bluuebunny/crossref_metadata_2025 huggingface dataset:
Cross sections for electron collisions with nitric oxide
Authors: Itikawa Yukikazu
Published: September 2016

Cross section data are reviewed for electron collisions with nitric oxide. Collision processes considered are total scattering, elastic scattering, momentum transfer, excitations of rotational, vibrational, and electronic states, ionization, and dissociative electron attachment. After a survey of the literature (up to the end of 2015), recommended values of the cross section are determined, as far as possible.
Rolling-based direct-transfer printing: A process for large-area transfer of micro- and nanostructures onto flexible substrates
Authors: Grierson D. S. , Flack F. S. , Lagally M. G. , Turner K. T.
Published: September 2016

A rolling-based printing approach for transferring arrays of patterned micro- and nano-structures directly from rigid fabrication substrates onto flexible substrates is presented. Transfer-printing experiments show that the new process can achieve high-yield and high-fidelity transfer of silicon nanomembrane components with diverse architectures to polyethylene terephthalate substrates over chip-scale areas (>1 × 1 cm2) in <0.3 s. The underlying mechanics of the process are investigated through finite element simulations of the contact and transfer process. These mechanics models provide guidance for controlling the contact area and strain in the flexible substrate during transfer, both of which are key for achieving reproducible and controlled component transfer over large areas.
Investigation of phonon transport and thermal boundary conductance at the interface of functionalized SWCNT and poly (ether-ketone)
Authors: Huang Haoxiang , Chen Liang , Varshney Vikas , Roy Ajit K. , Kumar Satish
Published: September 2016

Carbon nanostructures such as carbon nanotube (CNT), graphene, and carbon fibers can be used as fillers in amorphous polymers to improve their thermal properties. In this study, the effect of covalent bonding of CNT with poly(ether ketone) (PEK) on interfacial thermal interactions is investigated using non-equilibrium molecular dynamics simulations. The number of covalent bonds between (20, 20) CNT and PEK is varied in the range of 0–80 (0%–6.25%), and the thermal boundary conductance is computed. The analysis reveals that covalent functionalization of CNT atoms can enhance the thermal boundary conductance by an order of magnitude compared to the non-functionalized CNT-PEK interface at a high degree of CNT functionalization. Besides strengthening the thermal coupling, covalent functionalization is also shown to modify the phonon spectra of CNT. The transient spectral energy analysis shows that the crosslinks cause faster energy exchange from CNT to PEK in different frequency bands. The oxygen atom of hydroxyl group of PEK contributes energy transfer in the low frequency band, while aromatic and carbonyl carbon atoms play a more significant role in high frequency bands. In addition, by analyzing the relaxation time of the spectral temperature of different frequency bands of CNT, it is revealed that with increasing number of bonds, both lower frequency vibrational modes and higher frequency modes efficiently couple across the CNT-PEK interface and contribute in thermal energy transfer from CNT to the matrix.
In situ electron microscopy studies of electromechanical behavior in metals at the nanoscale using a novel microdevice-based system
Authors: Kang Wonmo , Beniam Iyoel , Qidwai Siddiq M.
Published: September 2016

Electrically assisted deformation (EAD) is an emerging technique to enhance formability of metals by applying an electric current through them. Despite its increasing importance in manufacturing applications, there is still an unresolved debate on the nature of the fundamental deformation mechanisms underlying EAD, mainly between electroplasticity (non-thermal effects) and resistive heating (thermal effects). This status is due to two critical challenges: (1) a lack of experimental techniques to directly observe fundamental mechanisms of material deformation during EAD, and (2) intrinsic coupling between electric current and Joule heating giving rise to unwanted thermally activated mechanisms. To overcome these challenges, we have developed a microdevice-based electromechanical testing system (MEMTS) to characterize nanoscale metal specimens in transmission electron microscopy (TEM). Our studies reveal that MEMTS eliminates the effect of Joule heating on material deformation, a critical advantage over macroscopic experiments, owing to its unique scale. For example, a negligible change in temperature (<0.02 °C) is predicted at ∼3500 A/mm2. Utilizing the attractive features of MEMTS, we have directly investigated potential electron-dislocation interactions in single crystal copper (SCC) specimens that are simultaneously subjected to uniaxial loading and electric current density up to 5000 A/mm2. Our in situ TEM studies indicate that for SCC, electroplasticity does not play a key role as no differences in dislocation activities, such as depinning and movement, are observed.
Novel silicon phases and nanostructures for solar energy conversion
Authors: Wippermann Stefan , He Yuping , Vörös Márton , Galli Giulia
Published: September 2016

Silicon exhibits a large variety of different bulk phases, allotropes, and composite structures, such as, e.g., clathrates or nanostructures, at both higher and lower densities compared with diamond-like Si-I. New Si structures continue to be discovered. These novel forms of Si offer exciting prospects to create Si based materials, which are non-toxic and earth-abundant, with properties tailored precisely towards specific applications. We illustrate how such novel Si based materials either in the bulk or as nanostructures may be used to significantly improve the efficiency of solar energy conversion devices.
Airgaps in nano-interconnects: Mechanics and impact on electromigration
Authors: Zahedmanesh Houman , Besser Paul R. , Wilson Christopher J. , Croes Kristof
Published: September 2016

