julilili42/papers huggingface dataset:
Numerical analysis of parabolic problems with dynamic boundary conditions
2016-05-22

Space and time discretizations of parabolic differential equations with dynamic boundary conditions are studied in a weak formulation that fits into the standard abstract formulation of parabolic problems, just that the usual L^2(Ω) inner product is replaced by an L^2(Ω) \\oplus L^2(Γ) inner product. The class of parabolic equations considered includes linear problems with time- and space-dependent coefficients and semilinear problems such as reaction-diffusion on a surface coupled to diffusion in the bulk. The spatial discretization by finite elements is studied in the proposed framework, with particular attention to the error analysis of the Ritz map for the elliptic bilinear form in relation to the inner product, both of which contain boundary integrals. The error analysis is done for both polygonal and smooth domains. We further consider mass lumping, which enables us to use exponential integrators and bulk-surface splitting for time integration.
An essential role for the baseplate protein Gp45 in phage adsorption to Staphylococcus aureus
2016-05-23

Abstract Despite the importance of phages in driving horizontal gene transfer (HGT) among pathogenic bacteria, the underlying molecular mechanisms mediating phage adsorption to S. aureus are still unclear. Phage φ11 is a siphovirus with a high transducing efficiency. Here, we show that the tail protein Gp45 localized within the φ11 baseplate. Phage φ11 was efficiently neutralized by anti-Gp45 serum and its adsorption to host cells was inhibited by recombinant Gp45 in a dose-dependent manner. Flow cytometry analysis demonstrated that biotin-labelled Gp45 efficiently stained the wild-type S. aureus cell but not the double knockout mutant Δ tarM/S , which lacks both α- and β-O-GlcNAc residues on its wall teichoic acids (WTAs). Additionally, adsorption assays indicate that GlcNAc residues on WTAs and O-acetyl groups at the 6-position of muramic acid residues in peptidoglycan are essential components of the φ11 receptor. The elucidation of Gp45-involved molecular interactions not only broadens our understanding of siphovirus-mediated HGT, but also lays the groundwork for the development of sensitive affinity-based diagnostics and therapeutics for S. aureus infection.
Spermidine, but not spermine, is essential for pigment pattern formation in zebrafish
2016-05-23

ABSTRACT Polyamines are small poly-cations essential for all cellular life. The main polyamines present in metazoans are putrescine, spermidine and spermine. Their exact functions are still largely unclear; however, they are involved in a wide variety of processes affecting cell growth, proliferation, apoptosis and aging. Here we identify idefix, a mutation in the zebrafish gene encoding the enzyme spermidine synthase, leading to a severe reduction in spermidine levels as shown by capillary electrophoresis-mass spectrometry. We show that spermidine, but not spermine, is essential for early development, organogenesis and colour pattern formation. Whereas in other vertebrates spermidine deficiency leads to very early embryonic lethality, maternally provided spermidine synthase in zebrafish is sufficient to rescue the early developmental defects. This allows us to uncouple them from events occurring later during colour patterning. Factors involved in the cellular interactions essential for colour patterning, likely targets for spermidine, are the gap junction components Cx41.8, Cx39.4, and Kir7.1, an inwardly rectifying potassium channel, all known to be regulated by polyamines. Thus, zebrafish provide a vertebrate model to study the in vivo effects of polyamines.
TLR1 Variant H305L Associated with Protection from Pulmonary Tuberculosis
2016-05-23

