julilili42/papers huggingface dataset:
Phenol‐soluble modulin α induces G2/M phase transition delay in eukaryotic HeLa cells
2015-02-03

ABSTRACT Staphylococcus aureus is a gram‐positive bacterium responsible for a wide range of infections. Host cell cycle alteration is a sophisticated mechanism used by pathogens to hijack the defense functions of host cells. We previously demonstrated that S. aureus MW2 (USA400) bacteria induced a G2/M phase transition delay in HeLa cells. We demonstrate here that this activity is triggered by culture supernatant compounds. Using size exclusion chromatography of the MW2 supernatant, followed by mass spectroscopy analysis of corresponding peaks, we identified phenol‐soluble modulin α (PSMα) peptides as the likely candidates for this effect. Indeed, synthetic PSMα 1 and PSMα3 caused a G2/M phase transition delay. The implication of PSMα in cell cycle alteration was confirmed by comparison of S. aureus Los Angeles County clone (LAC) wild‐type with the isogenic mutant LACΔpsmα , which lacks the psmα operon encoding PSMα1‐4. PSMα‐induced G2/M transition delay correlated with a decrease in the defensin genes expression suggesting a diminution of antibacterial functions of epithelial cells. By testing the supernatant of S. aureus human clinical isolates, we found that the degree of G2/M phase transition delay correlated with PSMα1 production. We show that PSMs secreted by S. aureus alter the host cell cycle, revealing a newly identified mechanism for fostering an infection.—Deplanche, M., Filho. R. A. E.‐A., Alekseeva, L., Ladier, E., Jardin, J., Henry, G., Azevedo, V., Miyoshi, A., Beraud, L., Laurent, F., Lina, G., Vandenesch, F., Steghens, J.‐P., Le Loir, Y., Otto, M., Götz, F., Berkova, N. Phenol‐soluble modulin α induces G2/M phase transition delay in eukaryotic HeLa cells. FASEB J. 29, 1950‐1959 (2015). www.fasebj.org
TLR Signaling-induced CD103-expressing Cells Protect Against Intestinal Inflammation
2015-02-03

The TLR-mediated amelioration of disease, the increase in CD103-expressing cells, and the beneficial function of TLR signal induction in hematopoietic cells indicate that the increased expression of TLRs in patients with inflammatory bowel disease might result in counterregulation of the host and serve in preventing disease.
On the relationship between negative affective priming and prefrontal cognitive control mechanisms
2015-02-03

Although several studies have examined inhibition of affective stimuli, valence-dependent cognitive control effects remain poorly understood. Behavioural and functional imaging (functional magnetic resonance imaging) data were collected from 17 healthy participants to examine neural correlates of the Negative Affective Priming (NAP) task. We created relative ratio scores considering the reaction times of prime trials in order to assess the amount of interference after the presentation of negative and positive distracter words. Behavioural results showed an attenuated NAP effect for negative distracters compared to neutral stimuli. Furthermore, priming negative distracters generated more interference by reacting to the probe target than positive distracters. Neuroimaging data revealed a stronger prefrontal activation during negative NAP trials compared to positive NAP and neutral control trials, which was reflected in a heightened activation of superior and middle frontal gyrus as well as parietal cortex. The findings show the impact of negative distracters on prefrontal response, contributing to the understanding of NAP effects in healthy subjects.
Next-to-leading order calculation for jets defined by a maximized jet function
2015-02-03

We present a next-to-leading order QCD calculation for the single-inclusive production of collimated jets at hadron colliders, when the jet is defined by maximizing a suitable jet function that depends on the momenta of final-state particles in the event. A jet algorithm of this type was initially proposed by Georgi and subsequently further developed into the class of "J(ET) algorithms." Our calculation establishes the infrared safety of the algorithms at this perturbative order. We derive analytical results for the relevant partonic cross sections. We discuss similarities and differences with respect to jets defined by cone or (anti-) k(t) algorithms and present numerical results for the Tevatron and the LHC.
Management Intensity Modifies Plant Diversity Effects on N Yield and Mineral N in Soil
2015-02-03

