bluuebunny/crossref_metadata_2025 huggingface dataset:
Biglycan stimulates VEGF expression in endothelial cells by activating the TLR signaling pathway
Authors: Hu Lei , Zang Ming-de , Wang He-xiao , Li Jian-fang , Su Li-ping , Yan Min , Li Chen , Yang Qiu-meng , Liu Bing-ya , Zhu Zheng-gang
Published: August 2016

Biglycan (BGN) is an important component of the extracellular matrix (ECM) that is implicated in a variety of human cancers. In our previous study, we reported that BGN was overexpressed in gastric cancer (GC) tissues and promoted cancer metastasis. Moreover, the tubular formation capacity in HUVECs was promoted by stimulation with culture media from BGN‐overexpressing GC cells, but the exact underlying mechanism is still unknown. The purpose of this study was to determine the role and molecular mechanism of BGN in VEGF expression in endothelial cells. We found that BGN stimulation of endothelial cells increased the interaction between NF‐kB and the HIF‐1α promoter, leading to enhanced promoter activity and increased HIF‐1α mRNA levels, as well as augmented HIF‐1 activity that resulted in VEGF expression. All of this was dependent on the interaction of BGN with its receptors, TLR2 and TLR4. Moreover, we found that BGN enhanced endothelial cell migration and proliferation, as well as tube formation, in a TLR signaling pathway‐dependent manner. In addition, endothelial cell‐derived VEGF in turn was found to act on GC cells and promotes their migration. The combined findings of our current and previous studies suggest that BGN secreted from GC cells into the tumor stroma promotes GC development, as well as its progression, potentially through the chronic activation of tumor angiogenesis.
How Do Gullies Form on Mars?
Authors: Stanley Sarah
Published: August 2016

New orbiter data support an important role for seasonal frost—not liquid water—in the formation of Martian gullies.
Microarray analysis and real-time PCR assay developed to find biomarkers for mercury-contaminated soil
Authors: Hou Jing , Liu Xinhui , Cui Baoshan , Bai Junhong , Wang Xiangke
Published: August 2016

The evaluation of mercury (Hg) toxicity in agricultural soil is of great concern because its bioavailability and bioaccumulation in organisms through the food chain can have adverse effects on human health.
Task- and Talker-Specific Gains in Auditory Training
Authors: Barcroft Joe , Spehar Brent , Tye-Murray Nancy , Sommers Mitchell
Published: August 2016

Purpose

This investigation focused on generalization of outcomes for auditory training by examining the effects of task and/or talker overlap between training and at test.

Method

Adults with hearing loss completed 12 hr of meaning-oriented auditory training and were placed in a group that trained on either multiple talkers or a single talker. A control group also completed 12 hr of training in American Sign Language. The experimental group’s training included a 4-choice discrimination task but not an open-set sentence test. The assessment phase included the same 4-choice discrimination task and an open-set sentence test, the Iowa Sentences Test (Tyler, Preece, & Tye-Murray, 1986).

Results

Improvement on 4-choice discrimination was observed in the experimental group as compared with the control group. Gains were (a) highest when the task and talker were the same between training and assessment; (b) second highest when the task was the same but the talker only partially so; and (c) third highest when task and talker were different.

Conclusions

The findings support applications of transfer-appropriate processing to auditory training and favor tailoring programs toward the specific needs of the individuals being trained for tasks, talkers, and perhaps, for stimuli, in addition to other factors.
Auditory Training With Frequent Communication Partners
Authors: Tye-Murray Nancy , Spehar Brent , Sommers Mitchell , Barcroft Joe
Published: August 2016

Purpose

Individuals with hearing loss engage in auditory training to improve their speech recognition. They typically practice listening to utterances spoken by unfamiliar talkers but never to utterances spoken by their most frequent communication partner (FCP)—speech they most likely desire to recognize—under the assumption that familiarity with the FCP's speech limits potential gains. This study determined whether auditory training with the speech of an individual's FCP, in this case their spouse, would lead to enhanced recognition of their spouse's speech.

Method

Ten couples completed a 6-week computerized auditory training program in which the spouse recorded the stimuli and the participant (partner with hearing loss) completed auditory training that presented recordings of their spouse.

Results

Training led participants to better discriminate their FCP's speech. Responses on the Client Oriented Scale of Improvement (Dillon, James, & Ginis, 1997) indicated subjectively that training reduced participants' communication difficulties. Peformance on a word identification task did not change.

Conclusions

Results suggest that auditory training might improve the ability of older participants with hearing loss to recognize the speech of their spouse and might improve communication interactions between couples. The results support a task-appropriate processing framework of learning, which assumes that human learning depends on the degree of similarity between training tasks and desired outcomes.
New Directions for Auditory Training: Introduction
Authors: Sommers Mitchell
Published: August 2016

Purpose

The purpose of this research forum article is to provide an overview of a collection of invited articles on contemporary issues in auditory training.
Low Gilbert damping in Co2FeSi and Fe2CoSi films
Authors: Sterwerf Christian , Paul Soumalya , Khodadadi Behrouz , Meinert Markus , Schmalhorst Jan-Michael , Buchmeier Mathias , Mewes Claudia K. A. , Mewes Tim , Reiss Günter
Published: August 2016

