bluuebunny/crossref_metadata_2025 huggingface dataset:
Damage Recovery by Reductive Chemistry after Methanol-Based Plasma Etch to Fabricate Magnetic Tunnel Junctions
Authors: Kinoshita Keizo , Yamamoto Tadashi , Honjo Hiroaki , Kasai Naoki , Ikeda Shoji , Ohno Hideo
Published: August 2012

The damage recovery process for magnetic tunnel junctions (MTJs) after methanol- (Me-OH) based plasma etch has been demonstrated. Me-OH and O2 plasma, which contain oxygen in the molecule, caused unavoidable modification of magnetic materials in the MTJ stack. For example, the magnetization saturation and MR ratio decreased. H2 base reductive plasma treatment was effective in recovering from this deterioration. No harmful side effects were observed in other aspects of MTJ performance such as MTJ resistance, hysteresis loop offset, and switching field. Heavier initial damage required a longer treatment time for recovery. Other types of reductive chemistry such as NH3 plasma deteriorated the MTJ when the treatment lasted more than 15 s, probably due to nitridation. The use of a highly selective Ar/Me-OH etch process along with He/H2 plasma recovery treatment is very promising for the MTJs' etch process to fabricate high-density magnetic random access memory (MRAM) and non-volatile logic devices.
High-Temperature Annealing by Subatmospheric-Pressure Radio-Frequency Capacitively Coupled Plasma
Authors: Miyake Masatoshi , Yokogawa Ken'etsu
Published: August 2012

High-temperature annealing was performed by a novel annealing system using subatmospheric-pressure radio-frequency capacitively coupled plasma (SAP-CCP). The heating characteristics and stability of discharge were studied. An electrode temperature of 1900 °C was obtained with a stable and uniform glow-like discharge. Also, the characteristics of annealing were investigated using silicon wafers implanted with boron ions accelerated by 5 kV at doses of 2.0×1015 cm-2. The sheet resistance decreased with increasing annealing temperature in the same manner as in conventional rapid thermal annealing. As a result, a sheet resistance of 86 Ω/sq was successfully achieved at an electrode temperature of 1080 °C without any surface roughness.
Modeling and Simulation of Nanoscale Surface Rippling during Plasma Etching of Si under Oblique Ion Incidence
Authors: Tsuda Hirotaka , Takao Yoshinori , Eriguchi Koji , Ono Kouichi
Published: August 2012

A three-dimensional atomic-scale cellular model (ASCeM-3D) has been developed to reproduce the evolution of feature profiles on atomic or nanometer scale during plasma etching. Emphasis was placed on the evolution of nanoscale surface features and roughness during Si etching in Cl2plasmas, with further attention being given to that of ripple structures on etched surfaces. Simulations were carried out for different ion incident angles from θi= 0 to 85°, with an ion incident energyEi= 100 eV, flux Γi0= 1.0 ×1016cm-2s-1, and neutral-to-ion flux ratio Γn0/Γi0= 100, which are typical in high-density plasma etching environments. Numerical results indicated that as the angle θiis increased, nanoscale concavo-convex features drastically change and ripple structures occur on etched surfaces. For θi= 0° or normal ion incidence, the surfaces are randomly roughened. For increased θi= 30–45° or oblique ion incidence, the ripples are formed perpendicular to the direction of ion incidence, while they are parallel to the direction of ion incidence for further increased θi= 75–80°. Analysis of ion trajectories implied that the ion reflection and concentration on microscopically roughened surfaces largely affect the surface roughening and rippling during plasma etching. These numerical approaches would become important to predict the nanoscale surface features and roughness, especially the line edge roughness (LER) formed on feature sidewalls, because experiments of oblique incidence of ions on surfaces are difficult in plasma environments.
Segmented Electrode Plasma Source with Anti-Phase Discharge
Authors: Sawada Ikuo , Morishima Masato , Saitoh Yukimasa
Published: August 2012

A new plasma source concept, consisting of segmented electrodes and an economical 13.56 MHz power generator, has been developed for the plasma-enhanced chemical vapor deposition (PECVD) of microcrystalline silicon thin films on large-area substrates. Using a plurality of rectangular column-type electrodes fed with RF (13.56 MHz) at various relative phases, a two-stage plasma, which consists of an upper and lower plasma, was generated. In the case of supplying the anti-phase RF, we could control the ion incident energy on a substrate to be lower, so as to keep the high crystallinity and high deposition rate during the film growth. The agreement between the observed light emission profiles from Ar or Ar/H2plasma and the numerically calculated ones was good, confirming the accuracy of the simulation model, and we performed the thin-film growth of microcrystal silicon with this new plasma source and H2/SiH4gas. Consequently, we could achieve a fast deposition rate of more than 1.5 nm/s with good crystallinity over 60%.
Focal Adhesion of Osteoblastic Cells on Titanium Surface with Amine Functionalities Formed by Plasma Polymerization
Authors: Song Heesang , Jung Sang Chul , Kim Byung Hoon
Published: August 2012

