bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of the intra-layer potential distributions and spatial currents on the performance of graphene SymFETs
Authors: Hasan Mehdi , Sensale-Rodriguez Berardi
Published: September 2015

In this paper, a two-dimensional (2-D) model for a graphene symmetric field effect transistor (SymFET), which considers (a) the intra-graphene layer potential distributions and (b) the internal current flows through the device, is presented and discussed. The local voltages along the graphene electrodes as well as the current-voltage characteristics of the device are numerically calculated based on a single-particle tunneling model. Our numerical results show that: (i) when the tunneling current is small, due to either a large tunneling thickness (≥ 2 atomic layers of BN) or a small coherence length, the voltage distributions along the graphene electrodes have almost zero variations upon including these distributed effects, (ii) when the tunnel current is large, due to either a small tunneling thickness (∼ 1 atomic layer of BN) or due to a large coherence length, the local voltage distributions along the graphene electrodes become appreciable and the device behavior deviates from that predicted by a 1-D approximation. These effects, which are not captured in one-dimensional SymFET models, can provide a better understanding about the electron dynamics in the device and might indicate potential novel applications for this proposed device.
Imaging a mouse’s brain through its skull
Authors: Wilson R. Mark
Published: September 2015

A modest change in the application of adaptive optics to light microscopy produces a dramatic increase in the field of view.
Lanthanide-doped upconversion nanoparticles
Authors: Bettinelli Marco , Carlos Luís , Liu Xiaogang
Published: September 2015

A new class of nanomaterials that convert near-IR radiation into tunable visible light has important implications for many fields of science and technology.
Climate change impacts: The growth of understanding
Authors: Weart Spencer
Published: September 2015

In this peculiar history, the main actors are committees and no seminal papers or scientific giants emerge. Seat-of-the-pants guesses made in the 1960s proved to be roughly correct, and the details are still being fleshed out today.
Photosynthetic fluorescence, from molecule to planet
Authors: Schlau-Cohen Gabriela S. , Berry Joseph
Published: September 2015

A small fraction of light absorbed by leaves is reemitted as fluorescence. Studies of that process at both large and small scales will help scientists better understand global photosynthesis and its connection to climate.
Substantial increase in concurrent droughts and heatwaves in the United States
Authors: Mazdiyasni Omid , AghaKouchak Amir
Published: September 2015

Significance

Climatic extremes cause significant damage to the environment and society, and can cause even more damage when multiple extremes occur simultaneously. This study shows that although there is no significant trend in meteorological drought, the concurrence of meteorological droughts and heatwaves shows statistically significant increases across the United States. We show that the tail of the distribution of concurrent drought and heatwave conditions has shifted toward more frequent and extreme concurrent extremes. Our study outlines a statistical approach for investigating continuous change in the cumulative distribution functions of climatic extremes.
Granular self-organization by autotuning of friction
Authors: Kumar Deepak , Nitsure Nitin , Bhattacharya S. , Ghosh Shankar
Published: September 2015

Significance

Self-organization is ubiquitous in nature, although a complete understanding of the phenomena in specific cases is rare. Here we elucidate a route to self-organization in a model granular system. The local rules of motion are extracted from the experiment. When converted into an algorithm, they simulate the main aspects of the experimental results. From this, a key ingredient for achieving robustness emerges, namely, a continuously variable relative fraction of time the objects spend in two distinct motional degrees of freedom, rolling and sliding. In so doing, they access a large range of effective friction coefficients that allows self-tuning of the system to adjust its response to changing environments and guarantees a protocol-insensitive unique final state, a previously unidentified paradigm for self-organization.
Beta oscillations define discrete perceptual cycles in the somatosensory domain
Authors: Baumgarten Thomas J. , Schnitzler Alfons , Lange Joachim
Published: September 2015

Significance

Our sensory system constantly receives multiple inputs, which are usually perceived as a seamless stream. Thus, perception is commonly regarded as a continuous process. Alternatively, a few phenomena and recent studies suggest that perception might work in a discrete and periodic sampling mode. In a human magnetoencephalography study, we challenged the common view of continuous perception. We demonstrate that neuronal oscillations in the alpha band and low beta band determine discrete perceptual sampling windows in primary somatosensory cortex. The current results elucidate how ongoing neuronal oscillations shape discrete perceptual cycles, which constitute the basis for a discontinuous and periodic nature of somatosensory perception.
Threat of plastic pollution to seabirds is global, pervasive, and increasing
Authors: Wilcox Chris , Van Sebille Erik , Hardesty Britta Denise
Published: September 2015

Significance

Plastic pollution in the ocean is a rapidly emerging global environmental concern, with high concentrations (up to 580,000 pieces per km
2
) and a global distribution, driven by exponentially increasing production. Seabirds are particularly vulnerable to this type of pollution and are widely observed to ingest floating plastic. We used a mixture of literature surveys, oceanographic modeling, and ecological models to predict the risk of plastic ingestion to 186 seabird species globally. Impacts are greatest at the southern boundary of the Indian, Pacific, and Atlantic Oceans, a region thought to be relatively pristine. Although evidence of population level impacts from plastic pollution is still emerging, our results suggest that this threat is geographically widespread, pervasive, and rapidly increasing.
Spin jam induced by quantum fluctuations in a frustrated magnet
Authors: Yang Junjie , Samarakoon Anjana , Dissanayake Sachith , Ueda Hiroaki , Klich Israel , Iida Kazuki , Pajerowski Daniel , Butch Nicholas P. , Huang Q. , Copley John R. D. , Lee Seung-Hun
Published: September 2015

