julilili42/papers huggingface dataset:
Designing forest biodiversity experiments: general considerations illustrated by a new large experiment in subtropicalChina
2013-10-14

Summary Biodiversity–ecosystem functioning ( BEF ) experiments address ecosystem‐level consequences of species loss by comparing communities of high species richness with communities from which species have been gradually eliminated. BEF experiments originally started with microcosms in the laboratory and with grassland ecosystems. A new frontier in experimental BEF research is manipulating tree diversity in forest ecosystems, compelling researchers to think big and comprehensively. We present and discuss some of the major issues to be considered in the design of BEF experiments with trees and illustrate these with a new forest biodiversity experiment established in subtropical C hina ( X ingangshan, J iangxi P rovince) in 2009/2010. Using a pool of 40 tree species, extinction scenarios were simulated with tree richness levels of 1, 2, 4, 8 and 16 species on a total of 566 plots of 25·8 × 25·8 m each. The goal of this experiment is to estimate effects of tree and shrub species richness on carbon storage and soil erosion; therefore, the experiment was established on sloped terrain. The following important design choices were made: (i) establishing many small rather than fewer larger plots, (ii) using high planting density and random mixing of species rather than lower planting density and patchwise mixing of species, (iii) establishing a map of the initial ‘ecoscape’ to characterize site heterogeneity before the onset of biodiversity effects and (iv) manipulating tree species richness not only in random but also in trait‐oriented extinction scenarios. Data management and analysis are particularly challenging in BEF experiments with their hierarchical designs nesting individuals within‐species populations within plots within‐species compositions. Statistical analysis best proceeds by partitioning these random terms into fixed‐term contrasts, for example, species composition into contrasts for species richness and the presence of particular functional groups, which can then be tested against the remaining random variation among compositions. We conclude that forest BEF experiments provide exciting and timely research options. They especially require careful thinking to allow multiple disciplines to measure and analyse data jointly and effectively. Achieving specific research goals and synergy with previous experiments involves trade‐offs between different designs and requires manifold design decisions.
Genome-Wide Identification of KANADI1 Target Genes
2013-10-14

Plant organ development and polarity establishment is mediated by the action of several transcription factors. Among these, the KANADI (KAN) subclade of the GARP protein family plays important roles in polarity-associated processes during embryo, shoot and root patterning. In this study, we have identified a set of potential direct target genes of KAN1 through a combination of chromatin immunoprecipitation/DNA sequencing (ChIP-Seq) and genome-wide transcriptional profiling using tiling arrays. Target genes are over-represented for genes involved in the regulation of organ development as well as in the response to auxin. KAN1 affects directly the expression of several genes previously shown to be important in the establishment of polarity during lateral organ and vascular tissue development. We also show that KAN1 controls through its target genes auxin effects on organ development at different levels: transport and its regulation, and signaling. In addition, KAN1 regulates genes involved in the response to abscisic acid, jasmonic acid, brassinosteroids, ethylene, cytokinins and gibberellins. The role of KAN1 in organ polarity is antagonized by HD-ZIPIII transcription factors, including REVOLUTA (REV). A comparison of their target genes reveals that the REV/KAN1 module acts in organ patterning through opposite regulation of shared targets. Evidence of mutual repression between closely related family members is also shown.
Being someone'sright handdoesn't always feel right: bodily experiences affect metaphoric language processing
2013-10-14

AbstractRecent research has found impact of bodily experiences on language understanding. However, there is no clear evidence whether previous experiences influence only literal linguistic expressions or whether they affect also the processing of metaphoric or idiomatic language. If bodily experiences influence understanding of metaphoric language, then left-handers should have more difficulties in processing metaphors that map good to the right and bad to the left than right-handers, as the underlying concept of such metaphors is at odds with their experiences. In our study, we found evidence for this assumption: In comparison to control conditions, left-handers processed linguistic left–right metaphors significantly slower than right-handers. This finding constitutes evidence for an influence of bodily experiences on metaphoric language processing.Keywords: embodimentbody-specificity hypothesishandednessmetaphors AcknowledgementsWe thank Daniel Casasanto and an anonymous reviewer for their helpful comments on an earlier version of the manuscript, Florian Wickelmaier for statistical advice on mixed-effect model analysis, and Sibylla Wolter, Matthias Hüttner, Jonathan Maier, Eduard Berndt and Lukas Eschstruth for data collection.FundingThis work was supported by a research grant from the German Research Foundation (DFG) to Barbara Kaup [SFB 833, project B4].Notes1. In lmer model syntax: RT ∼ Handedness × Sentence type + (1 + Handedness∣ Item) + (1 + Sentence type ∣ Subject).Additional informationFundingFunding: This work was supported by a research grant from the German Research Foundation (DFG) to Barbara Kaup [SFB 833, project B4].
Does an automated caliper placement system improve the quality of fetal biometry?
2013-10-14