To enhance the focal adhesion of osteoblastic cells on a titanium surface, plasma polymerized allyl amine (AAm) thin films were deposited by plasma polymerization. This plasma polymer functionalization of titanium is advantageous for osteoblastic focal adhesion formation. Such Ti surfaces are useful for the fabrication of titanium-based dental implants for enhancement of osseointegration.
Low-Temperature Deposition of Zinc Oxide Film by Plasma-Assisted Mist Chemical Vapor Deposition
Authors: Takenaka Kosuke , Okumura Yusuke , Setsuhara Yuichi
Published: August 2012

Zinc oxide (ZnO) film deposition using a plasma-assisted mist chemical vapor deposition (CVD) with an inductively-coupled plasma source has been performed and the effects of the plasma exposure on film properties have been investigated with oxygen mixture ratio as a parameter. With increasing oxygen mixture ratio to Ar+O2(10%), the X-ray diffraction (XRD) results showed evident peaks of ZnO(0002), indicating that highly c-axis-oriented films were grown at low substrate temperatures below 200 °C. The deposition rate of ZnO films was as high as 100 nm/min. ZnO films with an optical transmittance of 75% for the visible region and a band gap energy of 3.32 eV have been obtained by using plasma-assisted mist CVD.
Superstructures Based upon n- and p-Type Organic Semiconductors: Toward Light-Emitting Device Applications
Authors: Hayashi Waka , Terasaki Kohei , Kajiwara Kentaro , Yamao Takeshi , Hotta Shu
Published: August 2012

We have made organic light-emitting field-effect transistors (OLEFETs) using superstructures composed of layered n- and p-type organic semiconductor crystals. The superstructures are fabricated by lamination of the crystals via physical adsorption. The drain and source electrodes made of different kinds of metal are attached to both the upper and lower surfaces of each crystal. Under application of direct-current voltages to the drain and source electrodes, the superstructure OLEFETs emit bright light. The result indicates that the superstructures based on both types of organic crystals are useful for light-emitting devices.
A Dry Process for Polymer Nano-Microfibers Prepared by Electrospinning under Pressurized CO2
Authors: Murakami Wahyudiono , Machmudah Siti , Sasaki Mitsuru , Goto Motonobu
Published: August 2012

Electrospinning is known as an efficient technique for the fabrication of polymer nanoparticles and nanofibers. Various polymers have been successfully electrospun into ultrafine particles and fibers in recent years, mostly in solvent solution and some in melt form. In this study, electrospinning was conducted under pressurized carbon dioxide (CO2) to reduce the viscosity of polymer solution. The experiments were conducted at 313 K and ∼8.0 MPa. Poly(vinyl pyrrolidone) (PVP) in dichloromethane (DCM) was used as a polymer solution with 4 wt % of concentration. The applied voltage was 17 kV and the distance of nozzle and collector was 8 cm. The morphology and structure of the fibers produced were observed using scanning electron microscopy (SEM). Under pressurized CO2, PVP electrospun was produced without bead formation with diameter ranges of 608.50–7943.19 nm. These behaviors hold the potential to considerably improve devolatilization electrospinning processes.
High-Speed and Precise Gap Servo System for Near-Field Optical Recording
Authors: Koide Daiichi , Kajiyama Takeshi , Tokumaru Haruki , Takano Yoshimichi , Nabata Yuta , Ogata Tokoku , Miyazaki Toshimasa , Ohishi Kiyoshi
Published: August 2012

We propose a high-speed and precise gap servo control system that is based on the feed-forward control method that can reduce the harmonic disturbance (RHD-FFC) on a near-field optical recording system with a solid immersion lens. An optical disk of 1.2 mm thickness rotates with about 30 µmp–p of axial run-out. The axial run-out prevents a gap servo from performing precisely at high rotational speed. The RHD-FFC method can suppress harmonic disturbances of gap error signal and can perform at high speed while keeping less than 25 nm of gap length between an optical head and a rotational disk surface. We confirmed that the gap servo applying the RHD-FFC method performed precisely and achieved at high disk rotational speed of 11000 rpm with a 1.2-mm-thick optical disk with a track pitch of 0.16 µm, corresponding to a data capacity of 100 Gbyte.
Simplified Decoding of Trellis-Based Error-Correcting Modulation Codes Using the M-Algorithm for Holographic Data Storage
Authors: Kim Jinyoung , Lee Jaejin
Published: August 2012

In this paper, we investigate a simplified decoding method for the trellis-based error-correcting modulation codes using the M-algorithm for holographic data storage. The M-algorithm, which sacrifices the bit error rate performance, can reduce the Viterbi algorithm's complexity. When the M-algorithm is used in the trellis-based error-correcting modulation codes, common delay and complexity problems can be reduced.
Soft-Encoding Scheme of 3/4 Tone-Controllable Code for Channel Iteration of Low-Density Parity-Check Code on the Holographic Data Storage
Authors: Park Donghyuk , Lee Jaejin
Published: August 2012

In turbo equalization for holographic data storage (HDS) systems, an iterate-back signal must pass through a modulation coding process for channel iteration since the iterate-back signal is a demodulated signal and the input of a detector is modulated data. Also, the iterate-back signal is a soft-value, so the soft-input and soft-output (SISO) must be treated by a modulation code. A 3/4 tone-controllable (TC) code can control the ratio of ON and OFF pixels on each data page. The memory capacity of a holographic data storage system can be increased if we use a TC code. In this paper, we concatenate a 3/4 TC code and LDPC code, and then simulate the turbo equalization performance on a HDS channel. A SISO 3/4 TC code is needed for this simulation. Therefore, we propose a soft-encoding scheme for a SISO 3/4 TC code.
Proposal for Rewritable Microholographic Recording Using Polarization-Sensitive Materials
Authors: Katayama Ryuichi , Tominaga Shin
Published: August 2012