Thin highly textured Fe1+xCo2–xSi (0 ≤ x ≤ 1) films were prepared on MgO (001) substrates by magnetron co-sputtering. Magneto-optic Kerr effect (MOKE) and ferromagnetic resonance (FMR) measurements were used to investigate the composition dependence of the magnetization, the magnetic anisotropy, the gyromagnetic ratio, and the relaxation of the films. Both MOKE and FMR measurements reveal a pronounced fourfold anisotropy for all films. In addition, we found a strong influence of the stoichiometry on the anisotropy as the cubic anisotropy strongly increases with increasing Fe concentration. The gyromagnetic ratio is only weakly dependent on the composition. We find low Gilbert damping parameters for all films with values down to 0.0012±0.00010.0007 for Fe1.75Co1.25Si. The effective damping parameter for Co2FeSi is found to be 0.0018±0.00040.0034. We also find a pronounced anisotropic relaxation, which indicates significant contributions of two-magnon scattering processes that is strongest along the easy axes of the films. This makes thin Fe1+xCo2–xSi films ideal materials for the application in spin transfer-torque magnetic RAM (STT-MRAM) devices.
Role of melt behavior in modifying oxidation distribution using an interface incorporated model in selective laser melting of aluminum-based material
Authors: Gu Dongdong , Dai Donghua
Published: August 2016

A transient three dimensional model for describing the molten pool dynamics and the response of oxidation film evolution in the selective laser melting of aluminum-based material is proposed. The physical difference in both sides of the scan track, powder-solid transformation and temperature dependent physical properties are taken into account. It shows that the heat energy tends to accumulate in the powder material rather than in the as-fabricated part, leading to the formation of the asymmetrical patterns of the temperature contour and the attendant larger dimensions of the molten pool in the powder phase. As a higher volumetric energy density is applied (≥1300 J/mm3), a severe evaporation is produced with the upward direction of velocity vector in the irradiated powder region while a restricted operating temperature is obtained in the as-fabricated part. The velocity vector continuously changes from upward direction to the downward one as the scan speed increases from 100 mm/s to 300 mm/s, promoting the generation of the debris of the oxidation films and the resultant homogeneous distribution state in the matrix. For the applied hatch spacing of 50 μm, a restricted remelting phenomenon of the as-fabricated part is produced with the upward direction of the convection flow, significantly reducing the turbulence of the thermal-capillary convection on the breaking of the oxidation films, and therefore, the connected oxidation films through the neighboring layers are typically formed. The morphology and distribution of the oxidation are experimentally acquired, which are in a good agreement with the results predicted by simulation.
Analysis of stimulated Raman photoacoustics in frequency domain: A feasibility study
Authors: Li Gaoming , Gao Fei , Feng Xiaohua , Zheng Yuanjin
Published: August 2016

The frequency domain analysis of stimulated Raman Photoacoustic (PA) induced by laser pulses with Gaussian and rectangular temporal profiles is presented. Utilizing the pulsed laser with nanosecond and microsecond pulse width with Gaussian temporal profile, the frequency component of the PA signals cannot be differentiated between the stimulated Raman PA and the linear optical absorption PA, which is limited by the response bandwidth of biological tissue. When the laser pulses with rectangular temporal profile are used, we deduced the PA expression and numerically derived its frequency spectrum. The frequency components of PA signal induced by the stimulated Raman phonons is more than that induced by optical absorption in some low frequency ranges, which is inside the bandwidth of tissue system. Therefore, stimulated Raman PA signal can be distinguished from the linear optical absorption PA signal in frequency domain. Numerical simulations were conducted in this paper to demonstrate the proposition and feasibility of stimulated Raman PA in frequency domain, which will be experimentally validated in future work.
Analysis on vertical directional couplers with long range surface plasmons for multilayer optical routing
Authors: Alam B. , Veroli A. , Benedetti A.
Published: August 2016

A structure featuring vertical directional coupling of long-range surface plasmon polaritons between strip waveguides at λ = 1.55 μm is investigated with the aim of producing efficient elements that enable optical multilayer routing for 3D photonics. We have introduced a practical computational method to calculate the interaction on the bent part. This method allows us both to assess the importance of the interaction in the bent part and to control it by a suitable choice of the fabrication parameters that helps also to restrain effects due to fabrication issues. The scheme adopted here allows to reduce the insertion losses compared with other planar and multilayer devices.
Characterization of elastic interactions in GaAs/Si composites by optically pumped nuclear magnetic resonance
Authors: Wood Ryan M. , Tokarski John T. , McCarthy Lauren A. , Stanton Christopher J. , Bowers Clifford R.
Published: August 2016

Elastic interactions in GaAs/Si bilayer composite structures were studied by optically pumped nuclear magnetic resonance (OPNMR). The composites were fabricated by epoxy bonding of a single crystal of GaAs to a single crystal of Si at 373 K followed by selective chemical etching of the GaAs at room temperature to obtain a series of samples with GaAs thickness varying from 37 μm to 635 μm, while the Si support thickness remained fixed at 650 μm. Upon cooling to below 10 K, a biaxial tensile stress developed in the GaAs film due to differential thermal contraction. The strain perpendicular to the plane of the bilayer and localized near the surface of the GaAs was deduced from the quadrupolar splitting of the Gallium-71 OPNMR resonance. Strain relaxation by bowing of the composite was observed to an extent that depended on the relative thickness of the GaAs and Si layers. The variation of the strain with GaAs layer thickness was found to be in good agreement with a general analytical model for the elastic relationships in composite media.
Manipulation of superparamagnetic beads on patterned Au/Co/Au multilayers with perpendicular magnetic anisotropy
Authors: Jarosz A. , Holzinger D. , Urbaniak M. , Ehresmann A. , Stobiecki F.
Published: August 2016