Purpose: To examine the inter- and intra-operator repeatability of manual placement of callipers in the assessment of basic biometric measurements and to compare the results to an automated calliper placement system.
Pitfalls in echocardiography: Coarctation of the aorta presenting as dilative cardiomyopathy (DCM)
2013-10-14

The morphologic spectrum of aortic coarctation extends from discrete isthmic obstruction to tubular hypoplasia of the aortic arch. Neonates frequently present with congestive heart failure and critically reduced perfusion of the descending aorta following ductal closure. In infants and older children coarctation is often detected due to the presence of weak groin pulses, heart murmur or arterial hypertension. We report four infants with coarctation who presented with DCM and reviewed our patients to determine, whether this presentation represents an exception or is relevant for the differential diagnosis of children with DCM.
Sleep Improves Prospective Remembering by Facilitating Spontaneous-Associative Retrieval Processes
2013-10-15

Memories are of the past but for the future, enabling individuals to implement intended plans and actions at the appropriate time. Prospective memory is the specific ability to remember and execute an intended behavior at some designated point in the future. Although sleep is well-known to benefit the consolidation of memories for past events, its role for prospective memory is still not well understood. Here, we show that sleep as compared to wakefulness after prospective memory instruction enhanced the successful execution of prospective memories two days later. We further show that sleep benefited both components of prospective memory, i.e. to remember that something has to be done (prospective component) and to remember what has to be done (retrospective component). Finally, sleep enhanced prospective remembering particularly when attentional resources were reduced during task execution, suggesting that subjects after sleep were able to recruit additional spontaneous-associative retrieval processes to remember intentions successfully. Our findings indicate that sleep supports the maintenance of prospective memory over time by strengthening intentional memory representations, thus favoring the spontaneous retrieval of the intended action at the appropriate time.
MBL2Variations and Malaria Susceptibility in Indian Populations
2013-10-15

ABSTRACT Human mannose-binding lectin (MBL) encoded by the MBL2 gene is a pattern recognition protein and has been associated with many infectious diseases, including malaria. We sought to investigate the contribution of functional MBL2 gene variations to Plasmodium falciparum malaria in well-defined cases and in matched controls. We resequenced the 8.7 kb of the entire MBL2 gene in 434 individuals clinically classified with malaria from regions of India where malaria is endemic. The study cohort included 176 patients with severe malaria, 101 patients with mild malaria, and 157 ethnically matched asymptomatic individuals. In addition, 830 individuals from 32 socially, linguistically, and geographically diverse endogamous populations of India were investigated for the distribution of functional MBL2 variants. The MBL2 −221C ( X ) allelic variant is associated with increased risk of malaria (mild malaria odds ratio [OR] = 1.9, corrected P value [ P Corr ] = 0.0036; severe malaria OR = 1.6, P Corr = 0.02). The exon1 variants MBL2*B (severe malaria OR = 2.1, P Corr = 0.036; mild versus severe malaria OR = 2.5, P Corr = 0.039) and MBL2*C (mild versus severe malaria OR = 5.4, P Corr = 0.045) increased the odds of having malaria. The exon1 MBL2*D/*B/*C variant increased the risk for severe malaria (OR = 3.4, P Corr = 0.000045). The frequencies of low MBL haplotypes were significantly higher in severe malaria (14.2%) compared to mild malaria (7.9%) and asymptomatic (3.8%). The MBL2*LYPA haplotypes confer protection, whereas MBL2*LXPA increases the malaria risk. Our findings in Indian populations demonstrate that MBL2 functional variants are strongly associated with malaria and infection severity.
A Two-Hybrid-Receptor Assay Demonstrates Heteromer Formation as Switch-On for Plant Immune Receptors
2013-10-15

