bluuebunny/crossref_metadata_2025 huggingface dataset:
Coronary artery disease detected by coronary computed tomography angiography in adult survivors of childhood Hodgkin lymphoma
Authors: Mulrooney Daniel A. , Nunnery Sara E. , Armstrong Gregory T. , Ness Kirsten K. , Srivastava Deokumar , Donovan F. Daniel , Kurt Beth A. , Metzger Monika L. , Krasin Matthew J. , Joshi Vijaya , Durand Jean‐Bernard , Robison Leslie L. , Hudson Melissa M. , Flamm Scott D.
Published: July 2014

BACKGROUND

Survivors of Hodgkin lymphoma (HL) have significant cardiovascular risk and require long‐term surveillance. The current study assessed the prevalence of coronary artery disease (CAD) by coronary computed tomography angiography (CCTA) in adult survivors of childhood HL.

METHODS

Thirty‐one survivors of HL, 13 of whom (42%) were treated with radiotherapy (RT) only and 18 of whom (58%) were treated with multimodal therapy, underwent CCTA, echocardiography, electrocardiography (ECG), and treadmill stress testing. Obstructive CAD was defined as ≥50% occlusion of the left main or ≥70% occlusion of the left anterior descending, left circumflex, or right coronary arteries on CCTA. Echocardiograms with resting wall motion abnormalities or an ejection fraction <50%; ECGs with Q waves, ST abnormalities without Q waves, or T‐wave abnormalities without Q waves; and a J‐point depression of ≥1 mm with a horizontal or downsloping ST segment on stress testing were considered abnormal.

RESULTS

The prevalence of disease in participants (median age, 40 years [range, 26 years‐55 years]; median time from cancer diagnosis, 24 years [range, 17 years‐39 years]) was 39%, with 39 plaques detected among 12 survivors. Three participants (10%) treated with RT only had 4 obstructive lesions; 9 patients (29%; 5 of whom were treated with RT only and 4 of whom were treated with multimodal therapy) had nonobstructive lesions. Approximately 15% of lesions involved the left main, 21% involved the proximal left anterior descending, 18% involved the proximal right coronary, and 13% involved the proximal left circumflex arteries. Of the 12 participants found to have CAD by CCTA, 7 had a positive ECG, 1 had a positive echocardiogram, and 1 had a positive stress test.

CONCLUSIONS

CCTA identified CAD in a substantial percentage of survivors of HL and may be an effective screening modality for this population. Cancer 2014;120:3536–3544. © 2014 American Cancer Society.
The homeodomain transcription factor PITX2 is required for specifying correct cell fates and establishing angiogenic privilege in the developing cornea
Authors: Gage Philip J. , Kuang Chen , Zacharias Amanda L.
Published: July 2014

Background: Correct specification of cell lineages and establishing angiogenic privilege within the developing cornea are essential for normal vision but the mechanisms controlling these processes are poorly understood. Results: We show that the homeodomain transcription factor PItX2 is expressed in mesenchymal cells of the developing and mature cornea and use a temporal gene knockout approach to demonstrate that PITX2 is required for corneal morphogenesis and the specification of cell fates within the surface ectoderm and mesenchymal primordia. PITX2 is also required to establish angiogenic privilege in the developing cornea. Further, the expression of Dkk2 and suppression of canonical Wnt signaling activity levels are key mechanisms by which PITX2 specifies ocular surface ectoderm as cornea. In contrast, specifying the underlying mesenchyme to corneal fates and establishing angiogenic privilege in the cornea are less sensitive to DKK2 activity. Finally, the cellular expression patterns of FOXC2, PITX1, and BARX2 in Pitx2 and Dkk2 mutants suggest that these transcription factors may be involved in specifying cell fate and establishing angiogenic privilege within the corneal mesenchyme. However, they are unlikely to play a role in specifying cell fate within the corneal ectoderm. Conclusions: Together, these data provide important insights into the mechanisms regulating cornea development. Developmental Dynamics 243:1391–1400, 2014. © 2014 Wiley Periodicals, Inc.
Effects of flow alteration on Apple‐ring Acacia (Faidherbia albida) stands, Middle Zambezi floodplains, Zimbabwe
Authors: Gope Evelyn T. , Sass‐Klaassen Ute G. W. , Irvine Kenneth , Beevers Lindsay , Hes Edwin M. A.
Published: July 2014

The impounding of the Zambezi River by Kariba dam has regulated the river discharge of the Middle Zambezi river. This has been implicated in the failure of regeneration of Faidherbia albida in the downstream flood plain. This study aimed (1) to assess the effect of the altered flow regime of the river on the establishment and growth of F. albida on the Middle Zambezi floodplain and islands and (2) to test the potential of dendrochronology in detecting the age and long‐term growth rates of F. albida in response to flow regime.