Toll like receptors (TLR) are key elements of the innate immune response and involved in the recognition of pathogens. To test common and rare TLR variants involved in susceptibility or resistance to infection with Mycobacterium tuberculosis we screened the exons of the genes encoding TLR 1, 2, 4, and the adaptor molecule TIRAP in more than 4500 tuberculosis (TB) cases and controls from Ghana. The analysis yielded 109 variants with possible functional impact, including 101 non-synonymous variants, three stop-variants, and five indels. Association analyses yielded a significant result for the TLR1 variant rs3923647, conferring strong protection against TB (Odds ratio [OR] 0.21, CI confidence interval [CI] 0.05-0.6, Pnominal 1 x 10-3) when applying a recessive model of inheritance. Replication analyses with an additional 3370 Ghanaian cases and control samples, and with data from a recent TB study of 533 African-Americans confirmed the protective effect and resulted in a combined OR of 0.19, with a nominal P value of 2.2 x 10-5, and a corrected P value of 4.1 x 10-4. The SNP is located near the binding pocket of TLR1 and causes an amino acid exchange from histidine to leucine at position 305. The observed effect may, therefore, be attributable to structural changes in the recognition site of the TLR1 molecule, allowing to bind those mycobacterial ligands which preferentially may induce a protective immune response. This is supported by the analysis of BCG-stimulated peripheral blood mononuclear cells, showing increased induction of the proinflammatory cytokine IFN-γ in carriers of the mutant TLR1 rs3923647 TT genotype, compared to the IFN-γ levels of individuals with the AT and AA genotypes.
Plants adapted to warmer climate do not outperform regional plants during a natural heat wave
2016-05-23

Abstract With ongoing climate change, many plant species may not be able to adapt rapidly enough, and some conservation experts are therefore considering to translocate warm‐adapted ecotypes to mitigate effects of climate warming. Although this strategy, called assisted migration, is intuitively plausible, most of the support comes from models, whereas experimental evidence is so far scarce. Here we present data on multiple ecotypes of six grassland species, which we grew in four common gardens in Germany during a natural heat wave, with temperatures 1.4–2.0°C higher than the long‐term means. In each garden we compared the performance of regional ecotypes with plants from a locality with long‐term summer temperatures similar to what the plants experienced during the summer heat wave. We found no difference in performance between regional and warm‐adapted plants in four of the six species. In two species, regional ecotypes even outperformed warm‐adapted plants, despite elevated temperatures, which suggests that translocating warm‐adapted ecotypes may not only lack the desired effect of increased performance but may even have negative consequences. Even if adaptation to climate plays a role, other factors involved in local adaptation, such as biotic interactions, may override it. Based on our results, we cannot advocate assisted migration as a universal tool to enhance the performance of local plant populations and communities during climate change.
Magnetic Anisotropy in Functionalized Bipyridyl Cryptates
2016-05-23

The magnetic properties of molecular lanthanoid complexes are very important for a variety of scientific and technological applications, with the unique magnetic anisotropy being one of the most important features. In this context, a very rigid tris(bipyridine) cryptand was synthesized with a primary amine functionality for future bioconjugation. The magnetic anisotropy was investigated for the corresponding paramagnetic ytterbium cryptate. With the use of a combination of density functional theory calculations and lanthanoid-induced NMR shift analysis, the magnetic susceptibility tensor was determined and compared to the unfunctionalized cryptate analogue. The size and orientation of the axial and rhombic tensor components show remarkably great resilience toward the decrease of local symmetry around the metal and anion exchange in the inner coordination sphere. In addition, the functionalized ytterbium cryptate also exhibits efficient near-IR luminescence.
Dibaryons at COSY
2016-05-23

Experiments at the Juelich Cooler Synchrotron (COSY) have now found\\ncompelling evidence for a new resonant state in the two-baryon system with mass\\n2380 MeV and a width of 70 MeV. The structure, containing six valence quarks,\\nconstitutes a so-called dibaryon, either a hexaquark or a hadronic molecule.\\nThe present knowledge about the dibaryon as well as other implications and\\npossible future experiments are discussed.\\n
Bacterial adhesion to suture material in a contaminated wound model: Comparison of monofilament, braided, and barbed sutures
2016-05-24