Abstract Receptor kinases sense extracellular signals and trigger intracellular signaling and physiological responses. However, how does signal binding to the extracellular domain activate the cytoplasmic kinase domain? Activation of the plant immunoreceptor Flagellin sensing2 (FLS2) by its bacterial ligand flagellin or the peptide-epitope flg22 coincides with rapid complex formation with a second receptor kinase termed brassinosteroid receptor1 associated kinase1 (BAK1). Here, we show that the receptor pair of FLS2 and BAK1 is also functional when the roles of the complex partners are reversed by swapping their cytosolic domains. This reciprocal constellation prevents interference by redundant partners that can partially substitute for BAK1 and demonstrates that formation of the heteromeric complex is the molecular switch for transmembrane signaling. A similar approach with swaps between the Elongation factor-Tu receptor and BAK1 also resulted in a functional receptor/coreceptor pair, suggesting that a “two-hybrid-receptor assay” is of more general use for studying heteromeric receptor complexes.
Targeting Histidine Side Chains in Molecular Design through Nitrogen–Halogen Bonds
2013-10-15

Halogen bonds are directional noncovalent interactions that can be used to target electron donors in a protein binding site. In this study, we employ quantum chemical calculations to explore halogen···nitrogen contacts involving histidine side chains. We characterize the energetics on the MP2 level of theory using SCS-MP2 and CCSD(T)/CBS as reference calculations and elucidate their energy profile in suboptimal geometries. We derive simple rules allowing medicinal chemists and chemical biologists to easily determine preferred areas of interaction in a binding site and exploit them for scaffold decoration and design. Our work shows that nitrogen-halogen bonds are valuable interactions that are this far underexploited in patent applications, lead structure, and clinical candidate selection. We highlight their potential to increase binding affinities and suggest that they can significantly contribute to inducing and tuning subtype selectivities.
Impulsivity in Binge Eating Disorder: Food Cues Elicit Increased Reward Responses and Disinhibition
2013-10-16

According to these results, food-related reward sensitivity and rash-spontaneous behaviour, as the two components of impulsivity, are increased in BED in comparison with weight-matched and normal-weight controls. This indicates that BED represents a neurobehavioural phenotype of obesity that is characterised by increased impulsivity. Interventions for BED should target these special needs of affected patients.
Jakpot! New small molecules in autoimmune and inflammatory diseases
2013-10-16

Abstract Cytokines are key mediators of the development and homeostasis of haematopoietic cells, critical for host defense, but also for the development of autoimmune and inflammatory diseases such as psoriasis or rheumatoid arthritis ( RA ). Blocking cytokines activity by interfering with the ligand–receptor association has been successfully employed to treat several immune disorders. A subgroup of cytokines signals through receptors requiring the association with a family of cytoplasmic protein tyrosine kinases known as Janus kinases (Jaks). Jaks have recently gained significant attention as therapeutic targets in inflammation and autoimmunity, and several Jak inhibitory small molecules have been developed. The first two Jak inhibitors, tofacitinib and ruxolitinib, have been approved for the treatment of RA and primary myelofibrosis, respectively. Efficacy and safety data suggest that some of these oral Jak inhibitors as well as their topical formulations may soon enter the daily clinical practice for treating patients with psoriasis, lupus erythematosus or other inflammatory skin diseases. While biologics typically target one single cytokine, these new immunomodulators can inhibit signals from multiple cytokines intra‐cellularly and therefore could be useful when other therapies are ineffective. Thus, Jak inhibitors may replace some traditional immunosuppressive agents and help patients not responding to previous therapies.
Dealing With Omitted and Not-Reached Items in Competence Tests
2013-10-16

