bluuebunny/crossref_metadata_2025 huggingface dataset:
Trans10,cis15 18:2 Isolated from Beef Fat Does Not Have the Same Anti‐Adipogenic Properties as Trans10,cis12–18:2 in 3T3‐L1 Adipocytes
Authors: Vahmani Payam , Meadus William J. , Rolland David C. , Duff Pascale , Dugan Michael E. R.
Published: September 2016

During ruminal biohydrogenation of α‐linolenic acid, a non‐conjugated non‐methylene interrupted dienoic acid is formed containing a t10 double bond, namely t10,c15–18:2. The present study was designed to examine whether t10,c15–18:2 would exert similar anti‐adipogenic effects compared to t10,c12–18:2 in 3T3‐L1 adipocytes. Differentiated 3T3‐L1 adipocytes were treated with 35 or 70 µM of LNA, t10,c12–18:2, t10,c15–18:2, or bovine serum albumin (BSA) vehicle control for 120 h. Cellular triacylglycerol and protein were quantified using commercial colorimetric kits. Cells were analyzed for fatty acid composition and gene expression using gas chromatography and quantitative PCR, respectively. Trans10,cis12–18:2 decreased (P < 0.05) the adipocyte triacylglycerol (TAG) content, which was mainly related to a reduction in saturated fatty acids (SFA; e.g., 16:0 and 15:0) and cis monounsaturated fatty acids (c‐MUFA; e.g., c9–16:1 and c9–18:1). Trans10,cis12 also decreased (P < 0.05) the expression of genes related to fatty acid synthesis (ACACA, FASN), delta‐9 desaturation (SCD1), fatty acid elongation (ELOVL5), and fatty acid uptake (LPL) and upregulated (P < 0.05) the expression of the rate‐liming enzyme involved in fatty acid β‐oxidation (CPT1). In contrast, LNA and t10,c15–18:2 did not affect the gene expression and cellular content of the TAG, SFA, c‐MUFA, or SCD1 indices in adipocytes. Our findings suggest that t10,c15–18:2, despite having structural similarity to t10,c12–18:2 (presence of a trans‐10 double bond), does not exert anti‐adipogenic effects in 3T3‐L1 adipocytes.
Item response theory analysis of the Pain Self-Efficacy Questionnaire
Authors: Costa Daniel S.J. , Asghari Ali , Nicholas Michael K.
Published: September 2016

Background and aims

The Pain Self-Efficacy Questionnaire (PSEQ) is a 10-item instrument designed to assess the extent to which a person in pain believes s/he is able to accomplish various activities despite their pain. There is strong evidence for the validity and reliability of both the full-length PSEQ and a 2-item version. The purpose of this study is to further examine the properties of the PSEQ using an item response theory (IRT) approach.

Methods

We used the two-parameter graded response model to examine the category probability curves, and location and discrimination parameters of the 10 PSEQ items. In item response theory, responses to a set of items are assumed to be probabilistically determined by a latent (unobserved) variable. In the graded-response model specifically, item response threshold (the value of the latent variable for which adjacent response categories are equally likely) and discrimination parameters are estimated for each item. Participants were 1511 mixed, chronic pain patients attending for initial assessment at a tertiary pain management centre.

Results

All items except item 7 (‘I can cope with my pain without medication’) performed well in IRT analysis, and the category probability curves suggested that participants used the 7-point response scale consistently. Items 6 (‘I can still do many of the things I enjoy doing, such as hobbies or leisure activity, despite pain’), 8 (‘I can still accomplish most of my goals in life, despite the pain’) and 9 (‘I can live a normal lifestyle, despite the pain’) captured higher levels of the latent variable with greater precision.

Conclusions

The results from this IRT analysis add to the body of evidence based on classical test theory illustrating the strong psychometric properties of the PSEQ. Despite the relatively poor performance of Item 7, its clinical utility warrants its retention in the questionnaire.

Implications

The strong psychometric properties of the PSEQ support its use as an effective tool for assessing self-efficacy in people with pain.
Point-of-use Unit Based on Gravity Ultrafiltration Removes Waterborne Gastrointestinal Pathogens from Untreated Water Sources in Rural Communities
Authors: Chaidez Cristóbal , Ibarra-Rodríguez Juan R. , Valdez-Torres José Benigno , Soto Marcela , Gerba Charles P. , Castro-del Campo Nohelia
Published: September 2016

Objective

In developing countries, rural communities often face the lack of potable water infrastructure and must rely on untreated sources for drinking, which are often contaminated with waterborne pathogens. The use of home water treatment devices is seen as one means of reducing the risk of exposure to waterborne pathogens. The aim of this study was to evaluate the microbiological and physicochemical performance of a simple in-home point-of-use device based on gravity ultrafiltration through an ultrafilter membrane.

Methods

Twenty-five randomly selected households from 2 rural communities in Culiacán, Mexico, were enrolled. Water samples were collected before and after treatment and during storage for a period of 8 weeks. Heterotrophic bacteria, total coliforms, fecal coliforms, Escherichia coli, and Giardia spp were quantified, as well as various physicochemical parameters.