The effect of species loss on productivity were of comparable magnitude to changes in agricultural management. However, not only productivity but also the N cycle is relevant for food production comprising beneficial as well as threatening effects of agricultural management. Our objectives were to test whether grassland management (mowing two or four times a year; 0, 100, or 200 kg N/ha) (i) modifies N yield or soil Nmin concentrations and changes (ii) the effect of plant functional groups (legumes, grasses, non-leguminous small and tall herbs) on N yield or soil Nmin concentrations or (iii) the relationships between plant diversity and N yield or soil Nmin concentrations. We observed highest productivity under moderate management intensity which can be attributed to the growth-stimulating fertilizer effect associated with enough time for regrowth. With increasing management intensity, the positive effect of the presence of legumes on N yield and soil Nmin concentrations disappeared. Plant species richness was positively related to N yield with the most pronounced effect in the highly fertilized and frequently mown treatment. In the control (mown twice a year, non-fertilized), competition for nutrients very likely underlie plant species richness effects. Under higher management intensity, a combination of competition for light and adaption to mowing frequency seemed to be responsible for plant species richness effects. The concurrence of highest N yield in high-diversity mixtures under most intensive management indicates that some plant species must have more than compensated for the N uptake of non-adapted species that did not survive frequent mowing, highlighting the value of plant diversity as an insurance against anthropogenic disturbances including management measures.
Radiative Decay of Light Leptonic Magnetic Monopoles in an Extended Standard Model
2015-02-03

Abstract Based on the theory of Lochak and the experiments of Urutskoiev, it has been suggested by Urutskoiev that, during discharges in water (fluids), light leptonic magnetic monopoles can be created in order to understand accidents in power plants. In previous papers, it was demonstrated that these processes could and should be described within the effective electroweak sector of an extended Standard Model with symmetry breaking where, according to Lochak, the magnetic monopoles are considered as excited neutrinos. For massive excited neutrinos, no conservation of magnetic charge does exist, i.e., these particles can decay. The radiative decay is due to the transmutation of an excited neutrino into an ordinary neutrino. Details of the decay process are discussed, and it is shown that massive excited neutrinos are Majorana fermions that, owing to their magnetic charge, participate in electromagnetic processes, although this charge is not conserved. Numerical estimates for transition rates and emitted frequencies are given.
Can Internet Search Queries Help to Predict Stock Market Volatility?
2015-02-04

Abstract We study the dynamics of stock market volatility and retail investors' attention to the stock market. The latter is measured by internet search queries related to the leading stock market index. We find a strong co‐movement of the Dow Jones' realised volatility and the volume of search queries for its name. Furthermore, search queries Granger‐cause volatility: a heightened number of searches today is followed by an increase in volatility tomorrow. Including search queries in autoregressive models of realised volatility improves volatility forecasts in‐sample, out‐of‐sample, for different forecasting horizons, and in particular in high‐volatility phases.
Parasitic plants of the genus Cuscuta and their interaction with susceptible and resistant host plants
2015-02-04

By comparison with plant-microbe interaction, little is known about the interaction of parasitic plants with their hosts. Plants of the genus Cuscuta belong to the family of Cuscutaceae and comprise about 200 species, all of which live as stem holoparasites on other plants. Cuscuta spp. possess no roots nor fully expanded leaves and the vegetative portion appears to be a stem only. The parasite winds around plants and penetrates the host stems via haustoria, forming direct connections to the vascular bundles of their hosts to withdraw water, carbohydrates, and other solutes. Besides susceptible hosts, a few plants exist that exhibit an active resistance against infestation by Cuscuta spp. For example, cultivated tomato (Solanum lycopersicum) fends off Cuscuta reflexa by means of a hypersensitive-type response occurring in the early penetration phase. This report on the plant-plant dialog between Cuscuta spp. and its host plants focuses on the incompatible interaction of C. reflexa with tomato.
Fine-mapping identifies two additional breast cancer susceptibility loci at 9q31.2
2015-02-04

