julilili42/papers huggingface dataset:
A Decomposition of Local Labour-Market Conditions and Their Relevance for Inequalities in Transitions to Vocational Training
2017-06-13

We investigate to what extent individual transitions to vocational training in Germany have been affected by local labour-market conditions. A statistical decomposition approach is developed and applied, allowing for a systematic differentiation between long-term change, short-term fluctuations, and structural regional differences in labour-market conditions. To study individual-level consequences for transitions to vocational training, regionalized labour-market data are merged with longitudinal data from the National Educational Panel Study, and multivariate transition-rate models are fitted. The results indicate that structural differences between regions have had significant effects on the transition behaviour of school leavers, whereas temporary crises have been of only minor relevance. Moreover, different groups have been affected to different degrees by varying labour-market conditions. We also highlight the usefulness of our decomposition approach for a broader set of applications.
Investigating the origin of cyclical wind variability in hot massive stars – II. Hydrodynamical simulations of corotating interaction regions using realistic spot parameters for the O giant ξ Persei
2017-06-13

OB stars exhibit various types of spectral variability historically\\nassociated with wind structures, including the apparently ubiquitous discrete\\nabsorption components (DACs). These features have been proposed to be caused\\neither by magnetic fields or non-radial pulsations. In this second paper of\\nthis series, we revisit the canonical phenomenological hydrodynamical modelling\\nused to explain the formation of DACs by taking into account modern\\nobservations and more realistic theoretical predictions. Using constraints on\\nputative bright spots located on the surface of the O giant Persei\\nderived from high precision space-based broadband optical photometry obtained\\nwith the Microvariability and Oscillations of STars (MOST) space telescope, we\\ngenerate two-dimensional hydrodynamical simulations of co-rotating interaction\\nregions in its wind. We then compute synthetic ultraviolet (UV) resonance line\\nprofiles using Sobolev Exact Integration and compare them with historical\\ntimeseries obtained by the International Ultraviolet Explorer (IUE) to evaluate\\nif the observed behaviour of Persei's DACs is reproduced. Testing three\\ndifferent models of spot size and strength, we find that the classical pattern\\nof variability can be successfully reproduced for two of them: the model with\\nthe smallest spots yields absorption features that are incompatible with\\nobservations. Furthermore, we test the effect of the radial dependence of\\nionization levels on line driving, but cannot conclusively assess the\\nimportance of this factor. In conclusion, this study self-consistently links\\noptical photometry and UV spectroscopy, paving the way to a better\\nunderstanding of cyclical wind variability in massive stars in the context of\\nthe bright spot paradigm.\\n
A community proposal to integrate proteomics activities in ELIXIR
2017-06-13

<ns4:p>Computational approaches have been major drivers behind the progress of proteomics in recent years. The aim of this white paper is to provide a framework for integrating computational proteomics into ELIXIR in the near future, and thus to broaden the portfolio of omics technologies supported by this European distributed infrastructure. This white paper is the direct result of a strategy meeting on ‘The Future of Proteomics in ELIXIR’ that took place in March 2017 in Tübingen (Germany), and involved representatives of eleven ELIXIR nodes.</ns4:p><ns4:p> These discussions led to a list of priority areas in computational proteomics that would complement existing activities and close gaps in the portfolio of tools and services offered by ELIXIR so far. We provide some suggestions on how these activities could be integrated into ELIXIR’s existing platforms, and how it could lead to a new ELIXIR use case in proteomics. We also highlight connections to the related field of metabolomics, where similar activities are ongoing. This white paper could thus serve as a starting point for the integration of computational proteomics into ELIXIR. Over the next few months we will be working closely with all stakeholders involved, and in particular with other representatives of the proteomics community, to further refine this paper.</ns4:p>
The Entropy of Words—Learnability and Expressivity across More than 1000 Languages
2017-06-14

