Adsorption and desorption of three carbamate pesticides by illite, kaolinite and humic acid-clay complexes

In soils organic matter and clay minerals are often so associated that it is not clear that how the presence of organic matter influences the sorptive process of clay minerals.  So, in order to factor and quantify component contributions of mineral fractions and humic acid phase to the sorption of pesticides on clay minerals, adsorption and desorption of three carbamate pesticides oxamyl (I), S-Ethyl-N-(methyl carbamoyl)-oxythio acetimidate (II) and N-Phenyl (ethyl cabamoyl) propylcarbamate (III) by Na+, Ca2+ saturated illite, kaolinite and humic acid-clay complexes were investigated by batch experiments. The adsorption was more on illite than kaolinite and followed the order pesticide III > I > II, adsorption on Na-saturated clay samples was more than Ca-saturated. The presence of humic acid enhances the pesticide adsorption. A composite model for estimating pesticide adsorption, which assumes mineral and organic matter fraction individually as adsorbent phases, predicted sorption within a factor of 0.75-1.4 times the measured value. The desorption data indicated that humic acid retains more pesticide than clay mineral. XRD patterns showed that humic acid is restricted to the external surfaces of clay tactoids, denoting that clay mineral fractions in soils including those with organic coatings play an important role in the retention of polar carbamate pesticides

Observation of Dirac plasmons in a topological insulator

Plasmons are the quantized collective oscillations of electrons in metals and doped semiconductors. The plasmons of ordinary, massive electrons are since a long time basic ingredients of research in plasmonics and in optical metamaterials. Plasmons of massless Dirac electrons were instead recently observed in a purely two-dimensional electron system (2DEG)like graphene, and their properties are promising for new tunable plasmonic metamaterials in the terahertz and the mid-infrared frequency range. Dirac quasi-particles are known to exist also in the two-dimensional electron gas which forms at the surface of topological insulators due to a strong spin-orbit interaction. Therefore,one may look for their collective excitations by using infrared spectroscopy. Here we first report evidence of plasmonic excitations in a topological insulator (Bi2Se3), that was engineered in thin micro-ribbon arrays of different width W and period 2W to select suitable values of the plasmon wavevector k. Their lineshape was found to be extremely robust vs. temperature between 6 and 300 K, as one may expect for the excitations of topological carriers. Moreover, by changing W and measuring in the terahertz range the plasmonic frequency vP vs. k we could show, without using any fitting parameter, that the dispersion curve is in quantitative agreement with that predicted for Dirac plasmons.Comment: 11 pages, 3 figures, published in Nature Nanotechnology (2013

Investigation of pulsed laser induced dewetting in nanoscopic metal films

Hydrodynamic pattern formation (PF) and dewetting resulting from pulsed laser induced melting of nanoscopic metal films have been used to create spatially ordered metal nanoparticle arrays with monomodal size distribution on SiO_{\text{2}}/Si substrates. PF was investigated for film thickness h\leq7 nm < laser absorption depth \sim11 nm and different sets of laser parameters, including energy density E and the irradiation time, as measured by the number of pulses n. PF was only observed to occur for E\geq E_{m}, where E_{m} denotes the h-dependent threshold energy required to melt the film. Even at such small length scales, theoretical predictions for E_{m} obtained from a continuum-level lumped parameter heat transfer model for the film temperature, coupled with the 1-D transient heat equation for the substrate phase, were consistent with experimental observations provided that the thickness dependence of the reflectivity of the metal-substrate bilayer was incorporated into the analysis. The spacing between the nanoparticles and the particle diameter were found to increase as h^{2} and h^{5/3} respectively, which is consistent with the predictions of the thin film hydrodynamic (TFH) dewetting theory. These results suggest that fast thermal processing can lead to novel pattern formation, including quenching of a wide range of length scales and morphologies.Comment: 36 pages, 11 figures, 1 tabl

Algorithms: simultaneous error-correction and rooting for gene tree reconciliation and the gene duplication problem

<p>Abstract</p> <p>Background</p> <p>Evolutionary methods are increasingly challenged by the wealth of fast growing resources of genomic sequence information. Evolutionary events, like gene duplication, loss, and deep coalescence, account more then ever for incongruence between gene trees and the actual species tree. Gene tree reconciliation is addressing this fundamental problem by invoking the minimum number of gene duplication and losses that reconcile a rooted gene tree with a rooted species tree. However, the reconciliation process is highly sensitive to topological error or wrong rooting of the gene tree, a condition that is not met by most gene trees in practice. Thus, despite the promises of gene tree reconciliation, its applicability in practice is severely limited.</p> <p>Results</p> <p>We introduce the problem of reconciling unrooted and erroneous gene trees by simultaneously rooting and error-correcting them, and describe an efficient algorithm for this problem. Moreover, we introduce an error-corrected version of the gene duplication problem, a standard application of gene tree reconciliation. We introduce an effective heuristic for our error-corrected version of the gene duplication problem, given that the original version of this problem is NP-hard. Our experimental results suggest that our error-correcting approaches for unrooted input trees can significantly improve on the accuracy of gene tree reconciliation, and the species tree inference under the gene duplication problem. Furthermore, the efficiency of our algorithm for error-correcting reconciliation is capable of handling truly large-scale phylogenetic studies.</p> <p>Conclusions</p> <p>Our presented error-correction approach is a crucial step towards making gene tree reconciliation more robust, and thus to improve on the accuracy of applications that fundamentally rely on gene tree reconciliation, like the inference of gene-duplication supertrees.</p

An unusual case of low-grade tubulopapillary adenocarcinoma of the sinonasal tract