In this study, electromigration (EM) of interconnects (90 nm pitch) with airgaps was investigated using a combination of computational mechanics, analytical modelling, and EM experiments. EM experiments reveal that airgapped Cu lines without dielectric liner (non-capsulated) fail early by voiding in the EM tests due to oxidation and deterioration of interfacial adhesion at Cu interfaces. Also at high temperature regimes, extrusive failures under thermal compressive stresses were observed in airgapped Cu lines without dielectric liner. Therefore, Cu encapsulation using a conformal dielectric liner of adequate thickness is necessary in order to ensure hermeticity and provide endurance to the thermal and EM induced extrusive stresses. For an airgapped interconnect with a hermetic 5 nm PECVD conformal carbon doped silicon nitride (SiCN) liner deposited at 370 °C, a (jL)crit comparable to that of non-airgapped interconnects (with ultra-low-k dielectric 2.5 inter-layer dielectric) was predicted by the simulations. The process-oriented simulations reveal, however, that the tensile stress in Cu lines increases linearly with the thickness of the SiCN liner. Therefore, increasing the thickness of the dielectric liner beyond the minimum thickness required for hermeticity was found to impact the critical line length  (jL)crit adversely.
Twisted Fock representations of noncommutative Kähler manifolds
Authors: Sako Akifumi , Umetsu Hiroshi
Published: September 2016

We introduce twisted Fock representations of noncommutative Kähler manifolds and give their explicit expressions. The twisted Fock representation is a representation of the Heisenberg like algebra whose states are constructed by applying creation operators to a vacuum state. “Twisted” means that creation operators are not Hermitian conjugate of annihilation operators in this representation. In deformation quantization of Kähler manifolds with separation of variables formulated by Karabegov, local complex coordinates and partial derivatives of the Kähler potential with respect to coordinates satisfy the commutation relations between the creation and annihilation operators. Based on these relations, we construct the twisted Fock representation of noncommutative Kähler manifolds and give a dictionary to translate between the twisted Fock representations and functions on noncommutative Kähler manifolds concretely.
Structural analysis of polymer thin films using GISAXS in the tender X-ray region: Concept and design of GISAXS experiments using the tender X-ray energy at BL-15A2 at the Photon Factory
Authors: Takagi H. , Igarashi N. , Mori T. , Saijo S. , Nagatani Y. , Ohta H. , Yamamoto K. , Shimizu N.
Published: September 2016

If small angle X-ray scattering (SAXS) utilizing the soft X-ray region is available, advanced and unique experiments, which differ from traditional SAXS methods, can be realized. For example, grazing-incidence small angle X-ray scattering (GISAXS) using hard X-ray is a powerful tool for understanding the nanostructure in both vertical and lateral directions of thin films, while GISAXS utilizing the tender X-ray region (SX-GISAXS) enables depth-resolved analysis as well as a standard GISAXS analysis in thin films. Thus, at BL-15A2 at the Photon Factory, a dedicated diffractometer for SX-GISAXS (above 2.1 keV) was constructed. This diffractometer is composed of four vacuum chambers and can be converted into the vacuum state from the sample chamber in front of the detector surface. Diffractions are clearly observed until 12th peak when measuring collagen by SAXS with an X-ray energy of 2.40 keV and a camera length of 825 mm. Additionally, we conducted the model experiment using SX-GISAXS with an X-ray energy of 2.40 keV to confirm that a poly(methyl methacrylate)-poly(n-butyl acrylate) block copolymer thin film has a microphase-separated structure in the thin film, which is composed of lamellae aligned both parallel and perpendicular to the substrate surface. Similarly, in a polystyrene-poly(methyl methacrylate) block copolymer thin film, SX-GISAXS with 3.60 keV and 5.73 keV revealed that hexagonally packed cylinders are aligned parallel to the substrate surface. The incident angle dependence of the first order peak position of the qz direction obtained from experiments at various incident X-ray energies agrees very well with the theoretical one calculated from the distorted wave Born approximation.
Accurate and fast fiber transfer delay measurement based on phase discrimination and frequency measurement
Authors: Dong J. W. , Wang B. , Gao C. , Wang L. J.
Published: September 2016

An accurate and fast fiber transfer delay measurement method is demonstrated. As a key technique, a simple ambiguity resolving process based on phase discrimination and frequency measurement is used to overcome the contradiction between measurement accuracy and system complexity. The system achieves a high measurement accuracy of 0.2 ps with a 0.1 ps measurement resolution and a large dynamic range up to 50 km as well as no dead zone.
Influence of C or In buffer layer on photoluminescence behaviour of ultrathin ZnO film
Authors: Saravanan K. , Jayalakshmi G. , Krishnan R. , Sundaravel B. , Panigrahi B. K.
Published: September 2016