Significance

We report experimental evidence for a glassy state induced by quantum fluctuations, a spin jam, that is realized in SrCr

9
p

Ga

12-9
p

O
19
[SCGO(
p
)], a highly frustrated magnet, in which the magnetic Cr
3+
(s = 3/2) ions form a quasi-two-dimensional triangular system of bipyramids. Our new experimental data and our theoretical spin jam model provide, for the first time, to our knowledge, a coherent understanding of the existing experimental data of this fascinating system. Furthermore, our findings strongly support the possible existence of purely topological glassy states.
Mutual regulation between
Satb2
and
Fezf2
promotes subcerebral projection neuron identity in the developing cerebral cortex
Authors: McKenna William L. , Ortiz-Londono Christian F. , Mathew Thomas K. , Hoang Kendy , Katzman Sol , Chen Bin
Published: September 2015

Significance

Mutations in special AT-rich sequence-binding protein 2 (
Satb2
) cause severe intellectual deficiency in humans. However, its function in brain development is not completely understood. Our study focuses on the function of
Satb2
in specifying cortical projection neuron fates. We find that, although
Satb2
activates the expression of some subcerebral neuronal genes, it also inhibits the expression of other genes that are expressed in subcerebral neurons. We report that
Satb2
promotes
Fezf2
and
Sox5
expression in subcerebral neurons, and that
Fezf2
in turn inhibits high-level
Satb2
expression. We show that the mutual regulation between
Satb2
and
Fezf2
is essential for
Satb2
to promote subcerebral neuron fate.
Competitive exclusion by autologous antibodies can prevent broad HIV-1 antibodies from arising
Authors: Luo Shishi , Perelson Alan S.
Published: September 2015

Significance

Broadly neutralizing antibodies against HIV have recently been discovered, but their highly mutated nature and late emergence in infection make it difficult to infer how they arose. As a step to understanding their development, we investigate antibody–virus coevolution, using a mathematical model. Here we find that broadly neutralizing antibodies in principle may arise earlier and be less mutated, but that competition between broad responses and initial autologous antibody responses delays their emergence. It may be possible to reduce this competition and elicit broadly neutralizing antibodies earlier than previously thought by using a vaccine with diverse viral strains.
The adaptive radiation of lichen-forming Teloschistaceae is associated with sunscreening pigments and a bark-to-rock substrate shift
Authors: Gaya Ester , Fernández-Brime Samantha , Vargas Reinaldo , Lachlan Robert F. , Gueidan Cécile , Ramírez-Mejía Martín , Lutzoni François
Published: September 2015

Significance

The tempo of diversification of life can be accelerated by fortuitous ecological opportunity or by phenotypic innovation. In this study, we document how both factors are likely to have played a role in the origin and success of a major fungal lineage, the Teloschistaceae (comprising ∼1% of all fungi). Anthraquinone pigments are found in a widespread, but scattered, range of fungi and plants, but are particularly abundant in the lichen-forming Teloschistaceae, where they provide sunlight protection, especially needed when growing in arid deserts of the world. We found that anthraquinones evolved in these lichens, in conjunction with an ecological switch to exposed, rocky environments, allowing them to colonize swathes of unexploited habitats worldwide and sparking an acceleration in diversification.
Receptor sequestration in response to β-arrestin-2 phosphorylation by ERK1/2 governs steady-state levels of GPCR cell-surface expression
Authors: Paradis Justine S. , Ly Stevenson , Blondel-Tepaz Élodie , Galan Jacob A. , Beautrait Alexandre , Scott Mark G. H. , Enslen Hervé , Marullo Stefano , Roux Philippe P. , Bouvier Michel
Published: September 2015

Significance

ERK1/2 are important G protein-coupled receptor (GPCR) signaling effectors, but their role as possible GPCR regulators remains largely uncharted. We report that ERK1/2 activation leads to the phosphorylation of β-arrestin-2 on Ser14 and Thr276, promoting the intracellular sequestration of unliganded GPCRs. This subcellular redistribution results in the dampening of cell responsiveness to GPCRs’ ligand-mediated activation, positioning ERK1/2 as both a downstream effector and a negative regulator of GPCRs. Because ERK1/2 also is stimulated by receptor tyrosine kinases and is deregulated in many diseases, and because GPCRs respond to a large number of hormones and neurotransmitters, this newly uncovered regulatory process is poised to play a central role in controlling cell responsiveness in health and disease.
Micromechanics of cellularized biopolymer networks
Authors: Jones Christopher A. R. , Cibula Matthew , Feng Jingchen , Krnacik Emma A. , McIntyre David H. , Levine Herbert , Sun Bo
Published: September 2015

Significance

Mechanical interactions between cells, mediated by the elastic response of the extracellular matrix to active applied forces, play a critical role in developmental biology, wound healing, and cancer progression. This work applies sophisticated technical means, both in experiment and computational modeling, to investigate the micron-scale mechanics of a popular model of this medium, a collagen gel. The results obtained show clearly that on the cellular scale, there are significant spatial variations in the micromechanics due to network heterogeneities.
Electrostatic coating enhances bioavailability of insecticides and breaks pyrethroid resistance in mosquitoes
Authors: Andriessen Rob , Snetselaar Janneke , Suer Remco A. , Osinga Anne J. , Deschietere Johan , Lyimo Issa N. , Mnyone Ladslaus L. , Brooke Basil D. , Ranson Hilary , Knols Bart G. J. , Farenhorst Marit
Published: September 2015