Results

All of the untreated water samples contained high levels of indicator bacteria, but none were detected in the treated water fulfilling the requirements set by the Mexican Norm (NOM-127-SSA1-1994) and the World Health Organization guidelines for drinking water. However, indicator bacteria (fecal coliforms and E coli) were detected in every sample from water stored 24 hours after treatment.

Conclusion

This study demonstrated that point-of-use filters using gravity-fed ultrafilters are a low-cost, effective water treatment technology for water of poor microbial quality. However, further identification of the sources and mechanisms by which water is contaminated when stored after treatment will help with designing and implementing better strategies for keeping water safe for domestic use.
Mysterious Anomaly Interrupts Stratospheric Wind Pattern
Authors: Stanley Sarah
Published: September 2016

For the first time, scientists have observed a deviation from the typical alternating pattern of easterly and westerly winds in the equatorial stratosphere.
Delayed Launch Approved for Next Mars Mission
Authors: Wendel JoAnna
Published: September 2016

NASA has set a new 2018 launch date for a spacecraft to probe the Red Planet's interior, after instrument failure hobbled preparations for the mission.
Comparative proteomic assessment of matrisome enrichment methodologies
Authors: Krasny Lukas , Paul Angela , Wai Patty , Howard Beatrice A. , Natrajan Rachael C. , Huang Paul H.
Published: September 2016

The matrisome is a complex and heterogeneous collection of extracellular matrix (ECM) and ECM-associated proteins that play important roles in tissue development and homeostasis. While several strategies for matrisome enrichment have been developed, it is currently unknown how the performance of these different methodologies compares in the proteomic identification of matrisome components across multiple tissue types. In the present study, we perform a comparative proteomic assessment of two widely used decellularisation protocols and two extraction methods to characterise the matrisome in four murine organs (heart, mammary gland, lung and liver). We undertook a systematic evaluation of the performance of the individual methods on protein yield, matrisome enrichment capability and the ability to isolate core matrisome and matrisome-associated components. Our data find that sodium dodecyl sulphate (SDS) decellularisation leads to the highest matrisome enrichment efficiency, while the extraction protocol that comprises chemical and trypsin digestion of the ECM fraction consistently identifies the highest number of matrisomal proteins across all types of tissue examined. Matrisome enrichment had a clear benefit over non-enriched tissue for the comprehensive identification of matrisomal components in murine liver and heart. Strikingly, we find that all four matrisome enrichment methods led to significant losses in the soluble matrisome-associated proteins across all organs. Our findings highlight the multiple factors (including tissue type, matrisome class of interest and desired enrichment purity) that influence the choice of enrichment methodology, and we anticipate that these data will serve as a useful guide for the design of future proteomic studies of the matrisome.
Physics of solid–liquid interfaces: From the Young equation to the superhydrophobicity (Review Article)
Authors: Bormashenko Edward
Published: September 2016

The state-of-art in the field of physics of phenomena occurring at solid/liquid interfaces is presented. The notions of modern physics of wetting are introduced and discussed including: the contact angle hysteresis, disjoining pressure and wetting transitions. The physics of low temperature wetting phenomena is treated. The general variational approach to interfacial problems, based on the application of the transversality conditions to variational problems with free endpoints is presented. It is demonstrated that main equations, predicting contact angles, namely the Young, Wenzel, and Cassie–Baxter equations arise from imposing the transversality conditions on the appropriate variational problem of wetting. Recently discovered effects such as superhydrophobicity, the rose petal effect and the molecular dynamic of capillarity are reviewed.
Electrostatic charge-charge and dipole-dipole interactions near the surface of a medium with screening non-locality (Review Article)
Authors: Gabovich Alexander M. , Voitenko Alexander I.
Published: September 2016

Interaction energy between two point charges, WQQ′, or two point dipoles, WPP′, located in a medium with a constant dielectric permittivity near the plane surface of a metallic or semiconducting substrate with the spatial dispersion of its dielectric function has been revisited. The calculations were made on the basis of the Green's function method for layered systems. Long-range lateral asymptotics were found. The non-local character of screening in the substrates was shown to substantially modify the dependences of WQQ′ and WPP′ on the distance between the objects concerned. Thus, the purported conventional electrostatic interactions between adsorbed atoms and molecules (modeled by point charges and point dipoles) should be reconsidered making allowance for the substrate polarization. In particular, this factor may significantly influence the structure of electrostatic dipole lattices arising near the surfaces of solids, as well as the kinetics of charge or dipole motion over the surface.
Effects of phonon interference through long range interatomic bonds on thermal interface conductance
Authors: Han Haoxue , Feng Lei , Xiong Shiyun , Shiga Takuma , Shiomi Junichiro , Volz Sebastian , Kosevich Yuriy A.
Published: September 2016

We investigate the role of two-path destructive phonon interference induced by interatomic bonds beyond the nearest neighbor in the thermal conductance of a silicon-germanium-like metasurface. Controlled by the ratio between the second and first nearest-neighbor harmonic force constants, the thermal conductance across a germanium atomic plane in the silicon lattice exhibits a trend switch induced by the destructive interference of the nearest-neighbor phonon path with a direct path bypassing the defect atoms. We show that bypassing of the heavy isotope impurity is crucial to the realization of the local minimum in the thermal conductance. We highlight the effect of the second phonon path on the distinct behaviors of the dependence of the thermal conductance on the impurity mass ratio. All our conclusions are confirmed both by Green's Function calculations for the equivalent quasi-1D lattice models and by molecular dynamics simulations.
On the equivalence of two vacancy models applied to the electronic spectrum of materials with honeycomb lattice
Authors: Skrypnyk Y. V. , Loktev V. M.
Published: September 2016

