julilili42/papers huggingface dataset:
Managing the effects of multiple stressors on aquatic ecosystems under water scarcity. The GLOBAQUA project
2014-07-05

Water scarcity is a serious environmental problem in many European regions, and will likely increase in the near future as a consequence of increased abstraction and climate change. Water scarcity exacerbates the effects of multiple stressors, and thus results in decreased water quality. It impacts river ecosystems, threatens the services they provide, and it will force managers and policy-makers to change their current practices. The EU-FP7 project GLOBAQUA aims at identifying the prevalence, interaction and linkages between stressors, and to assess their effects on the chemical and ecological status of freshwater ecosystems in order to improve water management practice and policies. GLOBAQUA assembles a multidisciplinary team of 21 European plus 2 non-European scientific institutions, as well as water authorities and river basin managers. The project includes experts in hydrology, chemistry, biology, geomorphology, modelling, socio-economics, governance science, knowledge brokerage, and policy advocacy. GLOBAQUA studies six river basins (Ebro, Adige, Sava, Evrotas, Anglian and Souss Massa) affected by water scarcity, and aims to answer the following questions: how does water scarcity interact with other existing stressors in the study river basins? How will these interactions change according to the different scenarios of future global change? Which will be the foreseeable consequences for river ecosystems? How will these in turn affect the services the ecosystems provide? How should management and policies be adapted to minimise the ecological, economic and societal consequences? These questions will be approached by combining data-mining, field- and laboratory-based research, and modelling. Here, we outline the general structure of the project and the activities to be conducted within the fourteen work-packages of GLOBAQUA.
Translation-invariant quasi-free states for fermionic systems and the BCS approximation
2014-07-06

We study translation-invariant quasi-free states for a system of fermions with two-particle interactions. The associated energy functional is similar to the BCS functional but also includes direct and exchange energies. We show that for suitable short-range interactions, these latter terms only lead to a renormalization of the chemical potential, with the usual properties of the BCS functional left unchanged. Our analysis thus represents a rigorous justification of part of the BCS approximation. We give bounds on the critical temperature below which the system displays superfluidity.
mRNA vaccine CV9103 and CV9104 for the treatment of prostate cancer
2014-07-07

Among currently available vaccine strategies for cancer, nucleotide-based vaccination is an appealing treatment modality. Curevacs' mRNA containing vaccines (RNActive®) combine the beneficial properties of sufficient antigen-expression, autologous immune-stimulation and a high flexibility with respect to production and application. CV9103 and CV9104 are novel RNActive®-derived anticancer vaccines for the treatment of patients with prostate cancer. After successful phase I/II studies with documentation of good tolerability and favorable immune-activation of CV9103, the vaccine CV9104 is currently undergoing clinical testing in specific clinical settings such as castration resistant prostate cancer and as a neoadjuvant agent in men with high risk prostate cancer prior to surgery. This review discusses the available preclinical and clinical data on the anticancer vaccination treatment with RNActive®-derived anticancer-vaccines CV9103 and CV9104.
Phosphate‐Triggered Self‐Assembly of N‐[(Uracil‐5‐yl)methyl]urea: A Minimalistic Urea‐Derived Hydrogelator
2014-07-07

Abstract N ‐[(Uracil‐5‐yl)methyl]urea is reported as a minimalistic low‐molecular‐weight hydrogelator (LMWHG). The unusual phosphate‐induced assembly of this compound has been thoroughly investigated by IR, UV/Vis, and NMR spectroscopy, electron microscopy, and rheological experiments. This rare example of an anion‐triggered urea‐based LMWHG is the first example of a pyrimidine‐ and urea‐containing molecule that can be forced into self‐assembly in aqueous solution without additional aromatic or lipophilic groups. The gelator/phosphate ratio within the hydrogel was successfully determined by 31 P MAS NMR spectroscopy. The hydrogel exhibits a very fast and repeatable self‐healing property, and remarkable G ′ values. The viscoelastic properties of the hydrogel can easily be tuned by variation of the phosphate ratio.
inPHAP: Interactive visualization of genotype and phased haplotype data
2014-07-07