The magnetophoresis of water-suspended 4 μm-diameter superparamagnetic beads above topographically patterned, sputter deposited Ti(4 nm)/Au(60 nm)/[Co(0.7 nm)/Au(1 nm)] × 3 multilayers with perpendicular magnetic anisotropy was investigated. The results impressively demonstrate that the magnetic stray field landscape above the stripe structure when superimposed with an external, slowly rotating, field enables the directed transport of magnetic beads across the stripe panel with velocities up to 12 μm s−1.
Effect of atomic layer deposition temperature on current conduction in Al2O3 films formed using H2O oxidant
Authors: Hiraiwa Atsushi , Matsumura Daisuke , Kawarada Hiroshi
Published: August 2016

To develop high-performance, high-reliability gate insulation and surface passivation technologies for wide-bandgap semiconductor devices, the effect of atomic layer deposition (ALD) temperature on current conduction in Al2O3 films is investigated based on the recently proposed space-charge-controlled field emission model. Leakage current measurement shows that Al2O3 metal-insulator-semiconductor capacitors formed on the Si substrates underperform thermally grown SiO2 capacitors at the same average field. However, using equivalent oxide field as a more practical measure, the Al2O3 capacitors are found to outperform the SiO2 capacitors in the cases where the capacitors are negatively biased and the gate material is adequately selected to reduce virtual dipoles at the gate/Al2O3 interface. The Al2O3 electron affinity increases with the increasing ALD temperature, but the gate-side virtual dipoles are not affected. Therefore, the leakage current of negatively biased Al2O3 capacitors is approximately independent of the ALD temperature because of the compensation of the opposite effects of increased electron affinity and permittivity in Al2O3. By contrast, the substrate-side sheet of charge increases with increasing ALD temperature above 210 °C and hence enhances the current of positively biased Al2O3 capacitors more significantly at high temperatures. Additionally, an anomalous oscillatory shift of the current-voltage characteristics with ALD temperature was observed in positively biased capacitors formed by low-temperature (≤210 °C) ALD. This shift is caused by dipoles at the Al2O3/underlying SiO2 interface. Although they have a minimal positive-bias leakage current, the low-temperature-grown Al2O3 films cause the so-called blisters problem when heated above 400 °C. Therefore, because of the absence of blistering, a 450 °C ALD process is presently the most promising technology for growing high-reliability Al2O3 films.
Magnetic microstructure and magnetic properties of uniaxial itinerant ferromagnet Fe3GeTe2
Authors: León-Brito N. , Bauer E. D. , Ronning F. , Thompson J. D. , Movshovich R.
Published: August 2016

Magnetic force microscopy was used to observe the magnetic microstructure of Fe3GeTe2 at 4 K on the (001) surface. The surface magnetic structure consists of a two-phase domain branching pattern that is characteristic for highly uniaxial magnets in the plane perpendicular to the magnetic easy axis. The average surface magnetic domain width Ds = 1.3 μm determined from this pattern, in combination with intrinsic properties calculated from bulk magnetization data (the saturation magnetization Ms = 376 emu/cm3 and the uniaxial magnetocrystalline anisotropy constant Ku = 1.46 × 107 erg/cm3), was used to determine the following micromagnetic parameters for Fe3GeTe2 from phenomenological models: the domain wall energy γw = 4.7 erg/cm2, the domain wall thickness δw = 2.5 nm, the exchange stiffness constant Aex = 0.95 × 10−7 erg/cm, the exchange length lex = 2.3 nm, and the critical single domain particle diameter dc = 470 nm.
Simulation of microscale gas flow in heterogeneous porous media based on the lattice Boltzmann method
Authors: Zhao Jianlin , Yao Jun , Li Aifen , Zhang Min , Zhang Lei , Yang Yongfei , Sun Hai
Published: August 2016

A microscale multi-relaxation-time lattice Boltzmann model with the regularization procedure is adopted to simulate gas flow in different porous media. The diffuse reflection boundary condition is used to deal with the random solid boundaries. Because of the complex geometry of the pores, the characteristic length is no longer a constant but a function of the pore locations for the porous media. A rational method is proposed to obtain the local characteristic lengths of the porous media for the microscale gas flow simulations. The simulation results show that gas flow characteristics in different flow regions are notably different. In the continuum flow region and slip flow region, the gas flow abilities in different pores are quite different. The effect of heterogeneity of the porous media on gas velocity distribution is very obvious. As the Knudsen number increases, the differences of gas flow abilities in different pores decrease. For gas flow in the strong transition flow region and free molecular flow region, the gas flow abilities in small pores are similar to those in large pores and the effect of heterogeneity becomes small. Such phenomena are mainly caused by the different gas flow mechanisms in different flow regions. In addition, two commonly used apparent permeability calculation models are evaluated by the simulation results and a better coefficient for the Klinkenberg model is proposed according to the simulation results.
A multi-band spoof surface plasmon polariton coupling metasurface based on dispersion engineering
Authors: Dong Guoxiang , Shi Hongyu , Li Wei , He Yuchen , Zhang Anxue , Xu Zhuo , Wei Xiaoyong , Xia Song
Published: August 2016