On the basis of the tight-binding method, the Green's function for a material with honeycomb crystal lattice containing a vacancy was studied. Well-known and commonly used models for description of a single vacancy were considered, and their equivalence was analytically demonstrated. It was also shown that the contributions to the density of quasiparticle states from both sublattices of the honeycomb lattice are identical, except for zero energy, irrespective of which sublattice contains the vacancy.
Transmission of quasiparticle excitations through interfaces between two media (Review Article)
Authors: Kosevich Yu. A. , Syrkin E. S. , Tkachenko O. Yu.
Published: September 2016

The effect of the dynamic surface monolayer at the interface of a solid with superfluid helium on Kapitza thermal resistance is analyzed. A monolayer of impurity atoms adsorbed on a solid surface and weakly bound to the substrate is considered as a surface monolayer of this type. A resonance of phonons incident from the helium with oscillations in the two-dimensional system can cause a great increase in heat transfer through this kind of interface compared to an atomically clean boundary. Scalar and vector models of the interface are examined. New results from the macroscopic dynamics of an interface between two media are introduced in this review, with lattice anharmonicity (nonlinear effects) taken into account.
The origin of the conductivity maximum in molten salts. II. SnCl2 and HgBr2
Authors: Aravindakshan Nikhil P. , Kuntz Colin M. , Gemmell Kyle E. , Johnson Keith E. , East Allan L. L.
Published: September 2016

The phenomenon of electrical conductivity maxima of molten salts versus temperature during orthobaric (closed-vessel) conditions is further examined via ab initio simulations. Previously, in a study of molten BiCl3, a new theory was offered in which the conductivity falloff at high temperatures is due not to traditional ion association, but to a rise in the activation energy for atomic ions hopping from counterion to counterion. Here this theory is further tested on two more inorganic melts which exhibit conductivity maxima: another high-conducting melt (SnCl2, σmax = 2.81 Ω−1 cm−1) and a low-conducting one (HgBr2, σmax = 4.06 × 10−4 Ω−1 cm−1). First, ab initio molecular dynamics simulations were performed and again appear successful in reproducing the maxima for both these liquids. Second, analysis of the simulated liquid structure (radial distributions, species concentrations) was performed. In the HgBr2 case, a very molecular liquid like water, a clear Grotthuss chain of bromide transfers was observed in simulation when seeding the system with a HgBr+ cation and HgBr3− anion. The first conclusion is that the hopping mechanism offered for molten BiCl3 is simply the Grotthuss mechanism for conduction, applicable not just to H+ ions, but also to halide ions in post-transition-metal halide melts. Second, it is conjectured that the conductivity maximum is due to rising activation energy in network-covalent (halide-bridging) melts (BiCl3, SnCl2, PbCl2), but possibly a falling Arrhenius prefactor (collision frequency) for molecular melts (HgBr2).
Adsorption of ethylene on Sn and In terminated Si(001) surface studied by photoelectron spectroscopy and scanning tunneling microscopy
Authors: Zimmermann Petr , Sobotík Pavel , Kocán Pavel , Ošt’ádal Ivan , Vorokhta Mykhailo , Acres Robert George , Matolín Vladimír
Published: September 2016

Interaction of ethylene (C2H4) with Si(001)-Sn-2 × 2 and Si(001)-In-2 × 2 at room temperature has been studied using core level (C 1s) X-ray photoelectron spectroscopy with synchrotron radiation and scanning tunneling microscopy. Sn and In form similar dimer chains on Si(001)2 × 1, but exhibit different interaction with ethylene. While ethylene adsorbs on top of Sn dimers of the Si(001)-Sn-2 × 2 surface, the Si(001)-In-2 × 2 surface turned out to be inert. Furthermore, the reactivity of the Sn terminated surface is found to be considerably decreased in comparison with Si(001)2 × 1. According to the proposed adsorption model ethylene bonds to Sn dimers via [2 + 2] cycloaddition by interacting with their π dimer bonds. In contrast, indium dimers do not contain π bonds, which renders the In terminated Si(001) surface inert for ethylene adsorption.
Equilibrium crystal phases of triblock Janus colloids
Authors: Reinhart Wesley F. , Panagiotopoulos Athanassios Z.
Published: September 2016

Triblock Janus colloids, which are colloidal spheres decorated with attractive patches at each pole, have recently generated significant interest as potential building blocks for functional materials. Their inherent anisotropy is known to induce self-assembly into open structures at moderate temperatures and pressures, where they are stabilized over close-packed crystals by entropic effects. We present a numerical investigation of the equilibrium phases of triblock Janus particles with many different patch geometries in three dimensions, using Monte Carlo simulations combined with free energy calculations. In all cases, we find that the free energy difference between crystal polymorphs is less than 0.2 kBT per particle. By varying the patch fraction and interaction range, we show that large patches stabilize the formation of structures with four bonds per patch over those with three. This transition occurs abruptly above a patch fraction of 0.30 and has a strong dependence on the interaction range. Furthermore, we find that a short interaction range favors four bonds per patch, with longer range increasingly stabilizing structures with only three bonds per patch. By quantifying the effect of patch geometry on the stability of the equilibrium crystal structures, we provide insights into the fundamental design rules for constructing complex colloidal crystals.
From single molecules to water networks: Dynamics of water adsorption on Pt(111)
Authors: Naderian Maryam , Groß Axel
Published: September 2016