Results indicated an uneven age distribution of F. albida stands on relatively ‘new islands’, dominated by young trees, while the floodplain and the ‘old island’ exhibited an even‐aged stand but with a lack of regeneration, and a dying‐off of older trees. The lack of F. albida establishment on the floodplain was linked to the decreased occurrence of flooding events, associated with a decrease in alluvial deposits, soil moisture and groundwater recharge. These effects may be enhanced by impact from browsers on regeneration of trees. Tree‐ring analyses revealed the presence of distinct annual growth rings in F. albida and the applicability of dendrochronology for estimating F. albida population dynamics. The trees on the ‘new islands’ are younger and grow faster than those on the floodplain. Lack of competition and possible favourable moisture conditions suggest beneficial conditions for establishment and growth of the trees on the islands. Copyright © 2014 John Wiley & Sons, Ltd.
Transcriptional regulation of fatty acid production in higher plants: Molecular bases and biotechnological outcomes
Authors: Marchive Chloé , Nikovics Krisztina , To Alexandra , Lepiniec Loïc , Baud Sébastien
Published: July 2014

Acyl lipids are essential constituents found in every plant cell, where they fulfill diverse biological functions. Requirements for acyl chains depend on the cell type considered and vary greatly, implying a tight regulation of de novo fatty acid production in the plastids so that supply fits demand. Data generated by extensive transcriptome analyses carried out in various plant species and the characterization of the WRINKLED1 transcription factor in the model plant Arabidopsis thaliana have first established the importance of transcriptional regulation for modulating the rate of fatty acid production. The fatty acid biosynthetic pathway is indeed subjected to a system of global transcriptional control that coordinates the expression of most genes encoding enzymes of the pathway. Although much remains to be elucidated, the framework of the regulatory system controlling fatty acid biosynthesis in plants is coming into focus.

Practical applications: Fatty acids constitute the most abundant form of reduced carbon chains available from nature and plant oils represent the main renewable resource of these fatty acids. Plant oils therefore represent a highly valuable agricultural commodity, the demand for which is increasing rapidly. They are primarily used for food and feed, but they are increasingly being utilized as renewable sources of industrial feedstock and fuel. Knowledge regarding the regulation of fatty production is extensively exploited in the frame of genetic engineering for oilseed crop improvement.

Fatty acids constitute the most abundant form of reduced carbon chains available from nature and plant oils represent the main renewable resource of these fatty acids. Plant oils therefore represent a highly valuable agricultural commodity, the demand for which is increasing rapidly. They are primarily used for food and feed, but they are increasingly being utilized as renewable sources of industrial feedstock and fuel. Knowledge regarding the regulation of fatty production is extensively exploited in the frame of genetic engineering for oilseed crop improvement. Data generated by extensive transcriptome analyses carried out in various plant species and the characterization of the WRINKLED1 transcription factor in the model plant Arabidopsis thaliana have established the importance of transcriptional regulation for modulating the rate of fatty acid production. The fatty acid biosynthetic pathway is indeed subjected to a system of global transcriptional control that coordinates the expression of most genes encoding enzymes of the pathway. Recent advance suggest that WRINKLED1 activity may be modulated at the post‐translational level through homo‐dimerization, phosphorylation, and/or ubiquitination.
Magnetite NPs@C with Highly‐Efficient Peroxidase‐Like Catalytic Activity as an Improved Biosensing Strategy for Selective Glucose Detection
Authors: Arana Mercedes , Tettamanti Cecilia S. , Bercoff Paula G. , Rodríguez Marcela C.
Published: July 2014