ABSTRACT Contaminated suture material plays an important role in the physiopathology of surgical site infections. Recently, suture material has been developed characterized by barbs projecting from a monofilament base. Claimed advantages for barbed sutures are a shortened wound closure time and reduced maximum wound tension. It has also been suggested that these sutures would be advantageous microbiologically. The aim of this study was to test the microbiological characteristics of the barbed Quill in comparison to the monofilament Ethilon II and the braided sutures Vicryl and triclosan‐coated Vicryl Plus. In our study, sutures were cultivated on color‐change agar with Staphylococcus aureus , Staphylococcus epidermidis , Enterococcus faecium , Escherichia coli , and Pseudomonas aeruginosa and the halo size was measured. In a second study arm with longer cultivation bacterial growth was followed by antibiotic treatment. Ethilon II and Quill showed good comparable results, whereas large halos were found around Vicryl. Vicryl Plus results depended on triclosan sensitivity. After longer bacterial cultivation and antibiotic treatment, halos were up to 3.6 times smaller on Quill than on Vicryl ( p &lt; 0.001), but 1.4 times larger than on Ethilon II ( p &lt; 0.001) regarding S. aureus . Confocal microscopy analysis showed bacterial colonization between the braided filaments on Vicryl and beneath the barbs on Quill. From a microbiological perspective, barbed sutures can be recommended in aseptic surgery, but should only be used carefully in septic surgery. © 2016 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 35:925–933, 2017.
Circulating Omentin as a Novel Biomarker for Colorectal Cancer Risk: Data from the EPIC–Potsdam Cohort Study
2016-05-24

Abstract Omentin is a novel biomarker shown to exert metabolic, inflammatory, and immune-related properties and thereby could be implicated in the risk of colorectal cancer. So far, the association between omentin and colorectal cancer risk has not been evaluated in prospective cohort studies. We investigated the association between prediagnostic plasma omentin concentrations and risk of colorectal cancer in a case–cohort comprising 251 incident colorectal cancer cases diagnosed over a mean follow-up time of 10.4 years and 2,295 persons who remained free of cancer in the European Prospective Investigation into Cancer and Nutrition-Potsdam study. Hazard ratios as a measure of relative risk (RR) and 95% confidence intervals (CI) were computed using a Prentice-modified Cox regression. In a multivariable model adjusted for age, sex, education, dietary and lifestyle factors, body mass index (BMI), and waist circumference, higher omentin concentrations were associated with a higher colorectal cancer risk (RRcontinuously per doubling of omentin concentrations = 1.98; 95% CI, 1.45–2.73). Additional adjustment for metabolic biomarkers, including glycated hemoglobin, high-density lipoprotein cholesterol, and C-reactive protein, did not alter the results. In stratified analyses, the positive association between omentin and colorectal cancer risk was retained in participants with BMI &amp;lt; 30 (RRcontinuously per doubling of omentin concentrations = 2.26; 95% CI, 1.57–3.27), whereas among participants with BMI ≥ 30 no association was revealed (RRcontinuously per doubling of omentin concentrations = 1.07; 95% CI, 0.63–1.83; Pinteraction = 0.005). These novel findings provide the first lines of evidence for an independent association between prediagnostic omentin concentrations and colorectal cancer risk and suggest a potential interaction with the adiposity state of the individual. Cancer Res; 76(13); 3862–71. ©2016 AACR.
A Comparison of the Cheater Detection and the Unrelated Question Models: A Randomized Response Survey on Physical and Cognitive Doping in Recreational Triathletes
2016-05-24

The results suggest that the two models can provide converging prevalence estimates. The high rate of cheaters estimated by the CDM, however, suggests that the present results must be seen as a lower bound and that the true prevalence of doping might be considerably higher.
Differentially Isotope‐Labeled Nucleosomes To Study Asymmetric Histone Modification Crosstalk by Time‐Resolved NMR Spectroscopy
2016-05-24

Abstract Post‐translational modifications (PTMs) of histones regulate chromatin structure and function. Because nucleosomes contain two copies each of the four core histones, the establishment of different PTMs on individual “sister” histones in the same nucleosomal context, that is, asymmetric histone PTMs, are difficult to analyze. Here, we generated differentially isotope‐labeled nucleosomes to study asymmetric histone modification crosstalk by time‐resolved NMR spectroscopy. Specifically, we present mechanistic insights into nucleosomal histone H3 modification reactions in cis and in trans, that is, within individual H3 copies or between them. We validated our approach by using the H3S10phK14ac crosstalk mechanism, which is mediated by the Gcn5 acetyltransferase. Moreover, phosphorylation assays on methylated substrates showed that, under certain conditions, Haspin kinase is able to produce nucleosomes decorated asymmetrically with two distinct types of PTMs.
Influence of the Oil Phase and Topical Formulation on the Wound Healing Ability of a Birch Bark Dry Extract
2016-05-24