Significance

Conventional mosquito-control methods are becoming less effective in controlling mosquito-borne diseases because of widespread resistance against safe and recommended public health insecticides. Therefore innovative and effective alternatives are urgently needed. We present a novel method for exposing mosquitoes to insecticides that uses electrostatic forces to bind insecticide particles. Results show that this method increases exposure of mosquitoes to such an extent that even those that have developed high levels of resistance can be killed effectively. The ability to boost the efficacy of WHO-recommended insecticides provides a significant benefit to the field of vector-borne disease control and will further the development of novel resistance-breaking control tools.
Insect’s intestinal organ for symbiont sorting
Authors: Ohbayashi Tsubasa , Takeshita Kazutaka , Kitagawa Wataru , Nikoh Naruo , Koga Ryuichi , Meng Xian-Ying , Tago Kanako , Hori Tomoyuki , Hayatsu Masahito , Asano Kozo , Kamagata Yoichi , Lee Bok Luel , Fukatsu Takema , Kikuchi Yoshitomo
Published: September 2015

Significance

In general, animals have a mouth for feeding, an anus for defecation, and a gut connecting them for digestion and absorption. However, we discovered that the stinkbug’s gut is functionally disconnected in the middle by a previously unrecognized organ for symbiont sorting, which blocks food fluid and nonsymbiotic bacteria but selectively allows passing of a specific bacterial symbiont. Though very tiny and inconspicuous, the organ governs the configuration and specificity of stinkbug gut symbiosis, wherein the posterior gut region is devoid of food flow, populated by a specific bacterial symbiont, and transformed into an isolated organ for symbiosis. Mutant analyses showed that the symbiont’s flagellar motility is needed for passing the host organ, highlighting intricate host–symbiont interactions underpinning the symbiont sorting process.
Functional divisions for visual processing in the central brain of flying
Drosophila
Authors: Weir Peter T. , Dickinson Michael H.
Published: September 2015

Although anatomy is often the first step in assigning functions to neural structures, it is not always clear whether architecturally distinct regions of the brain correspond to operational units. Whereas neuroarchitecture remains relatively static, functional connectivity may change almost instantaneously according to behavioral context. We imaged panneuronal responses to visual stimuli in a highly conserved central brain region in the fruit fly,
Drosophila
, during flight. In one substructure, the fan-shaped body, automated analysis revealed three layers that were unresponsive in quiescent flies but became responsive to visual stimuli when the animal was flying. The responses of these regions to a broad suite of visual stimuli suggest that they are involved in the regulation of flight heading. To identify the cell types that underlie these responses, we imaged activity in sets of genetically defined neurons with arborizations in the targeted layers. The responses of this collection during flight also segregated into three sets, confirming the existence of three layers, and they collectively accounted for the panneuronal activity. Our results provide an atlas of flight-gated visual responses in a central brain circuit.
Label-free DNA imaging in vivo with stimulated Raman scattering microscopy
Authors: Lu Fa-Ke , Basu Srinjan , Igras Vivien , Hoang Mai P. , Ji Minbiao , Fu Dan , Holtom Gary R. , Neel Victor A. , Freudiger Christian W. , Fisher David E. , Xie X. Sunney
Published: September 2015

Significance

Microscopic imaging of DNA has to rely on the use of fluorescent staining, an exogenous labeling in biological and biomedical studies, which often leads to uncertainty with respect to the quality and homogeneity of the staining. Label-free imaging of DNA will enable noninvasive visualization of live cell nuclei in both human and animals. Spontaneous Raman microspectroscopy offers label-free chemical contrast for DNA imaging; however, its slow imaging speed hampers its wide application for in vivo and dynamic studies. Here we developed a novel and simple approach with multicolor stimulated Raman scattering microscopy to evaluate rapid DNA imaging, which can be applied to both in vivo DNA dynamic studies and instant label-free human skin cancer diagnosis.
Mode of interaction of TRIP13 AAA-ATPase with the Mad2-binding protein p31comet and with mitotic checkpoint complexes
Authors: Miniowitz-Shemtov Shirly , Eytan Ety , Kaisari Sharon , Sitry-Shevah Danielle , Hershko Avram
Published: September 2015

Significance

The mitotic checkpoint system is important to ensure accurate segregation of chromosomes in mitosis. It acts by the formation of a mitotic checkpoint complex (MCC), which inhibits the ubiquitin ligase anaphase-promoting complex/cyclosome (APC/C). When the checkpoint is turned off, MCC is disassembled by the joint action of an ATP-utilizing enzyme, thyroid receptor interacting protein 13 (TRIP13), and a Mad2-binding protein, p31comet. It is not well understood how p31comet targets TRIP13 to disassemble MCC. We show here that p31comet and MCC mutually promote the binding of each other to oligomeric TRIP13 and propose a model for the mode of the action of TRIP13 in MCC disassembly. Thus, the results reveal an important molecular mechanism in the inactivation of the mitotic checkpoint.
Expression of collagenase in Flavobacterium psychrophilum isolated from cold-water disease-affected ayu (Plecoglossus altivelis)
Authors: Nakayama Hitoshi , Tanaka Keisuke , Teramura Naoko , Hattori Shunji
Published: September 2015