We recently identified a novel susceptibility variant, rs865686, for estrogen-receptor positive breast cancer at 9q31.2. Here, we report a fine-mapping analysis of the 9q31.2 susceptibility locus using 43 160 cases and 42 600 controls of European ancestry ascertained from 52 studies and a further 5795 cases and 6624 controls of Asian ancestry from nine studies. Single nucleotide polymorphism (SNP) rs676256 was most strongly associated with risk in Europeans (odds ratios [OR] = 0.90 [0.88-0.92]; P-value = 1.58 × 10(-25)). This SNP is one of a cluster of highly correlated variants, including rs865686, that spans ∼14.5 kb. We identified two additional independent association signals demarcated by SNPs rs10816625 (OR = 1.12 [1.08-1.17]; P-value = 7.89 × 10(-09)) and rs13294895 (OR = 1.09 [1.06-1.12]; P-value = 2.97 × 10(-11)). SNP rs10816625, but not rs13294895, was also associated with risk of breast cancer in Asian individuals (OR = 1.12 [1.06-1.18]; P-value = 2.77 × 10(-05)). Functional genomic annotation using data derived from breast cancer cell-line models indicates that these SNPs localise to putative enhancer elements that bind known drivers of hormone-dependent breast cancer, including ER-α, FOXA1 and GATA-3. In vitro analyses indicate that rs10816625 and rs13294895 have allele-specific effects on enhancer activity and suggest chromatin interactions with the KLF4 gene locus. These results demonstrate the power of dense genotyping in large studies to identify independent susceptibility variants. Analysis of associations using subjects with different ancestry, combined with bioinformatic and genomic characterisation, can provide strong evidence for the likely causative alleles and their functional basis.
Kinase analysis in alcoholic hepatitis identifies p90RSK as a potential mediator of liver fibrogenesis
2015-02-04

p90RSK is upregulated in patients with chronic liver disease and mediates liver fibrogenesis in vivo and in vitro. These results suggest that the p90RSK pathway could be a new therapeutic approach for liver diseases characterised by advanced fibrosis.
On a conjecture of Lovász on circle-representations of simple 4-regular planar graphs
2015-02-04

Lovasz conjectured that every connected 4-regular planar graph admits a realization as a system of circles , i.e., it can be drawn on the plane utilizing a set of circles, such that the vertices of correspond to the intersection and touching points of the circles and the edges of are the arc segments among pairs of intersection and touching points of the circles. In this paper, we settle this conjecture. In particular, (a) we first provide tight upper and lower bounds on the number of circles needed in a realization of any simple 4-regular planar graph, (b) we affirmatively answer Lovasz's conjecture, if is 3-connected, and, (c) we demonstrate an infinite class of simple connected 4-regular planar graphs which are not 3-connected (i.e., either simply connected or biconnected) and do not admit realizations as a system of circles.
Coupled isotopes of plant wax and hemicellulose markers record information on relative humidity and isotopic composition of precipitation
2015-02-04

Abstract. The δ2H isotopic composition of leaf waxes is used increasingly for paleohydrological and -climate reconstructions. However, it is challenging to disentangle past changes in the isotopic composition of precipitation and changes in evapotranspirative enrichment of leaf water. We analyzed δ2H on n-alkanes and fatty acids in topsoils along a climate transect in Argentina, for which we had previously measured δ18O on plant-derived sugars. Our results indicate that leaf wax biomarker δ2H values (δ2Hlipids) primarily reflect δ2Hsource water (precipitation), but are modulated by evapotranspirative enrichment. A mechanistic model is able to produce the main trends in δ2Hlipids along the transect, but seems to slightly underestimate evapotranspirative enrichment in arid regions and overestimate it in grass-dominated ecosystems. Furthermore, the (i) coupling of the δ2Hlipid and δ18Osugar biomarker results and (ii) application of biosynthetic fractionation factors allows calculating the δ2H-δ18O isotopic composition of leaf water along the transect. This also yields the deuterium excess (d excess) of leaf water, which mainly reflects evapotranspirative enrichment, and can be used to model relative air humidity (RH). The high correlation of modeled (reconstructed based on biomarker results) and measured RH, as well as the good agreement between modeled and actual δ2H and δ18O of precipitation along the transect lends support to the coupled δ2Hlipid and δ18Osugar biomarker approach for future paleoclimate research.
Evaluating the Potential of Halogen Bonding in Molecular Design: Automated Scaffold Decoration Using the New Scoring Function XBScore
2015-02-05

We present a QM-derived empirical scoring function for the interaction between aromatic halogenated ligands and the carbonyl oxygen atom of the protein backbone. Applying this scoring function, we developed an algorithm that evaluates the potential of protein-bound ligands to form favorable halogen-bonding contacts upon scaffold decoration with chlorine, bromine, or iodine. Full recovery of all existing halogen bonds in the PDB involving the protein backbone was achieved with our protocol. Interestingly, the potential for introducing halogen bonds through scaffold decoration of unsubstituted aromatic carbon atoms appears to easily match the number of previously known halogen bonds. Our approach can thus be used as a blueprint for integration of halogen bonding into general empirical scoring functions, which at present ignore this interaction. Most importantly, we were able to identify a substantial number of protein-ligand complexes where the benefits and challenges of introducing a halogen bond by molecular design can be studied experimentally.
HIV Coinfection Enhances Complement Activation During Sepsis
2015-02-05

