julilili42/papers huggingface dataset:
DRI-Grass: A New Experimental Platform for Addressing Grassland Ecosystem Responses to Future Precipitation Scenarios in South-East Australia
2016-09-20

Climate models predict shifts in the amount, frequency and seasonality of rainfall. Given close links between grassland productivity and rainfall, such changes are likely to have profound effects on the functioning of grassland ecosystems and modify species interactions. Here, we introduce a unique, new experimental platform - DRI-Grass (<b>D</b>rought and <b>R</b>oot Herbivore <b>I</b>nteractions in a <b>Grass</b>land) - that exposes a south-eastern Australian grassland to five rainfall regimes [Ambient (AMB), increased amount (IA, +50%), reduced amount (RA, -50%), reduced frequency (RF, single rainfall event every 21 days, with total amount unchanged) and summer drought (SD, 12-14 weeks without water, December-March)], and contrasting levels of root herbivory. Incorporation of a belowground herbivore (root-feeding scarabs) addition treatment allows novel investigation of ecological responses to the twin stresses of altered rainfall and root herbivory. We quantified effects of permanently installed rain shelters on microclimate by comparison with outside plots, identifying small shelter effects on air temperature (-0.19°C day, +0.26°C night), soil water content (SWC; -8%) and photosynthetically active radiation (PAR; -16%). Shelters were associated with modest increases in net primary productivity (NPP), particularly during the cool season. Rainfall treatments generated substantial differences in SWC, with the exception of IA; the latter is likely due to a combination of higher transpiration rates associated with greater plant biomass in IA and the low water-holding capacity of the well-drained, sandy soil. Growing season NPP was strongly reduced by SD, but did not respond to the other rainfall treatments. Addition of root herbivores did not affect plant biomass and there were no interactions between herbivory and rainfall treatments in the 1st year of study. Root herbivory did, however, induce foliar silicon-based defenses in <i>Cynodon dactylon</i> and <i>Eragrostis curvula</i>. Rapid recovery of NPP following resumption of watering in SD plots indicates high functional resilience at the site, and may reflect adaptation of the vegetation to historically high variability in rainfall, both within- and between years. DRI-Grass provides a unique platform for understanding how ecological interactions will be affected by changing rainfall regimes and, specifically, how belowground herbivory modifies grassland resistance and resilience to climate extremes.
Female sexual dysfunction post radical cystectomy and urinary diversion
2016-09-20

Although female sexual function is an important predictor of health-related quality of life post radical cystectomy and urinary diversion, the available literature is not enough to provide proper information for surgeons and patients.
Water mold infection but not paternity induces selective filial cannibalism in a goby
2016-09-20

Abstract Many animals heavily invest in parental care but still reject at least some of their offspring. Although seemingly paradoxical, selection can favor parents to neglect offspring of particularly low reproductive value, for example, because of small survival chances. We here assess whether filial cannibalism ( FC ), where parents routinely eat some of their own young, is selective in response to individual offspring reproductive value. We performed two independent laboratory experiments in the common goby ( Pomatoschistus microps ) to test whether caring fathers preferentially cannibalize eggs of a given infection history and paternity. While males did not discriminate kin from nonkin eggs, they consumed significantly more eggs previously exposed to water mold compared to uninfected eggs. Our findings clearly show that parents differentiate between eggs based on differences in egg condition, and thus complement the prevailing view that FC arises for energetic reasons. By preventing the spread of microbial infections, the removal of molded eggs can constitute an important component of parental care and may represent a key driver of selective FC in a wide array of parental fish.
Long-term analysis of semilinear wave equations with slowly varying wave speed
2016-09-20