We propose a metasurface to achieve multi-band helicity dependent directional spoof surface plasmon polaritons (SPPs) coupling for circular polarized light in the microwave range. Our work shows that the coupling frequencies of spoof SPPs on the gradient metasurface are related to the dispersion relations of the metasurface, which indicate the desired coupling frequency can be manipulated by dispersion engineering. The proposed metasurface has counter-directional phase gradients for different helicity incidents and possesses multiple different dispersion relations by carefully designing the geometric parameters of each unit, which leads to the multi-band helicity-controlled directional spoof SPPs coupling. Both the simulation and experiment show that the multi-band helicity-controlled directional spoof SPPs coupling is achieved with a high efficiency.
Electronic states and electrical conductivity of the Si(111) native oxide surface adsorbed with electron donor tetrakis(dimethylamino)ethylene
Authors: Yoshimoto Shinya , Shiozawa Yuichiro , Koitaya Takanori , Noritake Hiroyuki , Mukai Kozo , Yoshinobu Jun
Published: August 2016

Electronic states and electrical conductivity of the native oxide Si(111) surface adsorbed with an electron donor tetrakis(dimethylamino)ethylene (TDAE) were investigated using ultraviolet photoelectron spectroscopy, X-ray photoelectron spectroscopy (XPS), and independently driven four-probe conductivity measurements. The formation of positively charged TDAE species is confirmed by the downward shift of the vacuum level by 1.45 eV, the absence of HOMO level in the valence band, and observation of the positively charged state in the N 1s XPS spectra. Si 2p XPS spectra and four-probe conductivity measurements revealed that TDAE adsorption induces an increase in downward band bending and a reduction in electrical resistance of the surface, respectively. The sheet conductivity and the electron density of the surface are 1.1 μS/◻ and 4.6 × 109 cm−2, respectively, after TDAE adsorption, and they are as high as 350% of the original surface. These results demonstrate that the electron density of the semiconductor surface is successfully controlled by the electron donor molecule TDAE.
First-principles study of twin grain boundaries in epitaxial BaSi2 on Si(111)
Authors: Baba Masakazu , Kohyama Masanori , Suemasu Takashi
Published: August 2016

Epitaxial films of BaSi2 on Si(111) for solar cell applications possess three epitaxial variants and exhibit a minority carrier diffusion length (ca. 9.4 μm) much larger than the domain size (ca. 0.2 μm); thus, the domain boundaries (DBs) between the variants do not act as carrier recombination centers. In this work, transmission electron microscopy (TEM) was used to observe the atomic arrangements around the DBs in BaSi2 epitaxial films on Si(111), and the most stable atomic configuration was determined by first-principles calculations based on density functional theory to provide possible interface models. Bright-field TEM along the a-axis of BaSi2 revealed that each DB was a twin boundary between two different epitaxial variants, and that Ba(II) atoms form hexagons containing central Ba(I) atoms in both the bulk and DB regions. Four possible interface models containing Ba(I)-atom interface layers were constructed, each consistent with TEM observations and distinguished by the relationship between the Si tetrahedron arrays in the two domains adjacent across the interface. This study assessed the structural relaxation of initial interface models constructed from surface slabs terminated by Ba(I) atoms or from zigzag surface slabs terminated by Si tetrahedra and Ba(II) atoms. In these models, the interactions or relative positions between Si tetrahedra appear to dominate the relaxation behavior and DB energies. One of the four interface models whose relationship between first-neighboring Si tetrahedra across the interface was the same as that in the bulk was particularly stable, with a DB energy of 95 mJ/m2. There were no significant differences in the partial densities of states and band gaps between the bulk and DB regions, and it was therefore concluded that such DBs do not affect the minority carrier properties of BaSi2.
In vivo visualization method by absolute blood flow velocity based on speckle and fringe pattern using two-beam multipoint laser Doppler velocimetry
Authors: Kyoden Tomoaki , Naruki Shoji , Akiguchi Shunsuke , Ishida Hiroki , Andoh Tsugunobu , Takada Yogo , Momose Noboru , Homae Tomotaka , Hachiga Tadashi
Published: August 2016

Two-beam multipoint laser Doppler velocimetry (two-beam MLDV) is a non-invasive imaging technique able to provide an image of two-dimensional blood flow and has potential for observing cancer as previously demonstrated in a mouse model. In two-beam MLDV, the blood flow velocity can be estimated from red blood cells passing through a fringe pattern generated in the skin. The fringe pattern is created at the intersection of two beams in conventional LDV and two-beam MLDV. Being able to choose the depth position is an advantage of two-beam MLDV, and the position of a blood vessel can be identified in a three-dimensional space using this technique. Initially, we observed the fringe pattern in the skin, and the undeveloped or developed speckle pattern generated in a deeper position of the skin. The validity of the absolute velocity value detected by two-beam MLDV was verified while changing the number of layers of skin around a transparent flow channel. The absolute velocity value independent of direction was detected using the developed speckle pattern, which is created by the skin construct and two beams in the flow channel. Finally, we showed the relationship between the signal intensity and the fringe pattern, undeveloped speckle, or developed speckle pattern based on the skin depth. The Doppler signals were not detected at deeper positions in the skin, which qualitatively indicates the depth limit for two-beam MLDV.
Generic phase diagram of binary superlattices
Authors: Tkachenko Alexei V.
Published: August 2016