Rewritable microholographic recording using polarization-sensitive materials has been proposed. Two types of optical configuration (i.e., single-channel detection and differential detection) have been presented. Recording operation is carried out by focusing two light beams with orthogonal polarization states in the recording medium. The polarization states of the two light beams are switched with switchable waveplates according to recording signal. The polarization directions of light in which the two light beams are synthesized are recorded in the recording medium as a polarization diffraction grating. Readout operation is carried out by focusing a light beam with a certain polarization state in the recording medium. A reflected light beam from the polarization diffraction grating is detected by a photodetector. The readout signal is obtained from the intensity or the polarization state of the reflected light beam. This technology features not only rewritability but also overwritability. Readout signal simulation considering polarization has demonstrated the validity of this technology.
Soft-Decision Viterbi Decoding Scheme and a New Reliability Metric for 4/6 Modulation Code in Holographic Data Storage
Authors: Kim Yongok , Kong Gyuyeol , Choi Sooyong
Published: August 2012

A soft-decision Viterbi decoding for a 4/6 modulation code is proposed in a holographic data storage system. Since the previous proposed soft-decision Viterbi decoding does not support a higher rate modulation codes than 1/2 rate modulation codes, we propose a new reliability metric to support the 4/6 modulation code. The reliability metric is used to calculate the branch metric on the trellis. For a better coding gain, we find a symbol mapping method for the modulation code which provides a large free distance on the trellis to have the enhanced error correcting capability. Simulation results show that the proposed scheme has about 2 dB coding gains than the conventional soft-decision Viterbi decoding scheme.
Reduction of Interlayer Crosstalk of Multilayer Optical Disc by Using Phase-Diversity Homodyne Detection
Authors: Ide Tatsuro , Osawa Kentaro , Mikami Hideharu , Watanabe Koichi
Published: August 2012

We theoretically and experimentally studied the effects of phase-diversity homodyne detection on the interlayer crosstalk of a multilayer optical disc by comparison with those of conventional intensity detection. From analytical studies, we clarified the differences in interlayer crosstalk of both detections. Interlayer crosstalk consists of two noises, the intensity of the stray light N
1 and the interference between the signal and stray light N
2. The noise N
1, which is dominant between these two, drastically decreases with layer spacing in phase-diversity homodyne detection owing to mismatch in the phase distribution between reference and stray light compared with that in intensity detection. Simulations and experiments on a dual-layer Blu-ray DiscTM having a layer spacing less than 10 µm demonstrated that phase-diversity homodyne detection provided higher tolerance to interlayer crosstalk than the conventional intensity detection.
Electrically-Generated Pure Spin Current in Graphene
Authors: Shiraishi Masashi
Published: August 2012

This article introduces the physical characteristics of pure spin current, especially the electrically generated pure spin current in graphene. Pure spin current is essentially different from charge current, since only spin angular momentum flows. A number of studies on the generation of pure spin current in graphene has been intensively performed, and various attractive physical features of the pure spin current have been clarified. Spin currentronics using graphene can open a new frontier in the field of spintronics.
Study of MgAl2O4(111) Spinel Surface Using Noncontact Atomic Force Microscopy
Authors: Okada Arifumi , Go Sekishu , Yoshimura Masamichi , Ishikawa Yo-ichi
Published: August 2012

The surface structures of MgAl2O4(111) were investigated using noncontact atomic force microscopy (nc-AFM), X-ray photoelectron spectroscopy (XPS), and energy-dispersive X-ray spectroscopy (EDS) attached with a scanning electron microscope (SEM). Two different specimens with different XPS Mg/Al intensity ratios were examined. The nc-AFM image of the sample with high Mg content shows formation of nanorods on the large steps and rough terraces. The nanorod is assumed to be MgO, which was precipitated from the MgO-rich solid solution. On the other hand, another sample (close to MgO:Al2O3=1:1) show flat terraces and relatively small step heights corresponding to one period of the (111) stacking sequence of MgAl2O4(111). Thus we found that the deviations of bulk compositions strongly affect the surface structures.
Investigations of Local Electrical Characteristics of a Pentacene Thin Film by Point-Contact Current Imaging Atomic Force Microscopy
Authors: Kimura Tomoharu , Miyato Yuji , Kobayashi Kei , Yamada Hirofumi , Matsushige Kazumi
Published: August 2012