This work reports the novel application of carbon‐coated magnetite nanoparticles (mNPs@C) as catalytic nanomaterial included in a composite electrode material (mNPs@C/CPE) taking advantages of their intrinsic peroxidase‐like activity. The nanostructured electrochemical transducer reveals an enhancement of the charge transfer for redox processes involving hydrogen peroxide. Likewise, mNPs@C/CPE demonstrated to be highly selective even at elevated concentrations of ascorbic acid and uric acid, the usual interferents of blood glucose analysis. Upon these remarkable results, the composite matrix was further modified by the addition of glucose oxidase as biocatalyst, in order to obtain a biosensing strategy (GOx/mNPs@C/CPE) with enhanced properties for the electrochemical detection of glucose. GOx/mNPs@C/CPE exhibit a linear range up to 7.5×10−3 mol L−1 glucose, comprising the entirely physiological range and incipient pathological values. The average sensitivity obtained at −0.100 V was (1.62±0.05)×105 nA L mol−1 (R2=0.9992), the detection limit was 2.0×10−6 M while the quantification limit was 6.1×10−6 mol L−1. The nanostructured biosensor demonstrated to have an excellent performance for glucose detection in human blood serum even for pathological values.
Pig Bone Derived Hierarchical Porous Carbon‐Supported Platinum Nanoparticles with Superior Electrocatalytic Activity Towards Oxygen Reduction Reaction
Authors: Liu Haijing , Cao Yinliang , Wang Feng , Zhang Weidong , Huang Yaqin
Published: July 2014

Hierarchical porous carbon (HPC) with nitrogen doped three dimension open macropore structure was prepared from pig bone, and applied for the support material for platinum nanoparticle (Pt NP) electrocatalyst. Compared with carbon black supported Pt NP electrocatalysts, the Pt/HPC exhibited larger electrochemical active surface area and enhanced catalytic properties for the oxygen reduction reaction (ORR) in terms of on‐set potential, current density, mass activity and stability. The superior catalytic activity is mainly attributed to the high surface area, hierarchical porous structures and the nitrogen‐doped surface properties of the HPC, indicating it is a promising support material for the ORR electrocatalysts.
Teleconnection and climatic oscillation in aquifer water level in Kumamoto plain, Japan
Authors: Dong Linyao , Shimada Jun , Kagabu Makoto , Fu Congsheng
Published: July 2014

Relative little is known about the interaction between climate change and groundwater. Analysis of aquifer response to climatic variability could improve the knowledge related to groundwater resource variations and therefore provides guidance on water resource management. In this work, seasonal and annual variations of groundwater levels in Kumamoto plain (Japan) and their possible interactions with climatic indices and El Niño Southern Oscillation (ENSO) were analyzed statistically. Results show the following: (1) The water level in the recharge area mainly fluctuates at 1‐ and 2‐year periods, whereas the significant periodicity for water level oscillation in the coastal aquifer is 0.5 year. (2) The aquifer water levels are possibly influenced by variability in precipitation, air temperature, barometric pressure, humidity variances and ENSO. Relative high correlations and large proportions of similarities in wavelet power patterns were found between these variables and water levels. (3) Aquifer response to climatic variances was evaluated using cross wavelet transform and wavelet coherence. In recharging aquifers, the ENSO‐induced annual variations in precipitation, air temperature, humidity and barometric pressure affect aquifer water levels. The precipitation, air temperature and humidity respond to ENSO with a 4‐, 6‐ and 8‐month time lag, respectively, whereas the ENSO imparts weak influence on the barometric pressure. Significant biennial variation of water levels during 1991–1995 is caused primarily by precipitation and humidity variations. In the coastal aquifer, the 0.5‐year variability in ENSO is transferred by precipitation, barometric pressure and humidity to aquifer water levels, and the precipitation/humidity influence is more significant comparing with the barometric pressure. Copyright © 2014 John Wiley & Sons, Ltd.
Dynamic contrast‐enhanced MRI of gastric cancer: Correlation of the perfusion parameters with pathological prognostic factors
Authors: Joo Ijin , Lee Jeong Min , Han Joon Koo , Yang Han‐Kwang , Lee Hyuk‐Joon , Choi Byung Ihn
Published: July 2014

Purpose

To investigate the feasibility of dynamic, contrast‐enhanced, magnetic resonance imaging (DCE‐MRI) for perfusion quantification of gastric cancers, and to correlate the DCE‐MRI parameters with the pathological prognostic factors.