Significance

Self-assembled superlattices represent one of the most promising trends in current nano- and colloidal sciences. Their potential applications range from photonics and plasmonics to catalysis and biomedical devices. This paper introduces a simple but general and remarkably rich theoretical model that provides an explanation for the observed morphological diversity and high degree of universality in superlattice self-assembly. The model describes binary system of mutually attractive sticky spheres of different sizes. An intuitive geometric procedure is used for constructing the phase diagram at variable composition and size ratio. The great conceptual value of this model is combined with its potential for predicting phase behavior for a broad range of self-assembly scenarios: DNA mediated, electrostatically driven, or induced by controlled drying.
FERONIA interacts with ABI2-type phosphatases to facilitate signaling cross-talk between abscisic acid and RALF peptide in
Arabidopsis
Authors: Chen Jia , Yu Feng , Liu Ying , Du Changqing , Li Xiushan , Zhu Sirui , Wang Xianchun , Lan Wenzhi , Rodriguez Pedro L. , Liu Xuanming , Li Dongping , Chen Liangbi , Luan Sheng
Published: August 2016

Significance

Receptor-like kinase FERONIA (FER) not only serves as a receptor for growth-regulating rapid alkalinization factor (RALF) peptide but also acts as an important node in a variety of other signaling pathways, including plant responses to hormones, pathogens, and abiotic stresses. However, the mechanism underlying FER actions in these signaling cross-talks remain largely unknown. Our previous work identified a molecular relay that allows FER to inhibit abscisic acid (ABA) response through activation of a small G protein to enhance the activity of the clade A protein phosphatase type 2C (PP2C) ABA Insensitive 2 (ABI2), a repressor of ABA response. In this study, we found that ABI2 can directly interact and dephosphorylate FER, providing a feedback mechanism for RALF activation of FER.
MYC-nick promotes cell migration by inducing fascin expression and Cdc42 activation
Authors: Anderson Sarah , Poudel Kumud Raj , Roh-Johnson Minna , Brabletz Thomas , Yu Ming , Borenstein-Auerbach Nofit , Grady William N. , Bai Jihong , Moens Cecilia B. , Eisenman Robert N. , Conacci-Sorrell Maralice
Published: August 2016

Significance

The MYC family of transcription factors is deregulated in a broad range of cancers and drives the expression of genes that mediate biomass accumulation and promote cell proliferation and tumor initiation. We find that MYC can also trigger tumor cell migration and metastasis independently of its transcriptional activity, via its conversion to MYC-nick, a truncated form of MYC localized in the cytoplasm. MYC-nick promotes reorganization of the actin cytoskeleton by inducing expression of the actin-bundling protein fascin and by activating the Rho GTPase Cdc42, both of which lead to formation of filopodia, cellular structures known to drive cell migration. Our work links the repurposing of the MYC transcription factor to altered cytoskeletal structure and tumor cell metastatic behavior.
The Impact of Blood Pressure and Visceral Adiposity on the Association of Serum Uric Acid With Albuminuria in Adults Without Full Metabolic Syndrome
Authors: Krajcoviechova Alena , Tremblay Johanne , Wohlfahrt Peter , Bruthans Jan , Tahir Muhmmad Ramzan , Hamet Pavel , Cifkova Renata
Published: August 2016

BACKGROUND

The impact of metabolic phenotypes on the association of uricemia with urinary albumin/creatinine ratio (uACR) remains unresolved. We evaluated the association between serum uric acid and uACR in persons with 0, and 1–2 metabolic syndrome (MetS) components and determined the modification effects of visceral adiposity index (VAI), mean arterial pressure (MAP), and fasting glucose on this association.

METHODS

Using data from a cross-sectional survey of a representative Czech population aged 25–64 years (n = 3612), we analyzed 1,832 persons without decreased glomerular filtration rate <60ml/min/1.73 m2, diabetes, and MetS. MetS components were defined using the joint statement of the leading societies.

RESULTS

Of the 1,832 selected participants, 64.1% (n = 1174) presented with 1–2 MetS components (age 46.3±11.2; men 51.7%), whereas 35.9% (n = 658) were free of any component (age 39.4±10.0; men 34.2 %). In fully adjusted multiple linear regression models for uricemia, uACR was an independent factor for increase in uric acid levels only in persons with 1–2 MetS components (standardized beta (Sβ) 0.048; P = 0.024); however, not in those without any component (Sβ 0.030; P = 0.264). Uric acid levels increased by the interaction of uACR with VAI (Sβ 0.06; P = 0.012), and of uACR with MAP (Sβ 0.05; P = 0.009). Finally, the association of uACR with uricemia was confined to persons whose VAI together with MAP were ≥the median of 1.35 and 98mm Hg, respectively (Sβ 0.190; P < 0.001).

CONCLUSIONS

We demonstrated a strong modification effect of VAI and MAP on the association between uACR and uricemia, which suggests obesity-related hypertension as the underlying mechanism.
A likelihood ratio-based method to predict exact pedigrees for complex families from next-generation sequencing data
Authors: Heinrich Verena , Kamphans Tom , Mundlos Stefan , Robinson Peter N , Krawitz Peter M
Published: August 2016

Motivation

Next generation sequencing technology considerably changed the way we screen for pathogenic mutations in rare Mendelian disorders. However, the identification of the disease-causing mutation amongst thousands of variants of partly unknown relevance is still challenging and efficient techniques that reduce the genomic search space play a decisive role. Often segregation- or linkage analysis are used to prioritize candidates, however, these approaches require correct information about the degree of relationship among the sequenced samples. For quality assurance an automated control of pedigree structures and sample assignment is therefore highly desirable in order to detect label mix-ups that might otherwise corrupt downstream analysis.