The collagenase activity and the fpcol gene were examined in Flavobacterium psychrophilum isolates from cold-water disease (CWD)-affected ayu, Plecoglossus altivelis. Collagenase expression was closely related to the accumulated mortality of CWD-affected ayu. RT-qPCR and bacterial challenge experiments showed that F. psychrophilum ayu isolate WA-1 expressed the fpcol gene more actively and was more virulent than ayu isolate WA-2. The amago (Oncorhynchus masou) isolate WB-1, which possesses a pseudo-fpcol gene, was not harmful to ayu. Hitherto, the well-studied metalloproteases Fpp1 and Fpp2 have been considered virulence factors. However, the most virulent isolate against ayu (WA-1) showed no Fpp activity because of a deletion mutation or an insertion of a transposon in the fpp genes. The less virulent WA-2 isolate showed only Fpp1 activity. Taken together, these results suggest that collagenolytic activity, but not Fpp activity, is related to the virulence of F. psychrophilum isolates in CWD-affected ayu.
Banking crises and social policy: the case of Latin America and the Caribbean
Authors: Gautam Rana S.
Published: September 2015

This paper examines the social policy consequences of systemic banking crises or financial crises in 13 Latin American and Caribbean countries between 1990 and 2010. It takes a rationalist approach to political economy to analyse the effect of these crises on aggregate social policy spending and on four distinct social welfare policy programmes – education, health, housing, and social security – benefits of which vary across social groups. The results indicate that banking crises have a statistically strong negative effect on aggregate social expenditure, but the impact is not uniform across the four programmes. While social security spending increases during the course of crises, health and education expenditures decrease in the same period. The results reinforce the view that distributional conflicts overshadow governments’ response and the burden of crises is unevenly shared in a heterogeneous society. These findings are robust to alternative specifications.
NOS1-derived nitric oxide promotes NF-κB transcriptional activity through inhibition of suppressor of cytokine signaling-1
Authors: Baig Mirza Saqib , Zaichick Sofia V. , Mao Mao , de Abreu Andre L. , Bakhshi Farnaz R. , Hart Peter C. , Saqib Uzma , Deng Jing , Chatterjee Saurabh , Block Michelle L. , Vogel Stephen M. , Malik Asrar B. , Consolaro Marcia E.L. , Christman John W. , Minshall Richard D. , Gantner Benjamin N. , Bonini Marcelo G.
Published: September 2015

The NF-κB pathway is central to the regulation of inflammation. Here, we demonstrate that the low-output nitric oxide (NO) synthase 1 (NOS1 or nNOS) plays a critical role in the inflammatory response by promoting the activity of NF-κB. Specifically, NOS1-derived NO production in macrophages leads to proteolysis of suppressor of cytokine signaling 1 (SOCS1), alleviating its repression of NF-κB transcriptional activity. As a result, NOS1−/− mice demonstrate reduced cytokine production, lung injury, and mortality when subjected to two different models of sepsis. Isolated NOS1−/− macrophages demonstrate similar defects in proinflammatory transcription on challenge with Gram-negative bacterial LPS. Consistently, we found that activated NOS1−/− macrophages contain increased SOCS1 protein and decreased levels of p65 protein compared with wild-type cells. NOS1-dependent S-nitrosation of SOCS1 impairs its binding to p65 and targets SOCS1 for proteolysis. Treatment of NOS1−/− cells with exogenous NO rescues both SOCS1 degradation and stabilization of p65 protein. Point mutation analysis demonstrated that both Cys147 and Cys179 on SOCS1 are required for its NO-dependent degradation. These findings demonstrate a fundamental role for NOS1-derived NO in regulating TLR4-mediated inflammatory gene transcription, as well as the intensity and duration of the resulting host immune response.
Kidins220/ARMS binds to the B cell antigen receptor and regulates B cell development and activation
Authors: Fiala Gina J. , Janowska Iga , Prutek Fabiola , Hobeika Elias , Satapathy Annyesha , Sprenger Adrian , Plum Thomas , Seidl Maximilian , Dengjel Jörn , Reth Michael , Cesca Fabrizia , Brummer Tilman , Minguet Susana , Schamel Wolfgang W.A.
Published: September 2015

B cell antigen receptor (BCR) signaling is critical for B cell development and activation. Using mass spectrometry, we identified a protein kinase D–interacting substrate of 220 kD (Kidins220)/ankyrin repeat–rich membrane-spanning protein (ARMS) as a novel interaction partner of resting and stimulated BCR. Upon BCR stimulation, the interaction increases in a Src kinase–independent manner. By knocking down Kidins220 in a B cell line and generating a conditional B cell–specific Kidins220 knockout (B-KO) mouse strain, we show that Kidins220 couples the BCR to PLCγ2, Ca2+, and extracellular signal-regulated kinase (Erk) signaling. Consequently, BCR-mediated B cell activation was reduced in vitro and in vivo upon Kidins220 deletion. Furthermore, B cell development was impaired at stages where pre-BCR or BCR signaling is required. Most strikingly, λ light chain–positive B cells were reduced sixfold in the B-KO mice, genetically placing Kidins220 in the PLCγ2 pathway. Thus, our data indicate that Kidins220 positively regulates pre-BCR and BCR functioning.
Fox reimbedding and Bing submanifolds
Authors: Nakamura Kei
Published: September 2015

Let

M
M

be an orientable closed connected

3
3

-manifold. We introduce the notion of an amalgamated Heegaard genus of

M
M

with respect to a closed separating

2
2

-manifold

F
F

, and use it to show that the following two statements are equivalent: (i) a compact connected 3-manifold

Y
Y

can be embedded in

M
M

so that the exterior of the image of

Y
Y

is a union of handlebodies; and (ii) a compact connected

3
3

-manifold

Y
Y

can be embedded in

M
M

so that every knot in

M
M

can be isotoped to lie within the image of

Y
Y

.

