julilili42/papers huggingface dataset:
The biosynthetic implications of late-stage condensation domain selectivity during glycopeptide antibiotic biosynthesis
2018-10-10

The condensation domain synthesising the last peptide bond in glycopeptide antibiotic biosynthesis has a preference for linear peptide substrates, with effective peptide formation linked to the rate of amino acid activation by the preceding adenylation domain.
Evidence for the Photoionization Absorption Edge in a Photospheric Radius Expansion X-Ray Burst from GRS 1747–312 in Terzan 6
2018-10-10

Abstract Thermonuclear X-ray bursts on the surface of neutron stars (NSs) can enrich the photosphere with metals, which may imprint photoionization edges on the burst spectra. We report here the discovery of absorption edges in the spectra of the type I X-ray burst from the NS low-mass X-ray binary GRS 1747−312 in Terzan 6 during observations by the Rossi X-ray Timing Explorer . We find that the edge energy evolves from 9.45 ± 0.51 to ∼6 keV and then back to 9.44 ± 0.40 keV during the photospheric radius expansion phase and remains at 8.06 ± 0.66 keV in the cooling tail. The photoionization absorption edges of hydrogen-like Ni, Fe, or an Fe/Ni mixture and the bound–bound transitions of metals may be responsible for the observed spectral features. The ratio of the measured absorption edge energy in the cooling tail to the laboratory value of the hydrogen-like Ni(Fe) edge energy allows us to estimate the gravitational redshift factor 1 + z = 1.34 ± 0.11(1 + z = 1.15 ± 0.09). The evolution of the spectral parameters during the cooling tail are well described by metal-rich atmosphere models. The combined constraints on the NS mass and radius from the direct cooling method and the tidal deformability strongly suggest very high atmospheric abundance of the iron group elements and limit the distance to the source to 11 ± 1 kpc.
Image and perception of physicians as barriers to inter-disciplinary cooperation? – the example of German occupational health physicians in the rehabilitation process: a qualitative study
2018-10-10

This example of cooperation between RPs, OPs, and PCPs suggests that negative and diverging perceptions about an out-group could create barriers in intra-professional and inter-disciplinary cooperation between physicians. These perspectives might also be useful in explaining problems at intersections between different specialties. We suggest examining the inter-group dimension of perception-based barriers to cooperation in future interventions to overcome problems caused by intra-professional and inter-disciplinary conflicts in addition to other barriers (i.e. organizational hurdles).
Glial Cells in the Fish Retinal Nerve Fiber Layer Form Tight Junctions, Separating and Surrounding Axons
2018-10-10

In the retina of teleost fish, cell addition continues throughout life involving proliferation and axonal growth. To study how this is achieved in a fully functioning retina, we investigated the nerve fiber layer (NFL) of the cichlid fish <i>Astatotilapia burtoni</i> for components that might regulate the extracellular environment. We hypothesized that growing axons are surrounded by different cell structures than signal conducting axons. Using immunohistochemistry and freeze fracture electron microscopy we found that the endfeet of Müller cells (MCs) expressed aquaporin-4 but not in high densities as in mammals. The presence of this water channel indicates the involvement of MCs in water homeostasis. Remarkably, we discovered conspicuous tight junctions in the retinal NFL. These tight junctions formed branching strands between myelin-like wrappings of ganglion cell axons that differed morphologically from any known myelin, and also an elaborate meshwork on large membrane faces between axons. We speculated that these tight junctions have additional functions than solely facilitating nerve conductance. Immunostainings against the adaptor protein ZO-1 labeled the NFL as did antibodies against the mammalian claudin-1, 3, and 19. Performing PCR analysis, we showed expression of claudin-1, 3, 5a, 5b, 9, 11, and 19 in the fish retina, claudins that typically occur at brain barriers or myelin. We could show by immunostains for doublecortin, a marker for differentiating neurons, that new axons are not surrounded by the myelin-like wrappings but only by the endfeet of MCs. We hypothesize that the tight junctions in the NFL of fish might contribute to the separation of an extracellular space around axons facilitating conductance, from a growth-promoting environment. For a functional test we applied Evans Blue dye to eye cup preparations which showed a retention of the dye in the NFL. This indicates that these remarkable tight junctions can indeed act as a diffusion barrier.
Xanthocidin Derivatives from the Endophytic Streptomyces sp. AcE210 Provide Insight into Xanthocidin Biosynthesis
2018-10-10