Materials and Methods

This prospective study was approved by our Institutional Review Board. Twenty‐seven patients with gastric cancers underwent DCE‐MRI using a free‐breathing, radial, gradient‐echo (GRE) sequence with k‐space weighted image contrast (KWIC) reconstruction on a 3T scanner. The DCE‐MRI parameters (volume transfer coefficient [Ktrans], reverse reflux rate constant [Kep], extracellular extravascular volume fraction [Ve], and initial area under the gadolinium concentration curve during the first 60 seconds [iAUC]) of gastric cancer and normal wall were measured and compared with each other using the Wilcoxon signed rank test. The relationship between the DCE‐MRI parameters of gastric cancer and the pathological prognostic factors were evaluated using the Mann–Whitney test or the Spearman rank correlation test.

Results

DCE‐MRIs were of diagnostic quality in 22 patients (81.5%). Ve and iAUC were significantly higher in gastric cancer than in normal gastric wall (P < 0.05). Ve showed significant positive correlation with T‐staging of gastric cancers (P < 0.05). Ktrans was significantly correlated with the grades of epidermal growth‐factor receptor expression (P < 0.05).

Conclusion

DCE‐MRI using a radial GRE with KWIC reconstruction is feasible for quantification of the perfusion dynamics of gastric cancers, and the DCE‐MRI parameters of gastric cancers may provide prognostic information. J. Magn. Reson. Imaging 2015;41:1608–1614. © 2014 Wiley Periodicals, Inc.
UTE imaging in the musculoskeletal system
Authors: Chang Eric Y. , Du Jiang , Chung Christine B.
Published: July 2014

Tissues, such as bone, tendon, and ligaments, contain a high fraction of components with "short" and "ultrashort" transverse relaxation times and therefore have short mean transverse relaxation times. With conventional magnetic resonance imaging (MRI) sequences that employ relatively long echo times (TEs), there is no opportunity to encode the decaying signal of short and ultrashort T2/T2* tissues before it has reached zero or near zero. The clinically compatible ultrashort TE (UTE) sequence has been increasingly used to study the musculoskeletal system. This article reviews the UTE sequence as well as various modifications that have been implemented since its introduction. These modifications have been used to improve efficiency or contrast as well as provide quantitative analysis. This article reviews several clinical musculoskeletal applications of UTE. J. Magn. Reson. Imaging 2015;41:870–883. © 2014 Wiley Periodicals, Inc.
Strategies for improved 3D small‐tip fast recovery imaging
Authors: Sun Hao , Fessler Jeffrey A. , Noll Douglas C. , Nielsen Jon‐Fredrik
Published: July 2014

Purpose

Small‐tip fast recovery (STFR) imaging is a recently proposed steady‐state sequence that has similar image contrast as balanced steady‐state free precession but has the potential to simultaneously remove banding artifacts and transient fluctuation. STFR relies on a “tip‐up” radiofrequency (RF) pulse tailored to the accumulated phase during the free precession (data acquisition) interval, designed to bring spins back to the longitudinal axis, thereby preserving transverse magnetization as longitudinal magnetization for the next pulse repetition time. We recently proposed an RF‐spoiled STFR sequence suitable for thin slab imaging, however, in many applications, e.g., functional magnetic resonance imaging or isotropic‐resolution structural imaging, three‐dimensional (3D) steady‐state imaging is desirable. Unfortunately, 3D STFR imaging is challenging due to the need for 3D tailored RF pulses. Here, we propose new strategies for improved 3D STFR imaging, based on (i) unspoiled imaging, and (ii) joint design of nonslice‐selective tip‐down/tip‐up RF pulses.

Theory and Methods

We derive an analytic signal model for the proposed unspoiled STFR sequence, and propose two strategies for designing the 3D tailored tip‐down/tip‐up RF pulses. We validate the analytic results using phantom and in vivo imaging experiments.