Results

We developed an algorithm based on likelihood ratios that discriminates between different classes of relationship for an arbitrary number of genotyped samples. By identifying the most likely class we are able to reconstruct entire pedigrees iteratively, even for highly consanguineous families. We tested our approach on exome data of different sequencing studies and achieved high precision for all pedigree predictions. By analyzing the precision for varying degrees of relatedness or inbreeding we could show that a prediction is robust down to magnitudes of a few hundred loci.

Availability and Implementation

A java standalone application that computes the relationships between multiple samples as well as a Rscript that visualizes the pedigree information is available for download as well as a web service at www.gene-talk.de.

Supplementary information

Supplementary data are available at Bioinformatics online.
Imbalanced multi-label learning for identifying antimicrobial peptides and their functional types
Authors: Lin Weizhong , Xu Dong
Published: August 2016

Motivation: With the rapid increase of infection resistance to antibiotics, it is urgent to find novel infection therapeutics. In recent years, antimicrobial peptides (AMPs) have been utilized as potential alternatives for infection therapeutics. AMPs are key components of the innate immune system and can protect the host from various pathogenic bacteria. Identifying AMPs and their functional types has led to many studies, and various predictors using machine learning have been developed. However, there is room for improvement; in particular, no predictor takes into account the lack of balance among different functional AMPs.

Results: In this paper, a new synthetic minority over-sampling technique on imbalanced and multi-label datasets, referred to as ML-SMOTE, was designed for processing and identifying AMPs’ functional families. A novel multi-label classifier, MLAMP, was also developed using ML-SMOTE and grey pseudo amino acid composition. The classifier obtained 0.4846 subset accuracy and 0.16 hamming loss.

Availability and Implementation: A user-friendly web-server for MLAMP was established at http://www.jci-bioinfo.cn/MLAMP.

Contacts:  linweizhong@jci.edu.cn or xudong@missouri.edu
Disrupting ER-associated protein degradation suppresses the abscission defect of a weak hae hsl2 mutant in Arabidopsis
Authors: Baer John , Taylor Isaiah , Walker John C.
Published: August 2016

In Arabidopsis thaliana , the process of abscission, or the shedding of unwanted organs, is mediated by two genes, HAESA ( HAE ) and HAESA-LIKE 2 ( HSL2 ), encoding receptor-like protein kinases (RLKs). The double loss-of-function mutant hae-3 hsl2-3 is completely deficient in floral abscission, but, interestingly, the hae-3 hsl2-9 mutant displays a less severe defect. This mutant was chosen for an ethyl methanesulfonate (EMS) screen to isolate enhancer and suppressor mutants, and two such suppressors are the focus of this study. Pooled DNA from the F 2 generation of a parental backcross was analyzed by genome sequencing to reveal candidate genes, two of which complement the suppressor phenotype. These genes, EMS-MUTAGENIZED BRI1 SUPPRESSOR 3 ( EBS3 ) and EBS4 , both encode mannosyltransferases involved in endoplasmic reticulum (ER)-associated degradation (ERAD) of proteins. Further analysis of these suppressor lines revealed that suppressor mutations are acting solely on the partially functional hsl2-9 mutant receptor to modify the abscission phenotype. Expressing a hsl2-9–yellow fluorescent protein (YFP) transgene in ebs3 mutants yields a higher fluorescent signal than in EBS3 / ebs3, suggesting that these mutants restore abscission by disrupting ERAD to allow accumulation of the hsl2-9 receptor, which probably escapes degradation to be trafficked to the plasma membrane to regain signaling.
Detection of burning ashes from thermonuclear X-ray bursts
Authors: Kajava J. J. E. , Nättilä J. , Poutanen J. , Cumming A. , Suleimanov V. , Kuulkers E.
Published: August 2016

When neutron stars (NS) accrete gas from low-mass binary companions, explosive nuclear burning reactions in the NS envelope fuse hydrogen and helium into heavier elements. The resulting thermonuclear (type-I) X-ray bursts produce energy spectra that are fit well with black bodies, but a significant number of burst observations show deviations from Planck spectra. Here we present our analysis of RXTE/PCA observations of X-ray bursts from the NS low-mass X-ray binary HETE J1900.1-2455. We have discovered that the non-Planckian spectra are caused by photoionization edges. The anticorrelation between the strength of the edges and the colour temperature suggests that the edges are produced by the nuclear burning ashes that have been transported upwards by convection and become exposed at the photosphere. The atmosphere model fits show that occasionally the photosphere can consist entirely of metals, and that the peculiar changes in blackbody temperature and radius can be attributed to the emergence and disappearance of metals in the photosphere. As the metals are detected already in the Eddington-limited phase, it is possible that a radiatively driven wind ejects some of the burning ashes into the interstellar space.
Single molecule tracking of Ace1p in Saccharomyces cerevisiae defines a characteristic residence time for non-specific interactions of transcription factors with chromatin
Authors: Ball David A , Mehta Gunjan D , Salomon-Kent Ronit , Mazza Davide , Morisaki Tatsuya , Mueller Florian , McNally James G , Karpova Tatiana S
Published: August 2016