Abstract Xanthocidin and six new derivatives were isolated from the endophytic Streptomyces sp. AcE210. Their planar structures were elucidated by 1D and 2D NMR spectroscopy as well as by HRMS. The absolute configuration of one compound was determined by using vibrational circular dichroism spectroscopy (VCD). The structural similarities of xanthocidin and some of the isolated xanthocidin congeners to the methylenomycins A, B, and C suggested that the biosynthesis of these compounds might follow a similar route. Feeding studies with isotopically labelled [ 13 C 5 ]‐ l ‐valine showed that instead of utilizing acetyl‐CoA as starter unit, which has been proposed for the methylenomycin biosynthesis, Streptomyces sp. AcE210 employs an isobutyryl‐CoA starter unit, resulting in a branched side chain in xanthocidin. Further evidence for a comparable biosynthesis was given by the analysis of the genome sequence of Streptomyces sp. AcE210 that revealed a cluster of homologues to the mmy genes involved in methylenomycin biosynthesis.
The U1 snRNP Subunit LUC7 Modulates Plant Development and Stress Responses via Regulation of Alternative Splicing
2018-10-11

Introns are removed by the spliceosome, a large macromolecular complex composed of five ribonucleoprotein subcomplexes (U snRNPs). The U1 snRNP, which binds to 5' splice sites, plays an essential role in early steps of the splicing reaction. Here, we show that <i>Arabidopsis thaliana</i> LETHAL UNLESS CBC7 (LUC7) proteins, which are encoded by a three-member gene family in Arabidopsis, are important for plant development and stress resistance. We show that LUC7 is a U1 snRNP accessory protein by RNA immunoprecipitation experiments and LUC7 protein complex purifications. Transcriptome analyses revealed that LUC7 proteins are not only important for constitutive splicing, but also affect hundreds of alternative splicing events. Interestingly, LUC7 proteins specifically promote splicing of a subset of terminal introns. Splicing of LUC7-dependent introns is a prerequisite for nuclear export, and some splicing events are modulated by stress in a LUC7-dependent manner. Taken together, our results highlight the importance of the U1 snRNP component LUC7 in splicing regulation and suggest a previously unrecognized role of a U1 snRNP accessory factor in terminal intron splicing.
Automatic Generation of Saliency-based Areas of Interest for the Visualization and Analysis of Eye-tracking Data
2018-10-11

Areas of interest (AOIs) are a powerful basis for the analysis and visualization of eye-tracking data. They allow to relate eyetracking metrics to semantic stimulus regions and to perform further statistics. In this work, we propose a novel method for the automated generation of AOIs based on saliency maps. In contrast to existing methods from the state-of-the-art, which generate AOIs based on eye-tracking data, our method generates AOIs based solely on the stimulus saliency, mimicking thus our natural vision. This way, our method is not only independent of the eye-tracking data, but allows to work AOI-based even for complex stimuli, such as abstract art, where proper manual definition of AOIs is not trivial. For evaluation, we cross-validate support vector machine classifiers with the task of separating visual scanpaths of art experts from those of novices. The motivation for this evaluation is to use AOIs as projection functions and to evaluate their robustness on different feature spaces. A good AOI separation should result in different feature sets that enable a fast evaluation with a widely automated work-flow. The proposed method together with the data shown in this paper is available as part of the software EyeTrace [?] http://www.ti.unituebingen. de/Eyetrace.1751.0.html.
Free fatty acid profiling in marine algae extract by LC‐MS/MS and isolation as well as quantification of the ω‐3 fatty acid hexadeca‐4,7,10,13‐tetraenoic acid
2018-10-11