Our result can be regarded as a common generalization of the reimbedding theorem by Fox (1948) and the characterization of

3
3

-sphere by Bing (1958), as well as more recent results of Hass and Thompson (1989) and Kobayashi and Nishi (1994).
Non-periodic bifurcations for surface diffeomorphisms
Authors: Horita Vanderlei , Muniz Nivaldo , Sabini Paulo
Published: September 2015

We prove that a “positive probability” subset of the boundary of the set of hyperbolic (Axiom A) surface diffeomorphisms with no cycles

H

\mathcal {H}

is constituted by Kupka-Smale diffeomorphisms: all periodic points are hyperbolic and their invariant manifolds intersect transversally. Lack of hyperbolicity arises from the presence of a tangency between a stable manifold and an unstable manifold, one of which is not associated to a periodic point. All these diffeomorphisms that we construct lie on the boundary of the same connected component of

H

\mathcal {H}

.
A hybrid bayesian approach for genome-wide association studies on related individuals
Authors: Yazdani A. , Dunson D. B.
Published: September 2015

Motivation: Both single marker and simultaneous analysis face challenges in GWAS due to the large number of markers genotyped for a small number of subjects. This large p small n problem is particularly challenging when the trait under investigation has low heritability.

Method: In this article, we propose a two-stage approach that is a hybrid method of single and simultaneous analysis designed to improve genomic prediction of complex traits. In the first stage, we use a Bayesian independent screening method to select the most promising SNPs. In the second stage, we rely on a hierarchical model to analyze the joint impact of the selected markers. The model is designed to take into account familial dependence in the different subjects, while using local-global shrinkage priors on the marker effects.

Results: We evaluate the performance in simulation studies, and consider an application to animal breeding data. The illustrative data analysis reveals an encouraging result in terms of prediction performance and computational cost.

Contact:  Akram.Yazdani@uth.tmc.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
NgsRelate: a software tool for estimating pairwise relatedness from next-generation sequencing data
Authors: Korneliussen Thorfinn Sand , Moltke Ida
Published: September 2015

Motivation: Pairwise relatedness estimation is important in many contexts such as disease mapping and population genetics. However, all existing estimation methods are based on called genotypes, which is not ideal for next-generation sequencing (NGS) data of low depth from which genotypes cannot be called with high certainty.

Results: We present a software tool, NgsRelate, for estimating pairwise relatedness from NGS data. It provides maximum likelihood estimates that are based on genotype likelihoods instead of genotypes and thereby takes the inherent uncertainty of the genotypes into account. Using both simulated and real data, we show that NgsRelate provides markedly better estimates for low-depth NGS data than two state-of-the-art genotype-based methods.

Availability: NgsRelate is implemented in C++ and is available under the GNU license at www.popgen.dk/software.

Contact: ida@binf.ku.dk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Filaments from the galaxy distribution and from the velocity field in the local universe
Authors: Libeskind Noam I. , Tempel Elmo , Hoffman Yehuda , Tully R. Brent , Courtois Hélène
Published: September 2015

The cosmic web that characterizes the large-scale structure of the Universe can be quantified by a variety of methods. For example, large redshift surveys can be used in combination with point process algorithms to extract long curvilinear filaments in the galaxy distribution. Alternatively, given a full 3D reconstruction of the velocity field, kinematic techniques can be used to decompose the web into voids, sheets, filaments and knots. In this Letter, we look at how two such algorithms – the Bisous model and the velocity shear web – compare with each other in the local Universe (within 100 Mpc), finding good agreement. This is both remarkable and comforting, given that the two methods are radically different in ideology and applied to completely independent and different data sets. Unsurprisingly, the methods are in better agreement when applied to unbiased and complete data sets, like cosmological simulations, than when applied to observational samples. We conclude that more observational data is needed to improve on these methods, but that both methods are most likely properly tracing the underlying distribution of matter in the Universe.
Encapsulation of Purple Maize Anthocyanins in Phosphorylated Starch by Spray Drying
Authors: García‐Tejeda Yunia Verónica , Salinas‐Moreno Yolanda , Hernández‐Martínez Ángel Ramón , Martínez‐Bustos Fernando
Published: September 2015

Phosphorylated starch was prepared and evaluated as an encapsulating agent for purple maize anthocyanins under several inlet air temperatures (130–170°C) and different concentrations (10–20%) of phosphorylated starch during the spray‐drying process. Phosphorylation was carried out by reactive extrusion with 4% sodium tripolyphosphate as a crosslinking agent at pH 5. The derivatization resulted in the loss of crystallinity, low viscosity, and high solubility of the starch. A band at 1,569 cm−1 in the FTIR spectrum attributed to the purple maize anthocyanins was observed in the microcapsules. The drying process yield ranged from 25.67 to 49.11%. The highest drying yield (49.11%) with encapsulation productivity of 87.63% resulted with 20% solids at 170°C. The higher the concentration of phosphorylated starch, the better the anthocyanin protection during the spray‐drying process was, in which smoother microcapsules were observed by scanning electron microscopy.
The Effects of Dexmedetomidine and Remifentanil on Hemodynamic Stability and Analgesic Requirement After Craniotomy: A Randomized Controlled Trial
Authors: Rajan Shobana , Hutcherson Matthew T. , Sessler Daniel I. , Kurz Andrea , Yang Dongsheng , Ghobrial Michael , Liu Jinbo , Avitsian Rafi
Published: September 2015

Background:

Anesthesia for craniotomies should blunt responses to noxious stimuli, whereas subsequently leaving patients sufficiently alert for early neurological evaluation. The aim was to compare postoperative blood pressure control, pain, and opioid requirement after anesthesia with dexmedetomidine versus remifentanil. We therefore tested 2 primary hypotheses: (1) intraoperative administration of dexmedetomidine provides better control of postoperative blood pressure than remifentanil; and (2) patients given dexmedetomidine have less postoperative pain and use less opioid.

