julilili42/papers huggingface dataset:
Hybridization increases invasive knotweed success
2014-01-02

Abstract Hybridization is one of the fundamental mechanisms by which rapid evolution can occur in exotic species. If hybrids show increased vigour, this could significantly contribute to invasion success. Here, we compared the success of the two invasive knotweeds, F allopia japonica and F . sachalinensis , and their hybrid, F . × bohemica, in competing against experimental communities of native plants. Using plant material from multiple clones of each taxon collected across a latitudinal gradient in Central Europe, we found that knotweed hybrids performed significantly better in competition with a native community and that they more strongly reduced the growth of the native plants. One of the parental species, F . sachalinensis , regenerated significantly less well from rhizomes, and this difference disappeared if activated carbon was added to the substrate, which suggests allelopathic inhibition of F . sachalinensis regeneration by native plants. We found substantial within‐taxon variation in competitive success in all knotweed taxa, but variation was generally greatest in the hybrid. Interestingly, there was also significant variation within the genetically uniform F . japonica , possibly reflecting epigenetic differences. Our study shows that invasive knotweed hybrids are indeed more competitive than their parents and that hybridization increased the invasiveness of the exotic knotweed complex.
Improving Soil Moisture Data Retrieval From Airborne L-Band Radiometer Data by Considering Spatially Varying Roughness
2014-01-02

This study presents the retrieval of near-surface soil moisture data below crop canopies (winter rye and winter barley) from airborne L-band radiometer observations using a radiative transfer model at very dry soil moisture conditions (<15 Vol.%). Using physically based models, the roughness parameterization plays a crucial role for the description of the surface emissivity. A two-step optimization procedure was performed for choosing an optimal roughness value to minimize the uncertainty of soil moisture estimates. A crop-type specific roughness parameterization within the model did not show satisfactory soil moisture results. Instead, a "pixel"-based (spatially varying) roughness parameter optimization provided significantly improved results, also indicating a strong relationship between the optimal roughness parameter value and the Normalized Difference Vegetation Index (NDVI) derived from imaging spectrometer data. Our results demonstrate the importance of treating surface roughness as spatially variable when retrieving soil moisture information from high spatial resolution L-band brightness temperature data. Furthermore, the results strongly indicate that a combination of passive microwave observations and optical remote sensing data of the vegetation improve the mapping and monitoring of surface soil moisture.
Inside Out – The New Literary Geographies of the Post-Apartheid City in Mpe's and Vladislavić's Johannesburg Writing
2014-01-02

This article examines the strategies used by Johannesburg writers Phaswane&#13;\\nMpe and Ivan Vladislavić in their texts Welcome to Our Hillbrow (2001) and&#13;\\nPortrait with Keys: The City of Johannesburg Unlocked (2006) to make sense&#13;\\nof the bewildering transformations of post-apartheid Johannesburg. The article&#13;\\nbegins by sketching the transformations of the city in the wake of the&#13;\\ndismantlement of apartheid-era segregation, sketching in particular the way in&#13;\\nwhich the city has been turned „inside-out‟. It then goes on to examine in the&#13;\\ntexts by Mpe‟s and Vladislavić‟s figures of the „inside-out‟, specifically Mpe‟s&#13;\\nuse of narratological loops and Vladislavić‟s implementation of the figure of the&#13;\\nMöbius strip, to show how these recent literary texts have attempted to elucidate&#13;\\nthe vertiginous demographic changes in the city.
Human Rights in a Plural Ethical Framework: A Questioning on the Threshold of Legal Orders
2014-01-02