The adsorption dynamics of water on Pt(111) was studied using ab initio molecular dynamics simulations based on density functional theory calculations including dispersion corrections. Sticking probabilities were derived as a function of initial kinetic energy and water coverage. In addition, the energy distribution upon adsorption was monitored in order to analyze the energy dissipation process. We find that on the water pre-covered surface the sticking probability is enhanced because of the attractive water-water interaction and the additional effective energy dissipation channels to the adsorbed water molecules. The water structures forming directly after the adsorption on the pre-covered surfaces do not necessarily correspond to energy minimum structures.
Rate theory of solvent exchange and kinetics of Li+ − BF4−/PF6− ion pairs in acetonitrile
Authors: Dang Liem X. , Chang Tsun-Mei
Published: September 2016

In this paper, we describe our efforts to apply rate theories in studies of solvent exchange around Li+ and the kinetics of ion pairings in lithium-ion batteries (LIBs). We report one of the first computer simulations of the exchange dynamics around solvated Li+ in acetonitrile (ACN), which is a common solvent used in LIBs. We also provide details of the ion-pairing kinetics of Li+-[BF4] and Li+-[PF6] in ACN. Using our polarizable force-field models and employing classical rate theories of chemical reactions, we examine the ACN exchange process between the first and second solvation shells around Li+. We calculate exchange rates using transition state theory and weighted them with the transmission coefficients determined by the reactive flux, Impey, Madden, and McDonald approaches, and Grote-Hynes theory. We found the relaxation times changed from 180 ps to 4600 ps and from 30 ps to 280 ps for Li+-[BF4] and Li+-[PF6] ion pairs, respectively. These results confirm that the solvent response to the kinetics of ion pairing is significant. Our results also show that, in addition to affecting the free energy of solvation into ACN, the anion type also should significantly influence the kinetics of ion pairing. These results will increase our understanding of the thermodynamic and kinetic properties of LIB systems.
Transient plasma potential in pulsed dual frequency inductively coupled plasmas and effect of substrate biasing
Authors: Mishra Anurag , Yeom Geun Young
Published: September 2016

An electron emitting probe in saturated floating potential mode has been used to investigate the temporal evolution of plasma potential and the effect of substrate RF biasing on it for pulsed dual frequency (2 MHz/13.56 MHz) inductively coupled plasma (ICP) source. The low frequency power (P2MHz) has been pulsed at 1 KHz and a duty ratio of 50%, while high frequency power (P13.56MHz) has been used in continuous mode. The substrate has been biased with a separate bias power at (P12.56MHz) Argon has been used as a discharge gas. During the ICP power pulsing, three distinct regions in a typical plasma potential profile, have been identified as ‘initial overshoot’, pulse ‘on-phase’ and pulse ‘off-phase’. It has been found out that the RF biasing of the substrate significantly modulates the temporal evolution of the plasma potential. During the initial overshoot, plasma potential decreases with increasing RF biasing of the substrate, however it increases with increasing substrate biasing for pulse ‘on-phase’ and ‘off-phase’. An interesting structure in plasma potential profile has also been observed when the substrate bias is applied and its evolution depends upon the magnitude of bias power. The reason of the evolution of this structure may be the ambipolar diffusion of electron and its dependence on bias power.
The role of conduction electrons in the formation of thermal boundary resistance of the metal-dielectric interface and resistivity of metal films, at low temperatures (Review Article)
Authors: Bezuglyj A. I. , Shklovskij V. A.
Published: September 2016

This review article is a discussion of the role played by conduction electrons in the formation of an effective acoustic transparency at the interface between narrow metal films and dielectric substrates with high thermal conductivity, within the framework of the acoustic mismatch between solids. We consider both steady and transient regimes of phonon radiation from metal films heated by electric current or short laser pulses, at low temperatures. We discuss in detail how the electron-phonon energy relaxation τe and the average exit time of the phonons from the films τes can be found using the experiment. A theoretical analysis of these problems is carried out using kinetic equations for the phonon and electron distribution functions. We examine the steady modes of relaxation and diffusion heat removal from the moving plane phase transition front in the film geometry. In most cases, we discuss the relationship between the theoretical results of the review authors and the existing experimental situation.
The structure of molten CuCl: Reverse Monte Carlo modeling with high-energy X-ray diffraction data and molecular dynamics of a polarizable ion model
Authors: Alcaraz Olga , Trullàs Joaquim , Tahara Shuta , Kawakita Yukinobu , Takeda Shin’ichi
Published: September 2016

