julilili42/papers huggingface dataset:
Segmental bronchi collapsibility: computed tomography-based quantification in patients with chronic obstructive pulmonary disease and correlation with emphysema phenotype, corresponding lung volume changes and clinical parameters
2016-12-01

Changes in collapsibility of 3<sup>rd</sup> generation bronchi in COPD grade IV patients is significantly lower than that in the trachea and the main bronchi. Collapsibility did not correlate with the reduction in lung volume but was significantly higher in lobes with homogeneous <i>vs</i>. heterogeneous emphysema phenotype. Changes in the 3<sup>rd</sup> generation bronchial calibres between inspiration and expiration are not predictive for the degree of small airway collapsibility and related airflow limitation.
LSTM Autoencoders for Dialect Analysis
2016-12-01

Computational approaches for dialectometry employed Levenshtein distance to compute an aggregate similarity between two dialects belonging to a single language group. In this paper, we apply a sequence-to-sequence autoencoder to learn a deep representation for words that can be used for meaningful comparison across dialects. In contrast to the alignment-based methods, our method does not require explicit alignments. We apply our architectures to three different datasets and show that the learned representations indicate highly similar results with the analyses based on Levenshtein distance and capture the traditional dialectal differences shown by dialectologists.
Creative Destruction and Asset Prices
2016-12-01

We relate Schumpeter’s notion of creative destruction to asset pricing, thereby offering a novel explanation of size and value premia. We argue that small-value firms must offer higher expected returns to compensate for the risk posed by serendipitous invention activity, whereas large-growth stocks provide protection against creative destruction and receive expected return discounts. A 2-factor model that accounts for creative-destruction risk effectively explains the cross-sectional return variation of size- and book-to-market-sorted portfolios. The estimated risk compensations associated with creative destruction are substantial and statistically significant, indicating their relevance for asset pricing.
Directed Rotational Motion of Birefringent Particles by Randomly Changing the Barrier Height at the Threshold in a Washboard Potential
2016-12-01

This communication presents a simulation study of the directed rotational motion of a birefringent spherical particle trapped in optical tweezers with randomly varying ellipticity of a trapping light at the point of threshold. When noise is not applied, the potential barrier due to the linear component of the polarization is simulated to be sufficient to prevent directed rotation till a certain threshold value of ellipticity. Random variations to the ellipticity cause random variations in the barrier height, including instants when the barrier is lower than the threshold energy level. It is due to this that the particle exhibits directed rotational motion at ellipticity lower than the threshold value. We also examine the rotational velocity of the birefringent particle as a function of the extent of zero-mean random noise applied to the ellipticity.
The search for sterile neutrinos with SOX-Borexino
2016-12-01

The aim of the SOX-Borexino project is to verify or falsify the existence of eV-scale sterile neutrinos. The existence of sterile neutrinos is suspected because of several anomalies, which were observed in previous experiments. A ~3.7 PBq electron antineutrino source made of 144 Ce will be installed below the Borexino detector at LNGS, Italy, to search for short-baseline oscillations of active-to-sterile neutrinos within the detector volume. Source delivery and beginning of data acquisition is planned for end of 2016, preliminary results are expected already in 2017.
Head measurements from 3D point clouds
2016-12-01

Head measurements are widely used in different fields as ergonomics, medicine and acoustics. In acoustics they are useful to create 3D virtual auditoriums, since the manipulation of the Head Related Transfer Function (HRTF) allows to virtually place sound sources. Despite the HRTF dependents on the physical characteristics of each person, a generic HRTF is frequently adopted in commercial systems because the user's anthropometric data is not always available. In this paper we present a scheme to calculate several head dimensions required to individualize the transfer function, however they can also be utilized in other applications. The measurements are calculated automatically on 3D models of the head acquired with an inexpensive RGBD sensor. Experiments performed with 80 point clouds of 20 subjects corroborate the potential of the proposed algorithm.
Mammalian organogenesis in deep time: tools for teaching and outreach
2016-12-01