A semilinear wave equation with slowly varying wave speed is considered in one to three space dimensions on a bounded interval, a rectangle or a box, respectively. It is shown that the action, which is the harmonic energy divided by the wave speed and multiplied with the diameter of the spatial domain, is an adiabatic invariant: it remains nearly conserved over long times, longer than any fixed power of the time scale of changes in the wave speed in the case of one space dimension, and longer than can be attained by standard perturbation arguments in the two- and three-dimensional cases. The long-time near-conservation of the action yields long-time existence of the solution. The proofs use modulated Fourier expansions in time.
Contributions to the functional morphology of caudate skulls: kinetic and akinetic forms
2016-09-20

A strongly ossified and rigid skull roof, which prevents parietal kinesis, has been reported for the adults of all amphibian clades. Our μ-CT investigations revealed that the Buresch’s newt ( Triturus ivanbureschi ) possess a peculiar cranial construction. In addition to the typical amphibian pleurokinetic articulation between skull roof and palatoquadrate associated structures, we found flexible connections between nasals and frontals (prokinesis), vomer and parasphenoid (palatokinesis), and between frontals and parietals (mesokinesis). This is the first description of mesokinesis in urodelans. The construction of the skull in the Buresch’s newts also indicates the presence of an articulation between parietals and the exocipitals, discussed as a possible kind of metakinesis. The specific combination of pleuro-, pro-, meso-, palato-, and metakinetic skull articulations indicate to a new kind of kinetic systems unknown for urodelans to this date. We discuss the possible neotenic origin of the skull kinesis and pose the hypothesis that the kinesis in T. ivanbureschi increases the efficiency of fast jaw closure. For that, we compared the construction of the skull in T. ivanbureschi to the akinetic skull of the Common fire salamander Salamandra salamandra . We hypothesize that the design of the skull in the purely terrestrial living salamander shows a similar degree of intracranial mobility. However, this mobility is permitted by elasticity of some bones and not by true articulation between them. We comment on the possible relation between the skull construction and the form of prey shaking mechanism that the species apply to immobilize their victims.
Extraction of ultrashort DNA molecules from herbarium specimens
2016-09-20

Abstract DNA extracted from herbarium specimens is highly fragmented and decays at a faster rate than DNA from ancient bones. Therefore, it is crucial to utilize extraction protocols that retrieve short DNA molecules. Improvements in extraction and library preparation protocols for animal remains have allowed efficient retrieval of molecules shorter than 50 bp. We adapted those improvements to extraction protocols for herbarium specimens and evaluated their performance by shotgun sequencing, which allows an accurate estimation of the distribution of fragment lengths. Extraction with PTB buffer decreased median fragment length by 35% when compared to CTAB. Modifying the binding conditions of DNA to silica allowed for an additional decrease of 10%. We did not observe a further decrease in length when we used single-stranded instead of double-stranded library preparation methods. Our protocol enables the retrieval of ultrashort molecules from herbarium specimens and will help to unlock the genetic information stored in herbaria.
Beyond data as representation: The performativity of Big Data in surveillance
2016-09-21

The article discusses problems of representative views of data and elaborates a concept of the performativity of data. It shows how data used for surveillance contributes in creating suspect subjectivities. In particular, the article focuses on the inductive or explorative processing of data and on the decoupling of data generation and analysis that characterize current use of data for surveillance. It lines out several challenges this poses to established accounts of surveillance: David Lyon’s concept of surveillance as social sorting and Haggerty and Ericson’s “surveillant assemblage”. These problems are attributed to a representationalist view, which focuses on the veracity of data. This can lead to ignoring problematic consequences of surveillance procedures and the full scope of affected persons. Building on an idea by Rita Raley, an alternative account of data as performative is proposed. Using Judith Butler’s concept of “citationality,” this account shows how surveillance is entangled with the production of subjects through data in general. Surveillance is reformulated as a particular way in which subjects are produced that is parasitical to other forms of subjectivation.
Hard times and European youth. The effect of economic insecurity on human values, social attitudes and well‐being
2016-09-21