We performed local electrical property measurements on a pentacene semiconducting thin film, which was connected to a Pt electrode, using point-contact current imaging atomic force microscopy (PCI-AFM). The measurements were conducted not only under ambient conditions, but also in a vacuum on the same film by employing theQ-control method to reduce the settling time of the cantilever oscillation amplitude. In both environments, the obtained current images showed that the current in the film gradually decreased with the increasing distance from the electrode. We also found differences in the threshold voltage among the grains and discontinuities in the apparent resistance at the grain boundaries, which suggest that the conductance of the thin film is limited by the grain boundaries. Moreover, by comparison of the measurement results on the same grains in air and in a vacuum, an increase in the current and a shift in the threshold voltage to a positive value in air were observed, which can be attributed to the exposure of the film to atmospheric oxygen.
Atomic-Resolution Imaging of Aragonite (001) Surface in Water by Frequency Modulation Atomic Force Microscopy
Authors: Araki Yuki , Tsukamoto Katsuo , Oyabu Noriaki , Kobayashi Kei , Yamada Hirofumi
Published: August 2012

Aragonite is a high-pressure phase of calcium carbonate crystals. However, aragonite is formed under normal pressure with the help of biomineralization. Although it is important to observe growth features to understand the growth mechanism of the aragonite surface, only a few research groups have succeeded in observing the growth steps. In this study, we performed observation of the (001) face of a natural aragonite crystal surface at the atomic scale by the newly developed frequency modulation atomic force microscopy (FM-AFM). On the (001) face of aragonite, several growth islands with flat terraces were observed. We have succeeded in obtaining atomic-resolution images of the pseudo-hexagonal arrangement of calcium ions on the terraces. We also obtained atomic-resolution images on the calcite (101̄4) face by FM-AFM, which highlights the difference in the surface atomic arrangements of the two polymorphs was clearly visualized.
Nuclear Organization and Genome Function
Authors: Van Bortle Kevin , Corces Victor G.
Published: August 2012

Long-range interactions between transcription regulatory elements play an important role in gene activation, epigenetic silencing, and chromatin organization. Transcriptional activation or repression of developmentally regulated genes is often accomplished through tissue-specific chromatin architecture and dynamic localization between active transcription factories and repressive Polycomb bodies. However, the mechanisms underlying the structural organization of chromatin and the coordination of physical interactions are not fully understood. Insulators and Polycomb group proteins form highly conserved multiprotein complexes that mediate functional long-range interactions and have proposed roles in nuclear organization. In this review, we explore recent findings that have broadened our understanding of the function of these proteins and provide an integrative model for the roles of insulators in nuclear organization.
Philip G. Saffman
Authors: Pullin D.I. , Meiron D.I.
Published: August 2012

This article surveys the contributions of Philip Geoffrey Saffman to our knowledge of fluid-dynamical phenomena both in nature and in the laboratory. We begin with Saffman's first work on fluid mechanics in Cambridge, England, in the mid-1950s and then describe the evolution of his ideas and research, over many diverse areas in fluid mechanics until his final paper in 2002. It is argued that Saffman brought a unique perspective to our interpretation of fluid mechanics as a broad scientific discipline that remains with us today.
Sociolegal Studies on Mexico
Authors: Ríos-Figueroa Julio
Published: August 2012

Mexico has undergone a peculiar transition to a democracy that in some aspects and places still exhibits traits of the authoritarian past. The combination of authoritarian shades and democratic glares, rich diversity in socioeconomic conditions across the country, and the recent availability of a wealth of information and systematized data make for a great deal of research opportunities for sociolegal scholarship. This article reviews recent sociolegal studies on courts and judicial behavior, public security and the criminal justice system, and legal culture, pointing to several empirical puzzles and open questions that are crying out for explanations and systematic empirical analysis.
Clinical Use of the Antiseptic Polihexanide for Genital Tract Infections
Authors: Koban I. , Bender C.P. , Assadian O. , Kramer A. , Hübner N.-O. ,   International Society of Chemotherapy Working Group Antiseptics; Working Section for Clinical Antiseptic of the German Society for Hospital Hygiene
Published: August 2012

Background: In clinical practice, treatment of genital tract infections is based on administration of either antibiotics or antiseptics. While antibiotics may be applied systemically or topically, antiseptics may be applied only topically. In case of bacterial vaginosis (BV), antibiotic therapy may often be limited and side effects due to systemic administration may develop. Polihexanide (PHMB) is a promising option for the topical treatment of genital tract infections, in particular BV and vaginitis. Method: A systematic search for publications on the use of PHMB for the treatment of genital infections in two electronic databases was performed. Titles, abstracts and citations were imported into a reference database. Duplicates were removed and two reviewers assessed each identified publication separately. Results: Among a total of 204 references, 3 prospective randomized trials were identified. Two trials treated BV infections with PHMB in comparison to clindamycin as antibiotic standard therapy with no significant differences either in safety or in efficacy. The third controlled trial investigated the clinical efficacy of PHMB compared to placebo in the treatment of human papilloma virus. Patients treated with PHMB daily for up to 16-weeks showed significantly higher (52%) clearance of genital warts as compared to patients treated with placebo (4%). Conclusion: PHMB may be a clinically effective alternative for the treatment of BV and human papilloma virus. Although PHMB-based antiseptics are available since the late 90s, controlled trials to investigate its clinical potential for antiseptic treatment are scant. Clinical use of antiseptics for the treatment of infectious diseases should be explored and supported further.
The Limits of Feedforward Vision: Recurrent Processing Promotes Robust Object Recognition when Objects Are Degraded
Authors: Wyatte Dean , Curran Tim , O'Reilly Randall
Published: August 2012