We study the effect of the indium or carbon buffer layer on the photoluminescence (PL) property of ZnO ultrathin films deposited on a Si(100) substrate. The surface morphology of the films obtained using scanning tunnelling microscopy shows spherical shaped ZnO nanoparticles of size ∼8 nm in ZnO/C/Si and ∼22 nm in ZnO/Si samples, while the ZnO/In/Si sample shows elliptical shaped ZnO particles. Further, the ZnO/C/Si sample shows densely packed ZnO nanoparticles in comparison with other samples. Strong band edge emission has been observed in the presence of In or C buffer layer, whereas the ZnO/Si sample exhibits poor PL emission. The influence of C and In buffer layers on the PL behaviour of ZnO films is studied in detail using temperature dependent PL measurements in the range of 4 K–300 K. The ZnO/C/Si sample exhibits a multi-fold enhancement in the PL emission intensity with well-resolved free and bound exciton emission lines. Our experimental results imply that the ZnO films deposited on the C buffer layer showed higher particle density and better exciton emission desired for optoelectronic applications.
Operation mechanism of high performance organic permeable base transistors with an insulated and perforated base electrode
Authors: Kaschura Felix , Fischer Axel , Klinger Markus P. , Doan Duy Hai , Koprucki Thomas , Glitzky Annegret , Kasemann Daniel , Widmer Johannes , Leo Karl
Published: September 2016

The organic permeable base transistor is a vertical transistor architecture that enables high performance while maintaining a simple low-resolution fabrication. It has been argued that the charge transport through the nano-sized openings of the central base electrode limits the performance. Here, we demonstrate by using 3D drift-diffusion simulations that this is not the case in the relevant operation range. At low current densities, the applied base potential controls the number of charges that can pass through an opening and the opening is the current limiting factor. However, at higher current densities, charges accumulate within the openings and in front of the base insulation, allowing for an efficient lateral transport of charges towards the next opening. The on-state in the current-voltage characteristics reaches the maximum possible current given by space charge limited current transport through the intrinsic semiconductor layers. Thus, even a small effective area of the openings can drive huge current densities, and further device optimization has to focus on reducing the intrinsic layer thickness to a minimum.
Depletion region surface effects in electron beam induced current measurements
Authors: Haney Paul M. , Yoon Heayoung P. , Gaury Benoit , Zhitenev Nikolai B.
Published: September 2016

Electron beam induced current (EBIC) is a powerful characterization technique which offers the high spatial resolution needed to study polycrystalline solar cells. Current models of EBIC assume that excitations in the p-n junction depletion region result in perfect charge collection efficiency. However, we find that in CdTe and Si samples prepared by focused ion beam (FIB) milling, there is a reduced and nonuniform EBIC lineshape for excitations in the depletion region. Motivated by this, we present a model of the EBIC response for excitations in the depletion region which includes the effects of surface recombination from both charge-neutral and charged surfaces. For neutral surfaces, we present a simple analytical formula which describes the numerical data well, while the charged surface response depends qualitatively on the location of the surface Fermi level relative to the bulk Fermi level. We find that the experimental data on FIB-prepared Si solar cells are most consistent with a charged surface and discuss the implications for EBIC experiments on polycrystalline materials.
Piezoelectric type acoustic energy harvester with a tapered Helmholtz cavity for improved performance
Authors: Khan Farid , Izhar
Published: September 2016

This paper reports an improved acoustic energy harvester with a tapered Helmholtz cavity. The harvester consists of a bimorph piezoelectric composite plate and a Helmholtz resonator (HR) with a tapered cavity. The architecture, operational mechanism, fabrication, and characterization of the harvesters are described. The harvesters are tested under sinusoidal sound pressure levels (SPLs) inside a lab as well as random SPLs in a real ambient acoustical environment. When a harvester with a tapered HR and without proof mass attached to its piezoelectric plate is characterized at a sinusoidal SPL of 130 dB, a maximum power of 90.6 μW is delivered to 1 kΩ load. In comparison, a similar harvester with a cylindrical shape HR produced a maximum power of 51.4 μW under the similar acoustic conditions. It is found that 76.26% increase in power is achieved with the tapered cavity for the HR. Furthermore, due to the attachment of a proof mass (0.84 g) with the harvester, its power production capability is further increased by 103.3%, from 90.6 to 184.18 μW. Moreover, in a real environment, the maximum voltage amplitudes of about 260 and 280 mV are produced by the harvester when placed in the surrounding of a motorbike and domestic electric generator, respectively.
Detailed characterization of the LLNL imaging proton spectrometer
Authors: Rasmus A. M. , Hazi A. U. , Manuel M. J.-E. , Kuranz C. C. , Klein S. R. , Belancourt P. X. , Fein J. R. , MacDonald M. J. , Drake R. P. , Pollock B. B. , Park J. , Williams G. J. , Chen H.
Published: September 2016

Ultra-intense short pulse lasers incident on solid targets (e.g., thin Au foils) produce well collimated, broad-spectrum proton beams. These proton beams can be used to characterize magnetic fields, electric fields, and density gradients in high energy-density systems. The LLNL-Imaging Proton Spectrometer (L-IPS) was designed and built [H. Chen et al., Rev. Sci. Instrum. 81, 10D314 (2010)] for use with such laser produced proton beams. The L-IPS has an energy range of 50 keV-40 MeV with a resolving power (E/dE) of about 275 at 1 MeV and 21 at 20 MeV, as well as a single spatial imaging axis. In order to better characterize the dispersion and imaging capability of this diagnostic, a 3D finite element analysis solver is used to calculate the magnetic field of the L-IPS. Particle trajectories are then obtained via numerical integration to determine the dispersion relation of the L-IPS in both energy and angular space.
Strengthening mechanism of super-hard nanoscale Cu/Al multilayers with negative enthalpy of mixing
Authors: Zhou Q. , Li S. , Huang P. , Xu K. W. , Wang F. , Lu T. J.
Published: September 2016