As of today, inPHAP is the only visual analytical tool that allows the user to explore unphased and phased haplotype data interactively. Due to its highly scalable design, inPHAP can be applied to large datasets with up to 100 GB of data, enabling users to visualize even large scale input data. inPHAP closes the gap between common visualization tools for unphased genotype data and introduces several new features, such as the visualization of phased data. inPHAP is available for download at http://bit.ly/1iJgKmX.
Upward-rightward planar drawings
2014-07-07

Upward drawing is a widely studied drawing convention for the visual representation of directed graphs. In an upward drawing vertices are mapped to distinct points of the plane, and edges are curves monotonically increasing in the vertical direction, according to their orientation. In particular, not all planar digraphs admit an upward planar drawing (i.e., an upward drawing with no edge crossing), and testing whether a planar digraph is upward planar drawable is NP-hard. Furthermore, straight-line upward planar drawings may require exponential area. In this paper we study a relaxation of upward drawings, called upward-rightward drawings; in such a drawing for any directed path from a vertex u to a vertex v it must be that either v is above u or v is to the right of u. In contrast with upward planarity, we prove that every planar digraph admits an upward-rightward planar drawing with straight-line edges and that this drawing can be computed in linear time and polynomial area.
Glycan Engagement by Viruses: Receptor Switches and Specificity
2014-07-08

A large number of viruses, including many human pathogens, bind cell-surface glycans during the initial steps of infection. Viral glycan receptors such as glycosaminoglycans and sialic acid–containing carbohydrates are often negatively charged, but neutral glycans such as histo–blood group antigens can also function as receptors. The engagement of glycans facilitates attachment and entry and, consequently, is often a key determinant of the host range, tissue tropism, pathogenicity, and transmissibility of viruses. Here, we review current knowledge about virus-glycan interactions using representative crystal structures of viral attachment proteins in complex with glycans. We illuminate the determinants of specificity utilized by different glycan-binding viruses and explore the potential of these interactions for switching receptor specificities within or even between glycan classes. A detailed understanding of these parameters is important for the prediction of binding sites where structural information is not available, and is invaluable for the development of antiviral therapeutics.
The effect of accretion on the measurement of neutron star mass and radius in the low-mass X-ray binary 4U 1608−52
2014-07-08

Spectral measurements of thermonuclear (type-I) X-ray bursts from low mass X-ray binaries have been used to measure neutron star (NS) masses and radii. A number of systematic issues affect such measurements and have raised concerns as to the robustness of the methods. We present analysis of the X-ray emission from bursts observed from 4U 1608-52 at various persistent fluxes. We find a strong dependence of the burst properties on the flux and spectral hardness of the persistent emission before burst. Bursts occurring during the low-accretion rate (hard) state exhibit evolution of the black body normalisation consistent with the theoretical predictions of NS atmosphere models. However, bursts occurring during the high-accretion rate (soft) state show roughly constant normalisation, which is inconsistent with the NS atmosphere models and therefore these bursts cannot be easily used to determine NS parameters. We analyse the hard-state burst to put the lower limit on the neutron star radius in 4U 1608-52 of 13 km (for masses 1.2-2.4 M ). The best agreement with the theoretical NS mass-radius relations is achieved for source distances in the range 3.1-3.7 kpc. We expect that the radius limit will be 10 per cent lower if spectral models including rapid rotation are used instead.
A Cohort Study of Paramedian Forehead Flap in 2 Stages (87 Flaps) and 3 Stages (100 Flaps)
2014-07-08