Triterpenes from the outer bark of birch are known for various pharmacological effects including enhanced wound healing (WH). A birch bark dry extract (TE) obtained by accelerated solvent extraction showed the ability to form oleogels when it is suspended in oils. Consistency of the oleogels and the dissolved amount of triterpenes varies largely with the used oil. Here we wanted to know to what extent different oils and formulations (oleogel versus o/w emulsion) influence WH. Looking at the plain oils, medium-chain triglycerides (MCT) enhanced WH (ca. 1.4-fold), while e.g. castor oil (ca.0.3-fold) or light liquid paraffin (LLP; ca. 0.5-fold) significantly decreased WH. Concerning the respective oleogels, TE-MCT showed no improvement although the solubility of the TE was high. In contrast, the oleogel of sunflower oil which alone showed a slight tendency to impair WH, enhanced WH significantly (ca. 1.6-fold). These results can be explained by release experiments where the release rate of betulin, the main component of TE, from MCT oleogels was significantly lower than from sunflower oil oleogels. LLP impaired WH as plain oil and even though it released betulin comparable to sunflower oil it still results in an overall negative effect of the oleogel on WH. As a further formulation option also surfactant free o/w emulsions were prepared using MCT, sunflower oil and LLP as a nonpolar oil phase. Depending on the preparation method (suspension or oleogel method) the distribution of the TE varied markedly and affected also release kinetics. However, the released betulin was clearly below the values measured with the respective oleogels. Consequently, none of the emulsions showed a significantly positive effect on WH. In conclusion, our data show that the oil used as a vehicle influences wound healing not only by affecting the release of the extract, but also by having its own vehicle effect on wound healing. This is also of importance for other applications where drugs have to be applied in non-polar vehicles because these solvents likely influence the outcome of the experiment substantially.
(E)-1-(Pyridin-4-yl)propan-1-one oxime
2016-05-24

The asymmetric unit of the title compound, C 8 H 10 N 2 O, contains two crystallographically independent molecules of slightly different conformation, which are linked via an intermolecular O—H...N hydrogen bond. The dihedral angle between the pyridine ring and the oxime plane of molecule A [2.09 (19)°] is smaller than in molecule B [16.50 (18)°].
Genome-wide analysis of chromatin packing in Arabidopsis thaliana at single-gene resolution
2016-05-25

The three-dimensional packing of the genome plays an important role in regulating gene expression. We have used Hi-C, a genome-wide chromatin conformation capture (3C) method, to analyze Arabidopsis thaliana chromosomes dissected into subkilobase segments, which is required for gene-level resolution in this species with a gene-dense genome. We found that the repressive H3K27me3 histone mark is overrepresented in the promoter regions of genes that are in conformational linkage over long distances. In line with the globally dispersed distribution of RNA polymerase II in A. thaliana nuclear space, actively transcribed genes do not show a strong tendency to associate with each other. In general, there are often contacts between 5′ and 3′ ends of genes, forming local chromatin loops. Such self-loop structures of genes are more likely to occur in more highly expressed genes, although they can also be found in silent genes. Silent genes with local chromatin loops are highly enriched for the histone variant H3.3 at their 5′ and 3′ ends but depleted of repressive marks such as heterochromatic histone modifications and DNA methylation in flanking regions. Our results suggest that, different from animals, a major theme of genome folding in A. thaliana is the formation of structural units that correspond to gene bodies.
Combining TMS and tACS for Closed-Loop Phase-Dependent Modulation of Corticospinal Excitability: A Feasibility Study
2016-05-25

The combination of different neuromodulation techniques facilitates highly specific brain state-dependent stimulation, and may constitute a valuable tool for exploring the physiological and therapeutic effect of phase-dependent stimulation, e.g., in the context of neurorehabilitation.
Evaluation of TRMM 3B43 Precipitation Data for Drought Monitoring in Jiangsu Province, China
2016-05-25