The choice associated with words is a fundamental property of natural languages. It lies at the heart of quantitative linguistics, computational linguistics and language sciences more generally. Information theory gives us tools at hand to measure precisely the average amount of choice associated with words: the word entropy. Here, we use three parallel corpora, encompassing ca. 450 million words in 1916 texts and 1259 languages, to tackle some of the major conceptual and practical problems of word entropy estimation: dependence on text size, register, style and estimation method, as well as non-independence of words in co-text. We present two main findings: Firstly, word entropies display relatively narrow, unimodal distributions. There is no language in our sample with a unigram entropy of less than six bits/word. We argue that this is in line with information-theoretic models of communication. Languages are held in a narrow range by two fundamental pressures: word learnability and word expressivity, with a potential bias towards expressivity. Secondly, there is a strong linear relationship between unigram entropies and entropy rates. The entropy difference between words with and without co-textual information is narrowly distributed around ca. three bits/word. In other words, knowing the preceding text reduces the uncertainty of words by roughly the same amount across languages of the world.
TP53 mutation and survival in aggressive B cell lymphoma
2017-06-14

TP53 is mutated in 20–25% of aggressive B‐cell lymphoma (B‐NHL). To date, no studies have addressed the impact of TP53 mutations in prospective clinical trial cohorts. To evaluate the impact of TP53 mutation to current risk models in aggressive B‐NHL, we investigated TP53 gene mutations within the RICOVER‐60 trial. Of 1,222 elderly patients (aged 61–80 years) enrolled in the study and randomized to six or eight cycles of CHOP‐14 with or without Rituximab (NCT00052936), 265 patients were analyzed for TP53 mutations. TP53 mutations were demonstrated in 63 of 265 patients (23.8%). TP53 mutation was associated with higher LDH (65% vs . 37%; p &lt; 0.001), higher international prognostic index‐Scores (IPI 4/5 27% vs . 12%; p = 0.025) and B‐symptoms (41% vs . 24%; p = 0.011). Patients with TP53 mutation were less likely to obtain a complete remission CR/CRu (CR unconfirmed) 61.9% (mut) vs . 79.7% (wt) ( p = 0.007). TP53 mutations were associated with decreased event‐free (EFS), progression‐free (PFS) and overall survival (OS) (median observation time of 40.2 months): the 3 year EFS, PFS and OS were 42% ( vs . 60%; p = 0.012), 42% ( vs . 67.5%; p &lt; 0.001) and 50% ( vs . 76%; p &lt; 0.001) for the TP53 mutation group. In a Cox proportional hazard analysis adjusting for IPI‐factors and treatment arms, TP53 mutation was shown to be an independent predictor of EFS (HR 1.5), PFS (HR 2.0) and OS (HR 2.3; p &lt; 0.001). TP53 mutations are independent predictors of survival in untreated patients with aggressive CD20+ lymphoma. TP53 mutations should be considered for risk models in DLBCL and strategies to improve outcome for patients with mutant TP53 must be developed.
Constraining black holes with light boson hair and boson stars using epicyclic frequencies and quasiperiodic oscillations
2017-06-14

Light bosonic fields are ubiquitous in extensions of the Standard Model. Even\\nwhen minimally coupled to gravity, these fields might evade the assumptions of\\nthe black-hole no-hair theorems and give rise to spinning black holes which can\\nbe drastically different from the Kerr metric. Furthermore, they allow for\\nself-gravitating compact solitons, known as (scalar or Proca) boson stars. The\\nquasi-periodic oscillations (QPOs) observed in the X-ray flux emitted by\\naccreting compact objects carry information about the strong-field region, thus\\nproviding a powerful tool to constrain deviations from Kerr's geometry and to\\nsearch for exotic compact objects. By using the relativistic precession model\\nas a proxy to interpret the QPOs in terms of geodesic frequencies, we\\ninvestigate how the QPO frequencies could be used to test the no-hair theorem\\nand the existence of light bosonic fields near accreting compact objects. We\\nshow that a detection of two QPO triplets with current sensitivity can already\\nconstrain these models, and that the future eXTP mission or a LOFT-like mission\\ncan set very stringent constraints on black holes with bosonic hair and on\\n(scalar or Proca) boson stars. The peculiar geodesic structure of compact\\nscalar/Proca boson stars implies that these objects can easily be ruled out as\\nalternative models for X-ray source GRO J1655-40.\\n
Improved mitral valve coaptation and reduced mitral valve annular size after percutaneous mitral valve repair (PMVR) using the MitraClip system
2017-06-14