Abstract Undaria pinnatifida (Wakame) alga contains high amounts of hexadeca‐4Z,7Z,10Z,13Z‐tetraenoic acid which was reported to decrease the efficiency of cisplatin chemotherapeutics. To obtain a fatty acid enriched extract of this ω‐3 poly‐unsaturated fatty acid as an analytical standard, Wakame was used as source material for its extraction. A two‐step extraction protocol consisting of a liquid‐liquid extraction followed by solid‐phase extraction with 3‐aminopropyl silica in accordance to a normal‐phase elution mode was developed. An ultra high performance liquid chromatography with electrospray ionization tandem mass spectrometry method based on sequential windowed acquisition of all theoretical fragment ion mass spectra allowed a simultaneous comprehensive group selective fatty acids profiling in untargeted manner and quantitative analysis of the targeted fatty acid. Hexadeca‐4Z,7Z,10Z,13Z‐tetraenoic acid was identified using high‐resolution product ion spectra. The quantitative method was based on d5‐deuterated hexadeca‐4Z,7Z,10Z,13Z‐tetraenoic acid which was employed as surrogate calibrant. Preliminary method validation was performed by evaluating detection and quantification limits, linear range, intra‐assay and inter‐day precision. Finally, a concentration of 421.2 ± 14.9 ng/mL (4% CV) of hexadeca‐4Z,7Z,10Z,13Z‐tetraenoic acid was determined in the extract which was further used as analytical standard.
Parkinson disease age of onset GWAS: defining heritability, genetic loci and a-synuclein mechanisms
2018-10-11

Abstract Increasing evidence supports an extensive and complex genetic contribution to Parkinson’s disease (PD). Previous genome-wide association studies (GWAS) have shed light on the genetic basis of risk for this disease. However, the genetic determinants of PD age of onset are largely unknown. Here we performed an age of onset GWAS based on 28,568 PD cases. We estimated that the heritability of PD age of onset due to common genetic variation was ~0.11, lower than the overall heritability of risk for PD (~0.27) likely in part because of the subjective nature of this measure. We found two genome-wide significant association signals, one at SNCA and the other a protein-coding variant in TMEM175 , both of which are known PD risk loci and a Bonferroni corrected significant effect at other known PD risk loci, INPP5F/BAG3 , FAM47E/SCARB2 , and MCCC1. In addition, we identified that GBA coding variant carriers had an earlier age of onset compared to non-carriers. Notably, SNCA , TMEM175 , SCARB2 , BAG3 and GBA have all been shown to either directly influence alpha-synuclein aggregation or are implicated in alpha-synuclein aggregation pathways. Remarkably, other well-established PD risk loci such as GCH1, MAPT and RAB7L1 /NUCKS1 (PARK16) did not show a significant effect on age of onset of PD. While for some loci, this may be a measure of power, this is clearly not the case for the MAPT locus; thus genetic variability at this locus influences whether but not when an individual develops disease. We believe this is an important mechanistic and therapeutic distinction. Furthermore, these data support a model in which alpha-synuclein and lysosomal mechanisms impact not only PD risk but also age of disease onset and highlights that therapies that target alpha-synuclein aggregation are more likely to be disease-modifying than therapies targeting other pathways.
Radiation Dose Optimization in Pediatric Chest CT: Major Indicators of Dose Exposure in 1695 CT Scans over Seven Years
2018-10-11