Data from competence tests usually show a number of missing responses on test items due to both omitted and not-reached items. Different approaches for dealing with missing responses exist, and there are no clear guidelines on which of those to use. While classical approaches rely on an ignorable missing data mechanism, the most recently developed model-based approaches account for nonignorable missing responses. Model-based approaches include the missing propensity in the measurement model. Although these models are very promising, the assumptions made in these models have not yet been tested for plausibility in empirical data. Furthermore, studies investigating the performance of different approaches have only focused on one kind of missing response at once. In this study, we investigated the performance of classical and model-based approaches in empirical data, accounting for different kinds of missing responses simultaneously. We confirmed the existence of a unidimensional tendency to omit items. Indicating nonignorability of the missing mechanism, missing tendency due to both omitted and not-reached items correlated with ability. However, results on parameter estimation showed that ignoring missing responses was sufficient to account for missing responses, and that the missing propensity was not needed in the model. The results from the empirical study were corroborated in a complete case simulation.
Erosion of dust aggregates
2013-10-16

Aims: The aim of this work is to gain a deeper insight into how much\\ndifferent aggregate types are affected by erosion. Especially, it is important\\nto study the influence of the velocity of the impacting projectiles. We also\\nwant to provide models for dust growth in protoplanetary disks with simple\\nrecipes to account for erosion effects.\\n Methods: To study the erosion of dust aggregates we employed a molecular\\ndynamics approach that features a detailed micro-physical model of the\\ninteraction of spherical grains. For the first time, the model has been\\nextended by introducing a new visco-elastic damping force which requires a\\nproper calibration. Afterwards, different sample generation methods were used\\nto cover a wide range of aggregate types.\\n Results: The visco-elastic damping force introduced in this work turns out to\\nbe crucial to reproduce results obtained from laboratory experiments. After\\nproper calibration, we find that erosion occurs for impact velocities of 5 m/s\\nand above. Though fractal aggregates as formed during the first growth phase\\nare most susceptible to erosion, we observe erosion of aggregates with rather\\ncompact surfaces as well.\\n Conclusions: We find that bombarding a larger target aggregate with small\\nprojectiles results in erosion for impact velocities as low as a few m/s. More\\ncompact aggregates suffer less from erosion. With increasing projectile size\\nthe transition from accretion to erosion is shifted to higher velocities. This\\nallows larger bodies to grow through high velocity collisions with smaller\\naggregates.\\n
Identification of Semicarbazones, Thiosemicarbazones and Triazine Nitriles as Inhibitors of Leishmania mexicana Cysteine Protease CPB
2013-10-16

Cysteine proteases of the papain superfamily are present in nearly all eukaryotes. They play pivotal roles in the biology of parasites and inhibition of cysteine proteases is emerging as an important strategy to combat parasitic diseases such as sleeping sickness, Chagas' disease and leishmaniasis. Homology modeling of the mature Leishmania mexicana cysteine protease CPB2.8 suggested that it differs significantly from bovine cathepsin B and thus could be a good drug target. High throughput screening of a compound library against this enzyme and bovine cathepsin B in a counter assay identified four novel inhibitors, containing the warhead-types semicarbazone, thiosemicarbazone and triazine nitrile, that can be used as leads for antiparasite drug design. Covalent docking experiments confirmed the SARs of these lead compounds in an effort to understand the structural elements required for specific inhibition of CPB2.8. This study has provided starting points for the design of selective and highly potent inhibitors of L. mexicana cysteine protease CPB that may also have useful efficacy against other important cysteine proteases.
Methylaluminum‐Supported Rare‐Earth‐Metal Dihydrides
2013-10-16

The super-bulky hydrotris(3-tert-butyl-5-methylpyrazolyl)borato ligand (TptBu,Me) allows the isolation of the monolanthanide complexes [TptBu,MeLn{(μ-H)AlMe3}2] (Ln=Y, Lu; see structure), which can be transformed into discrete non-agglomerated imide complexes [TptBu,MeLn{(μ-NC6H3Me2-2,6)(μ-H)AlMe2}] by reaction with dimethylaniline. Ln hydrido bonding is corroborated by 1H NMR spectroscopy through 1H–89Y coupling and 89Y DEPT45 NMR spectroscopy. As a service to our authors and readers, this journal provides supporting information supplied by the authors. Such materials are peer reviewed and may be re-organized for online delivery, but are not copy-edited or typeset. Technical support issues arising from supporting information (other than missing files) should be addressed to the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
CFC Legislation, Passive Assets and the Impact of the ECJ's Cadbury-Schweppes Decision
2013-10-16