According to one of the most famous and influential formulations by Michael Ignatieff, human rights can nowadays be considered to have acquired the status of a lingua franca.2 Every discourse on global and domestic justice is shaped and formulated by means of the semantics of human rights: from the realm of its theoretical implications, to that of its political implementation, to its legal codifications. Yet what captures the attention is the fact that this state of affairs, however indubitable on the side of its facticity, notably lacks a comparable character of indisputability on the side of its justificatory framework. In effect, while at its origin the human rights discourse could be said to have its foundation in the domain of a unifying natural law – either theologically or secularly conceived – and, likewise, during the age of revolutions, though abdicating its thick metaphysical grounding, could still defend its universal claim by relying on the very character of humanity (of human rights), no commensurable strategy of foundation could be assumed to persist into the current era. Today’s societies are simply more secularized and fragmented than they were two centuries ago. They explicitly reject a unitary and cohesive vision of morality. They cannot impose a single ethical standard of life upon their members. In simple words: these societies no longer build a universe, but a multiverse.3 Therefore, drawing on human rights as a (potentially) universal device for, say, establishing a minimal unitary cohesion, solving situations of conflict or promoting cooperation, can either be considered as an entirely unjustified endeavor, or at least one which leads to the formulation of an inevitable paradox, in that the very social contexts that spurn substantive forms of ethics are nevertheless called to adhere to a new kind of all-encompassing criteria of normativity. All this gives rise then to the overall impression, expressed from several perspectives,4 that the discourse of human rights ultimately represents none other than a new and odd Sittlichkeit which, because of its weak or nebulous foundation, turns out to be both profoundly illegitimate in the universal-reaching ethical claim it raises, and irreducibly violent when it comes to the forms of its implementation (and imposition) upon subjects and institutions. Notoriously, several contemporary legal discourses attempt to face such a predicament by systematically bypassing the ethical dimension of human rights and exclusively focusing on their legal aspects. Pragmatic as it may seem, such a legalistic shift, far from solving the most problematic issue at stake in the idea of human rights, ends up simply deferring it. For no unilateral approach – in our opinion – be it juridical or ethical, enables one to genuinely grasp the very thrust of human rights as such. Human rights are neither a purely ethical matter nor an exclusively legal concern, but
Male sex as a risk factor for the clinical course of skull base chordomas
2014-01-03

Object Chordomas of the skull base are rare and locally invasive and have a poor prognosis. The aim of this retrospective multicenter study was to evaluate the current pattern of care and clinical course and to identify prognostic factors. Methods A total of 47 patients (26 men; mean age 48.5 years) treated in 5 centers were included. Histology was centrally reviewed; additionally, semiquantitative N- and E-cadherin expression analysis was performed. Prognostic factors were obtained from multivariate regression models. For survival analysis the Kaplan-Meier method was used. Results The median follow-up period was 5.2 years. Complete resection, incomplete resection, and extended biopsy were performed in 14.9%, 80.9%, and 4.3% of patients, respectively. Surgical morbidity was not associated with extent of resection. Adjuvant radiation therapy was performed in 30 (63.8%) of 47 patients. The median progression-free survival (PFS) was 7.3 years. Complete resection prolonged median overall survival (OS) (p = 0.04). Male patients presented with worse PFS (4.8 years vs 9.8 years; p = 0.04) and OS (8.3 years vs not reached; p = 0.03) even though complete resection was exclusively achieved in the male subpopulation. Multivariate analysis confirmed male sex as the most important risk factor for tumor progression (p = 0.04) and death (p = 0.02). Age, duration of symptoms, initial Karnofsky Performance Scale score, brainstem compression, involvement of the petrous bone, infiltration of the dura mater, modality and dose of radiation therapy, and the E- and N-cadherin expression patterns did not gain prognostic relevance. Conclusions In skull base chordomas, male patients bear a higher risk of progressive disease and death. Male patients might benefit from more aggressive adjuvant therapy and/or from a closer follow-up schedule.
Upregulation of APP, ADAM10 and ADAM17 in the Denervated Mouse Dentate Gyrus
2014-01-03

