julilili42/papers huggingface dataset:
Physical analysis of an Antarctic ice core—towards an integration of micro- and macrodynamics of polar ice
2016-12-27

Microstructures from deep ice cores reflect the dynamic conditions of the drill location as well as the thermodynamic history of the drill site and catchment area in great detail. Ice core parameters (crystal lattice-preferred orientation (LPO), grain size, grain shape), mesostructures (visual stratigraphy) as well as borehole deformation were measured in a deep ice core drilled at Kohnen Station, Dronning Maud Land (DML), Antarctica. These observations are used to characterize the local dynamic setting and its rheological as well as microstructural effects at the EDML ice core drilling site (European Project for Ice Coring in Antarctica in DML). The results suggest a division of the core into five distinct sections, interpreted as the effects of changing deformation boundary conditions from triaxial deformation with horizontal extension to bedrock-parallel shear. Region 1 (uppermost approx. 450 m depth) with still small macroscopic strain is dominated by compression of bubbles and strong strain and recrystallization localization. Region 2 (approx. 450–1700 m depth) shows a girdle-type LPO with the girdle plane being perpendicular to grain elongations, which indicates triaxial deformation with dominating horizontal extension. In this region (approx. 1000 m depth), the first subtle traces of shear deformation are observed in the shape-preferred orientation (SPO) by inclination of the grain elongation. Region 3 (approx. 1700–2030 m depth) represents a transitional regime between triaxial deformation and dominance of shear, which becomes apparent in the progression of the girdle to a single maximum LPO and increasing obliqueness of grain elongations. The fully developed single maximum LPO in region 4 (approx. 2030–2385 m depth) is an indicator of shear dominance. Region 5 (below approx. 2385 m depth) is marked by signs of strong shear, such as strong SPO values of grain elongation and strong kink folding of visual layers. The details of structural observations are compared with results from a numerical ice sheet model (PISM, isotropic) for comparison of strain rate trends predicted from the large-scale geometry of the ice sheet and borehole logging data. This comparison confirms the segmentation into these depth regions and in turn provides a wider view of the ice sheet. This article is part of the themed issue ‘Microdynamics of ice’.
Dynamic recrystallization during deformation of polycrystalline ice: insights from numerical simulations
2016-12-27

The flow of glaciers and polar ice sheets is controlled by the highly anisotropic rheology of ice crystals that have hexagonal symmetry (ice lh). To improve our knowledge of ice sheet dynamics, it is necessary to understand how dynamic recrystallization (DRX) controls ice microstructures and rheology at different boundary conditions that range from pure shear flattening at the top to simple shear near the base of the sheets. We present a series of two-dimensional numerical simulations that couple ice deformation with DRX of various intensities, paying special attention to the effect of boundary conditions. The simulations show how similar orientations of c -axis maxima with respect to the finite deformation direction develop regardless of the amount of DRX and applied boundary conditions. In pure shear this direction is parallel to the maximum compressional stress, while it rotates towards the shear direction in simple shear. This leads to strain hardening and increased activity of non-basal slip systems in pure shear and to strain softening in simple shear. Therefore, it is expected that ice is effectively weaker in the lower parts of the ice sheets than in the upper parts. Strain-rate localization occurs in all simulations, especially in simple shear cases. Recrystallization suppresses localization, which necessitates the activation of hard, non-basal slip systems. This article is part of the themed issue ‘Microdynamics of ice’.
Achromatopsia mutations target sequential steps of ATF6 activation
2016-12-27

Significance The unfolded protein response regulator activating transcription factor 6 ( ATF6 ) was recently identified as a novel genetic cause of the cone photoreceptor disease achromatopsia. ATF6 upregulates genes that help cells cope with endoplasmic reticulum stress. We identified the pathomechanisms of all ATF6 achromatopsia mutations. Class 1 ATF6 mutants show impaired endoplasmic reticulum (ER)-to-Golgi trafficking and diminished production of the transcriptional activator fragment. Class 2 mutants encode the intact ATF6 transcriptional activator domain with full activity. Class 3 mutants have defective basic leucine zipper (bZIP) domains with abrogated function. Patient fibroblasts show increased apoptosis after ER stress. Our findings reveal that human ATF6 mutations interrupt distinct steps of ATF6 activation. ER stress-associated damage may underlie the pathology of achromatopsia arising from ATF6 .
Comparison of Different Risk Classification Systems in 558 Patients with Gastrointestinal Stromal Tumors after R0-Resection
2016-12-27