Mammals constitute a rich subject of study on evolution and development and provide model organisms for experimental investigations. They can serve to illustrate how ontogeny and phylogeny can be studied together and how the reconstruction of ancestors of our own evolutionary lineage can be approached. Likewise, mammals can be used to promote 'tree thinking' and can provide an organismal appreciation of evolutionary changes. This subject is suitable for the classroom and to the public at large given the interest and familiarity of people with mammals and their closest relatives. We present a simple exercise in which embryonic development is presented as a transformative process that can be observed, compared, and analyzed. In addition, we provide and discuss a freely available animation on organogenesis and life history evolution in mammals. An evolutionary tree can be the best tool to order and understand those transformations for different species. A simple exercise introduces the subject of changes in developmental timing or heterochrony and its importance in evolution. The developmental perspective is relevant in teaching and outreach efforts for the understanding of evolutionary theory today.
Prosody Predicts Contest Outcome in Non-Verbal Dialogs
2016-12-01

Non-verbal communication has important implications for inter-individual relationships and negotiation success. However, to what extent humans can spontaneously use rhythm and prosody as a sole communication tool is largely unknown. We analysed human ability to resolve a conflict without verbal dialogs, independently of semantics. We invited pairs of subjects to communicate non-verbally using whistle sounds. Along with the production of more whistles, participants unwittingly used a subtle prosodic feature to compete over a resource (ice-cream scoops). Winners can be identified by their propensity to accentuate the first whistles blown when replying to their partner, compared to the following whistles. Naive listeners correctly identified this prosodic feature as a key determinant of which whistler won the interaction. These results suggest that in the absence of other communication channels, individuals spontaneously use a subtle variation of sound accentuation (prosody), instead of merely producing exuberant sounds, to impose themselves in a conflict of interest. We discuss the biological and cultural bases of this ability and their link with verbal communication. Our results highlight the human ability to use non-verbal communication in a negotiation process.
Cover Picture: Debugging Eukaryotic Genetic Code Expansion for Site‐Specific Click‐PAINT Super‐Resolution Microscopy (Angew. Chem. Int. Ed. 52/2016)
2016-12-01

Cytoplasmic re-targeting of the pyrrolysine-based genetic code expansion machinery by using a nuclear export signal (NES) substantially increases the site-specific incorporation of clickable amino acids (green) into proteins in mammalian cells, as shown by E. A. Lemke and co-workers in their Communication on page 16172 ff. These clickable amino acids can then be modified with annealing sites for small DNA imaging strands (red) to enable high-contrast Click-PAINT super-resolution microscopy. Cytoplasmic re-targeting of the pyrrolysine-based genetic code expansion machinery by using a nuclear export signal (NES) substantially increases the site-specific incorporation of clickable amino acids (green) into proteins in mammalian cells, as shown by E. A. Lemke and co-workers in their Communication on page 16172 ff. These clickable amino acids can then be modified with annealing sites for small DNA imaging strands (red) to enable high-contrast Click-PAINT super-resolution microscopy. Zeolitic Imidazolate Frameworks Silanides Rhodium Single-Atom Catalysts
Parasite Infection, Carcinogenesis and Human Malignancy
2016-12-02

Cancer may be induced by many environmental and physiological conditions. Infections with viruses, bacteria and parasites have been recognized for years to be associated with human carcinogenicity. Here we review current concepts of carcinogenicity and its associations with parasitic infections. The helminth diseases schistosomiasis, opisthorchiasis, and clonorchiasis are highly carcinogenic while the protozoan Trypanosoma cruzi, the causing agent of Chagas disease, has a dual role in the development of cancer, including both carcinogenic and anticancer properties. Although malaria per se does not appear to be causative in carcinogenesis, it is strongly associated with the occurrence of endemic Burkitt lymphoma in areas holoendemic for malaria. The initiation of Plasmodium falciparum related endemic Burkitt lymphoma requires additional transforming events induced by the Epstein-Barr virus. Observations suggest that Strongyloides stercoralis may be a relevant co-factor in HTLV-1-related T cell lymphomas. This review provides an overview of the mechanisms of parasitic infection-induced carcinogenicity.
Diverse Activation Modes in the Hydroboration of Aldehydes and Ketones with Germanium, Tin, and Lead Lewis Pairs
2016-12-02