In vivo single molecule tracking has recently developed into a powerful technique for measuring and understanding the transient interactions of transcription factors (TF) with their chromatin response elements. However, this method still lacks a solid foundation for distinguishing between specific and non-specific interactions. To address this issue, we took advantage of the power of molecular genetics of yeast. Yeast TF Ace1p has only five specific sites in the genome and thus serves as a benchmark to distinguish specific from non-specific binding. Here, we show that the estimated residence time of the short-residence molecules is essentially the same for Hht1p, Ace1p and Hsf1p, equaling 0.12–0.32 s. These three DNA-binding proteins are very different in their structure, function and intracellular concentration. This suggests that (i) short-residence molecules are bound to DNA non-specifically, and (ii) that non-specific binding shares common characteristics between vastly different DNA-bound proteins and thus may have a common underlying mechanism. We develop new and robust procedure for evaluation of adverse effects of labeling, and new quantitative analysis procedures that significantly improve residence time measurements by accounting for fluorophore blinking. Our results provide a framework for the reliable performance and analysis of single molecule TF experiments in yeast.
Feasibility and efficacy of an extended trial of home-based working memory training for pediatric brain tumor survivors: a pilot study
Authors: Carlson-Green Bonnie , Puig Jennifer , Bendel Anne
Published: August 2016

Background.

Impaired working memory appears to play a key role in some of the neurocognitive late effects of pediatric brain tumor treatments, including declines in intellectual and executive functioning. Recent studies of pediatric cancer survivors suggest Cogmed® Working Memory Training is effective at improving working memory, although pediatric brain tumor survivors may demonstrate a less robust response than children with other cancers. The current study sought to determine if an extended course of Cogmed (35 sessions) was both feasible and efficacious for brain tumor survivors and if improvements were observable in near-transfer and far-transfer working memory measures as well as parent rating scores at 6 months post-treatment.

Methods.

Twenty pediatric brain tumor survivors ages 8 to 18 years with working memory deficits completed 35 sessions of Cogmed. Assessments of working memory and academic skills were completed at baseline, completion of training, and 6-month follow-up and parents completed questionnaires at baseline and 6-month follow-up.

Results.

Participants showed significant improvements in working memory at training completion and 6-month follow-up and math achievement at 6-month follow-up. Parents reported executive functioning improvements at follow-up as compared with baseline. Participants’ program-based working memory skills did not change significantly between sessions 25 and 35, suggesting that extended training did not provide additional benefit.

Conclusions.

This study replicates and extends previous research by: (1) demonstrating that brain tumor survivors at high risk for neurocognitive late effects can complete and benefit from working memory training, (2) identifying a point of diminished returns on training time investment, and (3) demonstrating benefits 6 months post-intervention.
Pivotal therapeutic trials for infiltrating gliomas and how they affect clinical practice
Authors: Lukas Rimas V , Mrugala Maciej M
Published: August 2016

The therapeutic landscape of the management of low- and high-grade infiltrating gliomas continues to evolve. Daily clinical decision making in neuro-oncology clinics across the US is frequently challenging, especially for anaplastic and low grade primary brain tumors. The focus of this review is centered on treatments which are approved by the FDA and/or featured in the NCCN Guidelines. Systemic therapy trials using a variety of agents such as temozolomide, bevacizumab, and procarbazine, lomustine, vincristine (PCV), and lastly trials of local therapies including surgical trials using carmustine impregnated wafers as well as trials investigating the administration of tumor treating fields are evaluated. Pivotal trials on the treatment of the primary brain tumors are discussed in detail along with associated correlative studies.
Low-dose Dexmedetomidine Improves Sleep Quality Pattern in Elderly Patients after Noncardiac Surgery in the Intensive Care Unit
Authors: Wu Xin-Hai , Cui Fan , Zhang Cheng , Meng Zhao-Ting , Wang Dong-Xin , Ma Jing , Wang Guang-Fa , Zhu Sai-Nan , Ma Daqing
Published: August 2016

Background

Patients admitted to the intensive care unit (ICU) after surgery often develop sleep disturbances. The authors tested the hypothesis that low-dose dexmedetomidine infusion could improve sleep architecture in nonmechanically ventilated elderly patients in the ICU after surgery.

Methods

This was a pilot, randomized controlled trial. Seventy-six patients age 65 yr or older who were admitted to the ICU after noncardiac surgery and did not require mechanical ventilation were randomized to receive dexmedetomidine (continuous infusion at a rate of 0.1 μg kg−1 h−1; n = 38) or placebo (n = 38) for 15 h, i.e., from 5:00 pm on the day of surgery until 8:00 am on the first day after surgery. Polysomnogram was monitored during the period of study-drug infusion. The primary endpoint was the percentage of stage 2 non–rapid eye movement (stage N2) sleep.

Results

Complete polysomnogram recordings were obtained in 61 patients (30 in the placebo group and 31 in the dexmedetomidine group). Dexmedetomidine infusion increased the percentage of stage N2 sleep from median 15.8% (interquartile range, 1.3 to 62.8) with placebo to 43.5% (16.6 to 80.2) with dexmedetomidine (difference, 14.7%; 95% CI, 0.0 to 31.9; P = 0.048); it also prolonged the total sleep time, decreased the percentage of stage N1 sleep, increased the sleep efficiency, and improved the subjective sleep quality. Dexmedetomidine increased the incidence of hypotension without significant intervention.