Background: Due to adjuvant treatment concepts for patients with R0-resected gastrointestinal stromal tumors (GIST), a reproducible and reliable risk classification system proved of utmost importance for optimal treatment of patients and prediction of prognosis. The aim of this study was to reevaluate the impact of five widely-applied and well-established GIST risk classification systems (i.e., scores by Fletcher, Miettinen, Huang, Joensuu, and TNM classification) on a series of 558 GIST patients with long-term follow-up after R0 resection. Methods: Tumor size, mitotic count and site were used in variable combination to predict high- and low risk patients by the use of the five risk classification models. For survival analyses disease-specific survival, disease-free survival and overall-survival were investigated. Patients with initial metastatic disease or incompletely resectable tumors were excluded. Results: All GIST classification models distinguished well between patients with high-risk and low-risk tumors and none of the five risk systems was superior to predict patient outcome. The models showed significant heterogeneity. There was no significant difference between the different risk-groups regarding overall-survival. Subdivision of GIST patients with very low- and low-risk appeared to be negligible. Conclusions: Currently applied GIST risk classification systems are comparable to predict high- or low-risk patients with initial non-metastatic and completely resected GIST. However, the heterogeneity of the high-risk group and the absence of differences in overall survival indicate the need for more precise tumor- and patient-related criteria for better stratification of GIST and identification of patients who would benefit best from adjuvant tyrosine kinase inhibitor therapy.
Nucleon tensor form factors in a relativistic confined quark model
2016-12-27

We present results for the isotriplet and isosinglet tensor form factors of\\nthe nucleon in the relativistic confined quark model. The model allows us to\\ncalculate not only their normalizations at and the related tensor\\ncharges, but also the full -dependence. Our results are compared to\\nexisting data and predictions of other theoretical approaches. We stress the\\nimportance of these form factors for the phenomenology of physics beyond the\\nStandard Model.\\n
Mapping of Surface-Exposed Epitopes of In Vitro and In Vivo Aggregated Species of Alpha-Synuclein
2016-12-27

Aggregated alpha-synuclein is the main component of Lewy bodies, intraneuronal deposits observed in Parkinson's disease and dementia with Lewy bodies. The objective of the study was to identify surface-exposed epitopes of alpha-synuclein in vitro and in vivo formed aggregates. Polyclonal immunoglobulin Y antibodies were raised against short linear peptides of the alpha-synuclein molecule. An epitope in the N-terminal region (1-10) and all C-terminal epitopes (90-140) were found to be exposed in an indirect enzyme-linked immunosorbent assay (ELISA) using recombinant monomeric, oligomeric, and fibrillar alpha-synuclein. In a phospholipid ELISA, the N-terminus and mid-region of alpha-synuclein (i.e., 1-90) were associated with phosphatidylserine and thus occluded from antibody binding. The antibodies that reacted most strongly with epitopes in the in vitro aggregates (i.e., 1-10 and epitopes between positions 90-140) also labeled alpha-synuclein inclusions in brains from transgenic (Thy-1)-h[A30P] alpha-synuclein mice and Lewy bodies and Lewy neurites in brains of patients with alpha-synucleinopathies. However, differences in reactivity were observed with the C-terminal antibodies when brain tissue from human and transgenic mice was compared. Taken together, the study shows that although similar epitopes are exposed in both in vitro and in vivo formed alpha-synuclein inclusions, structural heterogeneity can be observed between different molecular species.
Microdynamics of ice
2016-12-27

Understanding the dynamic behaviour of ice in glaciers, polar ice caps, sea ice and the icy planets of the Solar System is a major challenge, especially in a time of changing climate, amplified at the poles and exciting new space exploration. This theme issue of the Philosophical Transactions of the
Implementing Pharmacogenomics in Europe: Design and Implementation Strategy of the Ubiquitous Pharmacogenomics Consortium
2016-12-28