While economic downturns have adverse effects on young people's life chances, empirical studies examining whether and to what extent human values, social attitudes and well‐being indicators respond to sudden economic shocks are scarce. To assess the claim that human values are less affected by economic shocks than social attitudes and well‐being, two distinct yet related studies based on the European Social Survey ( ESS ) are conducted. The first employs a fixed effects pseudo‐panel analysis of the 2008–2014 ESS ‐waves to detect whether changes over time in the socio‐demographic group's unemployment risk and national youth unemployment affect individual dispositions to varying degrees. The second study captures micro‐ and cross‐national effects in the 2010 ESS cross‐section. Unique for this set‐up is that we can test whether the findings hold for over‐time changes in youth unemployment within countries (pseudo‐panel), as well as for cross‐country differences in youth unemployment (multilevel). Both studies indicate that political trust, satisfaction with the economy and subjective well‐being are lowered by economic risk and hardship, while social trust and self‐rated health are less affected by changes in youth unemployment. Secondly, human values are immune to economic risk, underscoring that values transcend specific situations and are therefore resistant against sudden economic shocks.
Proof-theoretic harmony: towards an intensional account
2016-09-21

Abstract In this paper we argue that an account of proof-theoretic harmony based on reductions and expansions delivers an inferentialist picture of meaning which should be regarded as intensional, as opposed to other approaches to harmony that will be dubbed extensional. We show how the intensional account applies to any connective whose rules obey the inversion principle first proposed by Prawitz and Schroeder-Heister. In particular, by improving previous formulations of expansions, we solve a problem with quantum-disjunction first posed by Dummett. As recently observed by Schroeder-Heister, however, the specification of an inversion principle cannot yield an exhaustive account of harmony. The reason is that there are more collections of elimination rules than just the one obtained by inversion which we are willing to acknowledge as being in harmony with a given collection of introduction rules. Several authors more or less implicitly suggest that what is common to all alternative harmonious collection of rules is their being interderivable with each other. On the basis of considerations about identity of proofs and formula isomorphism, we show that this is too weak a condition for a given collection of elimination rules to be in harmony with a collection of introduction rules, at least if the intensional picture of meaning we advocate is not to collapse on an extensional one.
Seeing the unseen? Illusory causal filling in FIFA referees, players, and novices
2016-09-21

Humans often falsely report having seen a causal link between two dynamic scenes if the second scene depicts a valid logical consequence of the initial scene. As an example, a video clip shows someone kicking a ball including the ball flying. Even if the video clip omitted the moment of contact (i.e., the causal link), participants falsely report having seen this moment. In the current study, we explored the interplay of cognitive-perceptual expertise and event perception by measuring the false-alarm rates of three groups with differing interests in football (soccer in North America) (novices, players, and FIFA referees). We used the event-completion paradigm with video footage of a real football match, presenting either complete clips or incomplete clips (i.e., with the contact moment omitted). Either a causally linked scene or an incoherent scene followed a cut in the incomplete videos. Causally linked scenes induced false recognitions in all three groups: although the ball contact moment was not presented, participants indicated that they had seen the contact as frequently when it was absent as in the complete condition. In a second experiment, we asked the novices to detect the ball contact moment when it was either visible or not and when it was either followed by a causally or non-causally linked scene. Here, instead of presenting pictures of the clip, the participants were give a two-alternative forced-choice task: "Yes, contact was visible", or "No, contact was not visible". The results of Experiment 1 indicate that conceptual interpretations of simple events are independent of expertise: there were no top-down effects on perception. Participants in Experiment 2 detected the ball contact moment significantly more often correctly in the non-causal than in the causal conditions, indicating that the effect observed in Experiment 1 was not due to a possibly influential design (e.g., inducing a false memory for the presented pictures). The theoretical as well as the practical implications are discussed.
Cooperative spontaneous emission from indistinguishable atoms in arbitrary motional quantum states
2016-09-21

