZI is a GaAs waveguide pattern epitaxially grown on a substrate<sup>3</sup>. As a first step towards nanostructuring the waveguide surface, chemical deposition of Au nanoparticles on GaAs transducers was established. For the use of MIR-MZI sensors in bioanalytical assay development, chemical immobilization of molecular recognition elements on GaAs transducers was carried out. The modified surfaces were characterized by atomic force microscopy (AFM), dark field microscopy, contact angle measurements and ellipsometric data as well as by a modified version of Reflectometric Interference Spectroscopy (RIfS)<sup>4</sup>. It was possible to monitor both the immobilization of gold nanoparticles and time-resolved specific binding using a model antibody antigen assay. After successful setup of relevant assays with RIfS, e.g. the detection of bacteria or endocrine disruptors, the assays are designed to be transferred onto the mid-infrared Mach-Zehnder interferometer.
Optical sensors for therapeutic drug monitoring of antidepressants for a better medication adjustment
2013-05-03

Therapeutic drug monitoring provides the attending physicians with detailed information on a patient's individual serum level especially during long-term medication. Due to the fact that each patient tolerates drugs or their metabolites differently a medication adjustment can reduce the number and intensity of noticeable side-effects. In particular, psychotropic drugs can cause unpleasant side-effects that affect a patient's life almost as much as the mental disease itself. The tricyclic antidepressants amitriptyline is commonly used for treatment of depressions and was selected for the development of an immunoassay using the direct optical sensor technique Reflectometric Interference Spectroscopy (RIfS). RIfS is a simple, robust and label-free method for direct monitoring of binding events on glass surfaces. Binding to the surface causes a shift of the interference spectrum by a change of the refractive index or physical thickness. This technique can be used for time-resolved observation of association and dissociation of amitriptyline (antigen) and a specific antibody using the binding inhibition test format. An amitriptyline derivative is immobilized on the sensor surface and a specific amount of antibodies can bind to the surface unless the binding is inhibited by free amitriptyline in a sample. No fluorescent label is needed making the whole assay less expensive than label-based methods. With this recently developed immunoassay amitriptyline concentrations in buffer (PBS) can easily be detected down to 500 ng/L.
Recognition as a challenging label-free optical sensing system
2013-05-03

Optical biosensors are increasingly used in application areas of environmental analysis, healthcare and food safety. The quality of the biosensor's results depends on the interaction layer, the detection principles, and evaluation strategies, not only on the biopolymer layer but also especially on recognition elements. Using label-free optical sensing, non-specific interaction between sample and transducer has to be reduced, and the selectivity of recognition elements has to be improved. For this reason, strategies to avoid non-specific interaction even in blood and milk are discussed, a variety of upcoming recognition is given. Based on the classification of direct optical detection methods, some examples for the above mentioned applications are reviewed. Trends as well as advantages of parallel multisport detection for kinetic evaluation are also part of the lecture.
Ray-tracing study of theeROSITAtelescope
2013-05-03

We perform ray-tracing simulations aimed at investigating the impact on the overall sensitivity of eROSITA of possible small errors in the mechanical shaping and positioning of the baffle rings above the mirror modules, to estimate to what extent they may contribute to degrade the efficiency of the baffle in eliminating the stray-light at the focal plane as well as to increase at the same time the vignetting, then reducing the effective area of the mirrors. Through the simulations we identify the ranges of acceptable tolerances.
Phages of Staphylococcus aureus and their impact on host evolution
2013-05-06

Most of the dissimilarity between Staphylococcus aureus strains is due to the presence of mobile genetic elements such as bacteriophages or pathogenicity islands. These elements provide the bacteria with additional genes that enable them to establish a new lifestyle that is often accompanied by a shift to increased pathogenicity or a jump to a new host. S. aureus phages may carry genes coding for diverse virulence factors such as Panton-Valentine leukocidin, staphylokinase, enterotoxins, chemotaxis-inhibitory proteins, or exfoliative toxins. Phages also mediate the transfer of pathogenicity islands in a highly coordinated manner and are the primary vehicle for the horizontal transfer of chromosomal and extra-chromosomal genes. Here, we summarise recent advances regarding phage classification, genome organisation and function of S. aureus phages with a particular emphasis on their role in the evolution of the bacterial host.
Presynaptic maturation in auditory hair cells requires a critical period of sensory-independent spiking activity
2013-05-06