This study demonstrates mechanical approximation of both mitral valve annulus edges with improved mitral valve annular coaptation by PMVR using the MitraClip® system, which correlates with residual MR in patients with MR.
Discovery of N-{4-[5-(4-Fluorophenyl)-3-methyl-2-methylsulfanyl-3H-imidazol-4-yl]-pyridin-2-yl}-acetamide (CBS-3595), a Dual p38α MAPK/PDE-4 Inhibitor with Activity against TNFα-Related Diseases
2017-06-14

The anti-inflammatory potential of p38 mitogen-activated protein kinase (MAPK) inhibitors was coincidentally expanded to a dual inhibition of p38α MAPK and phosphodiesterase 4 (PDE4), and the potential benefits arising from the blockage of both inflammation-related enzymes were thoroughly investigated. The most promising compound, CBS-3595 (1), was successively evaluated in in vitro experiments as well as in ex vivo and in vivo preclinical studies after administration of 1 to rodents, dogs, and monkeys. The resulting data clearly indicated a potent suppression of tumor necrosis factor alpha release. For reconfirming the findings of the animal studies when administering 1 to healthy human volunteers, a phase I clinical trial was conducted. Apart from further information regarding the pharmacokinetic and pharmacodynamic characteristics of 1, it was demonstrated that dual inhibition of p38α MAPK and PDE4 is able to synergistically attenuate the excessive anti-inflammatory response.
Estimating a Representative Value and Proportion of True Zeros for Censored Analytical Data with Applications to Contaminated Site Assessment
2017-06-14

This paper demonstrates a maximum likelihood (ML)-based approach to derive representative ("best guess") contaminant concentrations from data with censored values (e.g., less than the detection limit). The method represents an advancement over existing techniques because it is capable of estimating the proportion of measurements that are true zeros and incorporating varying levels of censorship (e.g., sample specific detection limits, changes through time in method detection). The ability of the method to estimate the proportion of true zeros is validated using precipitation data. The stability and flexibility of the method are demonstrated with stochastic simulation, a sensitivity analysis, and unbiasedness analysis including varying numbers of significant digits. A key aspect of this paper is the application of the statistical analysis to real site rock core contaminant concentration data collected within a plume at two locations using high resolution depth-discrete sampling. Comparison of the representative values for concentrations at each location along the plume center-line shows a larger number of true zeros and generally lower concentrations at the downgradient location according to the conceptual site model, leading to improved estimates of attenuation with distance and/or time and associated confidence; this is not achievable using deterministic methods. The practical relevance of the proposed method is that it provides an improved basis for evaluating change (spatial, temporal, or both) in environmental systems.
Mito-xenophagic killing of bacteria is coordinated by a metabolic switch in dendritic cells
2017-06-14

Abstract Chlamydiae are bacterial pathogens that grow in vacuolar inclusions. Dendritic cells (DCs) disintegrate these compartments, thereby eliminating the microbes, through auto/xenophagy, which also promotes chlamydial antigen presentation via MHC I. Here, we show that TNF-α controls this pathway by driving cytosolic phospholipase (cPLA)2-mediated arachidonic acid (AA) production. AA then impairs mitochondrial function, which disturbs the development and integrity of these energy-dependent parasitic inclusions, while a simultaneous metabolic switch towards aerobic glycolysis promotes DC survival. Tubulin deacetylase/autophagy regulator HDAC6 associates with disintegrated inclusions, thereby further disrupting their subcellular localisation and stability. Bacterial remnants are decorated with defective mitochondria, mito-aggresomal structures, and components of the ubiquitin/autophagy machinery before they are degraded via mito-xenophagy. The mechanism depends on cytoprotective HSP25/27, the E3 ubiquitin ligase Parkin and HDAC6 and promotes chlamydial antigen generation for presentation on MHC I. We propose that this novel mito-xenophagic pathway linking innate and adaptive immunity is critical for effective DC-mediated anti-bacterial resistance.
Simultaneous spike-time locking to multiple frequencies
2017-06-14