We investigate superradiance and subradiance of indistinguishable atoms with\\nquantized motional states, starting with an initial total state that factorizes\\nover the internal and external degrees of freedom of the atoms. Due to the\\npermutational symmetry of the motional state, the cooperative spontaneous\\nemission, governed by a recently derived master equation [F. Damanet et al.,\\nPhys. Rev. A 93, 022124 (2016)], depends only on two decay rates and\\n and a single parameter describing the\\ndipole-dipole shifts. We solve the dynamics exactly for atoms,\\nnumerically for up to 30 atoms, and obtain the large- -limit by amean-field\\napproach. We find that there is a critical difference that\\ndepends on beyond which superradiance is lost. We show that exact\\nnon-trivial dark states (i.e. states other than the ground state with vanishing\\nspontaneous emission) only exist for , and that those states\\n(dark when ) are subradiant when .\\n
Arsenic trioxide potentiates the effectiveness of etoposide in Ewing sarcomas
2016-09-21

Ewing sarcomas (ES) are rare mesenchymal tumours, most commonly diagnosed in children and adolescents. Arsenic trioxide (ATO) has been shown to efficiently and selectively target leukaemic blasts as well as solid tumour cells. Since multidrug resistance often occurs in recurrent and metastatic ES, we tested potential additive effects of ATO in combination with the cytostatic drugs etoposide and doxorubicin. The Ewing sarcoma cell lines A673, RD-ES and SK-N-MC as well as mesenchymal stem cells (MSC) for control were treated with ATO, etoposide and doxorubicin in single and combined application. Viability and proliferation (MTS assay, colony formation, 3D spheroid culture) as well as cell death induction (western blot analysis, flow cytometry) were analysed. In the MTS viability assays ATO treatment significantly reduced the metabolic activity of all three ES cell lines (A673, RD-ES and SK-N-MC) examined. Moreover, all ES cell lines were sensitive to etoposide, whereas MSC remained unaffected by the drug concentrations used. With the exception of ATO in RD-ES cells, all drugs induced apoptosis in the ES cell lines, indicated by caspase-3 and PARP cleavage. Combination of the agents potentiated the reduction of viability as well as the inhibitory effect on clonal growth. In addition, cell death induction was obviously enhanced in RD-ES and SK-N-MC cells by a combination of ATO and etoposide compared to single application. Summarised, the combination of low dose, physiologically easily tolerable ATO with commonly used etoposide and doxorubicin concentrations efficiently and selectively suppressed viability and colony formation in ES cell lines, whereas a combination of ATO and etoposide was favourable for cell death induction. In addition to an increase of the effectiveness of the cytostatic drugs and prevention of potential drug resistance, this approach may also reduce toxicity effects, since the individual doses can be reduced.
P01.11 The transcriptional coactivator PGC-1a promotes defence against reactive oxygen species (ROS) and proliferation in human glioma cells
2016-09-21

AbstractGene expression of many signalling pathways and metabolic programs is regulated at the transcriptional level by DNA binding coactivators. These coactivators act in a tissue-specific-manner and are responsive to different physiological stimuli like nutrient supply and temperature. One of these coactivators, Peroxisome proliferator-activated receptor- coactivator (PGC)-1α, is a master regulator of mitochondrial biogenesis, controls antioxidative responses and coordinates posttranscriptional events. The activity of PGC-1a is regulated by growth factor receptor signaling and the AMP-activated protein kinase (AMPK) pathway, both of which are crucial for the growth and metabolism of tumors. Further, because variable nutritional environments require tumor cells to adapt their energy metabolism, we asked whether PGC-1α is involved in growth, resistance against nutrient depletion and metabolic flexibility of glioma cells.We found that PGC-1α is expressed in a subset of established and primary glioma cells. Surprisingly, while suppression of PGC-1α expression by sh-RNA in U343MG glioma cells reduced glucose consumption and lactate production, it did not reduce oxygen consumption or mitochondrial mass. PGC-1α-sh cells had impaired proliferation and migration in vitro. Compatible to the known PGC-1α’s functions in reactive oxygen species (ROS) metabolism, glioma cells lacking PGC-1α expression had reduced RNA levels of proteins involved in (ROS) detoxification mechanism, and these cells were more susceptible to death induction by H2O2 compared to control cells. Interestingly, the PGC-1α-knock-down conferred protection against hypoxia-induced cell death. In an in-vivo-xenograft experiment, tumors formed by PGC-1α-suppressed glioma cells grew much slower than control tumors.In summary, PGC-1α is expressed in glioma cells and has an important role in growth and resistance against ROS in these cells. As the oxygen consumption in PGC-1α-sh cells was not significantly impaired, the presented effects of PGC-1α seemingly do not depend on the well-established functions of PGC-1α on mitochondrial oxidative phosphorylation. Further experiments are underway to analyse in more detail the metabolic and cellular functions of PGC-1α.
OS2.4 Expression and relevance of tumoral and stromal MHC class II in gliomas
2016-09-21