Everyday vision requires robustness to a myriad of environmental factors that degrade stimuli. Foreground clutter can occlude objects of interest, and complex lighting and shadows can decrease the contrast of items. How does the brain recognize visual objects despite these low-quality inputs? On the basis of predictions from a model of object recognition that contains excitatory feedback, we hypothesized that recurrent processing would promote robust recognition when objects were degraded by strengthening bottom–up signals that were weakened because of occlusion and contrast reduction. To test this hypothesis, we used backward masking to interrupt the processing of partially occluded and contrast reduced images during a categorization experiment. As predicted by the model, we found significant interactions between the mask and occlusion and the mask and contrast, such that the recognition of heavily degraded stimuli was differentially impaired by masking. The model provided a close fit of these results in an isomorphic version of the experiment with identical stimuli. The model also provided an intuitive explanation of the interactions between the mask and degradations, indicating that masking interfered specifically with the extensive recurrent processing necessary to amplify and resolve highly degraded inputs, whereas less degraded inputs did not require much amplification and could be rapidly resolved, making them less susceptible to masking. Together, the results of the experiment and the accompanying model simulations illustrate the limits of feedforward vision and suggest that object recognition is better characterized as a highly interactive, dynamic process that depends on the coordination of multiple brain areas.
Domestic Violence In India: Cases Under The Protection Of Women From Domestic Violence Act, 2005
Authors: Bhatia Manjeet
Published: August 2012

After prolonged lobbying, the Protection of Women from Domestic Violence Act of 2005 was implemented in India in October 2006. The Act soon gave rise to cases. This article is based on a preliminary study using questionnaire-based interviews of litigants in Delhi who were involved in cases under the Act. Primary data, taken from all the Delhi Metropolitan Magistrates Courts at that time, concern the background of those who used the law, the litigation process, implementation of the law and the forms of violence addressed. The article seeks to assess the effectiveness of this new legislation and examines specifically what kinds of people bring actions under this new gender-specific law. In addition, qualitative assessment of the perceptions of different kinds of violence by complainants and respondents provides deeper insights into ongoing and potential contestations over gender-based violence.
Emotion, engagement and meaning in strong experiences of music performance
Authors: Lamont Alexandra
Published: August 2012

This paper explores the emotions connected with music performance. Performing music provides the potential to attain wellbeing via the hedonic and eudaimonic routes, appealing to pleasure, engagement and meaning (Seligman, 2002). To date, most research exploring emotions amongst performers has focused on these components separately, exploring positive or negative affect, flow, or the development of performer identity. In the current study, 35 university students (mean age 20.6 years) gave free reports of their strongest, most intense experiences of performing music. Accounts were content analyzed using the Strong Experiences of Music Descriptive System (Gabrielsson & Lindström Wik, 2003), and also analyzed for the components of wellbeing using an idiographic approach. Four basic types of response were characterized, emphasizing: (1) negative and positive emotions and personal engagement; (2) negative and positive emotions, engagement and meaning; (3) positive emotion and meaning; or (4) positive emotions, engagement, and meaning. The emphasis on the eudaimonic route to wellbeing (through engagement and meaning) shows that young musicians do have valuable and rewarding experiences with the potential to sustain long-term motivation to engage with practical music-making. The value of the positive psychology framework is also demonstrated by its applicability to descriptions of strong experiences of performing music.
Bed Bugs: They ARE Back!
Authors: Sciscione Patricia
Published: August 2012

Recently there has been a resurgence of bed bugs in all facets of our society. Bed bugs have even been found in schools, causing unnecessary exclusion of students and unfounded hysteria. School nurses are again called upon to be front-line sources of information to quell the hysteria and confusion related to this unsavory condition. By arming themselves with the best evidence regarding proper identification of bed bugs and their bites and information about integrated prevention measures to control transmission of infestations, school nurses can contribute to the control and management of bed bugs and aid in the overall battle against this “new and improved” invasion of the bed bugs.
FluShuffle and FluResort: new algorithms to identify reassorted strains of the influenza virus by mass spectrometry
Authors: Lun Aaron TL , Wong Jason WH , Downard Kevin M
Published: August 2012

Background

Influenza is one of the oldest and deadliest infectious diseases known to man. Reassorted strains of the virus pose the greatest risk to both human and animal health and have been associated with all pandemics of the past century, with the possible exception of the 1918 pandemic, resulting in tens of millions of deaths. We have developed and tested new computer algorithms, FluShuffle and FluResort, which enable reassorted viruses to be identified by the most rapid and direct means possible. These algorithms enable reassorted influenza, and other, viruses to be rapidly identified to allow prevention strategies and treatments to be more efficiently implemented.

Results

The FluShuffle and FluResort algorithms were tested with both experimental and simulated mass spectra of whole virus digests. FluShuffle considers different combinations of viral protein identities that match the mass spectral data using a Gibbs sampling algorithm employing a mixed protein Markov chain Monte Carlo (MCMC) method. FluResort utilizes those identities to calculate the weighted distance of each across two or more different phylogenetic trees constructed through viral protein sequence alignments. Each weighted mean distance value is normalized by conversion to a Z-score to establish a reassorted strain.