Materials and Methods:

Adults having elective brain tumor excisions under balanced general anesthesia with endotracheal intubation were randomized to an infusion of remifentanil (0.08 to 0.15 μg/kg/min, n=71) or dexmedetomidine (0.2 to 0.7 μg/kg/h, n=68). Patients also received propofol, rocuronium, fentanyl, and sevoflurane. The mean arterial pressure (MAP) and pain were recorded at 15, 30, 45, 60, and 90 postoperative minutes. Outcomes were assessed with joint hypothesis testing, evaluating noninferiority and superiority.

Results:

Compared with remifentanil, the use of dexmedetomidine was associated with reduced postoperative MAP (88±12 vs. 98±11 mm Hg), with estimated mean difference (97.5% confidence interval) of −10 (−13, −4) mm Hg, P<0.001, and mean visual analog pain score (2.9±2.6 vs. 5.1±2.4 points), with estimated mean difference of −5 (−10, −3) points, P<0.001, and required less median opioid consumption (5 [0, 10] vs. 10 [7, 15] mg morphine equivalents), with estimated median difference of −5 (−10, −3) mg, P<0.001. Dexmedetomidine was both noninferior and superior to remifentanil in maintaining postoperative hemodynamics and providing improved pain control.

Conclusions:

Intraoperative dexmedetomidine better controlled postoperative MAP and provided superior analgesia in patients undergoing craniotomy.
A Comparison of Macintosh and Airtraq Laryngoscopes for Endotracheal Intubation in Adult Patients With Cervical Spine Immobilization Using Manual In Line Axial Stabilization: A Prospective Randomized Study
Authors: Vijayakumar Vinodhadevi , Rao Shwethapriya , Shetty Nanda
Published: September 2015

Background:

During cervical spine immobilization using Manual In Line Axial Stabilization (MILS), it is difficult to visualize the larynx by aligning the oropharyngeolaryngeal axes using Macintosh laryngoscope. Theoretically, Airtraq an anatomically shaped blade with endotracheal tube guide channel offers advantage over Macintosh. We hypothesized that intubation would be easier and faster with Airtraq compared with Macintosh laryngoscope.

Materials and Methods:

Ninety anesthetized adult patients with normal airways were intubated by experienced anesthesiologists after cervical immobilization with MILS either with Macintosh or Airtraq. Primary outcomes compared were successful intubation, and degree of difficulty of intubation as assessed by Intubation Difficulty Scale (IDS) score. Secondary outcomes compared were duration of laryngoscopy and intubation, degree of difficulty of intubation as assessed by Numerical Rating Scale score, soft tissue, and dental trauma.

Results:

All 90 patients were successfully intubated in the first attempt. Intubation as assessed by IDS score was easier in Airtraq (84.44%) in contrast to slight difficulty in the Macintosh (77.78%) group; Numerical Rating Scale score was easy in both the groups (Airtraq—91.12%; Macintosh—93.34%). The median (interquartile range [IQR]) time for laryngoscopy, (12 s [IQR, 8 to 17.5) vs. 8 s [IQR, 6 to 12]); total duration for intubation (25 s [IQR, 20-33] vs. 22 s [IQR, 18-27.5]) were prolonged in Airtraq group in comparison to Macintosh group.

Conclusions:

In anesthetized adult patients with MILS compared with Macintosh, Airtraq provides equal success rate of intubation, statistically significant (although clinically insignificant) longer duration for laryngoscopy and intubation. Intubation with Airtraq was significantly easier than Macintosh as assessed by the IDS score.
Frontal Sinus Mucocele Formation as a Late Complication of External Dacrocystorhinostomy
Authors: Malik Adeela , Syed Irfan , Osborne Sarah , Toma Abbad
Published: September 2015

Two cases of frontal sinus mucocele post external approach dacrocystorhinostomy (DCR) surgery are reported. The possible anatomical causes of this condition are discussed and in particular, attention is drawn to the consideration of frontal sinus mucocele in patients presenting with frontal sinus symptoms post-DCR surgery.
The Impact of Pelvic Floor and Lower Gastrointestinal Symptoms on Quality of Life in Women With Systemic Sclerosis
Authors: Umar Sarah B. , Griffing Leroy , Garcia Heidi , Foxx-Orenstein Amy E. , DiBaise John K. , Crowell Michael D.
Published: September 2015

Background:

Systemic sclerosis (SSc) patients with gastrointestinal (GI) involvement have a lower quality of life (QoL) and while the impact of upper GI symptoms on QoL in SSc patients has been described few data exist on the presence and impact of lower gastrointestinal (LGI) and pelvic floor symptoms in SSc. Our goal was to assess the prevalence of these symptoms in women with SSc and evaluate their impact on QoL. A secondary hypothesis was that the impact of LGI symptoms on QoL is mediated by depression.