The development of neural circuits relies on spontaneous electrical activity that occurs during immature stages of development. In the developing mammalian auditory system, spontaneous calcium action potentials are generated by inner hair cells (IHCs), which form the primary sensory synapse. It remains unknown whether this electrical activity is required for the functional maturation of the auditory system. We found that sensory-independent electrical activity controls synaptic maturation in IHCs. We used a mouse model in which the potassium channel SK2 is normally overexpressed, but can be modulated in vivo using doxycycline. SK2 overexpression affected the frequency and duration of spontaneous action potentials, which prevented the development of the Ca 2+ -sensitivity of vesicle fusion at IHC ribbon synapses, without affecting their morphology or general cell development. By manipulating the in vivo expression of SK2 channels, we identified the “critical period” during which spiking activity influences IHC synaptic maturation. Here we provide direct evidence that IHC development depends upon a specific temporal pattern of calcium spikes before sound-driven neuronal activity.
Reforestation Sites Show Similar and Nested AMF Communities to an Adjacent Pristine Forest in a Tropical Mountain Area of South Ecuador
2013-05-06

Arbuscular mycorrhizae are important for growth and survival of tropical trees. We studied the community of arbuscular mycorrhizal fungi in a tropical mountain rain forest and in neighbouring reforestation plots in the area of Reserva Biológica San Francisco (South Ecuador). The arbuscular mycorrhizal fungi were analysed with molecular methods sequencing part of the 18 S rDNA. The sequences were classified as Operational Taxonomic Units (OTUs). We found high fungal species richness with OTUs belonging to Glomerales, Diversisporales and Archaeosporales. Despite intensive sampling, the rarefaction curves are still unsaturated for the pristine forest and the reforestation plots. The communities consisted of few frequent and many rare species. No specific interactions are recognizable. The plant individuals are associated with one to ten arbuscular mycorrhizal fungi and mostly with one to four. The fungal compositions associated with single plant individuals show a great variability and variety within one plant species. Planted and naturally occurring plants show high similarities in their fungal communities. Pristine forest and reforestation plots showed similar richness, similar diversity and a significantly nested structure of plant-AMF community. The results indicate that small-scale fragmentation presently found in this area has not destroyed the natural AMF community, at least yet. Thus, the regeneration potential of natural forest vegetation at the tested sites is not inhibited by a lack of appropriate mycobionts.
Osteonectin Expression in Surrounding Stroma of Craniopharyngiomas
2013-05-06

Craniopharyngioma is an epithelial tumor of the sellar region with a high survival rate but a high rate of recurrence, especially in children. Hypothalamic involvement, tumor recurrence, and multiple treatments result in clinical deterioration and impaired quality of life. Using immunohistochemistry, we investigated the expression pattern of osteonectin, a marker of tumor invasion and aggressive behavior, in 43 cases of craniopharyngioma. We observed a positive correlation of osteonectin expression in connective-type stromal tissue surrounding the epithelial tumor cells of craniopharyngioma with the extent of central nervous system infiltration and recurrence rate ( P &lt; .001). Given the previous success of chemotherapeutic agents that target the tumor microenvironment, our findings on osteonectin expression in stroma of craniopharyngiomas might, hopefully, be a guide to find newer prognostic markers capable of estimating the risk of progression or recurrence. They may also aid in the development of therapeutics that target tumor microenvironment to improve patient outcome.
Invasive fibroblasts: Fundamental difference between sporadic inclusion body myositis and polymyositis
2013-05-06

ABSTRACT Introduction : Sporadic inclusion body myositis (sIBM) is a progressive disease that leads to extensive muscle weakness. The aim of this study was to determine whether the number and distribution of fibroblasts differ in sIBM when compared with polymyositis. Methods : Immunofluorescence double labeling was performed on 35 biopsies with antibodies directed against perlecan and CD90, procollagen I, CD34, and CD105. In addition, nonserial ultrathin sections were studied from 3 biopsies of each condition. Results : Fibroblasts expressing CD90 and CD34 accumulated in the endomysial compartment in polymyositis and sIBM. In addition, cells expressing CD90 were found beneath the basal lamina in both conditions. At the ultrastructural level in polymyositis, fibroblasts invaded the myofiber, with focal destruction of the basement membrane. In sIBM, by contrast, invasive fibroblasts were ensheathed by the intact myofiber basement membrane. Conclusions : The impact of intruding fibroblasts on satellite cells remains to be established. Muscle Nerve 49 : 175–180, 2014
A poor man’s BLASTX—high-throughput metagenomic protein database search using PAUDA
2013-05-07

Abstract Summary: In the context of metagenomics, we introduce a new approach to protein database search called PAUDA, which runs ∼10 000 times faster than BLASTX, while achieving about one-third of the assignment rate of reads to KEGG orthology groups, and producing gene and taxon abundance profiles that are highly correlated to those obtained with BLASTX. PAUDA requires &amp;lt;80 CPU hours to analyze a dataset of 246 million Illumina DNA reads from permafrost soil for which a previous BLASTX analysis (on a subset of 176 million reads) reportedly required 800 000 CPU hours, leading to the same clustering of samples by functional profiles. Availability: PAUDA is freely available from: http://ab.inf.uni-tuebingen.de/software/pauda. Also supplementary method details are available from this website. Contact: daniel.huson@uni-tuebingen.de or xiechao@bic.nus.edu.sg