Conclusions

The new FluShuffle and FluResort algorithms can correctly identify the origins of influenza viral proteins and the number of reassortment events required to produce the strains from the high resolution mass spectral data of whole virus proteolytic digestions. This has been demonstrated in the case of constructed vaccine strains as well as common human seasonal strains of the virus. The algorithms significantly improve the capability of the proteotyping approach to identify reassorted viruses that pose the greatest pandemic risk.
Evolution of the Rdr1 TNL-cluster in roses and other Rosaceous species
Authors: Terefe-Ayana Diro , Kaufmann Helgard , Linde Marcus , Debener Thomas
Published: August 2012

Background

The resistance of plants to pathogens relies on two lines of defense: a basal defense response and a pathogen-specific system, in which resistance (R) genes induce defense reactions after detection of pathogen-associated molecular patterns (PAMPS). In the specific system, a so-called arms race has developed in which the emergence of new races of a pathogen leads to the diversification of plant resistance genes to counteract the pathogens’ effect. The mechanism of resistance gene diversification has been elucidated well for short-lived annual species, but data are mostly lacking for long-lived perennial and clonally propagated plants, such as roses. We analyzed the rose black spot resistance gene, Rdr1, in five members of the Rosaceae: Rosa multiflora, Rosa rugosa, Fragaria vesca (strawberry), Malus x domestica (apple) and Prunus persica (peach), and we present the deduced possible mechanism of R-gene diversification.

Results

We sequenced a 340.4-kb region from R. rugosa orthologous to the Rdr1 locus in R. multiflora. Apart from some deletions and rearrangements, the two loci display a high degree of synteny. Additionally, less pronounced synteny is found with an orthologous locus in strawberry but is absent in peach and apple, where genes from the Rdr1 locus are distributed on two different chromosomes. An analysis of 20 TIR-NBS-LRR (TNL) genes obtained from R. rugosa and R. multiflora revealed illegitimate recombination, gene conversion, unequal crossing over, indels, point mutations and transposable elements as mechanisms of diversification.

A phylogenetic analysis of 53 complete TNL genes from the five Rosaceae species revealed that with the exception of some genes from apple and peach, most of the genes occur in species-specific clusters, indicating that recent TNL gene diversification began prior to the split of Rosa from Fragaria in the Rosoideae and peach from apple in the Spiraeoideae and continued after the split in individual species. Sequence similarity of up to 99% is obtained between two R. multiflora TNL paralogs, indicating a very recent duplication.

Conclusions

The mechanisms by which TNL genes from perennial Rosaceae diversify are mainly similar to those from annual plant species. However, most TNL genes appear to be of recent origin, likely due to recent duplications, supporting the hypothesis that TNL genes in woody perennials are generally younger than those from annuals. This recent origin might facilitate the development of new resistance specificities, compensating for longer generation times in woody perennials.
Heart Disease and Left Ventricular Rotation – A Systematic Review and Quantitative Summary
Authors: Phillips Aaron A , Cote Anita T , Bredin Shannon SD , Warburton Darren ER
Published: August 2012

Background

Left ventricular (LV) rotation is increasingly examined in those with heart disease. The available evidence measuring LV rotation in those with heart diseases has not been systematically reviewed.

Methods

To review systematically the evidence measuring LV rotational changes in various heart diseases compared to healthy controls, literature searches were conducted for appropriate articles using several electronic databases (e.g., MEDLINE, EMBASE). All randomized-controlled trials, prospective cohort and case–controlled studies that assessed LV rotation in relation to various heart conditions were included. Three independent reviewers evaluated each investigation’s quality using validated scales. Results were tabulated and levels of evidence assigned.

Results

A total of 1,782 studies were found through the systematic literature search. Upon review of the articles, 47 were included. The articles were separated into those investigating changes in LV rotation in participants with: aortic stenosis, myocardial infarction, hypertrophic cardiomyopathy, dilated cardiomyopathy, non-compaction, restrictive cardiomyopathy/ constrictive pericarditis, heart failure, diastolic dysfunction, heart transplant, implanted pacemaker, coronary artery disease and cardiovascular disease risk factors. Evidence showing changes in LV rotation due to various types of heart disease was supported by evidence with limited to moderate methodological quality.

Conclusions

Despite a relatively low quality and volume of evidence, the literature consistently shows that heart disease leads to marked changes in LV rotation, while rotational systolic-diastolic coupling is preserved. No prognostic information exists on the potential value of rotational measures of LV function. The literature suggests that measures of LV rotation may aid in diagnosing subclinical aortic stenosis and diastolic dysfunction.
Double-blind, placebo-controlled first in human study to investigate an oral vaccine aimed to elicit an immune reaction against the VEGF-Receptor 2 in patients with stage IV and locally advanced pancreatic cancer
Authors: Niethammer Andreas G , Lubenau Heinz , Mikus Gerd , Knebel Philipp , Hohmann Nicolas , Leowardi Christine , Beckhove Philipp , Akhisaroglu Mustafa , Ge Yingzi , Springer Marco , Grenacher Lars , Buchler Markus W , Koch Moritz , Weitz Jürgen , Haefeli Walter E , Schmitz-Winnenthal Friedrich H
Published: August 2012

Background

The investigational oral DNA vaccine VXM01 targets the vascular endothelial growth factor receptor 2 (VEGFR-2) and uses Salmonella typhi Ty21a as a vector. The immune reaction elicited by VXM01 is expected to disrupt the tumor neovasculature and, consequently, inhibit tumor growth. VXM01 potentially combines the advantages of anti-angiogenic therapy and active immunotherapy.