To our knowledge, our study is the largest series published to date and the first one to compare the prevalence of forehead flap necrosis in the 2- versus the 3-stage technique for paramedian forehead flaps. We found no evidence that the use of a 3-stage forehead flap lowers the prevalence of necrosis. Until larger multicenter studies or meta-analyses can be conducted, smaller yet well-conducted studies such as the present one provide critical data and represent an important contribution to the field. Future research should investigate whether the 3-stage technique produces better aesthetic results than the 2-stage technique.
Optical dating and soil micromorphology at MacCauley's Beach, New South Wales, Australia
2014-07-08

Abstract The ability to position landscapes in a context of time and space is a particular goal of Quaternary science research. The lack of context for dating samples published previously for MacCauley's Beach, an important site for the reconstruction of Australian sea levels, warranted a re‐evaluation of both the site stratigraphy and chronology. In this study, we combined optically stimulated luminescence (OSL) dating of sedimentary quartz grains and soil micromorphology of the same samples to improve our understanding of the depositional history and chronology of the sediments. This combination allowed the contextualization of samples not only in time and space, but also in terms of their depositional histories. The latter is important in OSL dating, where pre‐, syn‐ and post‐depositional processes can all influence the accuracy and precision of the final age estimates. The sediment profile at MacCauley's Beach is made up of three major units. The basal mottled mud layer has undergone extensive pedogenesis since deposition, and only a minimum age of 14.7 ± 2.7 ka could be calculated. The overlying grey mud, with OSL ages from the bottom and top of the unit of 10.0 ± 0.7 and 7.7 ± 0.5 ka, respectively, shows evidence of soil structure collapse. This unit correspond to the onset of the mid‐Holocene sea‐level high stand for this region. The overlying sand layer was first deposited at 7.5 ± 0.4 ka, with deposition continuing beyond 6.6 ± 0.4 ka. Not only does the chronology presented constrain the timing of deposition (and the extent of post‐depositional processes) at MacCauley's Beach, but the methodological approach used here can be applied to any site to aid in the interpretation of formation processes and assess their influence on OSL age determination. Copyright © 2014 John Wiley &amp; Sons, Ltd.
Well-being in amyotrophic lateral sclerosis: a pilot experience sampling study
2014-07-08

Objective: The aim of this longitudinal study was to identify predictors of instantaneous well-being in patients with amyotrophic lateral sclerosis (ALS). Based on flow theory well-being was expected to be highest when perceived demands and perceived control were in balance, and that thinking about the past would be a risk factor for rumination which would in turn reduce well-being. Methods: Using the experience sampling method, data on current activities, associated aspects of perceived demands, control, and well-being were collected from 10 patients with ALS three times a day for two weeks. Results: Results show that perceived control was uniformly and positively associated with well-being, but that demands were only positively associated with well-being when they were perceived as controllable. Mediation analysis confirmed thinking about the past, but not thinking about the future, to be a risk factor for rumination and reduced well-being. Discussion: Findings extend our knowledge of factors contributing to well-being in ALS as not only perceived control but also perceived demands can contribute to well-being. They further show that a focus on present experiences might contribute to increased well-being.
A Neurodegenerative Vascular Burden Index and the Impact on Cognition
2014-07-09