Abstract Phase locking of neural firing is ubiquitously observed in the brain and occurs when neurons fire at a particular phase of a periodic signal. Here we study in detail how spikes of single neurons can simultaneously lock to multiple distinct frequencies at the example of p-type electroreceptor afferents in the electrosensory system of the Gymnotiform weakly electric fish Apteronotus leptorhynchus . We identify key elements for multiple frequency locking, study its determining factors and limits, and provide concise mathematical models reproducing our main findings. Our findings provide another example how rate and temporal codes can coexist and complement each other in single neurons, and demonstrate that sensory coding in p-type electroreceptor afferents provides a much richer representation of the sensory environment than commonly assumed. Since the underlying mechanisms are not specific to the electrosensory system, our results could provide the basis for studying multiple-frequency locking in other systems.
Testing the Kerr Black Hole Hypothesis Using X-Ray Reflection Spectroscopy
2017-06-15

Abstract We present the first X-ray reflection model for testing the assumption that the metric of astrophysical black holes is described by the Kerr solution. We employ the formalism of the transfer function proposed by Cunningham. The calculations of the reflection spectrum of a thin accretion disk are split into two parts: the calculation of the transfer function and the calculation of the local spectrum at any emission point in the disk. The transfer function only depends on the background metric and takes into account all the relativistic effects (gravitational redshift, Doppler boosting, and light bending). Our code computes the transfer function for a spacetime described by the Johannsen metric and can easily be extended to any stationary, axisymmetric, and asymptotically flat spacetime. Transfer functions and single line shapes in the Kerr metric are compared to those calculated from existing codes to check that we reach the necessary accuracy. We also simulate some observations with NuSTAR and LAD/eXTP and fit the data with our new model to show the potential capabilities of current and future observations to constrain possible deviations from the Kerr metric.
Observed changes in maximum and minimum temperatures in Xinjiang autonomous region, China
2017-06-15

ABSTRACT Changes in maximum and minimum temperature ( T max and T min ) are analysed to assess the regional extent of global warming in Xinjiang autonomous region, China, for the period of 1961–2015. Two nonlinear, non‐stationary signal‐processing methods – the Bernaola‐Galván algorithm and the ensemble empirical mode decomposition method – are applied on daily time series of observations from 53 meteorological stations. Statistically significant abrupt change points are identified in 1996 in both annual T max and T min time series averaged for the whole province, while another one is identified in 1976 in the annual T min time series only. At local scale, most stations experience one abrupt change point in annual T max in the 1990s, but two or three change points in annual T min , mainly in the 1980s and 1990s. After the abrupt change points, the frequency and probability density of T max in summer and T min in winter are skewed towards the hotter part of the probability distribution. It is found that the hot temperature extremes in summer occur concurrently with El Niño events. Further results suggest that anomalies in geopotential height at 500 hPa can be associated with the hottest and coldest months. The key regions of the anomalies are over the east of the Ural Mountains and the North Atlantic, while the geopotential height anomalies over Greenland and the east of the Ural Mountains are closely related to the hot and cold spells.
Organ transplantation scandal influencing corneal donation rate
2017-06-15

In the majority of countries, there is a shortage of donor corneas for corneal transplantations. This study investigated the impact of organ transplantation scandals on corneal donation rate at the University Hospital Tübingen. Each deceased patient was considered as a potential corneal donor. An ophthalmic resident handled with stable methods of procedures the corneal donor procurement from 2009 to 2015. The rates of corneal donation were examined and analyzed. Among the 5712 hospital deaths, consent for corneal donation was obtained in 711 cases. The mean annual corneal donation rate was 12.4%. Since 2009, the donation rate per year could be increased with exception of 2013 and 2015. In the end of 2012 and 2014 two huge organ donation scandals were known in Germany. In the following years 2013 and 2015 corneal donation rate decreased significantly (<i>P</i>=0.0181 and <i>P</i>=0.0006). We concluded that transplantation scandals have a significant impact on corneal donation rate. Improving professional's performance through full transparency and honesty is very important to earn trust of potential donors and their families.
SANDPUMA: ensemble predictions of nonribosomal peptide chemistry reveal biosynthetic diversity across Actinobacteria
2017-06-16