Despite scientific and clinical advances in the field of pharmacogenomics (PGx), application into routine care remains limited. Opportunely, several implementation studies and programs have been initiated over recent years. This article presents an overview of these studies and identifies current research gaps. Importantly, one such gap is the undetermined collective clinical utility of implementing a panel of PGx‐markers into routine care, because the evidence base is currently limited to specific, individual drug‐gene pairs. The Ubiquitous Pharmacogenomics (U‐PGx) Consortium, which has been funded by the European Commission's Horizon‐2020 program, aims to address this unmet need. In a prospective, block‐randomized, controlled clinical study (PREemptive Pharmacogenomic testing for prevention of Adverse drug REactions [PREPARE]), pre‐emptive genotyping of a panel of clinically relevant PGx‐markers, for which guidelines are available, will be implemented across healthcare institutions in seven European countries. The impact on patient outcomes and cost‐effectiveness will be investigated. The program is unique in its multicenter, multigene, multidrug, multi‐ethnic, and multihealthcare system approach.
Wormholes versus black holes: quasinormal ringing at early and late times
2016-12-28

Recently it has been argued that the phantom thin-shell wormholes matched\\nwith the Schwarzschild space-time near the Schwarzschild radius ring like\\nSchwarzschild black holes at early times, but differently at late times\\n(arXiv:1602.07309). Here we consider perturbations of the wormhole which was\\nconstructed without thin-shells: the Bronnikov-Ellis wormhole supported by the\\nphantom matter and electromagnetic field. This wormhole solution is known to be\\nstable under specific equation of state of the phantom matter. We show that if\\none does not use the above thin-shell matching, the wormhole, depending on the\\nvalues of its parameters, either rings as the black hole at all times or rings\\ndifferently also at all times. The wormhole's spectrum, investigated here,\\nposses a number of distinctive features.\\n In the final part we have considered general properties of scattering around\\narbitrary rotating traversable wormholes. We have found that symmetric and\\nnon-symmetric (with respect to the throat) wormholes are qualitatively\\ndifferent in this respect: First, superradiance is allowed only if for those\\nnon-symmetric wormholes for which the asymptotic values of the rotation\\nparameters are different on both sides from the throat. Second, the symmetric\\nwormholes cannot mimic effectively the ringing of a black hole at a few various\\ndominant multipoles at the same time, so that the future observations of\\nvarious events should easily tell the symmetric wormhole from a black hole.\\n
Evaluation of transmit efficiency and SAR for a tight fit transceiver human head phased array at 9.4 T
2016-12-28

Ultra‐high field (UHF, ≥7 T) tight fit transceiver phased arrays improve transmit (Tx) efficiency ( B 1 + /√ P ) in comparison with Tx‐only arrays, which are usually larger to fit receive (Rx)‐only arrays inside. One of the major problems limiting applications of tight fit arrays at UHFs is the anticipated increase of local tissue heating, which is commonly evaluated by the local specific absorption rate (SAR). To investigate the tradeoff between Tx efficiency and SAR when a tight fit UHF human head transceiver phased array is used instead of a Tx‐only/Rx‐only RF system, a single‐row eight‐element prototype of a 400 MHz transceiver head phased array was constructed. The Tx efficiency and SAR of the array were evaluated and compared with that of a larger Tx‐only array, which could also be used in combination with an 18‐channel Rx‐only array. Data were acquired on the Siemens Magnetom whole body 9.4 T human MRI system. Depending on the head size, positioning and the RF shim strategy, the smaller array provides from 11 to 23% higher Tx efficiency. In general, the Tx performance, evaluated as B 1 + /√SAR, i.e. the safety excitation efficiency (SEE), is also not compromised. The two arrays provide very similar SEEs evaluated over 1000 random RF shim sets. We demonstrated that, in general, the tight fit transceiver array improves Tx performance without compromising SEE. However, in specific cases, the SEE value may vary, favoring one of the arrays, and therefore must be carefully evaluated.
Gestational diabetes alters the fetal heart rate variability during an oral glucose tolerance test: a fetal magnetocardiography study
2016-12-28