The disintegrin and metalloproteinases ADAM10 and ADAM17 are regarded as the most important α-secretases involved in the physiological processing of amyloid precursor protein (APP) in brain. Since it has been suggested that processing of APP by α-secretases could be involved in the reorganization of the brain following injury, we studied mRNA expression of the two α-secretases Adam10 and Adam17, the ß-secretase Bace1, and the App-gene family (App, Aplp1, Aplp2) in the dentate gyrus of the mouse following entorhinal denervation. Using laser microdissection, tissue was harvested from the outer molecular layer and the granule cell layer of the denervated dentate gyrus. Expression levels of candidate genes were assessed using Affymetrix GeneChip Mouse Gene 1.0 ST arrays and reverse transcription-quantitative PCR, revealing an upregulation of Adam10 mRNA and Adam17 mRNA in the denervated outer molecular layer and an upregulation of Adam10 mRNA and App mRNA in the dentate granule cell layer. Immunolabeling for ADAM10 or ADAM17 in combination with markers for astro- and microglia revealed an increased labeling of ADAM10 and ADAM17 in the denervated outer molecular layer that was associated with reactive astrocytes but not with microglia. Collectively, these data show that denervation affects the expression level of APP and its two most important α-secretases. This suggests that APP-processing could be shifted towards the non-amyloidogenic pathway in denervated areas of the brain and, thus, towards the formation of neuroprotective APP cleavage products, such as APPsα.
HESS J1818–154, a new composite supernova remnant discovered in TeV gamma rays and X-rays
2014-01-03

Composite supernova remnants (SNRs) constitute a small subclass of the\\nremnants of massive stellar explosions where non-thermal radiation is observed\\nfrom both the expanding shell-like shock front and from a pulsar wind nebula\\n(PWN) located inside of the SNR. These systems represent a unique evolutionary\\nphase of SNRs where observations in the radio, X-ray, and -ray regimes\\nallow the study of the co-evolution of both these energetic phenomena. In this\\narticle, we report results from observations of the shell-type SNR G15.4+0.1\\nperformed with the High Energy Stereoscopic System (H.E.S.S.) and XMM-Newton. A\\ncompact TeV -ray source, HESSJ1818-154, located in the center and\\ncontained within the shell of G15.4+0.1 is detected by H.E.S.S. and featurs a\\nspectrum best represented by a power-law model with a spectral index of and an integral flux of\\nF 0.42 )=( cm s . Furthermore, a recent\\nobservation with XMM-Newton reveals extended X-ray emission strongly peaked in\\nthe center of G15.4+0.1. The X-ray source shows indications of an\\nenergy-dependent morphology featuring a compact core at energies above 4 keV\\nand more extended emission that fills the entire region within the SNR at lower\\nenergies. Together, the X-ray and VHE -ray emission provide strong\\nevidence of a PWN located inside the shell of G15.4+0.1, and this SNR can\\ntherefore be classified as a \\\\emph{composite} based on these observations. The\\nradio, X-ray, and -ray emission from the PWN is compatible with a\\none-zone leptonic model that requires a low average magnetic field inside the\\nemission region. An unambiguous counterpart to the putative pulsar, which is\\nthought to power the PWN, has been detected neither in radio nor in X-ray\\nobservations of G15.4+0.1.\\n
Correction: Roscovitine-induced Apoptosis in Neutrophils and Neutrophil Progenitors Is Regulated by the Bcl-2-Family Members Bim, Puma, Noxa and Mcl-1
2014-01-03

Neutrophil granulocyte (neutrophil) apoptosis plays a key role in determining inflammation in infectious and noninfectious settings.Recent work has shown that inhibitors of cyclin-dependent kinases (cdk) such as roscovitine can potently induce neutrophil apoptosis and reduce inflammation.Using a conditional Hoxb8-expression system we tested the participation of Bcl-2-family proteins to roscovitine-induced apoptosis in mouse neutrophils and in neutrophil progenitor cells.Bcl-2 strongly protected against roscovitine-induced apoptosis in neutrophils.The isolated loss of either Bim or noxa provided significant, partial protection while protection through combined loss of Bim and noxa or Bim and Puma was only slightly greater than this individual loss.The only substantial change in protein levels observed was the loss of Mcl-1, which was not transcriptional and was inhibited by proteasome blockade.In progenitor cells there was no protection by the loss of Bim alone but substantial protection by the loss of both Bim and Puma; surprisingly, strongest protection was seen by the isolated loss of noxa.The pattern of protein expression and Mcl-1-regulation in progenitor cells was very similar to the one observed in differentiated neutrophils.In addition, roscovitine strongly inhibited proliferation in progenitor cells, associated with an accumulation of cells in G2/M-phase.
Comment: Why do nondopaminergic features in Parkinson disease matter?
2014-01-04