We present unusual high hardness (up to 7.7 GPa) achieved in Cu/Al multilayers relative to monolithic Cu and Al films (∼2 GPa and ∼1 GPa, respectively). Nanotwins and stacking faults (SFs) were proposed to be the main contributors of hardness enhancement, especially when h < 5 nm. Using molecular dynamics simulations of deposition, we demonstrated that intermixing near Cu/Al interface was paramount in stabilizing the SFs in both Cu and Al layers. Our experimental results indicated that the high strength caused by layer intermixing was in sharp contrast to the general belief that only sharp interface structures could strengthen the multilayers.
Better batteries through architecture
Authors: Chang Sung
Published: September 2016

Easing the tortuous path for lithium ions improves electrode performance.
Can MAGIS work magic for separating stable isotopes?
Authors: Feder Toni
Published: September 2016

Atomic beams, optical pumping, and magnet geometry are the crux of a fledgling method that may help meet the demand for pure isotopes.
Experience of clinical supervisors of international medical graduates in an Australian district hospital
Authors: Henderson David , McGrath Pam D. , Patton Mary Anne
Published: September 2016

Objective Herein we record the experience of clinical supervisors of international medical graduates (IMGs) working as junior staff in a district hospital by examining supervisor perspectives on IMG performance, the factors affecting their performance and the requirements of supervision under these circumstances. Methods The present study had an open-ended exploratory qualitative design. Thirteen 13 open-ended, in-depth interviews were undertaken with supervisors of IMGs employed in a public district hospital in Queensland, Australia. Results The supervisors reported that, although performance was an individual and variable characteristic, IMGs tended to perform less well than Australian graduates and required more intensive supervision. Factors that affected performance were motivation and experience, and specifically lack of familiarity with the Australian healthcare system, lack of recent of practice, education, language, communication and cultural factors. English language proficiency was regarded as crucial to performance. Conclusions The additional work required to supervise IMGs in order to enable them to perform at a satisfactory level and successfully integrate into the Australian healthcare system needs to be recognised and resourced. Assistance with attaining proficiency in English and with communication skills over and above the standard required to pass the International English Language Testing System examination should be seriously considered as a means of improving performance. What is known about the topic? To date, there is little research available about the experience of supervisors of IMGs in Australia. What does this paper add? The findings of the present study make an important contribution to the literature by examining the critical role clinical supervisors of IMGs have in helping IMGs adapt to the Australian healthcare system and ensuring that they are able to provide quality health care. It identifies current challenges and highlights areas in need of attention to ensure a strong healthcare system for Australia. What are the implications for practitioners? Supervisors of IMGs need recognition of the extra time and expertise required in their role if they are to be effectively supported in their endeavours to integrate IMGs into the Australian health workforce. More attention needs to be given to the development of English language proficiency of IMGs, including colloquial usage, and communication in medical practice.
Genomic prediction for carcass traits in Japanese Black cattle using single nucleotide polymorphism markers of different densities
Authors: Ogawa Shinichiro , Matsuda Hirokazu , Taniguchi Yukio , Watanabe Toshio , Kitamura Yuki , Tabuchi Ichiro , Sugimoto Yoshikazu , Iwaisaki Hiroaki
Published: September 2016

Genomic prediction (GP) of breeding values using single nucleotide polymorphism (SNP) markers can be conducted even when pedigree information is unavailable, providing phenotypes are known and marker data are provided. While use of high-density SNP markers is desirable for accurate GP, lower-density SNPs can perform well in some situations. In the present study, GP was performed for carcass weight and marbling score in Japanese Black cattle using SNP markers of varying densities. The 1791 fattened steers with phenotypic data and 189 having predicted breeding values provided by the official genetic evaluation using pedigree data were treated as the training and validation populations respectively. Genotype data on 565837 autosomal SNPs were available and SNPs were selected to provide different equally spaced SNP subsets of lower densities. Genomic estimated breeding values (GEBVs) were obtained using genomic best linear unbiased prediction incorporating one of two types of genomic relationship matrices (G matrices). The GP accuracy assessed as the correlation between the GEBVs and the corrected records divided by the square root of estimated heritability was around 0.85 for carcass weight and 0.60 for marbling score when using 565837 SNPs. The type of G matrix used gave no substantial difference in the results at a given SNP density for traits examined. Around 80% of the GP accuracy was retained when the SNP density was decreased to 1/1000 of that of all available SNPs. These results indicate that even when a SNP panel of a lower density is used, GP may be beneficial to the pre-selection for the carcass traits in Japanese Black young breeding animals.
Temporal patterns in the size of the main commercial shark species of Western Australia
Authors: Braccini Matias
Published: September 2016