The results of the structural properties of molten copper chloride are reported from high-energy X-ray diffraction measurements, reverse Monte Carlo modeling method, and molecular dynamics simulations using a polarizable ion model. The simulated X-ray structure factor reproduces all trends observed experimentally, in particular the shoulder at around 1 Å−1 related to intermediate range ordering, as well as the partial copper-copper correlations from the reverse Monte Carlo modeling, which cannot be reproduced by using a simple rigid ion model. It is shown that the shoulder comes from intermediate range copper-copper correlations caused by the polarized chlorides.
High-temperature adult-plant resistance to stripe rust in facultative winter wheat
Authors: Akin Beyhan , Chen Xian Ming , Morgunov Alex , Zencirci Nusret , Wan Anmin , Wang Meinan
Published: September 2016

Stripe (yellow) rust, caused by Puccinia striiformis Westend. f. sp. tritici Erikss., is one of the most damaging diseases in wheat and is especially damaging for winter and facultative wheat. The objective of this study was to understand stripe rust resistance in 100 wheat and facultative wheat entries from the International Winter Wheat Improvement Program by conducting experiments in a greenhouse and in four field environments in Washington State, USA, and by genotyping molecular markers linked to Yr genes. Percentages of entries resistant to the rust races at the seedling stage were: PST-17, 44%; PST-37, 32%; PST-43, 45%; PST-45, 49%; PST-116, 18%; PST-100, 17%; and PST-127, 8%. Molecular markers were positive for genes Yr9, Yr17, and Yr18 and negative for Yr5, Yr10, and Yr15. Yr18 was present in 44 entries (44%). By using the highly virulent races PST-127 and PST-100 under controlled conditions, 16 entries were shown to have high-temperature adult-plant (HTAP) resistance and resistant–moderately resistant field reactions at all four field sites. Resistant entries, especially those with HTAP resistance, were also identified in the field experiments.
Expression of amphicarpy in Vigna lanceolata morphotypes and their hybrids and implications for cultivar development
Authors: Lawn R. J. , Bielig L. M.
Published: September 2016

Amphicarpy is an adaptation that enhances persistence under various environmental stresses, including heavy grazing, through the production of both aerial and underground seeds on the same plant. The trait occurs in several Australian endemic tropical herbaceous legumes, including Vigna lanceolata. The objective of the current research was to compare aerial and underground reproductive structures in six amphicarpic morphotypes of V. lanceolata (four perennials and two annuals), and in hybrids among these morphotypes and also with a seventh, non-amphicarpic perennial morphotype. The aim was to establish how easily the trait might be manipulated in a breeding program to develop improved amphicarpic cultivars, for ley and forage purposes. In the four amphicarpic perennials, the underground fruiting structures formed on leafless underground stems or rhizomes, and in all four, amphicarpy was habitual, i.e. individual plants routinely developed both aerial and underground fruiting structures. In the two annuals, the underground fruiting structures developed on specialised axillary geotropic stems that arose along the prostrate aerial stems and penetrated the soil or leaf litter. One of the annuals exhibited habitual amphicarpy, whereas the other was opportunistic, in that the underground fruiting structures developed only where aerial stems became covered with soil or leaf litter. F1 hybrids between the two annual morphotypes exhibited habitual amphicarpy, indicating dominance of habitual over opportunistic amphicarpy. F1 hybrids between the four perennial amphicarpic morphotypes were all amphicarpic, reflecting the similar expression of the trait in these forms. By contrast, when these four were crossed with the non-amphicarpic perennial, none of the viable F1 hybrids exhibited amphicarpy, suggesting dominance for non-expression. Many of the perennial F1 hybrids were self-sterile, but in the hybrids that were at least partially fertile, many more geocarpic than aerial seeds were produced, raising the possibility that in the wild, amphicarpy may facilitate the persistence of chance natural outcrosses that might otherwise not survive. The results suggested that it would be feasible to develop amphicarpic annual and amphicarpic perennial cultivars for, respectively, ley and forage purposes.
Crop Choice, School Participation, and Child Labor in Developing Countries: Cotton Expansion in Burkina Faso
Authors: Kazianga Harounan , Makamu Francis
Published: September 2016

We estimate the effects of changes in cotton adoption on children's schooling and child labor in rural Burkina Faso. Using time and spatial variations, we find evidence that expansion of cotton farming has led to an increase in enrollment and to a reduction of participation in child labor for girls. There are, however, no detectable effects on boys. In theory, cotton adoption could increase household income, leading to increased demand for schooling and reduced child labor. On the other hand, because children are productive on cotton farms, adoption of cotton could increase the opportunity cost of child time and the demand for child labor. We provide suggestive evidence showing that boys are more productive than girls on cotton farms. Taken together, the results suggest that the income effect from cotton adoption might have been larger than the wage effect for girls, hence the overall positive impacts on school enrollment for girls.
HAPRAP: a haplotype-based iterative method for statistical fine mapping using GWAS summary statistics
Authors: Zheng Jie , Rodriguez Santiago , Laurin Charles , Baird Denis , Trela-Larsen Lea , Erzurumluoglu Mesut A , Zheng Yi , White Jon , Giambartolomei Claudia , Zabaneh Delilah , Morris Richard , Kumari Meena , Casas Juan P , Hingorani Aroon D ,   UCLEB Consortium, Evans David M , Gaunt Tom R , Day Ian N M
Published: September 2016

Motivation

Fine mapping is a widely used approach for identifying the causal variant(s) at disease-associated loci. Standard methods (e.g. multiple regression) require individual level genotypes. Recent fine mapping methods using summary-level data require the pairwise correlation coefficients (r2) of the variants. However, haplotypes rather than pairwise r2, are the true biological representation of linkage disequilibrium (LD) among multiple loci. In this article, we present an empirical iterative method, HAPlotype Regional Association analysis Program (HAPRAP), that enables fine mapping using summary statistics and haplotype information from an individual-level reference panel.