Abstract Summary Nonribosomally synthesized peptides (NRPs) are natural products with widespread applications in medicine and biotechnology. Many algorithms have been developed to predict the substrate specificities of nonribosomal peptide synthetase adenylation (A) domains from DNA sequences, which enables prioritization and dereplication, and integration with other data types in discovery efforts. However, insufficient training data and a lack of clarity regarding prediction quality have impeded optimal use. Here, we introduce prediCAT, a new phylogenetics-inspired algorithm, which quantitatively estimates the degree of predictability of each A-domain. We then systematically benchmarked all algorithms on a newly gathered, independent test set of 434 A-domain sequences, showing that active-site-motif-based algorithms outperform whole-domain-based methods. Subsequently, we developed SANDPUMA, a powerful ensemble algorithm, based on newly trained versions of all high-performing algorithms, which significantly outperforms individual methods. Finally, we deployed SANDPUMA in a systematic investigation of 7635 Actinobacteria genomes, suggesting that NRP chemical diversity is much higher than previously estimated. SANDPUMA has been integrated into the widely used antiSMASH biosynthetic gene cluster analysis pipeline and is also available as an open-source, standalone tool. Availability and implementation SANDPUMA is freely available at https://bitbucket.org/chevrm/sandpuma and as a docker image at https://hub.docker.com/r/chevrm/sandpuma/ under the GNU Public License 3 (GPL3). Supplementary information Supplementary data are available at Bioinformatics online.
Systemic therapy of ocular and cutaneous rosacea in children
2017-06-16

Abstract Background In paediatric rosacea, ocular symptoms are often predominant. Literature about systemic therapy of paediatric ocular rosacea is sparse, though. Objective Analysis of children with ocular rosacea treated systemically, particularly addressing remission and recurrence rates. Methods Retrospective study reviewing the medical records of children with ocular rosacea treated with systemic antibiotic therapy. Nine of 19 patients were chosen for detailed analysis. To our knowledge, this is the first study in paediatric ocular rosacea requiring systemic therapy with a larger patient group and a longer follow‐up (mean follow‐up = 30.2 months). Results 17 patients (89.5%) suffered from blepharitis, 15 patients (78.9%) from conjunctivitis, twelve patients (63.2%) from chalazia/styes and nine female patients (47.4%) from corneal involvement. We used erythromycin ( n = 9) or roxithromycin ( n = 1) in patients younger than 8 years and doxycycline ( n = 8) or minocycline ( n = 1) in patients older than 8 years. Seven of nine patients treated with erythromycin, one of eight patients treated with doxycycline and the patient treated with minocycline achieved a complete remission of ocular and cutaneous symptoms. Two of nine patients treated with erythromycin, seven of eight patients treated with doxycycline and the patient treated with roxithromycin achieved a partial remission. Relapses occurred in the patient treated with minocycline (cutaneous), two of eight patients treated with doxycycline (ocular and cutaneous) and one of nine patients treated with erythromycin (cutaneous). Conclusion To achieve a complete remission of cutaneous and ocular rosacea, a long‐term anti‐inflammatory treatment of at least 6 months is necessary. The relapse rates seem to be lower than in adults especially in the patients treated with erythromycin.
The U1 snRNP subunit LUC7 controls plant development and stress response through alternative splicing regulation
2017-06-16

Abstract Introns are removed by the spliceosome, a large macromolecular complex composed of five ribonucleoprotein subcomplexes (U snRNP). The U1 snRNP, which binds to 5’ splice sites, plays an essential role in early steps of the splicing reaction. Here, we show that Arabidopsis 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 are U1 snRNP accessory proteins by RNA immunoprecipitation experiments and LUC7 protein complex purifications. Transcriptome analyses revealed that LUC7 proteins are not only important for constitutive splicing, but also affects 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.