Purpose To analyze possible influencing factors on radiation exposure in pediatric chest CT using different approaches for radiation dose optimization and to determine major indicators for dose development. Materials and Methods In this retrospective study at a clinic with maximum care facilities including pediatric radiology, 1695 chest CT examinations in 768 patients (median age: 10 years; range: 2 days to 17.9 years) were analyzed. Volume CT dose indices, effective dose, size-specific dose estimate, automatic dose modulation (AEC), and high-pitch protocols (pitch ≥ 3.0) were evaluated by univariate analysis. The image quality of low-dose examinations was compared to higher dose protocols by non-inferiority testing. Results Median dose-specific values annually decreased by an average of 12 %. High-pitch mode (n = 414) resulted in lower dose parameters (p &lt; 0.001). In unenhanced CT, AEC delivered higher dose values compared to scans with fixed parameters (p &lt; 0.001). In contrast-enhanced CT, the use of AEC yielded a significantly lower radiation dose only in patients older than 16 years (p = 0.04). In the age group 6 to 15 years, the values were higher (p &lt; 0.001). The diagnostic image quality of low-dose scans was non-inferior to high-dose scans (2.18 vs. 2.14). Conclusion Radiation dose of chest CT was reduced without loss of image quality in the last decade. High-pitch scanning was an independent factor in this context. Dose reduction by AEC was limited and only relevant for patients over 16 years. Key Points Citation Format
Sending expats or hiring locals? The impact of communication barriers on foreign subsidiary CEO staffing
2018-10-11

Communication between headquarters (HQs) and foreign subsidiaries of multinational corporations (MNCs) is crucial for coordination, control, and knowledge transfer, but language barriers and geographic distance impede this exchange. Hypothesising that MNCs react to these hurdles by appointing subsidiary top managers with adequate communication skills, we investigate how the native language barrier, foreign language barrier, and geographic distance between HQs and a foreign subsidiary influence the choice between parent and host/third country nationals as subsidiary CEOs. Testing our hypotheses on a sample of 101 staffing decisions made by German firms in 33 countries, we find a negligible effect of the native language barrier, but establish that a foreign language barrier enhances and higher geographic distance lowers firms' propensity to staff subsidiary CEO positions with parent country nationals. An MNC's international experience was found to moderate these relationships.
Strategies for addressing collinearity in multivariate linguistic data
2018-10-12

When multiple correlated predictors are considered jointly in regression modeling, estimated coefficients may assume counterintuitive and theoretically uninterpretable values. We survey several statistical methods that implement strategies for the analysis of collinear data: regression with regularization (the elastic net), supervised component generalized linear regression, and random forests. Methods are illustrated for a data set with a wide range of predictors for segment duration in a German speech corpus. Results broadly converge, but each method has its own strengths and weaknesses. Jointly, they provide the analyst with somewhat different but complementary perspectives on the structure of collinear data.
Smaller medial temporal lobe volumes in individuals with subjective cognitive decline and biomarker evidence of Alzheimer's disease—Data from three memory clinic studies
2018-10-12

Abstract Introduction Previous studies showed associations of brain volume differences and biomarker evidence for Alzheimer's disease (AD) in subjective cognitive decline (SCD). The consistency of this finding across SCD studies has not been investigated. Methods We studied gray matter volume differences between SCD subjects with and without cerebrospinal fluid biomarker evidence for AD across three European memory clinic samples (German Center for Neurodegenerative Diseases Longitudinal Cognitive Impairment and Dementia study, Amsterdam, Barcelona). Analysis of covariance models with samples and cerebrospinal fluid biomarkers as between‐subject factors were calculated. Results A significant main effect for AD biomarker (Aβ 42 − &gt; Aβ 42 +) in the left medial temporal lobe (MTL) was found, with the absence of main effects for sample or interaction effects between AD biomarker and sample. This indicates consistent lower left MTL volume across three samples in SCD subjects with abnormal Aβ 42 levels. Discussion Our results support the model that in the presence of AD pathology, SCD corresponds to the late preclinical stage (stage 2 of AD) with smaller MTL volumes.
Molecular structure of the substrate-induced thin-film phase of tetracene
2018-10-12

We present a combined experimental and theoretical study to solve the unit-cell and molecular arrangement of the tetracene thin film (TF) phase. TF phases, also known as substrate induced phases (SIPs), are polymorphs that exist at interfaces and decisively impact the functionality of organic thin films, e.g., in a transistor channel, but also change the optical spectra due to the different molecular packing. As SIPs only exist in textured ultrathin films, their structure determination remains challenging compared to bulk materials. Here, we use grazing incidence X-ray diffraction and atomistic simulations to extract the TF unit-cell parameters of tetracene together with the atomic positions within the unit-cell.
A new multicopter based unmanned aerial system for pollen and spores collection in the atmospheric boundary layer
2018-10-12