Results

Simulations with individual-level genotypes show that the results of HAPRAP and multiple regression are highly consistent. In simulation with summary-level data, we demonstrate that HAPRAP is less sensitive to poor LD estimates. In a parametric simulation using Genetic Investigation of ANthropometric Traits height data, HAPRAP performs well with a small training sample size (N < 2000) while other methods become suboptimal. Moreover, HAPRAP’s performance is not affected substantially by single nucleotide polymorphisms (SNPs) with low minor allele frequencies. We applied the method to existing quantitative trait and binary outcome meta-analyses (human height, QTc interval and gallbladder disease); all previous reported association signals were replicated and two additional variants were independently associated with human height. Due to the growing availability of summary level data, the value of HAPRAP is likely to increase markedly for future analyses (e.g. functional prediction and identification of instruments for Mendelian randomization).

Availability and Implementation

The HAPRAP package and documentation are available at http://apps.biocompute.org.uk/haprap/

Supplementary information

Supplementary data are available at Bioinformatics online.
popSTR: population-scale detection of STR variants
Authors: Kristmundsdóttir Snædís , Sigurpálsdóttir Brynja D , Kehr Birte , Halldórsson Bjarni V
Published: September 2016

Motivation

Microsatellites, also known as short tandem repeats (STRs), are tracts of repetitive DNA sequences containing motifs ranging from two to six bases. Microsatellites are one of the most abundant type of variation in the human genome, after single nucleotide polymorphisms (SNPs) and Indels. Microsatellite analysis has a wide range of applications, including medical genetics, forensics and construction of genetic genealogy. However, microsatellite variations are rarely considered in whole-genome sequencing studies, in large due to a lack of tools capable of analyzing them.

Results

Here we present a microsatellite genotyper, optimized for Illumina WGS data, which is both faster and more accurate than other methods previously presented. There are two main ingredients to our improvements. First we reduce the amount of sequencing data necessary for creating microsatellite profiles by using previously aligned sequencing data. Second, we use population information to train microsatellite and individual specific error profiles. By comparing our genotyping results to genotypes generated by capillary electrophoresis we show that our error rates are 50% lower than those of lobSTR, another program specifically developed to determine microsatellite genotypes.

Availability and Implementation

Source code is available on Github: https://github.com/DecodeGenetics/popSTR
signeR: an empirical Bayesian approach to mutational signature discovery
Authors: Rosales Rafael A , Drummond Rodrigo D , Valieris Renan , Dias-Neto Emmanuel , da Silva Israel T
Published: September 2016

Motivation

Mutational signatures can be used to understand cancer origins and provide a unique opportunity to group tumor types that share the same origins and result from similar processes. These signatures have been identified from high throughput sequencing data generated from cancer genomes by using non-negative matrix factorisation (NMF) techniques. Current methods based on optimization techniques are strongly sensitive to initial conditions due to high dimensionality and nonconvexity of the NMF paradigm. In this context, an important question consists in the determination of the actual number of signatures that best represent the data. The extraction of mutational signatures from high-throughput data still remains a daunting task.

Results

Here we present a new method for the statistical estimation of mutational signatures based on an empirical Bayesian treatment of the NMF model. While requiring minimal intervention from the user, our method addresses the determination of the number of signatures directly as a model selection problem. In addition, we introduce two new concepts of significant clinical relevance for evaluating the mutational profile. The advantages brought by our approach are shown by the analysis of real and synthetic data. The later is used to compare our approach against two alternative methods mostly used in the literature and with the same NMF parametrization as the one considered here. Our approach is robust to initial conditions and more accurate than competing alternatives. It also estimates the correct number of signatures even when other methods fail. Results on real data agree well with current knowledge.

Availability and Implementation

signeR is implemented in R and C ++, and is available as a R package at http://bioconductor.org/packages/signeR.

Supplementary information

Supplementary data are available at Bioinformatics online.
Technology and tuberculosis control: the OUT-TB Web experience
Authors: Guthrie Jennifer L , Alexander David C , Marchand-Austin Alex , Lam Karen , Whelan Michael , Lee Brenda , Furness Colin , Rea Elizabeth , Stuart Rebecca , Lechner Julia , Varia Monali , McLean Jennifer , Jamieson Frances B
Published: September 2016

Objective: Develop a tool to disseminate integrated laboratory, clinical, and demographic case data necessary for improved contact tracing and outbreak detection of tuberculosis (TB).

Methods: In 2007, the Public Health Ontario Laboratories implemented a universal genotyping program to monitor the spread of TB strains within Ontario. Ontario Universal Typing of TB (OUT-TB) Web utilizes geographic information system (GIS) technology with a relational database platform, allowing TB control staff to visualize genotyping matches and microbiological data within the context of relevant epidemiological and demographic data.