In its Cadbury-Schweppes decision of 12 September 2006 (C-196/04), the ECJ decided that the UK CFC rules, which were implemented to subject low taxed passive income of foreign affiliates to UK corporate tax, implied an infringement of the freedom of establishment. Consequently, many EU countries including Germany changed their legislation. The paper discusses to which extent the ECJ ruling has impacted on the allocation of passive assets in German multinationals. Using firm level data we find evidence for an increased preference for low-tax European countries compared to non-European countries.
Spectral and temporal properties of the supergiant fast X-ray transient IGR J18483–0311 observed by INTEGRAL
2013-10-16

IGR J18483-0311 is a supergiant fast X-ray transient whose compact object is\\nlocated in a wide (18.5 d) and eccentric (e~0.4) orbit, which shows sporadic\\noutbursts that reach X-ray luminosities of ~1e36 erg/s. We investigated the\\ntiming properties of IGR J18483-0311 and studied the spectra during bright\\noutbursts by fitting physical models based on thermal and bulk Comptonization\\nprocesses for accreting compact objects. We analysed archival INTEGRAL data\\ncollected in the period 2003-2010, focusing on the observations with IGR\\nJ18483-0311 in outburst. We searched for pulsations in the INTEGRAL light\\ncurves of each outburst. We took advantage of the broadband observing\\ncapability of INTEGRAL for the spectral analysis. We observed 15 outbursts,\\nseven of which we report here for the first time. This data analysis almost\\ndoubles the statistics of flares of this binary system detected by INTEGRAL. A\\nrefined timing analysis did not reveal a significant periodicity in the\\nINTEGRAL observation where a ~21s pulsation was previously detected. Neither\\ndid we find evidence for pulsations in the X-ray light curve of an archival\\nXMM-Newton observation of IGR J18483-0311. In the light of these results the\\nnature of the compact object in IGR J18483-0311 is unclear. The broadband X-ray\\nspectrum of IGR J18483-0311 in outburst is well fitted by a thermal and bulk\\nComptonization model of blackbody seed photons by the infalling material in the\\naccretion column of a neutron star. We also obtained a new measurement of the\\norbital period using the Swift/BAT light curve.\\n
Correction: LPS Structure and PhoQ Activity Are Important for Salmonella Typhimurium Virulence in the Galleria mellonella Infection Model
2013-10-16

The larvae of the wax moth, Galleria mellonella, have been used experimentally to host a range of bacterial and fungal pathogens.In this study we evaluated the suitability of G. mellonella as an alternative animal model of Salmonella infection.Using a range of inoculum doses we established that the LD 50 of Salmonella Typhimurium strain NCTC 12023 was 3.6 × 10 3 bacteria per larva.Further, a set of isogenic mutant strains depleted of known virulence factors was tested to identify determinants essential for S. Typhimurium pathogenesis.Mutants depleted of one or both of the type III secretion systems encoded by Salmonella Pathogenicity Islands 1 and 2 showed no virulence defect.In contrast, we observed reduced pathogenic potential of a phoQ mutant indicating an important role for the PhoPQ two-component signal transduction system.Lipopolysaccharide (LPS) structure was also shown to influence Salmonella virulence in G. mellonella.A waaL (rfaL) mutant, which lacks the entire O-antigen (OAg), was virtually avirulent, while a wzz ST /wzz fepE double mutant expressing only a very short OAg was highly attenuated for virulence.Furthermore, shortly after infection both LPS mutant strains showed decreased replication when compared to the wild type in a flow cytometry-based competitive index assay.In this study we successfully established a G. mellonella model of S. Typhimurium infection.By identifying PhoQ and LPS OAg length as key determinants of virulence in the wax moth larvae we proved that there is an overlap between this and other animal model systems, thus confirming that the G. mellonella infection model is suitable for assessing aspects of Salmonella virulence function.