Study:

Women with SSc (n=175) attending an outpatient scleroderma clinic completed multiple validated questionnaires. Pelvic floor and LGI symptoms included fecal incontinence (FI), urinary incontinence (UI), dual incontinence (DI), chronic constipation, diarrhea, and pelvic pain. The Student t tests adjusted for multiple comparisons were used to evaluate group differences at the 0.05 level.

Results:

Complete data were available for 160 women. FI was reported by 65, UI by 64, DI by 40, chronic constipation by 94, diarrhea by 82, and pelvic pain by 35 of SSc patients. Overall QoL was reduced in SSc patients with FI (0.96 vs. 0.63; P=0.007), UI (0.96 vs. 0.65; P=0.01), DI (1.11 vs. 0.67; P=0.002), and pelvic pain (1.01 vs. 0.70; P=0.04). Antidepressant use was reported by 26%. The negative impact on QoL in patients with pelvic floor symptoms was partially mediated by depression.

Conclusions:

Women with SSc suffer from an increased prevalence of LGI and pelvic floor symptoms including FI, UI, diarrhea, constipation, and pelvic pain and this effect seems to be partially mediated by depression.
Health‐Related Quality of Life in Spanish Children With Coeliac Disease
Authors: Barrio Josefa , Román Enriqueta , Cilleruelo MaLuz , Márquez Manuela , Mearin MaLuisa , Fernández Cristina
Published: September 2015

Objectives:

The aim of the study was to assess health‐related quality of life (HRQOL) using the Coeliac Disease Dutch Questionnaire (CDDUX) in Spanish children with coeliac disease.

Methods:

The CDDUX was cross‐culturally adapted according to international consensus guidelines. HRQOL was assessed in coeliac members of the Madrid Coeliac Association ages 8 to 18 years using the adapted CDDUX. Cronbach α coefficient was determined as a measure of intraquestionnaire reliability and intraclass correlation coefficients as a measure of reliability between scores awarded by children and parents. Demographic and clinical variables associated with HRQOL were also assessed.

Results:

A total of 1602 children of 3122 registered Madrid Coeliac Association members ages 8 to 18 years were invited to participate. The questionnaire was completed by 480 families (30%): 214 only by parents, 214 by parents and their children, and 52 only by children. Cronbach α coefficient for the total score for parents was 0.90, and for children 0.88 (0.75–0.90 by scales). Mean total (standard deviation [SD]) HRQOL scores in children and parents were 55.5 (SD 12.7) and 53.89 (SD 12.19), respectively, with no differences detected in paired comparisons between the 2 groups. Significantly worse HRQOL scores were recorded in children showing a nonclassical clinical presentation, in those not adhering to treatment and in those reporting difficulties in following the diet.

Conclusions:

The CDDUX questionnaire emerged as reliable for use in Spanish children with celiac disease. Overall, both children and parents felt the disease had no substantial negative impacts on patient HRQOL.
Prevalence of Anterior Cutaneous Nerve Entrapment Syndrome in a Pediatric Population With Chronic Abdominal Pain
Authors: Siawash Murid , de Jager‐Kievit Jenneke W.A. , Ten Walther Tjon A. , Roumen Rudi M. , Scheltinga Marc R.
Published: September 2015

Objective:

Anterior cutaneous nerve entrapment syndrome (ACNES) is a frequently overlooked condition causing chronic abdominal pain (CAP). The objective of the present study was to investigate the rate of ACNES in a pediatric outpatient cohort with CAP.

Methods:

A cross‐sectional cohort study was conducted in a population 10 to 18 years of age consulting a pediatric outpatient department with new‐onset CAP during a 2 years’ time period. All individuals were identified through a standard hospital registration system. History, physical examination, diagnosis, and success of treatment were obtained in patients who were diagnosed as having ACNES.

Results:

Twelve of 95 adolescents with CAP were found to be experiencing ACNES. Carnett sign was positive at the lateral border of the rectus abdominus muscle in all 12. Altered skin sensation was present in 11 of 12 patients with ACNES. Six weeks after treatment (1–3 injections, n = 5; neurectomy, n = 7), pain was absent in 11 patients.

Conclusions:

ACNES is present in 1 of 8 adolescents presenting with CAP to a pediatric outpatient department of a teaching hospital. Simple physical examinational testing allows for the diagnosis. Treatments including nerve blocks or surgery are beneficial in most.
Standardizing Falls Reporting: Using Data From Adverse Event Reporting to Drive Quality Improvement
Authors: Gardner Lea Anne , Bray Phyllis J. , Finley Edward , Sterner Carly , Ignudo Thomas L. , Stauffer Cherie L. , Kincaid Shawn A. , Marella William M.
Published: September 2015

Objective

To enhance the value of the Pennsylvania Patient Safety Reporting System (PA-PSRS) falls reports by developing a falls reporting program that standardizes falls reporting and provides timely benchmarked falls rates and process measurement reports hospitals can use to identify areas of improvement in their falls program.

Methods

The new PA-PSRS falls reporting program requires adherence to standardized definitions of falls to generate standardized, customizable analytic reports. An advisory committee and statewide survey guided the development of the program, data definitions, system features and functionality, and methods for stratifying reporting criteria.