HIV activates the complement system, predominantly via the classical pathway, and causes increased C4 activation and consumption during sepsis. HIV-induced complement activation may contribute to tissue injury during chronic infection and acute intercurrent bacterial infections.
Nickel‐Triad Complexes of a Side‐on Coordinating Distannene
2015-02-05

Abstract NHC adducts of the stannylene Trip 2 Sn (Trip=2,4,6‐triisopropylphenyl) were reacted with zero‐valent Ni, Pd, and Pt precursor complexes to cleanly yield the respective metal complexes featuring a three‐membered ring moiety Sn‐Sn‐M along with carbene transfer onto the metal and complete substitution of the starting ligands. Thus the easily accessible NHC adducts to stannylenes are shown to be valuable precursors for transition‐metal complexes with an unexpected SnSn bond. The complexes have been studied by X‐ray diffraction and NMR spectroscopy as well as DFT calculations. The compounds featuring the structural motif of a distannametallacycle comprised of a [(NHC) 2 M 0 ] fragment and Sn 2 Trip 4 represent rare higher congeners of the well‐known olefin complexes. DFT calculations indicate the presence of a π‐type Sn–Sn interaction in these first examples for acyclic distannenes symmetrically coordinating to a zero‐valent transition metal.
Co-detection of Panton-Valentine leukocidin encoding genes and cotrimoxazole resistance in Staphylococcus aureus in Gabon: implications for HIV-patientsâ€™ care
2015-02-05

Patients infected with the human immunodeficiency virus (HIV) are frequently exposed to antimicrobial agents. This might have an impact on the resistance profile, genetic background and virulence factors of colonizing Staphylococcus aureus. Sub-Saharan Africa is considered to be endemic for Panton-Valentine leukocidin (PVL) positive S. aureus which can be associated with skin and soft tissue infections (SSTI). We compared S. aureus from nasal and pharyngeal swabs from HIV patients (n = 141) and healthy controls (n = 206) in Gabon in 2013, and analyzed determinants of colonization with PVL positive isolates in a cross-sectional study. S. aureus isolates were screened for the presence of selected virulence factors (incl. PVL) and were subjected to antimicrobial susceptibility testing and genotyping. In HIV patients, S. aureus was more frequently detected (36.9 vs. 31.6%) and the isolates were more frequently PVL positive than in healthy controls (42.1 vs. 23.2%). The presence of PVL was associated with cotrimoxazole resistance (OR = 25.1, p < 0.001) and the use of cotrimoxazole was a risk factor for colonization with PVL positive isolates (OR = 2.5, p = 0.06). PVL positive isolates were associated with the multilocus sequence types ST15 (OR = 5.6, p < 0.001) and ST152 (OR = 62.1, p < 0.001). Participants colonized with PVL positive isolates reported more frequently SSTI in the past compared to carriers of PVL negative isolates (OR = 2.7, p = 0.01). In conclusion, the novelty of our study is that cotrimoxazole might increase the risk of SSTI in regions where cotrimoxazole resistance is high and associated with PVL. This finding needs to be confirmed in prospective studies.
Does your body count? Embodied influences on the preferred counting direction of preschoolers
2015-02-06

Many studies confirm that preschoolers from left-to-right reading societies count from left to right, which reflects the cultural direction of their spatial-numerical associations (SNAs). Other factors, not directly related to cultural experience, have not yet been systematically examined as potential determinants of counting direction in preschool children. In this study, we test one such determinant, i.e. whether and how counting direction is related to body-centred reference frames, such as a preferred hand in different spatial-motoric settings. We first asked preschoolers to count spontaneously. Then, we asked them to use a particular hand to count objects presented close to or far away from their bodies. An overall left-to-right counting dominance was replicated, but it was modulated by a counting hand in both tasks: Children preferred to start counting from an object ipsilateral to the hand used. This pattern increased when stimuli were in a position close to the body. We conclude that early counting preferences of preliterate children are embodied. The SNAs which were assessed are not only related to culture but also to situated individual bodily reference frames.
Characterization of the Gut Microbiota of Papua New Guineans Using Reverse Transcription Quantitative PCR
2015-02-06