<p>Abstract</p> <p>Background</p> <p>Low-grade papillary adenocarcinomas of the sinonasal tract are rare neoplasms. Over recent years, little doubt remains that this tumour represents a separate entity based on morphology, ultrastructural features and behaviour. We outline a case of this rare entity displaying a not hitherto described immunophenotype.</p> <p>Case presentation</p> <p>A 32 year old man presented recurrent epistaxis was evaluated with endoscopy which revealed a well circumscribed pedunculated mass lesion in left nares. The mass was arising from the nasal septum which was excised along with the mass. The biopsy revealed low-grade, non-intestinal type sinonasal tubulopapillary adenocarcinoma.</p> <p>Conclusion</p> <p>TTF-1 immunoreactivity in absence of thyroid or pulmonary primary in the present case remains an enigma. However, this raises the possibility of the utility of this antibody to predict a better clinical outcome in the subset of low grade non-intestinal sinonasal adenocarcinoma. More cases of similar morphological appearance may need to be examined for TTF-1 immunoreactivity and clinically followed up to establish this theory.</p

Modifying the surface electronic properties of YBa2Cu3O7-delta with cryogenic scanning probe microscopy

We report the results of a cryogenic study of the modification of YBa2Cu3O7-delta surface electronic properties with the probe of a scanning tunneling microscope (STM). A negative voltage applied to the sample during STM tunneling is found to modify locally the conductance of the native degraded surface layer. When the degraded layer is removed by etching, the effect disappears. An additional surface effect is identified using Scanning Kelvin Probe Microscopy in combination with STM. We observe reversible surface charging for both etched and unetched samples, indicating the presence of a defect layer even on a surface never exposed to air.Comment: 6 pages, 4 figures. To appear in Superconductor Science and Technolog

HapTree: A Novel Bayesian Framework for Single Individual Polyplotyping Using NGS Data

As the more recent next-generation sequencing (NGS) technologies provide longer read sequences, the use of sequencing datasets for complete haplotype phasing is fast becoming a reality, allowing haplotype reconstruction of a single sequenced genome. Nearly all previous haplotype reconstruction studies have focused on diploid genomes and are rarely scalable to genomes with higher ploidy. Yet computational investigations into polyploid genomes carry great importance, impacting plant, yeast and fish genomics, as well as the studies of the evolution of modern-day eukaryotes and (epi)genetic interactions between copies of genes. In this paper, we describe a novel maximum-likelihood estimation framework, HapTree, for polyploid haplotype assembly of an individual genome using NGS read datasets. We evaluate the performance of HapTree on simulated polyploid sequencing read data modeled after Illumina sequencing technologies. For triploid and higher ploidy genomes, we demonstrate that HapTree substantially improves haplotype assembly accuracy and efficiency over the state-of-the-art; moreover, HapTree is the first scalable polyplotyping method for higher ploidy. As a proof of concept, we also test our method on real sequencing data from NA12878 (1000 Genomes Project) and evaluate the quality of assembled haplotypes with respect to trio-based diplotype annotation as the ground truth. The results indicate that HapTree significantly improves the switch accuracy within phased haplotype blocks as compared to existing haplotype assembly methods, while producing comparable minimum error correction (MEC) values. A summary of this paper appears in the proceedings of the RECOMB 2014 conference, April 2–5.National Science Foundation (U.S.) (NSF/NIH BIGDATA Grant R01GM108348-01)National Science Foundation (U.S.) (Graduate Research Fellowship)Simons Foundatio

Evidence for the role of EPHX2 gene variants in anorexia nervosa.

Anorexia nervosa (AN) and related eating disorders are complex, multifactorial neuropsychiatric conditions with likely rare and common genetic and environmental determinants. To identify genetic variants associated with AN, we pursued a series of sequencing and genotyping studies focusing on the coding regions and upstream sequence of 152 candidate genes in a total of 1205 AN cases and 1948 controls. We identified individual variant associations in the Estrogen Receptor-ß (ESR2) gene, as well as a set of rare and common variants in the Epoxide Hydrolase 2 (EPHX2) gene, in an initial sequencing study of 261 early-onset severe AN cases and 73 controls (P=0.0004). The association of EPHX2 variants was further delineated in: (1) a pooling-based replication study involving an additional 500 AN patients and 500 controls (replication set P=0.00000016); (2) single-locus studies in a cohort of 386 previously genotyped broadly defined AN cases and 295 female population controls from the Bogalusa Heart Study (BHS) and a cohort of 58 individuals with self-reported eating disturbances and 851 controls (combined smallest single locus P&lt;0.01). As EPHX2 is known to influence cholesterol metabolism, and AN is often associated with elevated cholesterol levels, we also investigated the association of EPHX2 variants and longitudinal body mass index (BMI) and cholesterol in BHS female and male subjects (N=229) and found evidence for a modifying effect of a subset of variants on the relationship between cholesterol and BMI (P&lt;0.01). These findings suggest a novel association of gene variants within EPHX2 to susceptibility to AN and provide a foundation for future study of this important yet poorly understood condition

Dynamics of multi-stage infections on networks

This paper investigates the dynamics of infectious diseases with a nonexponentially distributed infectious period. This is achieved by considering a multistage infection model on networks. Using pairwise approximation with a standard closure, a number of important characteristics of disease dynamics are derived analytically, including the final size of an epidemic and a threshold for epidemic outbreaks, and it is shown how these quantities depend on disease characteristics, as well as the number of disease stages. Stochastic simulations of dynamics on networks are performed and compared to output of pairwise models for several realistic examples of infectious diseases to illustrate the role played by the number of stages in the disease dynamics. These results show that a higher number of disease stages results in faster epidemic outbreaks with a higher peak prevalence and a larger final size of the epidemic. The agreement between the pairwise and simulation models is excellent in the cases we consider