Objective Gestational diabetes mellitus (GDM) potentially harms the child before birth. We previously found GDM to be associated with developmental changes in the central nervous system. We now hypothesise that GDM may also impact on the fetal autonomic nervous system under metabolic stress like an oral glucose tolerance test (OGTT). Design We measured heart rate variability (HRV) of mothers and fetuses during a three‐point OGTT using fetal magnetocardiography (fMCG). Setting Measurements were performed in the fMEG Centre in Tübingen. Population After exclusion of 23 participants, 13 pregnant women with GDM and 36 pregnant women with normal glucose tolerance were examined. Methods All women underwent the same examination setting with OGTT during which fMCG was recorded three times. Main outcome measure(s) Parameters of heart rate variability were measured. Results Compared with mothers with normal glucose regulation, mothers with GDM showed increased heart rate but no significant differences of maternal HRV. In contrast, HRV in fetuses of mothers with GDM differed from those in the metabolically healthy group regarding standard deviation normal to normal beat (SDNN) ( P = 0.012), low‐frequency band ( P = 0.008) and high‐frequency band ( P = 0.031). These HRV parameters exhibit a decrease only in GDM fetuses during the second hour of the OGTT. Conclusions These results show an altered response of the fetal autonomic nervous system to metabolic stress in GDM‐complicated pregnancies. Hence, disturbances in maternal glucose metabolism might not only impact on the central nervous system of the fetus but may also affect the fetal autonomic nervous system. Tweetable abstract Metabolic stress reveals a different response of fetal autonomic nervous system in GDM‐complicated pregnancies.
Cytotoxic Effects of Rapana venosa Hemocyanin on Bladder Cancer Permanent Cell Lines
2016-12-28

The cytotoxic activities of hemocyanin from Rapana venosa and its structural subunits with different oligosaccharide structures are studied in vitro on the bladder cancer permanent cell lines CAL-29, T-24, and the normal urothelial cell line HL 10/29.A significant cytotoxic effect against these tumor cells was observed for the functional unit RvH1-c after a treatment in contrast to native RvH and its structural subunits.Cells, treated with RvH1-c, show a mixture of both, necrotic and apoptotic cells.Cytotoxicity of RvH1-c is probably due to specific oligosaccharide structures exposed on the surface of the glycoprotein.
Optomechanical damping of a nanomembrane inside an optical ring cavity
2016-12-28

We experimentally and theoretically investigate mechanical nanooscillators coupled to the light in an optical ring resonator made of dielectric mirrors. We identify an optomechanical damping mechanism that is fundamentally different to the well known cooling in standing wave cavities. While, in a standing wave cavity the mechanical oscillation shifts the resonance frequency of the cavity in a ring resonator the frequency does not change. Instead the position of the nodes is shifted with the mechanical excursion. We derive the damping rates and test the results experimentally with a silicon-nitride nanomembrane. It turns out that scattering from small imperfections of the dielectric mirror coatings has to be taken into account to explain the value of the measured damping rate. We extend our theoretical model and regard a second reflector in the cavity that captures the effects of mirror back scattering. This model can be used to also describe the situation of two membranes that both interact with the cavity fields. This may be interesting for future work on synchronization of distant oscillators that are coupled by intracavity light fields.
On the (in)definiteness of impersonal pronouns
2016-12-28

This paper addresses the question whether impersonal pronouns should be analyzed as indefinite or definite expressions based on their discourse anaphoric potential. I present new data that support the claim that impersonal pronouns should be analyzed as neither (see Koenig &amp; Mauner 1999). I sketch a formal analysis that captures this behaviour. Furthermore, I show that the availability of quantificational variability effects for impersonal pronouns is not foolproof evidence for their indefiniteness as is usually assumed in the literature (see Malamud 2013).
Conditional antecedents containing the German discourse particle denn: a corpus study
2016-12-28