Declines in the mean size of harvested organisms may indicate overexploitation. In the present study, temporal patterns in the mean size of the four main commercial shark species of Western Australia were evaluated. Unlike commonly observed for other shark populations, there were no strong temporal patterns in the mean size of gummy, dusky and whiskery sharks, whereas the mean size of sandbar sharks showed a gradual increase since 1993. These observations add further evidence that sharks can be fished sustainably when adequate monitoring, assessment and management actions are implemented.
As through a glass, darkly: the future of sexually transmissible infections among gay, bisexual and other men who have sex with men
Authors: Stenger Mark Richard , Baral Stefan , Stahlman Shauna , Wohlfeiler Dan , Barton Jerusha E. , Peterman Thomas
Published: September 2016

The trajectory of sexually transmissible infection (STI) incidence among gay and other men who have sex with men (MSM) suggests that incidence will likely remain high in the near future. STIs were hyperendemic globally among MSM in the decades preceding the HIV epidemic. Significant changes among MSM as a response to the HIV epidemic, caused STI incidence to decline, reaching historical nadirs in the mid-1990s. With the advent of antiretroviral treatment (ART), HIV-related mortality and morbidity declined significantly in that decade. Concurrently, STI incidence resurged among MSM and increased in scope and geographic magnitude. By 2000, bacterial STIs were universally resurgent among MSM, reaching or exceeding pre-HIV levels. While the evidence base necessary for assessing the burden STIs among MSM, both across time and across regions, continues to be lacking, recent progress has been made in this respect. Current epidemiology indicates a continuing and increasing trajectory of STI incidence among MSM. Yet increased reported case incidence of gonorrhoea is likely confounded by additional screening and identification of an existing burden of infection. Conversely, more MSM may be diagnosed and treated in the context of HIV care or as part of routine management of pre-exposure prophylaxis (PrEP), potentially reducing transmission. Optimistically, uptake of human papillomavirus (HPV) vaccination may lead to a near-elimination of genital warts and reductions in HPV-related cancers. Moreover, structural changes are occurring with respect to sexual minorities in social and civic life that may offer new opportunities, as well as exacerbate existing challenges, for STI prevention among MSM.
Dealing with pre-exposure prophylaxis-associated condom migration: changing the paradigm for men who have sex with men
Authors: Crosby Richard A.
Published: September 2016

The behavioural aspects of pre-exposure prophylaxis (PrEP) are challenging, particularly the issue of condom migration. Three vital questions are: (1) at the population-level, will condom migration lead to increases in non-viral sexually transmissible infections?; (2) how can clinic-based counselling best promote the dual use of condoms and PrEP?; and (3) in future PrEP trials, what are the ‘best practices’ that should be used to avoid type 1 and type 2 errors that arise without accounting for condom use behaviours? This communication piece addresses each question and suggests the risk of a ‘PrEP only’ focus to widening health disparities.
Long noncoding RNA #32 contributes to antiviral responses by controlling interferon-stimulated gene expression
Authors: Nishitsuji Hironori , Ujino Saneyuki , Yoshio Sachiyo , Sugiyama Masaya , Mizokami Masashi , Kanto Tatsuya , Shimotohno Kunitada
Published: September 2016

Significance

Here, we describe a key feature of the long noncoding RNA (lncRNA) involved in innate immunity. We identified 182 lncRNAs that were highly modulated in poly(I:C)-treated hepatocyte cells. Of these, lncRNA#32 regulated the level of IFN-stimulated genes under both unstimulated and type I IFN-stimulated conditions through interactions with hnRNPU and ATF2, and therefore plays an important role in antiviral immunity.
Parent-of-origin effects of A1CF and AGO2 on testicular germ-cell tumors, testicular abnormalities, and fertilization bias
Authors: Carouge Delphine , Blanc Valerie , Knoblaugh Sue E. , Hunter Robert J. , Davidson Nicholas O. , Nadeau Joseph H.
Published: September 2016

Significance

Usually diagnosed in young men, testicular germ cell tumors (TGCTs) originate from abnormalities in germ cells during fetal development. Testicular cancer is a complex disease combining multiple genetic variants and environmental factors. The discovery of unconventional inheritance for TGCT risk both in humans and mice highlighted the major contribution of epigenetic mechanisms. The current work identifies two TGCT modifiers, the RNA-binding proteins apolipoprotein B mRNA-editing enzyme complex 1 (APOBEC1) complementation factor (A1CF) and Argonaute 2 (AGO2), respectively involved in RNA editing and RNA silencing. These results help us better understand the epigenetic control of germ-cell fate, urogenital development, and gamete functions.
New nutrients exert fundamental control on dissolved organic carbon accumulation in the surface Atlantic Ocean
Authors: Romera-Castillo Cristina , Letscher Robert T. , Hansell Dennis A.
Published: September 2016

Significance

Oceanic dissolved organic carbon (DOC) is, at 662 ± 32 petagrams of carbon (Pg C), one of Earth's major, exchangeable carbon reservoirs. With its large inventory and biologic turnover, the pool has been invoked as a principal source/sink of atmospheric CO
2
driving paleoclimate variations. Controls on past source/sink functions remain unknown, but insights can be gleaned from the modern ocean. Here, we find that new nutrients introduced to the euphotic zone exert a fundamental and predictable control on the net production of DOC, in turn playing a large part in determining the surface distribution and concentrations of the pool. Climate-driven changes in surface ocean renewal of nutrients will ultimately control the source term, dictating the inventory of carbon residing in marine DOC.
A preliminary investigation on the relationship between gut microbiota and gene expressions in peripheral mononuclear cells of infants with autism spectrum disorders
Authors: Inoue Ryo , Sakaue Yuko , Sawai Chihiro , Sawai Toshihiro , Ozeki Motoyuki , Romero-Pérez Gustavo A , Tsukahara Takamitsu
Published: September 2016