Mutation-derived neo-epitopes have emerged as promising targets in immune-therapy of glioma. These neo-epitopes are often presented on MHC class II rather than MHC class I molecules, as exemplified by the mutant IDH1 neoepitope. Thus, MHC class II expression may strongly determine the effectiveness of those approaches. However, the expression patterns of MHC class II in diffuse glioma and possible correlations with the extent of T cell infiltration and outcome remain elusive. Here, we analyzed formalin-fixed paraffin-embedded glioma samples of the NOA-04 study collective, glioma cell lines and primary cells, and TCGA glioma expression data for the relevance of MHC class II expression. MHC class II expression was found in 80/82 glioma samples (98%) with expression attributable to tumor cells in 11/83 (13%). Expression on tumor cells was associated with an increased infiltration of CD4+ and CD8+ T-cells (p=0.002 and p<0.001). In the TCGA glioma dataset (TCGA, Nature 2008) MHC class II expression was associated with expression patterns reflecting a Th-mediated immune response. Neural and mesenchymal subtypes were associated with higher levels of MHC class II expression among gliobastoma, while IDH mutant 1p/19q co-deleted low-grade glioma harbored low levels of MHC class II. Presentation of epitopes was demonstrated by ligandome screening that identified up to 552 MHC class II ligands. Expression of MHC class II on tumor cells per se and high levels of infiltration with CD8+ cells were associated with unfavorable time-to-progression in the NOA04 study cohort (p=0.0414 and p=0.0479, respectively). In glioblastoma, high expression of MHC class II per se was associated with unfavorable overall survival in the TCGA dataset (p=0.032). The effect in glioblastoma was higher when confining the analysis on samples with low levels of MGMT expression (p=0.006). Our data provide evidence for the functional expression of MHC class II in diffuse glioma. These findings have implications for treatment approaches aiming at inducing a MHC class II restricted immune response such as the IDH1R132H vaccine.
OS2.1 Immune responses to a mutation-specific peptide vaccine targeting IDH1R132H in patients with IDH1R132H-mutated gliomas
2016-09-21

Immunotherapeutic concepts for brain tumors have been hampered by lack of selective measures to target the CNS and lack of truly tumor-specific antigens. But the concept of an immune privileged CNS has to be questioned due to survey of the brain by specific T-cells, CNS autoimmunity and presence of lymphatics. As tumor-specific antigens, mutated antigens have come into focus for all tumor entities. Mutations in the gene for isocitrate dehydrogenase 1 frequently occur in diffuse gliomas, mostly astrocytomas, resulting in a point mutation (mostly IDH1R132H). IDH1R132H is an ideal tumor-specific antigen, because it is tumor-specific, homogenously expressed and considered a driving mutation in glioma. Preclinical studies have shown that mutation-specific Th cell responses spontaneously occur in patients with IDH1-mutated gliomas and that a peptide vaccine encoding IDH1R132H is therapeutic in a humanized mouse tumorÂ model.