We discuss the semantic contribution and distribution of conditional antecedents containing the discourse particle denn (“antecedents with denn”, abbreviated as AWD). We propose that AWDs occur only in contexts where (i) the speaker does not believe the antecedent proposition p to hold, and (ii) the truth of p has been nonexplicitly (= tacitly) proposed. To gain a better understanding of (ii), we conduct two corpus studies. The first study investigates the relative location of AWDs with respect to their consequents. We find that unlike antecedents of regular hypothetical conditionals, AWDs occur significantly more often after the material in the consequent and parenthetically inside this material than before it. In a second study, we investigate the position of the tacit proposal relative to the AWD. We find that it typically precedes the AWD. Both results are in accordance with (ii). We then present a classification of the types of tacit proposals that we find with AWDs: speakers use AWDs to qualify their own statements or to doubt proposals of others, in both cases managing potential updates to the common ground.
Transatlantic crossing in the 1920s and 30s – the trajectories of the European poetic and scientific avant-garde in Brazil
2016-12-28

This article focuses on four paradigmatic cases of travelers. The central part concerns Dina Lévi-Strauss who gave the first course on modern ethnography in Brazil. She transfered the very latest: her projects include the founding of an ethnographic museum modeled on the “Musée de l`Homme”. Claude Lévi-Strauss and Fernand Braudel traveled to São Paulo as members of the French mission, which played an important role in the founding of the University of São Paulo. For political reasons Claude Lévi-Strauss’ contract at the University was not renewed in 1937. Blaise Cendrars was already a famous poet when he crossed the Atlantic in 1924. Fascism in Europe and World War II interrupted the careers of these four travelers as well as their interchanges with Brazil and their Brazilian friendships. But Brazilian experiences of Claude Lévi-Strauss and Braudel are crucial for their successful careers, after 1945.----------------------------------------------------------------------------------------------------Travessia transatlântica nos anos 1920 e 1930: as trajetórias da vanguarda poética e científica europeia no BrasilO artigo trata de quatro casos paradigmáticos de viajantes. A parte central está dedicada a Dina Lévi-Strauss, quem ministrou o primeiro curso de etnografia moderna no Brasil, apresentando nele o que havia de mais recente em sua época; seus projetos ainda incluíam a fundação de um museu etnográfico concebido a partir do modelo do “Musée de l’Homme”. Por sua vez, Claude Lévi-Strauss e Fernand Braudel viajaram a São Paulo como membros da Missão francesa, que teve um papel importante na fundação da Universidade de São Paulo, mesmo que, por razões políticas, o contrato de Claude Lévi-Strauss não tenha sido renovado pela Universidade em 1937. Antes deles, Blaise Cendrars era já um poeta famoso quando cruzou o Atlântico em 1924. O fascismo na Europa e a Segunda Guerra Mundial interromperam as carreiras destes quatro viajantes tanto quanto seus intercâmbios com o Brasil e com seus amigos brasileiros. Contudo, as experiências que Claude Lévi-Strauss e Braudel levaram a cabo no Brasil foram cruciais para o sucesso de suas respectivas carreiras após 1945.---Artigo em inglês.
High-Quality Draft Genome Sequence of the Actinobacterium Nocardia terpenica IFM 0406, Producer of the Immunosuppressant Brasilicardins, Using Illumina and PacBio Technologies
2016-12-29

ABSTRACT The bacterium Nocardia terpenica IFM 0406 is known as the producer of the immunosuppressant brasilicardin A. Here, we report the completely sequenced genome of strain IFM 0406, which facilitates the heterologous expression of the brasilicardin biosynthetic gene cluster but also unveils the intriguing biosynthetic capacity of the strain to produce secondary metabolites.
The chronology and duration of the prehistoric ditched enclosures: the case of Marroquíes Bajos (Jaén)
2016-12-30

The time spans of the so-called ditched enclosures are key to a better understanding of a type of site characterised by complex palimpsests. Several conclusions can be drawn from the 16 radiocarbon dates obtained from Ditch 4 at Marroquíes Bajos. According to Bayesian modelling, the filling process began in 2510-2310 cal BC at 2 σ and ended in 2115-1795 cal BC at 2 σ, making them the most recent ditched enclosure with depositional activity in Iberia. Comparison with the dating from other sections of Ditch 4 challenges the traditional assumption that radiocarbon samples obtained from deposits at the bottom of the ditch provide the best dates for its construction. The process by which different sections of the same Ditch 4 were filled at different times suggests that its general outline is more the result of an aggregation of segments than of a single build-up.