Satellite-based precipitation monitoring at high spatial resolution is crucial for assessing the water and energy cycles at the global and regional scale. Based on the recently released 7th version of the Multi-satellite Precipitation Analysis (TMPA) product of the Tropical Rainfall Measuring Mission (TRMM), and the monthly precipitation data (3B43) are evaluated using observed monthly precipitation from 65 meteorological stations in Jiangsu Province, China, for the period 1998–2014. Additionally, the standardized precipitation index (SPI), which is derived by a nonparametric approach, is employed to investigate the suitability of the TRMM 3B43 precipitation data for drought monitoring in Jiangsu Province. The temporal correlations between observations and the TRMM 3B43 precipitation data show, in general, reasonable agreement for different time scales. However, in summer, only 50% of the stations present correlation coefficients that are statistically significant at the 95% confidence interval. The overall best agreement of TRMM 3B43 precipitation data at seasonal scale tends to occur in autumn (SON). The comparative analysis of the calculated SPI time series suggests that the accuracy of TRMM3B43 decreases with increasing time scale. Stations with significant correlation coefficients also become less spatially homogeneous with increasing time scale. In summary, the findings demonstrate that TRMM 3B43 precipitation data can be used for reliable short-term drought monitoring in Jiangsu province, while temporal-spatial limitations exist for longer time scales.
Integrative analysis of the West African Ceraceosorus africanus sp. nov. provides insights into the diversity, biogeography, and evolution of the enigmatic Ceraceosorales (Fungi: Ustilaginomycotina)
2016-05-25

The order Ceraceosorales (Ustilaginomycotina) currently includes the single genus Ceraceosorus, with one species, Ceraceosorus bombacis, parasitic on Bombax ceiba in India. The diversity, biogeography, evolution, and phylogenetic relationships of this order are still relatively unknown. Here, a second species of Ceraceosorus is described from West Africa as a novel species, Ceraceosorus africanus, infecting Bombax costatum in Benin, Ghana, and Togo. This species produces conspicuous fructifications, similar to corticioid basidiomata when mature, but sorus-like in early stages of ontogenetic development. The fructifications cover much of the leaf surface and resemble leaf blight. This contrasts with the inconspicuous fructifications of C. bombacis comprising small spots scattered over the lower leaf surface that resemble leaf spot. Both species of Ceraceosorus differ in several micromorphological traits, infect different host plant species in widely separated geographical areas, and are separated by a considerable genetic distance in 28S rDNA and RPB2 genes. The distinct corticioid fructification of C. africanus is a unique morphological trait within the Ustilaginomycotina. Molecular phylogenetic analyses of a single gene dataset (D1/D2 28S rDNA) supported the monophyly of the two Ceraceosorus species and the Ceraceosorales and their placement within the Ustilaginomycotina. Molecular phylogenetic analyses of a multigene dataset (18S/5.8S/28S rDNA/RPB2/TEF1) revealed Exobasidium rhododendri (Exobasidiales) as the closest relative of Ceraceosorus, both clustering together with Entyloma calendulae (Entylomatales), indicating affinities to the Exobasidiomycetes. This phylogenetic placement is in agreement with ultrastructural characteristics (presence of local interaction zone and interaction apparatus) reported for the Ceraceosorales, Entylomatales, and Exobasidiales.
Leveraging FDSOI through body bias domain partitioning and bias search
2016-05-25

In FDSOI, sophisticated body biasing schemes can greatly reduce leakage or improve performance as well as efficiency. This paper proposes algorithms to determine body bias domain candidates which then merge those to reach a desired number of domains. Domain candidates are determined using an activation based approach, analyzing mapped verilog netlists to identify which parts of the design are used under specified conditions. Body bias domain partitionings are then determined based on activation and the timing of the partitioned parts. The algorithms include a body bias assignment algorithm to reach given timing goals with multiple domains and cross-domain resource sharing. The approach is compatible with any synthesis optimization and is resource sharing aware. Using an implementation of the proposed algorithms, overall leakage can be significantly reduced in all scenarios while obtaining the same benefits of body biasing. The method is evaluated in STMicro's 28nm FDSOI and Renesas's 65nm SOTB.