Methods/Design

This phase I trial examines the safety, tolerability, and immunological and clinical responses to VXM01. The randomized, placebo-controlled, double blind dose-escalation study includes up to 45 patients with locally advanced and stage IV pancreatic cancer. The patients will receive four doses of VXM01 or placebo in addition to gemcitabine as standard of care. Doses from 106 cfu up to 1010 cfu of VXM01 will be evaluated in the study. An independent data safety monitoring board (DSMB) will be involved in the dose-escalation decisions. In addition to safety as primary endpoint, the VXM01-specific immune reaction, as well as clinical response parameters will be evaluated.

Discussion

The results of this study shall provide the first data regarding the safety and immunogenicity of the oral anti-VEGFR-2 vaccine VXM01 in cancer patients. They will also define the recommended dose for phase II and provide the basis for further clinical evaluation, which may also include additional cancer indications.

Trial registration

EudraCT No.: 2011-000222-29, NCT01486329, ISRCTN68809279
Sex differences in response to maximal exercise stress test in trained adolescents
Authors: Fomin Åsa , Ahlstrand Mattias , Schill Helena Gyllenhammar , Lund Lars H , Ståhlberg Marcus , Manouras Aristomenis , Gabrielsen Anders
Published: August 2012

Background

Sex comparisons between girls and boys in response to exercise in trained adolescents are missing and we investigated similarities and differences as a basis for clinical interpretation and guidance.

Methods

A total of 24 adolescent females and 27 adolescent males aged 13–19 years underwent a maximal bicycle exercise stress test with measurement of cardiovascular variables, cardiac output, lung volumes, metabolic factors/lactate concentrations and breath-by-breath monitoring of ventilation, and determination of peak VO2.

Results

Maximum heart rate was similar in females (191 ± 9 bpm) and males (194 ± 7 bpm), cardiac index at maximum exercise was lower in females (7.0 ± 1.0 l/min/m2) than in males (8.3 ± 1.4 l/min/m2, P < 0.05). Metabolic responses and RQ at maximum exercise were similar (females: 1.04 ± 0.06 vs. males: 1.05 ± 0.05). Peak VO2 was lower in females (2.37 ± 0.34 l/min) than in males (3.38 ± 0.49 l/min, P < 0.05). When peak VO2 was normalized to leg muscle mass sex differences disappeared (females: 161 ± 21 ml/min/kg vs. males: 170 ± 23 ml/min/kg). The increase in cardiac index during exercise is the key factor responsible for the greater peak VO2 in adolescent boys compared to girls.

Conclusions

Differences in peak VO2 in adolescent boys and girls disappear when peak VO2 is normalized to estimated leg muscle mass and therefore provide a tool to conduct individual and intersex comparisons of fitness when evaluating adolescent athletes in aerobic sports.
Prevalence and determinants of complementary and alternative medicine use among infertile patients in Lebanon: a cross sectional study
Authors: Ghazeeri Ghina S , Awwad Johnny T , Alameddine Mohamad , Younes Zeina MH , Naja Farah
Published: August 2012

Background

Complementary and alternative medicine (CAM) is widely used for the treatment of infertility. While the Middle East and North Africa region has been shown to house one of the fastest growing markets of CAM products in the world, research describing the use of CAM therapies among Middle-Eastern infertile patients is minimal. The aim of this study is to examine the prevalence, characteristics and determinants of CAM use among infertile patients in Lebanon.

Methods

A cross sectional survey design was used to carry out face-to-face interviews with 213 consecutive patients attending the Assisted Reproductive Unit at a major academic medical center in Beirut. The questionnaire comprised three sections: socio-demographic and lifestyle characteristics, infertility-related aspects and information on CAM use. The main outcome measure was the use of CAM modalities for infertility treatment. Determinants of CAM use were assessed through the logistic regression method.

Results

Overall, 41% of interviewed patients reported using a CAM modality at least once for their infertility. There was a differential by gender in the most commonly used CAM therapies; where males mostly used functional foods (e.g. honey & nuts) (82.9%) while females mostly relied on spiritual healing/prayer (56.5%). Factors associated with CAM use were higher household income (OR: 0.305, 95% CI: 0.132–0.703) and sex, with females using less CAM than males (OR: 0.12, 95% CI: 0.051–0.278). The older patients were diagnosed with infertility, the lower the odds of CAM use (p for trend <0.05). Almost half of the participants (48%) were advised on CAM use by their friends, and only 13% reported CAM use to their physician.