Results

Three real-time falls outcomes and 2 falls process reports with multiple configurable options were created. A falls dashboard was developed based on gaps in falls risk assessment processes identified in PA-PSRS falls event reports. Six months after launching the program, 41.3% of Pennsylvania hospitals enrolled. The Authority's annual survey indicated 82.9% of participating hospitals found that the new falls analytic reports were somewhat useful to very useful. Preliminary impact on the falls with harm rate has been limited, a less than 1% reduction, but the ability to identify specific organizational and patient risk factors in a timely manner provides hospitals with opportunities to target falls prevention resources more effectively.

Conclusions

The PA-PSRS falls reporting program's standardized definition of falls offers new analytic reports that include falls rates with benchmarking data and a falls dashboard. The benchmarking data allow hospitals to compare themselves to peer hospitals statewide. The newly expanded PA-PSRS falls reporting program has turned an adverse event-reporting program into a quality improvement tool.
Genome-wide annotation of microRNA primary transcript structures reveals novel regulatory mechanisms
Authors: Chang Tsung-Cheng , Pertea Mihaela , Lee Sungyul , Salzberg Steven L. , Mendell Joshua T.
Published: September 2015

Precise regulation of microRNA (miRNA) expression is critical for diverse physiologic and pathophysiologic processes. Nevertheless, elucidation of the mechanisms through which miRNA expression is regulated has been greatly hindered by the incomplete annotation of primary miRNA (pri-miRNA) transcripts. While a subset of miRNAs are hosted in protein-coding genes, the majority of pri-miRNAs are transcribed as poorly characterized noncoding RNAs that are 10's to 100's of kilobases in length and low in abundance due to efficient processing by the endoribonuclease DROSHA, which initiates miRNA biogenesis. Accordingly, these transcripts are poorly represented in existing RNA-seq data sets and exhibit limited and inaccurate annotation in current transcriptome assemblies. To overcome these challenges, we developed an experimental and computational approach that allows genome-wide detection and mapping of pri-miRNA structures. Deep RNA-seq in cells expressing dominant-negative DROSHA resulted in much greater coverage of pri-miRNA transcripts compared with standard RNA-seq. A computational pipeline was developed that produces highly accurate pri-miRNA assemblies, as confirmed by extensive validation. This approach was applied to a panel of human and mouse cell lines, providing pri-miRNA transcript structures for 1291/1871 human and 888/1181 mouse miRNAs, including 594 human and 425 mouse miRNAs that fall outside protein-coding genes. These new assemblies uncovered unanticipated features and new potential regulatory mechanisms, including links between pri-miRNAs and distant protein-coding genes, alternative pri-miRNA splicing, and transcripts carrying subsets of miRNAs encoded by polycistronic clusters. These results dramatically expand our understanding of the organization of miRNA-encoding genes and provide a valuable resource for the study of mammalian miRNA regulation.
Isolation of Peroxisomes from Yeast
Authors: Cramer Jana , Effelsberg Daniel , Girzalsky Wolfgang , Erdmann Ralf
Published: September 2015

Peroxisomes are multifunctional, dynamic organelles present in nearly all eukaryotic cells. Determining their structural and functional characteristics often requires obtaining isolated and purified peroxisomes via subcellular fractionation. Subcellular fractionation techniques are generally based on a three-step procedure: preparation of a cell-free homogenate (postnuclear supernatant), generation of an organellar pellet by differential centrifugation, and density gradient centrifugation. Here we introduce methods for small-scale isolation of peroxisomes from yeast cells using different gradient media as well as large-scale purification using a two-step gradient centrifugation.
Construction of Multifragment Plasmids by Homologous Recombination in Yeast
Authors: van Leeuwen Jolanda , Andrews Brenda , Boone Charles , Tan Guihong
Published: September 2015

Over the past decade, the focus of cloning has shifted from constructing plasmids that express a single gene of interest to creating multigenic constructs that contain entire pathways or even whole genomes. Traditional cloning methods that rely on restriction digestion and ligation are limited by the number and size of fragments that can efficiently be combined. Here, we focus on the use of homologous-recombination-based DNA manipulation in the yeast Saccharomyces cerevisiae for the construction of plasmids from multiple DNA fragments. Owing to its simplicity and high efficiency, cloning by homologous recombination in yeast is very accessible and can be applied to high-throughput construction procedures. Its applications extend beyond yeast-centered purposes and include the cloning of large mammalian DNA sequences and entire bacterial genomes.
Total Internal Reflection Fluorescence Microscopy
Authors: Yildiz Ahmet , Vale Ronald D.
Published: September 2015

The goal in fluorescence microscopy is to detect the signal of fluorescently labeled molecules with great sensitivity and minimal background noise. In epifluorescence microscopy, it is difficult to observe weak signals along the optical axis, owing to the overpowering signal from the out-of-focus particles. Confocal microscopy uses a small pinhole to produce thin optical sections (∼500 nm), but the pinhole rejects some of the in-focus photons as well. Total internal reflection fluorescence microscopy (TIRFM) is a wide-field illumination technique that illuminates only the molecules near the glass coverslip. It has become widely used in biological imaging because it has a significantly reduced background and high temporal resolution capability. TIRFM has been used to study proteins in vitro as well as signaling cascades by hormones and neurotransmitters, intracellular cargo transport, actin dynamics near the plasma membrane, and focal adhesions in living cells. Because TIRF illumination is restricted to the glass–water interface and does not penetrate the specimen, it is well suited for studying the interaction of molecules within or near the cell membrane in living cells.