Conclusions

In nonmechanically ventilated elderly patients who were admitted to the ICU after noncardiac surgery, the prophylactic low-dose dexmedetomidine infusion may improve overall sleep quality.
Apelin Compared With Dobutamine Exerts Cardioprotection and Extends Survival in a Rat Model of Endotoxin-Induced Myocardial Dysfunction*
Authors: Chagnon Frederic , Coquerel David , Salvail Dany , Marsault Eric , Dumaine Robert , Auger-Messier Mannix , Sarret Philippe , Lesur Olivier
Published: August 2016

Objective:

Dobutamine is the currently recommended β-adrenergic inotropic drug for supporting sepsis-induced myocardial dysfunction when cardiac output index remains low after preload correction. Better and safer therapies are nonetheless mandatory because responsiveness to dobutamine is limited with numerous side effects. Apelin-13 is a powerful inotropic candidate that could be considered as an alternative noncatecholaminergic support in the setting of inflammatory cardiovascular dysfunction.

Design:

Interventional controlled experimental animal study.

Setting:

Tertiary care university-based research institute.

Subjects:

One hundred ninety-eight adult male rats.

Interventions:

Using a rat model of “systemic inflammation–induced cardiac dysfunction” induced by intraperitoneal lipopolysaccharide injection (10 mg/kg), hemodynamic efficacy, cardioprotection, and biomechanics were assessed under IV osmotic pump infusions of apelin-13 (0.25 μg/kg/min) or dobutamine (7.5 μg/kg/min).

Measurements and Main Results:

In this model and in both in vivo and ex vivo studies, apelin-13 compared with dobutamine provoked distinctive effects on cardiac function: 1) optimized cardiac energy–dependent workload with improved cardiac index and lower vascular resistance, 2) upgraded hearts’ apelinergic responsiveness, and 3) consecutive downstream advantages, including increased urine output, enhanced plasma volume, reduced weight loss, and substantially improved overall outcomes. In vitro studies confirmed that these apelin-13–driven processes encompassed a significant and rapid reduction in systemic cytokine release with dampening of myocardial inflammation, injury, and apoptosis and resolution of associated molecular pathways.

Conclusions:

In this inflammatory cardiovascular dysfunction, apelin-13 infusion delivers distinct and optimized hemodynamic support (including positive fluid balance), along with cardioprotective effects, modulation of circulatory inflammation and extended survival.
Long-Pulsed 532-Nm Neodymium-Doped Yttrium Aluminium Garnet Laser for Treatment of Facial Plane Warts in 160 Yemeni Patients
Authors: Alshami Mohammad Ali , Mohana Mona Jameel , Alshami Ahlam Mohammad
Published: August 2016

BACKGROUND

Warts in general and plane warts in particular pose a therapeutic challenge for dermatologists. Many treatment modalities exist, with variable success rates, side effect profiles, and precautions. The long-pulsed 532-nm neodymium-doped yttrium aluminium garnet (LP Nd:YAG) laser has not been previously used for this indication.

OBJECTIVE

This study was conducted to assess the efficacy and safety of the LP Nd:YAG laser for treating facial plane warts.

MATERIALS AND METHODS

A total of 160 Yemeni patients (62 women, 98 men; age range, 5–55 years) were exposed to 1 laser treatment session with the following parameters: wavelength, 532 nm; pulse duration, 20 millisecond; spot size, 2 to 3 mm; and fluence, 25 J/cm2. The end point was graying or whitening of the lesion. Color photographs were taken before and immediately after treatment and at follow-up visits 1, 4, and 16 weeks after the laser session.

RESULTS

An overall clearance rate of 92% after only one session was achieved, with minimal and transient side effects.

CONCLUSION

The LP Nd:YAG laser is safe and effective for treating facial plane warts, with a success rate of 92% after only one session.
GSK-3β Inhibitor CHIR-99021 Promotes Proliferation Through Upregulating β-Catenin in Neonatal Atrial Human Cardiomyocytes
Authors: Wang Shoubao , Ye Lincai , Li Minghui , Liu Jinfen , Jiang Chuan , Hong Haifa , Zhu Hongbin , Sun Yanjun
Published: August 2016

Background:

The renewal capacity of neonate human cardiomyocytes provides an opportunity to manipulate endogenous cardiogenic mechanisms for supplementing the loss of cardiomyocytes caused by myocardial infarction or other cardiac diseases. GSK-3β inhibitors have been recently shown to promote cardiomyocyte proliferation in rats and mice, thus may be ideal candidates for inducing human cardiomyocyte proliferation.

Methods:

Human cardiomyocytes were isolated from right atrial specimens obtained during routine surgery for ventricle septal defect and cultured with either GSK-3β inhibitor (CHIR-99021) or β-catenin inhibitor (IWR-1). Immunocytochemistry was performed to visualize 5-ethynyl-2′-deoxyuridine (EdU)–positive or Ki67-positive cardiomyocytes, indicative of proliferative cardiomyocytes.

Results:

GSK-3β inhibitor significantly increased β-catenin accumulation in cell nucleus, whereas β-catenin inhibitor significantly reduced β-catenin accumulation in cell plasma. In parallel, GSK-3β inhibitor increased EdU-positive and Ki67-positive cardiomyocytes, whereas β-catenin inhibitor decreased EdU-positive and Ki67-positive cardiomyocytes.

Conclusions:

These results indicate that GSK-3β inhibitor can promote human atrial cardiomyocyte proliferation. Although it remains to be determined whether the observations in atrial myocytes could be directly applicable to ventricular myocytes, the current findings imply that Wnt/β-catenin pathway may be a valuable pathway for manipulating endogenous human heart regeneration.