Abstract Intramolecular germylene, stannylene, and plumbylene Lewis pairs were reacted with hexanal and yielded the cyclic addition products only with the germanium and tin reagents. In further reactivity studies, the hydroboration of aldehydes and ketones catalyzed by intramolecular germylene, stannylene, and plumbylene Lewis pairs was studied. In the case of the cyclic germylene Lewis pair, the product of the oxidative addition of pinacolborane at the germylene moiety was observed. According to stoichiometric as well as catalytic experiments, the intramolecular germylene Lewis pair acts as a catalyst in the hydroboration of aldehydes and ketones. The homologous stannylene Lewis pair forms a reactive tin hydride during the catalysis, which can also act as a catalyst in this transformation.
Skull shape variation in extant and extinct Testudinata and its relation to habitat and feeding ecology
2016-12-02

Abstract Turtles (Testudinata) are a diverse group of reptiles that conquered a broad set of habitats and feeding ecologies over the course of their well‐documented evolutionary history. We here investigate the cranial shape of 171 representatives of the turtle lineage and the relationship of shape to different habitat and diet preferences using two‐dimensional geometric morphometrics. The skull shape of extant turtles correlates with both ecological proxies, but is more affected by habitat than diet. However, the application of these correlations to extinct turtles produces mostly flawed results, as least when compared to external data such as sedimentary environment, highlighting that the morphospace held by extant turtles is not necessarily the optimal location in tree space for a particular ecology. The inability of this study to correctly predict the ecology of extinct turtles is likely related to the fact that the shape of turtle skulls is dominated by the emarginations and jaw closure mechanisms, two shape features unrelated to habitat or feeding ecology. This indicates that various specializations that are apparent in the skull only contribute little to overall shape.
Decaying dark matter search with NuSTAR deep sky observations
2016-12-02

We present the results of the search for decaying dark matter with particle\\nmass in the 6-40 keV range with NuSTAR deep observations of COSMOS and ECDFS\\nempty sky fields. We show that main contribution to the decaying dark matter\\nsignal from the Milky Way galaxy comes through the aperture of the NuSTAR\\ndetector, rather than through the focusing optics. High sensitivity of the\\nNuSTAR detector, combined with the large aperture and large exposure times of\\nthe two observation fields allow us to improve previously existing constraints\\non the dark matter decay time by up to an order of magnitude in the mass range\\n10-30 keV. In the particular case of the nuMSM sterile neutrino dark matter,\\nour constraints impose an upper bound m&lt;20 keV on the dark matter particle\\nmass. We report detection of four unidentified spectral lines in our data set.\\nThese line detections are either due to the systematic effects (uncertainties\\nof calibrations of the NuSTAR detectors) or have an astrophysical origin. We\\ndiscuss different possibilities for testing the nature of the detected lines.\\n
Experimental and simulation approach for process optimization of atomic layer deposited thin films in high aspect ratio 3D structures
2016-12-02

The authors present a new method to determine film thicknesses and sticking coefficients (SC) of precursor molecules for atomic layer deposition (ALD) in high aspect ratio three dimensional (3D) geometries as they appear in microelectromechanical system manufacturing. The method combines a specifically designed experimental test structure with the theoretical predictions from a novel 3D Monte Carlo process simulation for large structures. The authors exemplify our method using Al2O3 and SiO2 ALD processes. SCs for trimethylaluminium and bis-diethyl aminosilane (BDEAS) are extracted. The SC for BDEAS is determined for the first time.
Temperature dependence of the sticking coefficients of bis-diethyl aminosilane and trimethylaluminum in atomic layer deposition
2016-12-02