Results: OUT-TB Web is currently available to the 8 health units responsible for >85% of Ontario’s TB cases and is a valuable tool for TB case investigation. Users identified key features to implement for application enhancements, including an e-mail alert function, customizable heat maps for visualizing TB and drug-resistant cases, socioeconomic map layers, a dashboard providing TB surveillance metrics, and a feature for animating the geographic spread of strains over time.

Conclusion: OUT-TB Web has proven to be an award-winning application and a useful tool. Developed and enhanced using regular user feedback, future versions will include additional data sources, enhanced map and line-list filter capabilities, and development of a mobile app.
Are there two types of pulsars?
Authors: Contopoulos I.
Published: September 2016

In order to investigate the importance of dissipation in the pulsar magnetosphere, we decided to combine force-free with Aristotelian electrodynamics. We obtain solutions that are ideal (non-dissipative) everywhere except in an equatorial current sheet where Poynting flux from both hemispheres converges and is dissipated into particle acceleration and radiation. We find significant dissipative losses (up to about 50 per cent of the pulsar spin-down luminosity), similar to what is found in global Particle-In-Cell simulations in which particles are provided only on the stellar surface. We conclude that there might indeed exist two types of pulsars, strongly dissipative ones with particle injection only from the stellar surface, and ideal (weakly dissipative) ones with particle injection in the outer magnetosphere and in particular at the Y-point.
A strong-lensing elliptical galaxy in the MaNGA survey
Authors: Smith Russell J.
Published: September 2016

I report discovery of a new galaxy-scale gravitational lens system, identified using public data from the Mapping Galaxies at Apache Point Observatory (MaNGA) survey, as part of a systematic search for lensed background line emitters. The lens is SDSS J170124.01+372258.0, a giant elliptical galaxy with velocity dispersion σ = 256 km s−1, at a redshift of zl = 0.122. After modelling and subtracting the target galaxy light, the integral-field data cube reveals [O ii], [O iii] and Hβ emission lines corresponding to a source at zs = 0.791, forming an identifiable ring around the galaxy centre. If the ring is formed by a single lensed source, then the Einstein radius is REin ≈ 2.3 arcsec, projecting to ∼5 kpc at the distance of the lens. The total projected lensing mass is MEin = (3.6 ± 0.6) × 1011 Mȯ, and the total J-band mass-to-light ratio is 3.0 ± 0.7 solar units. Plausible estimates of the likely dark matter content could reconcile this with a Milky Way-like initial mass function (IMF), for which M/L ≈ 1.5 is expected, but heavier IMFs are by no means excluded with the present data. An alternative interpretation of the system, with a more complex source plane, is also discussed. The discovery of this system bodes well for future lens searches based on MaNGA and other integral-field spectroscopic surveys.
Report on the Fifth PANDA Symposium on “Anesthesia and Neurodevelopment in Children”
Authors: Miller Tonya L.K. , Park Raymond , Sun Lena S.
Published: September 2016

On April 16 and 17, 2016, the Pediatric Anesthesia and Neurodevelopment Assessment (PANDA) study held its fifth biennial symposium at the Morgan Stanley Children’s Hospital of New York. The PANDA symposium has served as a key forum for clinicians, researchers, and other major stakeholders to gather and review the current state of preclinical and clinical research related to anesthetic neurotoxicity in children. Goals of the meeting included assessing how current knowledge has translated and impacted clinical care of patients who may be at risk, and future directions for research and policy. The program participants represented a diverse group with a shared concern of potential anesthetic neurotoxicity in children. It included clinicians, preclinical and clinical researchers as well as representatives from government organizations (FDA [Food and Drug Administration] and National Institutes of Health). A total of 135 attended the symposium.
Summary of the Update Session on Clinical Neurotoxicity Studies
Authors: Pinyavat Teeda , Warner David O. , Flick Randall P. , McCann Mary Ellen , Andropoulos Dean B. , Hu Danquig , Sall Jeffrey W. , Spann Marisa N. , Ing Caleb
Published: September 2016

During the Fifth Pediatric Anesthesia Neurodevelopmental Assessment Symposium, experts and stakeholders met to present and discuss recent advances made in the study of neurodevelopmental outcomes after exposure to anesthetic drugs in infants and children. This article summarizes the update of 5 ongoing clinical studies: General Anesthesia compared to Spinal Anesthesia, Toxicity of Remifentanil and Dexmedetomidine, Mayo Anesthesia Safety in Kids, the University of California San Francisco human cohort study, and Columbia University Medical Center Neonatal Magnetic Resonance Imaging study. The purpose of this summary is to discuss the contributions and limitations of these studies, how they fit into the published literature, and what questions remain to be answered.
Optimal Timing of Surgical Procedures in Pediatric Patients
Authors: Ko Riva R. , Pinyavat Teeda , Stylianos Steven , Lambert Sarah M. , Anderson Richard C. , Gallin Pamela F. , Maxwell Lynne G. , Ward Christopher G. , Deshpande Jayant K. , Houck Constance S.
Published: September 2016