Conclusions

The considerably high use of CAM modalities among Lebanese infertile patients, added to a poor CAM use disclosure to physicians, underscore the need to integrate CAM into the education and training of health professionals, as well as enhance infertile patients' awareness on safe use of CAM products.
RETRACTED ARTICLE: The proto-oncogene c-src is involved in primordial follicle activation through the PI3K, PKC and MAPK signaling pathways
Authors: Du Xiao-Yu , Huang Jian , Xu Liang-Quan , Tang Dan-Feng , Wu Lei , Zhang Li-Xia , Pan Xiao-Ling , Chen Wei-Yun , Zheng Li-Ping , Zheng Yue-Hui
Published: August 2012

Background

C-src is an evolutionarily conserved proto-oncogene that regulates cell proliferation, differentiation and apoptosis. In our previous studies, we have reported that another proto-oncogene, c-erbB2, plays an important role in primordial follicle activation and development. We also found that c-src was expressed in mammalian ovaries, but its functions in primordial follicle activation remain unclear. The objective of this study is to investigate the role and mechanism of c-src during the growth of primordial follicles.

Methods

Ovaries from 2-day-old rats were cultured in vitro for 8 days. Three c-src-targeting and one negative control siRNA were designed and used in the present study. PCR, Western blotting and primordial follicle development were assessed for the silencing efficiency of the lentivirus c-src siRNA and its effect on primordial follicle onset. The expression of c-src mRNA and protein in primordial follicle growth were examined using the PCR method and immunohistochemical staining. Furthermore, the MAPK inhibitor PD98059, the PKC inhibitor Calphostin and the PI3K inhibitor LY294002 were used to explore the possible signaling pathways of c-src in primordial folliculogenesis.

Results

The results showed that Src protein was distributed in the ooplasmic membrane and the granulosa cell membrane in the primordial follicles, and c-src expression level increased with the growth of primordial follicle. The c-src -targeting lentivirus siRNAs had a silencing effect on c-src mRNA and protein expression. Eight days after transfection of rat ovaries with c-src siRNA, the GFP fluorescence in frozen ovarian sections was clearly discernible under a fluorescence microscope, and its relative expression level was 5-fold higher than that in the control group. Furthermore, the c-src-targeting lentivirus siRNAs lowered its relative expression level 1.96 times. We also found that the development of cultured primordial follicles was completely arrested after c-src siRNA knockdown of c-src expression. Furthermore, our studies demonstrated that folliculogenesis onset was inhibited by Calphostin, PD98059 or LY294002 treatment,but none of them down-regulated c-src expression. In contrast, the expression levels of p-PKC, p-ERK1/2 and p-PI3K in the follicles were clearly decreased by c-src siRNA transfection. Correspondingly, both Calphostin and LY294002 treatment resulted in a decrease in the p-PKC level in follicles, but no change was observed in the PD98059 group. Finally, LY294002 treatment decreased the p-PI3K expression level in the follicles, but no changes were observed in the PD98059 and Calphostin groups.

Conclusions

C-src plays an important role in regulating primordial follicle activation and growth via the PI3K-PKC- ERK1/2 pathway.
Neurog1 and Neurog2 coordinately regulate development of the olfactory system
Authors: Shaker Tarek , Dennis Daniel , Kurrasch Deborah M , Schuurmans Carol
Published: August 2012

Background

Proneural genes encode basic helix–loop–helix transcription factors that specify distinct neuronal identities in different regions of the nervous system. In the embryonic telencephalon, the proneural genes Neurog1 and Neurog2 specify a dorsal regional identity and glutamatergic projection neuron phenotype in the presumptive neocortex, but their roles in cell fate specification in the olfactory bulb, which is also partly derived from dorsal telencephalic progenitors, have yet to be assessed. Given that olfactory bulb development is guided by interactions with the olfactory epithelium in the periphery, where proneural genes are also expressed, we investigated the roles of Neurog1 and Neurog2 in the coordinated development of these two olfactory structures.

Results

Neurog1/2 are co-expressed in olfactory bulb progenitors, while only Neurog1 is widely expressed in progenitors for olfactory sensory neurons in the olfactory epithelium. Strikingly, only a remnant of an olfactory bulb forms in Neurog1
−/−
;Neurog2
−/− double mutants, while this structure is smaller but distinguishable in Neurog1
−/− single mutants and morphologically normal in Neurog2

−/−
single mutants. At the cellular level, fewer glutamatergic mitral and juxtaglomerular cells differentiate in Neurog1
−/−
;Neurog2
−/− double-mutant olfactory bulbs. Instead, ectopic olfactory bulb interneurons are derived from dorsal telencephalic lineages in Neurog1
−/−
;Neurog2
−/− double mutants and to a lesser extent in Neurog2

−/−
single mutants. Conversely, cell fate specification is normal in Neurog1

−/−
olfactory bulbs, but aberrant patterns of cell proliferation and neuronal migration are observed in Neurog1

−/−
single and Neurog1
−/−
;Neurog2
−/− double mutants, probably contributing to their altered morphologies. Finally, in Neurog1

−/−
and Neurog1
−/−
;Neurog2
−/− embryos, olfactory sensory neurons in the epithelium, which normally project to the olfactory bulb to guide its morphogenesis, fail to innervate the olfactory bulb.

Conclusions

We have identified a cell autonomous role for Neurog1/ 2 in specifying the glutamatergic identity of olfactory bulb neurons. Furthermore, Neurog1 (and not Neurog2) is required to guide olfactory sensory neuron innervation of the olfactory bulb, the loss of which results in defects in olfactory bulb proliferation and tissue morphogenesis. We thus conclude that Neurog1/2 together coordinate development of the olfactory system, which depends on tissue interactions between the olfactory bulb and epithelium.