In this paper, the authors present the temperature dependent sticking coefficient (SC) of bis-diethyl aminosilane (BDEAS) and trimethylaluminum (TMA) in atomic layer deposition. SiO2 from BDEAS and ozone at substrate temperatures between 200 and 350 °C as well as Al2O3 from TMA and water deposited at substrate temperatures between 150 and 300 °C was deposited on our likewise in this journal published cavity test structures. The SC of BDEAS shows an Arrhenius dependence while for TMA no temperature dependent SC could be resolved. The activation energy for BDEAS which is extracted from a linear fit to the Arrhenius diagram is compared to the value gained by density functional theory calculations from the literature. Furthermore, the different growth behavior of BDEAS and TMA under substrate temperature considerations is identified with different deposition regimes as proposed in the literature.
Involvement of NFAT Transcription Factors in NK Cell Reactivity
2016-12-02

Abstract NK cells are lymphoid components of innate immunity and play an important role in tumor immunosurveillance. One of the major transcriptional regulators in lymphoid cells is NFAT (Nuclear Factor of Activated T Cells), as highlighted by its important role in T and B cell development and function. With regard to NK cells, available data indicate that NFAT is dispensable for development. However, several lines of evidence including the observation that the immunosuppressive drugs cyclosporin A and tacrolimus, which mediate their effects through inhibition of calcineurin and consecutively NFAT, influence NK reactivity implicate a role of this family of transcription factors in NK cell reactivity and function. Here we employed different genetic mouse models on the C57BL/6 background to directly study the functional role of NFAT in NK cells. We found that except for NFAT3 mRNA and protein of all family members (NFAT 1, 2, 4 and 5) was expressed in resting NK cells of wild type (WT) mice with NFAT1, 2 and 4 being most abundantly detectable. When we employed NK cells with knockout (KO) of NFAT 1, 2, and 4 in comparative in vitro analyses, we surprisingly found that lack of NFAT resulted in enhanced NK cell activation, degranulation and release of immunomodulatory cytokines like IFN-γ after co-culture with YAC-1 target cells as well as increased production of granzyme B and perforin after cytokine activation. The inhibitory effect of NFAT on NK cell effector function was further confirmed in vivo by employing WT and germ line NFAT KO animals in the syngeneic B16 melanoma model, which revealed a significantly reduced metastatic burden in NFAT KO mice. Depletion of NK cells in this model system in turn resulted in increased metastasis, however, with WT animals displaying significantly higher metastatic burden compared to NFAT KO mice. As this pointed to the fact that NFAT influences metastasis via both NK-dependent and independent mechanisms, we further generated mice with a NK cell-specific (conditional Ncr1-Cre dependent) NFAT2 KO. When these animals were employed again in analyses of B16 lung metastasis, comparative analyses with WT animals confirmed the inhibitory effect of NFAT on NK tumor immunosurveillance. Taken together, these results provide the first direct evidence for the functional involvement of NFAT in NK cell antitumor reactivity and, in contrast to T and B cells, identify NFAT as a negative regulator of NK cell function. Disclosures No relevant conflicts of interest to declare.
Ibrutinib Abrogates TREM-1 Mediated Neutrophil Activation
2016-12-02

Abstract Triggering receptor expressed on myeloid cells 1 (TREM-1) is an activating receptor on neutrophils (PMN) and important in the innate host defence against microbial pathogens. Here we examined the influence of the Bruton tyrosine kinase (BTK) inhibitor ibrutinib on TREM-1 dependent activation of human PMNs. Firstly, ibrutinib specifically inhibited TREM-1 mediated PMN activation of the oxidative burst and CD62L shedding, whereas TLR mediated activation remained unaffected. Correspondingly, ibrutinib suppressed ERK phosphorylation after TREM-1, but not after TLR ligation. To clarify whether this TREM-1 specific effect of ibrutinib was also relevant in vivo, we treated mice with ibrutinib, and analyzed fungal clearance in vivo upon pulmonary challenge with A. fumigatus and PMN activation ex vivo upon TREM-1 or TLR ligation, again finding that TREM-1, but not TLR induced activation was suppressed. Equivalent results were obtained in PMNs of six lymphoma patients under treatment with ibrutinib. In summary, BTK plays an important role in TREM-1 mediated PMN activation, providing a potential mechanism for the frequently observed infectious complications in patients treated with ibrutinib, and fosters studies using this drug as a novel tool to modulate TREM-1 activity for therapeutic purposes, i. e. in sepsis or autoimmune diseases. Disclosures Hess: Pfizer: Honoraria; Janssen: Honoraria; Celgene: Honoraria; Roche, CTI, Pfizer, Celgene: Research Funding; Roche: Honoraria; Novartis: Honoraria.
Taming the Late Quaternary phylogeography of the Eurasiatic wild ass through ancient and modern DNA
2016-12-02