Abstract. The application of a new particle collection system (PCS) onboard a multicopter unmanned aerial vehicle (UAV) is presented as a new unmanned aerial system (UAS) approach for in-situ measurement of the concentration of aerosol particles such as pollen grains and spores in the atmospheric boundary layer (ABL). A newly developed impactor is used for high efficiency particle extraction onboard the multicopter UAV. An air volume flow of 0.2 m3 per minute through the impactor is provided by a battery powered blower and measured with an onboard mass flow sensor. A bell mouth shaped air intake of the PCS is arranged and oriented on the multicopter UAV to provide substantially isokinetic sampling conditions by advantageously using the airflow pattern generated by the propellers of the multicopter UAV. More than thirty aerosol particle collection flights were carried out near Tübingen in March 2017 at altitudes of up to 300 m above ground level (a.g.l.), each with a sampled air volume of 2 m3. Pollen grains and spores of various genera as well as charcoal and fine dust particles were collected and specific concentrations of up to 100 particles per m3 were determined by visual microscopic analysis. The pollen concentration values measured with the new UAS matches well with the pollen concentration data published by the Stiftung Deutscher Polleninformationsdienst (PID) and by MeteoSchweiz. A major advantage of the new multicopter based UAS is the possibility of the identification of collected aerosol particles and the measurement of their concentration with high temporal and spatial resolution, which can be used inter alia to improve the data base for modelling the propagation of aerosol particles in the ABL.
Sulfated RaxX, which represents an unclassified group of ribosomally synthesized post-translationally modified peptides, binds a host immune receptor
2018-10-13

ABSTRACT The rice immune receptor XA21 is activated by the sulfated microbial peptide RaxX (required for a ctivation of X A21-mediated immunity X ) produced by Xanthomonas oryzae pv. oryzae ( Xoo ). Mutational studies and targeted proteomics revealed that RaxX is processed and secreted by the protease/transporter RaxB, whose function can be partially fulfilled by a noncognate p eptidase- c ontaining transporter B (PctB). RaxX is cleaved at a Gly-Gly motif, yielding a mature peptide that retains the necessary elements for RaxX function as an immunogen and host peptide hormone mimic. These results indicate that RaxX is a founding member of a previously unclassified and understudied group of tyrosine sulfated RiPPs ( ri bosomally synthesized, p ost-translationally modified p eptides). We further demonstrate that sulfated RaxX directly binds XA21 with high affinity. This work reveals a complete, previously uncharacterized biological process: bacterial RiPP biosynthesis, secretion, binding to a eukaryotic receptor and triggering of a robust host immune response.
Slovenian adaptation of the Morningness-Eveningness-Stability Scales improved (MESSi)
2018-10-14

Circadian preference can be measured by a set of questionnaires. While accepting the biological correlates as a good convergent criterion, researchers criticized currently used questionnaires because of their design, weighted number of items, unbalanced scoring or uneven Likert scales. This led to the development of a composite questionnaire, the Morningness-Eveningness-Stability-Scales improved (MESSi). The MESSi contains three constructs: morning affect (MA), eveningness (EV) and stability/distinctness (DI). The aim of this study was a preliminary assessment of a Slovenian translation of the MESSi. Students of five different study programs from the University of Ljubljana, Faculty of Education, participated in the study (N = 275). The scales fit to a three-factor solution, based on exploratory and confirmatory factor analysis. Cronbach’s α were 0.82 (MA), 0.85 (EV), and 0.69 (DI). After allowing covariances (loading onto the same factor) the model fit was good (RMSEA = 0.055). Nearly all sleep-wake variables were correlated with MA and EV in the expected direction. As a conclusion, we can propose to use the MESSi also in Slovenia.