Fecal and blood samples of infants with autism spectrum disorders (ASD) and healthy infants were analyzed to investigate the association of altered gut microbiota and ASD development. 16S rRNA gene-based sequencing found that, unlike those of healthy infants, feces of ASD infants had significantly higher and lower abundance of genera Faecalibacterium and Blautia, respectively. Moreover, DNA microarray analysis of peripheral blood mononuclear cells (PBMC) detected more highly than low expressed genes in ASD infants than in healthy infants. Gene Ontology analysis revealed that differentially expressed genes between ASD and healthy infants were involved in interferon (IFN)-γ and type-I IFN signaling pathways. Finally, strong positive correlations between expression of IFN signaling-associated genes in PBMC and fecal abundance of Faecalibacterium were found. Our results strongly suggested that altered gut microbiota in infants resulted from ASD development and was associated with systemic immunity dysregulation, especially chronic inflammation.
Direct Alloying of Steel with Nickel Concentrate
Authors: Nokhrina O I , Rozhikhina I D , Proshunin I E
Published: September 2016

A technology of alloying steel with nickel reduced from nickel concentrate is analysed and developed. Limits of reduction concentration areas are defined. An optimal composition of nickel concentrate pellets and a method of feeding them into the furnace are deduced from experiments. It is proved that when pellets made of nickel concentrate and coke are added into the charge during steel smelting by the technology of alloyed scrap remelting, nickel recovery achieves 92-95%. The technology was tested by smelting DSP-40 steel.
Each regular paratopological group is completely regular
Authors: Banakh Taras , Ravsky Alex
Published: September 2016

We prove that a semiregular topological space

X
X

is completely regular if and only if its topology is generated by a normal quasi-uniformity. This characterization implies that each regular paratopological group is completely regular. This resolves an old problem in the theory of paratopological groups, which stood open for about 60 years. Also we define a natural uniformity on each paratopological group and using this uniformity prove that each (first countable) Hausdorff paratopological group is functionally Hausdorff (and submetrizable). This resolves another two known open problems in the theory of paratopological groups.
Exit times densities of the Bessel process
Authors: Serafin Grzegorz
Published: September 2016

We examine the density functions of the first exit times of the Bessel process from the intervals

[
0
,
1
)

[0,1)

and

(
0
,
1
)

(0,1)

. First, we express them by means of the transition density function of the killed process. Using that relationship we provide precise estimates and asymptotics of the exit time densities. In particular, the results hold for the first exit time of the

n
n

-dimensional Brownian motion from a ball.
Adams operations on classical compact Lie groups
Authors: Fok Chi-Kwong
Published: September 2016

Let

G
G

be

U
(
n
)

U(n)

,

S
U
(
n
)

SU(n)

,

S
p
(
n
)

Sp(n)

or

S
p
i
n
(
n
)

Spin(n)

. In this short note we give explicit general formulas for Adams operations on

K
∗

(
G
)

K^*(G)

and eigenvectors of Adams operations on

K
∗

(
U
(
n
)
)

K^*(U(n))

.
Spindle function inXenopusoocytes involves possible nanodomain calcium signaling
Authors: Li Ruizhen , Leblanc Julie , He Kevin , Liu X. Johné
Published: September 2016

Intracellular calcium transients are a universal phenomenon at fertilization and are required for egg activation, but the exact role of Ca2+in second-polar-body emission remains unknown. On the other hand, similar calcium transients have not been demonstrated during oocyte maturation, and yet, manipulating intracellular calcium levels interferes with first-polar-body emission in mice and frogs. To determine the precise role of calcium signaling in polar body formation, we used live-cell imaging coupled with temporally precise intracellular calcium buffering. We found that BAPTA-based calcium chelators cause immediate depolymerization of spindle microtubules in meiosis I and meiosis II. Surprisingly, EGTA at similar or higher intracellular concentrations had no effect on spindle function or polar body emission. Using two calcium probes containing permutated GFP and the calcium sensor calmodulin (Lck-GCaMP3 and GCaMP3), we demonstrated enrichment of the probes at the spindle but failed to detect calcium increase during oocyte maturation at the spindle or elsewhere. Finally, endogenous calmodulin was found to colocalize with spindle microtubules throughout all stages of meiosis. Our results—most important, the different sensitivities of the spindle to BAPTA and EGTA—suggest that meiotic spindle function in frog oocytes requires highly localized, or nanodomain, calcium signaling.
Effects of anchor structure and glycosylation of Fcγ receptor III on ligand binding affinity
Authors: Jiang Ning , Chen Wei , Jothikumar Prithiviraj , Patel Jaina M. , Shashidharamurthy Rangaiah , Selvaraj Periasamy , Zhu Cheng
Published: September 2016