Parkinson disease (PD) is a progressive multisystem disorder affecting both dopaminergic and nondopaminergic neurons. Whereas dopaminergic (mainly motor) symptoms are well-defined, the nondopaminergic symptoms (mainly nonmotor, such as depression, cognitive decline, anxiety, apathy, fatigue, sleep disorders, sensory symptoms, postural control deficits, orthostatic hypotension, and urogenital and gastrointestinal symptoms) are frequently missed or neglected during routine clinical visits; consequently, they are underinvestigated and undertreated. The neglect of nondopaminergic symptoms is surprising because i) they occur in almost all patients with PD throughout the course of the disease,(1) and can even precede the occurrence of the classic motor symptoms; ii) they affect almost all aspects of daily life; and iii) have a greater effect on health-related quality of life than dopaminergic symptoms.(2) During the last decade, several initiatives have addressed this deficit with specific assessment procedures for application in clinical practice and research.(1.)
Quantitative Phosphoproteome Analysis of Bacillus subtilis Reveals Novel Substrates of the Kinase PrkC and Phosphatase PrpC
2014-01-05

Reversible protein phosphorylation on serine, threonine, and tyrosine (Ser/Thr/Tyr) residues plays a critical role in regulation of vital processes in the cell. Despite of considerable progress in our understanding of the role of this modification in bacterial physiology, the dynamics of protein phosphorylation during bacterial growth has rarely been systematically addressed. In addition, little is known about in vivo substrates of bacterial Ser/Thr/Tyr kinases and phosphatases. An excellent candidate to study these questions is the Gram-positive bacterium Bacillus subtilis, one of the most intensively investigated bacterial model organism with both research and industrial applications. Here we employed gel-free phosphoproteomics combined with SILAC labeling and high resolution mass spectrometry to study the proteome and phosphoproteome dynamics during the batch growth of B. subtilis. We measured the dynamics of 1666 proteins and 64 phosphorylation sites in five distinct phases of growth. Enzymes of the central carbon metabolism and components of the translation machinery appear to be highly phosphorylated in the stationary phase, coinciding with stronger expression of Ser/Thr kinases. We further used the SILAC workflow to identify novel putative substrates of the Ser/Thr kinase PrkC and the phosphatase PrpC during stationary phase. The overall number of putative substrates was low, pointing to a high kinase and phosphatase specificity. One of the phosphorylation sites affected by both, PrkC and PrpC, was the Ser281 on the oxidoreductase YkwC. We showed that PrkC phosphorylates and PrpC dephosphorylates YkwC in vitro and that phosphorylation at Ser281 abolishes the oxidoreductase activity of YkwC in vitro and in vivo. Our results present the most detailed phosphoproteomic analysis of B. subtilis growth to date and provide the first global in vivo screen of PrkC and PrpC substrates.
Winning the Cold War: Anti-Communism, Informal Diplomacy, and the Transnational Career of Jean Violet
2014-01-05

The multifaceted career of the French lawyer, political advisor, voluntary intelligence officer, and anti-communist "freelancer" Jean Violet illustrates the growing importance of "informal diplomacy" during the second half of the twentieth century. In highlighting the decisive steps in Violet's political life, aimed at defeating the communist regimes and "winning the cold war", this paper discusses the role played by private and non-state actors in the development of a transnational European and transatlantic policy after World War II as well as the extension and professionalization of the informal diplomatic sector since the 1960s which was accompanied by an increasing lack of democratic legitimacy.
Dysregulation of Neurotrophic and Haematopoietic Growth Factors in Alzheimer’s Disease: From Pathophysiology to Novel Treatment Strategies
2014-01-06