A wide range of vascular burden factors has been identified to impact vascular function and structure as indicated by carotid intima-media thickness (IMT). On the basis of their impact on IMT, vascular factors may be selected and clustered in a vascular burden index (VBI). Since many vascular factors increase the risk of Alzheimer's disease (AD), a multifactorial neurodegenerative VBI may be related to early pathological processes in AD and cognitive decline in its preclinical stages. We investigated an elderly cohort at risk for neurodegeneration (TREND study, n = 1102) for the multifactorial influence of vascular burden factors on IMT measured by ultrasound. To create a VBI for this cohort, vascular factors and their definitions (considering medical history, medication, and/or blood marker data) were selected based on their statistical effects on IMT in multiple regressions including age and sex. The impact of the VBI on cognitive performance was assessed using the Trail-Making Test (TMT) and the consortium to establish a registry for Alzheimer's disease (CERAD) neuropsychological battery. IMT was significantly predicted by age (standardized β = 0.26), sex (0.09; males > females) and the factors included in the VBI: obesity (0.18), hypertension (0.14), smoking (0.08), diabetes (0.07), and atherosclerosis (0.05), whereas other cardiovascular diseases or hypercholesterolemia were not significant. Individuals with 2 or more VBI factors compared to individuals without had an odds ratio of 3.17 regarding overly increased IMT ( ≥ 1.0 mm). The VBI showed an impact on executive control [log(TMT B-A), p = 0.047] and a trend toward decreased global cognitive function (CERAD total score, p = 0.057) independent of age, sex, and education. A VBI established on the basis of IMT may help to identify individuals with overly increased vascular burden linked to decreased cognitive function indicating neurodegenerative processes. The longitudinal study of this risk cohort will reveal the value of the VBI as prodromal marker for cognitive decline and AD.
Endless: A Purine‐Binding RNA Motif that Can Be Expressed in Cells
2014-07-09

Abstract It is becoming increasingly clear that nature uses RNAs extensively for regulating vital functions of the cell, and short sequences are frequently used to suppress gene expression. However, controlling the concentration of small molecules intracellularly through designed RNA sequences that fold into ligand‐binding structures is difficult. The development of “ endless ”, a triplex‐based folding motif that can be expressed in mammalian cells and binds the second messenger 3′,5′‐cyclic guanosine monophosphate (cGMP), is described. In vitro, DNA or RNA versions of endless show low micromolar to nanomolar dissociation constants for cGMP. To test its functionality in vivo, four endless RNA motifs arranged in tandem were co‐expressed with a fluorescent cGMP sensor protein in murine vascular smooth muscle cells. Nitric oxide induced endogenous cGMP signals were suppressed in endless ‐expressing cells compared to cells expressing a control motif, which suggests that endless can act as a genetically encoded cGMP sink to modulate signal transduction in cells.
Meat abstinence and its positive environmental effect: Examining the fasting etiquettes of the Ethiopian Orthodox Church
2014-07-09

Meat abstinence, as is practiced in some religions, has a positive impact on reducing the damages that the process of meat production inflicts on the environment. The Ethiopian Orthodox Christians observe fasting by abstaining from meat for more than half a year, and this seems to do the environment and economy some good. Religion has been playing a regulatory role between ever-increasing meat demands and the country’s fast-growing meat and live animal exports. The article concludes that individuals' tendency to drift from religious life practices, coupled with a growing middle class that can afford to buy meat regularly, and the country’s need to maximize foreign currency through meat and livestock exportation, is likely to see Ethiopia introduce intensive livestock production in the not too distant future, to meet domestic meat demands and increase livestock export earnings.
Explanation of Counterion Effects in Gold(I)-Catalyzed Hydroalkoxylation of Alkynes
2014-07-10

Using gold(I)-catalyzed hydroalkoxylation of alkynes as a model reaction with a well-known mechanism, a systematic experimental study was conducted to disclose the influence of the counterion X– of a gold catalyst LAuNCMe+ X– on every step of the catalytic cycle. The overall ion effect is determined as a superposition of several effects, operating on different steps of the reaction mechanism. All effects were explained from a position of hydrogen bonding, coordination chemistry at gold, and affinity for a proton.
A novel Arabidopsis CHITIN ELICITOR RECEPTOR KINASE 1 (CERK1) mutant with enhanced pathogen‐induced cell death and altered receptor processing
2014-07-10