Isoforms of the Fcγ receptor III (FcγRIII or CD16) are cell surface receptors for the Fc portion of IgG and important regulators of humoral immune responses. Different ligand binding kinetics of FcγRIII isoforms are obtained in three dimensions by surface plasmon resonance and in two dimensions by a micropipette adhesion frequency assay. We show that the anchor structure of CD16 isoforms isolated from the cell membrane affects their binding affinities in a ligand-specific manner. Changing the receptor anchor structure from full to partial to none decreases the ligand binding affinity for human IgG1 (hIgG1) but increases it for murine IgG2a (mIgG2a). Removing N-glycosylation from the CD16 protein core by tunicamycin also increases the ligand binding affinity. Molecular dynamics simulations indicate that deglycosylation at Asn-163 of CD16 removes the steric hindrance for the CD16-hIgG1 Fc binding and thus increases the binding affinity. These results highlight an unexpected sensitivity of ligand binding to the receptor anchor structure and glycosylation and suggest their respective roles in controlling allosterically the conformation of the ligand binding pocket of CD16.
Detecting horizontal gene transfer by mapping sequencing reads across species boundaries
Authors: Trappe Kathrin , Marschall Tobias , Renard Bernhard Y.
Published: September 2016

Motivation

Horizontal gene transfer (HGT) is a fundamental mechanism that enables organisms such as bacteria to directly transfer genetic material between distant species. This way, bacteria can acquire new traits such as antibiotic resistance or pathogenic toxins. Current bioinformatics approaches focus on the detection of past HGT events by exploring phylogenetic trees or genome composition inconsistencies. However, these techniques normally require the availability of finished and fully annotated genomes and of sufficiently large deviations that allow detection and are thus not widely applicable. Especially in outbreak scenarios with HGT-mediated emergence of new pathogens, like the enterohemorrhagic Escherichia coli outbreak in Germany 2011, there is need for fast and precise HGT detection. Next-generation sequencing (NGS) technologies facilitate rapid analysis of unknown pathogens but, to the best of our knowledge, so far no approach detects HGTs directly from NGS reads.

Results

We present Daisy, a novel mapping-based tool for HGT detection. Daisy determines HGT boundaries with split-read mapping and evaluates candidate regions relying on read pair and coverage information. Daisy successfully detects HGT regions with base pair resolution in both simulated and real data, and outperforms alternative approaches using a genome assembly of the reads. We see our approach as a powerful complement for a comprehensive analysis of HGT in the context of NGS data.

Availability and Implementation

Daisy is freely available from http://github.com/ktrappe/daisy.

Contact

renardb@rki.de

Supplementary information

Supplementary data are available at Bioinformatics online.
Pathway-based approach using hierarchical components of collapsed rare variants
Authors: Lee Sungyoung , Choi Sungkyoung , Kim Young Jin , Kim Bong-Jo ,   T2d-Genes Consortium, Hwang Heungsun , Park Taesung
Published: September 2016

Motivation

To address ‘missing heritability’ issue, many statistical methods for pathway-based analyses using rare variants have been proposed to analyze pathways individually. However, neglecting correlations between multiple pathways can result in misleading solutions, and pathway-based analyses of large-scale genetic datasets require massive computational burden. We propose a Pathway-based approach using HierArchical components of collapsed RAre variants Of High-throughput sequencing data (PHARAOH) for the analysis of rare variants by constructing a single hierarchical model that consists of collapsed gene-level summaries and pathways and analyzes entire pathways simultaneously by imposing ridge-type penalties on both gene and pathway coefficient estimates; hence our method considers the correlation of pathways without constraint by a multiple testing problem.

Results

Through simulation studies, the proposed method was shown to have higher statistical power than the existing pathway-based methods. In addition, our method was applied to the large-scale whole-exome sequencing data with levels of a liver enzyme using two well-known pathway databases Biocarta and KEGG. This application demonstrated that our method not only identified associated pathways but also successfully detected biologically plausible pathways for a phenotype of interest. These findings were successfully replicated by an independent large-scale exome chip study.

Availability and Implementation

An implementation of PHARAOH is available at http://statgen.snu.ac.kr/software/pharaoh/.

Contact

tspark@stats.snu.ac.kr

Supplementary information

Supplementary data are available at Bioinformatics online.
Snowball: strain aware gene assembly of metagenomes
Authors: Gregor I. , Schönhuth A. , McHardy A. C.
Published: September 2016

Motivation

Gene assembly is an important step in functional analysis of shotgun metagenomic data. Nonetheless, strain aware assembly remains a challenging task, as current assembly tools often fail to distinguish among strain variants or require closely related reference genomes of the studied species to be available.

Results

We have developed Snowball, a novel strain aware gene assembler for shotgun metagenomic data that does not require closely related reference genomes to be available. It uses profile hidden Markov models (HMMs) of gene domains of interest to guide the assembly. Our assembler performs gene assembly of individual gene domains based on read overlaps and error correction using read quality scores at the same time, which results in very low per-base error rates.

Availability and Implementation

The software runs on a user-defined number of processor cores in parallel, runs on a standard laptop and is available under the GPL 3.0 license for installation under Linux or OS X at https://github.com/hzi-bifo/snowball.