&lt;div&gt;&lt;p&gt;There has been considerable interest in composition of gut microbiota in recent years, leading to a better understanding of the role the gut microbiota plays in health and disease. Most studies have been limited in their geographical and socioeconomic diversity to high-income settings, and have been conducted using small sample sizes. To date, few analyses have been conducted in low-income settings, where a better understanding of the gut microbiome could lead to the greatest return in terms of health benefits. Here, we have used quantitative real-time polymerase chain reaction targeting dominant and sub-dominant groups of microorganisms associated with human gut microbiome in 115 people living a subsistence lifestyle in rural areas of Papua New Guinea. Quantification of &lt;i&gt;Clostridium coccoides&lt;/i&gt; group, &lt;i&gt;C. leptum&lt;/i&gt; subgroup, &lt;i&gt;C. perfringens&lt;/i&gt;, &lt;i&gt;Bacteroides fragilis&lt;/i&gt; group, &lt;i&gt;Bifidobacterium&lt;/i&gt;, &lt;i&gt;Atopobium&lt;/i&gt; cluster, &lt;i&gt;Prevotella&lt;/i&gt;, Enterobacteriaceae, &lt;i&gt;Enterococcus&lt;/i&gt;, &lt;i&gt;Staphylococcus&lt;/i&gt;, and &lt;i&gt;Lactobacillus&lt;/i&gt; spp. was conducted. Principle coordinates analysis (PCoA) revealed two dimensions with &lt;i&gt;Prevotella&lt;/i&gt;, clostridia, &lt;i&gt;Atopobium&lt;/i&gt;, Enterobacteriaceae, &lt;i&gt;Enterococcus&lt;/i&gt; and &lt;i&gt;Staphylococcus&lt;/i&gt; grouping in one dimension, while &lt;i&gt;B. fragilis&lt;/i&gt;, &lt;i&gt;Bifidobacterium&lt;/i&gt; and &lt;i&gt;Lactobacillus&lt;/i&gt; grouping in the second dimension. Highland people had higher numbers of most groups of bacteria detected, and this is likely a key factor for the differences revealed by PCoA between highland and lowland study participants. Age and sex were not major determinants in microbial population composition. The study demonstrates a gut microbial composition with some similarities to those observed in other low-income settings where traditional diets are consumed, which have previously been suggested to favor energy extraction from a carbohydrate rich diet.&lt;/p&gt;&lt;/div&gt;
Synthesis and Photoluminescence Properties of the Red‐Emitting Phosphor Mg3(BN2)N Doped with Eu2+
2015-02-06

Abstract Mg 3 (BN 2 )N was prepared by solid state metathesis reactions and several europium (Eu 2+ ) doped samples were prepared to discover novel red‐emitting photoluminescent (PL) materials. It turned out that the undoped and doped samples showed very broad deep‐red photoluminescence ranging from about 500 nm into the near infrared. Due to the similar spectra of the undoped and doped samples and unusually high FWHM values of about 5780 cm –1 we conclude that the luminescence process originates from defect sites. This was confirmed by decay measurements which show that the decay constants for all samples were in the range of several milliseconds.
Mitochondrial Genomes of Giant Deers Suggest their Late Survival in Central Europe
2015-02-06

The giant deer Megaloceros giganteus is among the most fascinating Late Pleistocene Eurasian megafauna that became extinct at the end of the last ice age. Important questions persist regarding its phylogenetic relationship to contemporary taxa and the reasons for its extinction. We analyzed two large ancient cervid bone fragments recovered from cave sites in the Swabian Jura (Baden-Württemberg, Germany) dated to 12,000 years ago. Using hybridization capture in combination with next generation sequencing, we were able to reconstruct nearly complete mitochondrial genomes from both specimens. Both mtDNAs cluster phylogenetically with fallow deer and show high similarity to previously studied partial Megaloceros giganteus DNA from Kamyshlov in western Siberia and Killavullen in Ireland. The unexpected presence of Megaloceros giganteus in Southern Germany after the Ice Age suggests a later survival in Central Europe than previously proposed. The complete mtDNAs provide strong phylogenetic support for a Dama-Megaloceros clade. Furthermore, isotope analyses support an increasing competition between giant deer, red deer, and reindeer after the Last Glacial Maximum, which might have contributed to the extinction of Megaloceros in Central Europe.