The Pediatric Anesthesia Neuro Development Assessment (PANDA) team at the Anesthesiology Department at Columbia University Medical Center held its fifth biennial symposium to discuss issues regarding potential neurotoxicity of anesthetic agents in pediatric patients. Overall optimal surgical timing as well as a “critical window” for surgery on a specialty specific basis are areas of focus for the American Academy of Pediatrics Surgical Advisory Panel. An ad hoc panel of pediatric surgical experts representing general surgery, urology, neurosurgery, and ophthalmology was assembled for this meeting and provided a dialogue focused on the benefits of early intervention versus potential anesthetic risk, addressing parental concerns, and the need for continued interdisciplinary collaboration in this area.
Sevoflurane Impairs Growth Cone Motility in Dissociated Murine Neurons
Authors: Ryu Yun Kyoung , Mathena Reilley P. , Lim Sanghee , Kwak Minhye , Xu Michael , Mintz Cyrus D.
Published: September 2016

Background:

Early postnatal exposure to general anesthetic agents causes a lasting impairment in learning and memory in animal models. One hypothesis to explain this finding is that exposure to anesthetic agents during critical points in neural development disrupts the formation of brain circuitry. Here, we explore the effects of sevoflurane on the neuronal growth cone, a specialization at the growing end of axons and dendrites that is responsible for the targeted growth that underlies connectivity between neurons.

Methods:

Dissociated neuronal cultures were prepared from embryonic mouse neocortex. Time-lapse images of live growth cones exposed to anesthetics were taken using differential interference contrast microscopy, and the rate of change of the area of the lamellipodia and the speed of the filopodial tip were quantified as measures of motility. The involvement of the p75 neurotropin receptor (p75NTR) was tested using inhibitors applied to the media and by a coimmunoprecipitation assay.

Results:

The rate of lamellipodial area change and filopodial tip velocity in both axonal and dendritic growth cones was significantly reduced with sevoflurane exposure between 2% and 6%. Motility could be substantially restored by treatment with Y27632 and TAT-peptide 5, which are inhibitors of Rho Kinase and p75NTR, respectively. Sevoflurane results in reduced coimmunoprecipitation of Rho-Guanosine-5′-diphosphate dissociation inhibitor after pulldown with p75NTR.

Conclusions:

Sevoflurane interferes with growth cone motility, which is a critical process in brain circuitry formation. Our data suggest that this may occur through an action on the p75NTR, which promotes growth inhibitory signaling by the Rho pathway.
Lisfranc injuries in children and adolescents
Authors: Hill Jaclyn F. , Heyworth Benton E. , Lierhaus Anneliese , Kocher Mininder S. , Mahan Susan T.
Published: September 2016

In this descriptive analysis of pediatric Lisfranc injuries, records of 56 children treated for bony or ligamentous Lisfranc injuries over a 12-year period were reviewed. Overall, 51% of fractures and 82% of sprains were sports-related (P=0.03). A total of 34% of the cohort underwent open reduction internal fixation, which was more common among patients with closed physes (67%). Full weight bearing was allowed in open reduction internal fixation patients at a mean of 14.5 weeks, compared to 6.5 weeks in the nonoperative group. Complications were rare (4%) and included physeal arrest in one patient and a broken, retained implant in one patient.
Cost analysis and performance in distal pediatric forearm fractures: is a short-arm cast superior to a sugar-tong splint?
Authors: Acree Joshua S. , Schlechter John , Buzin Scott
Published: September 2016

The aim of this study is to compare splint versus cast immobilization for maintaining alignment following closed reduction of distal 1/3 radius and both-bone forearm fractures. We performed a retrospective review of patient records between 5 and 14 years old with a distal 1/3 radius or radius and ulna fracture requiring reduction. A cost comparison was also performed using facility costs for materials. Reduction was maintained with acceptable alignment in most cases (94%). Although a sugar-tong splint slightly maintained fracture alignment better, this was not significant. Cost analysis favored initial placement of a short-arm cast ($23.59) versus a splint with later cast conversion ($26.95). Pediatric patients with a distal 1/3 radius and/or both-bone fracture requiring reduction maintain postreduction alignment irrespective of the immobilization method used, but initial placement of a short-arm cast is more cost-effective.
Septic shoulder presenting as a shoulder dislocation in the pediatric patient: a case report
Authors: Maguire Kathleen J. , Otsuka Norman Y.
Published: September 2016

Shoulder dislocation is relatively uncommon in the younger pediatric population. Because of the relative strength of the surrounding soft tissue structures of the shoulder compared with the proximal humeral physis, subluxation or dislocation resulting from a traumatic event or application of force is rare and instead a proximal humeral physeal injury occurs. Case presentation – We present a 5-year-old male who presented to the office with post-traumatic left shoulder pain for about 1 week. Radiographs of the left shoulder indicated inferior subluxation of the humeral head. He was ultimately diagnosed and treated for a septic shoulder. Septic arthritis of the glenohumeral joint accounts for about 3% of all septic arthritis cases. About half of the pediatric patients with a septic arthritis will present with a concomitant osteomyelitis about the joint involved. Widening of the glenohumeral joint and subluxation clinically as well as radiographically have been described in cases of large joint effusions because of an increase in intra-articular fluid in adults. This inferior subluxation is often noted without a frank dislocation. The case described in this report is unique in that this is the first to describe a pediatric septic shoulder presenting as a shoulder subluxation. Given the rarity of pediatric shoulder dislocations and subluxations, the pediatric orthopaedist and pediatrician should maintain a suspicion for a septic joint. Level of evidence: Level V.