Alzheimer's disease (AD) is the leading cause of dementia in the elderly. Growth factors have been demonstrated to act in a synergistic way in angiogenesis and neurogenesis contributing to self-healing powers of the adult human brain. A growing body of evidence demonstrates that levels of many growth factors (neurotrophins and hematopoietins) are altered in cerebrospinal fluid and peripheral blood from AD patients and in animal models of AD. The present review summarizes the role of several neurotrophic growth factors (e.g., BDNF, SCF, NGF, GDNF) and haematopoietic growth factors (e.g., G-CSF, VEGF, SDF-1) in AD. Moreover, we summarize recent studies evaluating the diagnostic and prognostic value of growth factor levels in blood and cerebrospinal fluid in patients with AD and discuss the potential role of these growth factors as a promising new therapeutic approach in AD.
Superradiance-tidal friction correspondence
2014-01-06

Since the work of Hartle in the 1970s, and the subsequent development of the\\nthe Membrane Paradigm approach to black hole physics it has been widely\\naccepted that superradiant scattering of gravitational waves bears strong\\nsimilarities with the phenomenon of ``tidal friction'' (well-known from\\nNewtonian gravity) operating in binary systems of viscous material bodies. In\\nthis paper we revisit the superradiance-tidal friction analogy within the\\ncontext of ultracompact relativistic bodies. We advocate that as long as these\\nbodies have non-zero viscosity they should undergo tidal friction that can be\\nconstrued as a kind of superradiant scattering from the point of view of the\\ndynamics of an orbiting test-body. In addition we consider the presence of\\nanisotropic matter, which is required for at least some ultracompact bodies, if\\nthey are to sustain a radius very close to the gravitational radius. We find\\nthat the tidal friction/superradiance output is enhanced with increasing\\nanisotropy and that strongly anisotropic systems exhibit an unconventional\\nresponse to tidal and centrifugal forces. Finally, we make contact with the\\nartificial system comprising a black hole with its horizon replaced by a mirror\\n(sometimes used as a proxy for ultracompact material bodies) and discuss\\nsuperradiance and tidal friction in relation to it.\\n
Correction: Screening for Protein-DNA Interactions by Automatable DNA-Protein Interaction ELISA
2014-01-06

DNA-binding proteins (DBPs), such as transcription factors, constitute about 10% of the protein-coding genes in eukaryotic genomes and play pivotal roles in the regulation of chromatin structure and gene expression by binding to short stretches of DNA.Despite their number and importance, only for a minor portion of DBPs the binding sequence had been disclosed.Methods that allow the de novo identification of DNA-binding motifs of known DBPs, such as protein binding microarray technology or SELEX, are not yet suited for high-throughput and automation.To close this gap, we report an automatable DNA-protein-interaction (DPI)-ELISA screen of an optimized double-stranded DNA (dsDNA) probe library that allows the high-throughput identification of hexanucleotide DNA-binding motifs.In contrast to other methods, this DPI-ELISA screen can be performed manually or with standard laboratory automation.Furthermore, output evaluation does not require extensive computational analysis to derive a binding consensus.We could show that the DPI-ELISA screen disclosed the full spectrum of binding preferences for a given DBP.As an example, AtWRKY11 was used to demonstrate that the automated DPI-ELISA screen revealed the entire range of in vitro binding preferences.In addition, protein extracts of AtbZIP63 and the DNA-binding domain of AtWRKY33 were analyzed, which led to a refinement of their known DNA-binding consensi.Finally, we performed a DPI-ELISA screen to disclose the DNA-binding consensus of a yet uncharacterized putative DBP, AtTIFY1.A palindromic TGATCA-consensus was uncovered and we could show that the GATC-core is compulsory for AtTIFY1 binding.This specific interaction between AtTIFY1 and its DNA-binding motif was confirmed by in vivo plant one-hybrid assays in protoplasts.Thus, the value and applicability of the DPI-ELISA screen for de novo binding site identification of DBPs, also under automatized conditions, is a promising approach for a deeper understanding of gene regulation in any organism of choice.