Summary Plants detect pathogens by sensing microbe‐associated molecular patterns ( MAMP s) through pattern recognition receptors. Pattern recognition receptor complexes also have roles in cell death control, but the underlying mechanisms are poorly understood. Here, we report isolation of cerk1 ‐4, a novel mutant allele of the A rabidopsis chitin receptor CERK 1 with enhanced defense responses. We identified cerk1 ‐4 in a forward genetic screen with barley powdery mildew and consequently characterized it by pathogen assays, mutant crosses and analysis of defense pathways. CERK 1 and CERK 1‐4 proteins were analyzed biochemically. The cerk1 ‐4 mutation causes an amino acid exchange in the CERK 1 ectodomain. Mutant plants maintain chitin signaling capacity but exhibit hyper‐inducible salicylic acid concentrations and deregulated cell death upon pathogen challenge. In contrast to chitin signaling, the cerk1 ‐4 phenotype does not require kinase activity and is conferred by the N ‐terminal part of the receptor. CERK 1 undergoes ectodomain shedding, a well‐known process in animal cell surface proteins. Wild‐type plants contain the full‐length CERK 1 receptor protein as well as a soluble form of the CERK 1 ectodomain, whereas cerk1 ‐4 plants lack the N ‐terminal shedding product. Our work suggests that CERK 1 may have a chitin‐independent role in cell death control and is the first report of ectodomain shedding in plants.
Pathways to care: how superdiversity shapes the need for navigational assistance
2014-07-10

Abstract The recently developed sociological concept of superdiversity provides a potentially interesting and useful way of developing an understanding of life in contemporary Europe. Here we report on research based on individual narratives about access to health care, as described by a range of people from very different sociocultural backgrounds in four European countries. This article notes the frequent appearance in first‐person narratives of the need for navigational assistance in the form of knowledge, cultural competence and orientation that facilitate the identification and use of pathways to health care. Our dataset of 24 semi‐structured interviews suggests that, in the context of needing health care, the feeling of being a ‘stranger in a strange land’ is common in people from a wide range of backgrounds. In social settings characterised by transnationalism and cultural heterogeneity, it is important to understand the need for navigational assistance, particularly at times of uncertainty, in the design and delivery of health services. The relationship between the inhabitants of contemporary Europe and the healthcare systems available in the places where they live is dominated by both complexity and contingency – and this is the cultural field in which navigation operates.
Structural and Spectroscopic Characterization of Tin–Tin Double Bonds in Cyclic Distannenes
2014-07-10

Three cyclic distannenes, 1, 3, and 4, and one spacer-bridged bis(stannylene), 2, were prepared and thoroughly investigated by single-crystal X-ray diffraction in the solid state, by variable-temperature (VT) 119Sn NMR, VT 1H NMR, 13C NMR, and UV–vis spectroscopy in solution, and by quantum chemical calculations. The tin(II) compounds feature rigid 9,9-dimethylxanthene or naphthalene backbones and very bulky m-terphenyl substituents ArR [=C6H3-2,6-{C6H2-2,4,6-R3}2; R = Me (1, 3), i-Pr (2, 4)]. For distannenes 3 and 4, the strain of the naphthalene backbone results in rather short tin–tin distances of 2.7299(3) and 2.7688(2) Å, respectively, whereas the xanthene backbone produces long tin–tin distances of 3.0009(7) Å for distannene 1 and 4.2779(7) Å for the spacer-bridged bis(stannylene) 2. In comparison to the AriPr substituents, the less bulky ArMe substituents give rise to stronger trans-bending of the distannenes; moreover, DFT calculations indicate that, in contrast to AriPr, the ArMe substituents allow for asymmetric distortion of the trans-bending in dynamic processes. The oxidation products of distannene 1 and bis(stannylene) 2 reveal rare structural motifs: dihydroxydistannoxane 5 and bis(dihydroxystannane) 6, respectively, which feature terminal Sn–OH functionalities. The reaction of distannene 1 with 1 equiv of potassium chloride in the presence of the cryptating agent 222 results in the formation of the unusual stannyl stannide 7. A modified synthesis protocol for the preparation of distannene 1 yields in one step the stannyl stannylene 8 with a center of chirality at the stannyl tin atom. The series 1, 7, and 8 represents a variation of electronic tin–tin interactions.