Contact

AMC14@helmholtz-hzi.de,a.schoenhuth@cwi.nl

Supplementary information

Supplementary data are available at Bioinformatics online.
Estimating real cell size distribution from cross-section microscopy imaging
Authors: Lenz Michael , Roumans Nadia JT , Vink Roel G , van Baak Marleen A , Mariman Edwin CM , Arts Ilja CW , de Kok Theo M , Ertaylan Gökhan
Published: September 2016

Motivation

Microscopy imaging is an essential tool for medical diagnosis and molecular biology. It is particularly useful for extracting information about disease states, tissue heterogeneity and cell specific parameters such as cell type or cell size from biological specimens. However, the information obtained from the images is likely to be subjected to sampling and observational bias with respect to the underlying cell size/type distributions.

Results

We present an algorithm, Estimate Tissue Cell Size/Type Distribution (EstiTiCS), for the adjustment of the underestimation of the number of small cells and the size of measured cells while accounting for the section thickness independent of the tissue type. We introduce the sources of bias under different tissue distributions and their effect on the measured values with simulation experiments. Furthermore, we demonstrate our method on histological sections of paraffin-embedded adipose tissue sample images from 57 people from a dietary intervention study. This data consists of measured cell size and its distribution over the dietary intervention period at four time points. Adjusting for the bias with EstiTiCS results in a closer fit to the true/expected adipocyte size distribution with earlier studies. Therefore, we conclude that our method is suitable as the final step in estimating the tissue wide cell type/size distribution from microscopy imaging pipeline.

Availability and Implementation

Source code and its documentation are available at https://github.com/michaelLenz/EstiTiCS. The whole pipeline of our method is implemented in R and makes use of the ‘nloptr’ package. Adipose tissue data used for this study are available on request.

Contact

Michael.Lenz@Maastrichtuniversity.nl, Gokhan.Ertaylan@Maastrichtuniversity.nl
Simultaneous discovery of cancer subtypes and subtype features by molecular data integration
Authors: Le Van Thanh , van Leeuwen Matthijs , Carolina Fierro Ana , De Maeyer Dries , Van den Eynden Jimmy , Verbeke Lieven , De Raedt Luc , Marchal Kathleen , Nijssen Siegfried
Published: September 2016

Motivation

Subtyping cancer is key to an improved and more personalized prognosis/treatment. The increasing availability of tumor related molecular data provides the opportunity to identify molecular subtypes in a data-driven way. Molecular subtypes are defined as groups of samples that have a similar molecular mechanism at the origin of the carcinogenesis. The molecular mechanisms are reflected by subtype-specific mutational and expression features. Data-driven subtyping is a complex problem as subtyping and identifying the molecular mechanisms that drive carcinogenesis are confounded problems. Many current integrative subtyping methods use global mutational and/or expression tumor profiles to group tumor samples in subtypes but do not explicitly extract the subtype-specific features. We therefore present a method that solves both tasks of subtyping and identification of subtype-specific features simultaneously. Hereto our method integrates` mutational and expression data while taking into account the clonal properties of carcinogenesis. Key to our method is a formalization of the problem as a rank matrix factorization of ranked data that approaches the subtyping problem as multi-view bi-clustering.

Results

We introduce a novel integrative framework to identify subtypes by combining mutational and expression features. The incomparable measurement data is integrated by transformation into ranked data and subtypes are defined as multi-view bi-clusters. We formalize the model using rank matrix factorization, resulting in the SRF algorithm. Experiments on simulated data and the TCGA breast cancer data demonstrate that SRF is able to capture subtle differences that existing methods may miss.

Availability and Implementation

The implementation is available at: https://github.com/rankmatrixfactorisation/SRF.

Contact

kathleen.marchal@intec.ugent.be, siegfried.nijssen@cs.kuleuven.be

Supplementary information

Supplementary data are available at Bioinformatics online.
Causality modeling for directed disease network
Authors: Bang Sunjoo , Kim Jae-Hoon , Shin Hyunjung
Published: September 2016

Motivation

Causality between two diseases is valuable information as subsidiary information for medicine which is intended for prevention, diagnostics and treatment. Conventional cohort-centric researches are able to obtain very objective results, however, they demands costly experimental expense and long period of time. Recently, data source to clarify causality has been diversified: available information includes gene, protein, metabolic pathway and clinical information. By taking full advantage of those pieces of diverse information, we may extract causalities between diseases, alternatively to cohort-centric researches.

Method

In this article, we propose a new approach to define causality between diseases. In order to find causality, three different networks were constructed step by step. Each step has different data sources and different analytical methods, and the prior step sifts causality information to the next step. In the first step, a network defines association between diseases by utilizing disease–gene relations. And then, potential causalities of disease pairs are defined as a network by using prevalence and comorbidity information from clinical results. Finally, disease causalities are confirmed by a network defined from metabolic pathways.

Results

The proposed method is applied to data which is collected from database such as MeSH, OMIM, HuDiNe, KEGG and PubMed. The experimental results indicated that disease causality that we found is 19 times higher than that of random guessing. The resulting pairs of causal-effected diseases are validated on medical literatures.

Availability and Implementation

http://www.alphaminers.net

Contact

shin@ajou.ac.kr

Supplementary information

Supplementary data are available at Bioinformatics online.