Abstract Taxonomic over-splitting of extinct or endangered taxa, due to an incomplete knowledge of both skeletal morphological variability and the geographical ranges of past populations, continues to confuse the link between isolated extant populations and their ancestors. This is particularly problematic with the genus Equus. To more reliably determine the evolution and phylogeographic history of the endangered Asiatic wild ass, we studied the genetic diversity and inter-relationships of both extinct and extant populations over the last 100,000 years, including samples throughout its previous range from Western Europe to Southwest and East Asia. Using 229 bp of the mitochondrial hypervariable region, an approach which allowed the inclusion of information from extremely poorly preserved ancient samples, we classify all non-African wild asses into nine clades that show a clear phylogeographic structure revealing their phylogenetic history. This study places the extinct European wild ass, E. hydruntinus , the phylogeny of which has been debated since the end of the 19 th century, into its phylogenetic context within the Asiatic wild asses and reveals recent gene flow events between populations currently regarded as separate species. The phylogeographic organization of clades resulting from these efforts can be used not only to improve future taxonomic determination of a poorly characterized group of equids, but also to identify historic ranges, interbreeding events between various populations, and the impact of ancient climatic changes. In addition, appropriately placing extant relict populations into a broader phylogeographic and genetic context can better inform ongoing conservation strategies for this highly endangered species.
HLA Class I-Specific Effects in AML with Mutated Nucleophosmin
2016-12-02

Abstract Background We have recently identified a skewed distribution of class I human leukocyte antigens (HLA) among patients with AML and mutated nucleophosmin gene (NPMc+ AML). A lower frequency of several HLA allelic groups in the NPMc+ AML patient cohort was in good correlation with the results of theoretical predictions for high-affinity immunopeptides derived from NPM1, suggesting that an anti-NPM1 immune response could prevent leukemia development in patients with a suitable HLA class I type. Aim We here present more detailed analysis of HLA-specific features, in a much larger cohort (N = 357) of AML patients with NPM1 mutation (type A/D) from several centers in the Czech Republic, Germany and Poland. Results Most importantly, we confirmed the lower incidence of B ́40 and C ́07 allelic groups in NPMc+ AML compared to the normal values. The moderate decrease of A ́02 allelic group frequency became statistically significant in this larger patient cohort (see Table). On the other hand, no difference in HLA class II frequencies was found compared to the normal distribution. Furthemore, patients with B ́07 allelic group had a significantly better prognosis, but only in the absence of Flt-3-ITD mutations (p = 0.049, see Figure). HLA typing was performed by molecular methods in a subgroup of patients (N = 73), allowing for discrimination between C ́07 alleles. In this subgroup, C*07:01, but not C*07:02/04 expression was associated with better overall survival (p = 0.036), in agreement with theoretical predictions. Conclusion Our results support the hypothesis that anti-NPM1 immune response reduces AML development and contributes to a better outcome of NPMc+ AML patients with suitable HLA class I type (including at least A ́02, B ́07, B ́40 and C*07:01). Furthermore, NPMc+ immunogenicity is caused rather by its aberrant localization than by the generation of a unique aminoacid sequence. Figure Figure. Disclosures Schetelig: Sanofi: Honoraria. Thiede:AgenDix: Employment, Other: Ownership.