Results

Our analytic model and imaging experiments demonstrate that the proposed unspoiled STFR sequence is less sensitive to tip‐up excitation error compared to the corresponding spoiled sequence, and may, therefore, be an attractive candidate for 3D imaging. The proposed “joint” RF pulse design method, in which we formulate the tip‐down/tip‐up RF pulse design task as a magnitude least squares problem, produces modest improvement over a simpler “Separate” design approach. Using the proposed unspoiled sequence and joint RF pulse design, we demonstrate proof‐of‐principle 3D STFR brain images with balanced steady‐state free precession‐like signal properties but with reduced banding.

Conclusion

Using the proposed unspoiled sequence and joint RF pulse design, STFR brain images in a 3D region of interest with balanced steady‐state free precession‐like signal properties but with reduced banding can be obtained. Magn Reson Med 72:389–398, 2014. © 2013 Wiley Periodicals, Inc.
Boveri at 100: Boveri, chromosomes and cancer
Authors: Heim Sverre
Published: July 2014

Microscopic studies of chromosomes in cells cultured from leukaemias and solid tumours have helped confirm the central tenet of Boveri's somatic mutation theory of cancer, namely that acquired chromosomal aberrations of susceptible target cells may cause their neoplastic transformation. Cancer cytogenetics – especially when used together with appropriate molecular genetic investigations of tumour parenchyma cells – offers diagnostic and prognostic information, insights into the clonal composition and evolution of neoplasms, and information about how the observed gains, losses and balanced relocations work pathogenetically. In the future, one may expect cancer cytogenetics to focus not only on how the various aberrations contribute to tumourigenesis, but also on why and how they occur, as well as on the biological meaning behind the polyclonality detected in several epithelial neoplasms. Finally, the study of different nuclear compartments during interphase may add to our understanding of how large‐scale numerical and structural karyotypic aberrations may disturb normal controls of cell division and death to induce neoplastic transformation. Copyright © 2014 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd
Modification of asphalt using polymer‐forming monomer
Authors: Chung Kyungho , Park Moonsoo , Mun Sungho , Ohm Byungsik , Yoo Pyeongjun , Hong Youngkeun
Published: July 2014

A polymer‐forming monomer, dimethylphenol, was incorporated into neat asphalt at 180°C and tensile strength and rutting resistance of the asphalt improved dramatically. We found that polymerization occurred autonomously in the asphalt with some asphalt components and oxygen molecules in the air. The polymer produced was poly(phenylene oxide) (PPO), and its components were vanadium and its oxides. An increase in both the number and weight average molecular weights of PPO indicated a progress of polymerization. An increase in molecular weight contributed to an increase in the melting temperature, tensile strength, and rutting resistance parameter. NMR and IR spectra illustrate the corresponding peaks of PPO. DSC data reveals that the polymer has a melting temperature of 223°C, confirming the presence of PPO. Moreover, the asphalt containing a purported PPO displayed a 35.4% crystallinity, compared to the amorphous structure of asphalt. POLYM. ENG. SCI., 55:1128–1132, 2015. © 2014 Society of Plastics Engineers
Analysis of pellet shaping kinetics at the die opening in underwater pelletizing processes
Authors: Kast Oliver , Geiger Kalman , Grünschloss Eberhard , Bonten Christian
Published: July 2014

Underwater pelletizing of thermoplastic materials has gained high importance within the chemical and the compounding industry. It is known for producing comparatively spherical pellets with good bulk characteristics. Pellet shapes are determined by the viscous and elastic properties of the melt as well as various process conditions. Therefore, deformation of the melt strands because of the water flow at the die‐hole opening may result in undesired shapes. This is particularly the case when processing polymers of low viscosity. This paper defines an analytical framework describing the pellet formation at the die‐hole opening. Furthermore, a nondimensional DS number is developed as a measure for the deformation sensitivity of different polymer materials. In order to validate this approach, a new camera system and video recording method has been developed, which allows for a visual analysis of the cutting process in underwater pelletizing systems. Examining different materials at various process parameters, this paper identifies the main parameters responsible for pellet deformation and demonstrates how the DS number can be used to anticipate these effects. POLYM. ENG. SCI., 55:1170–1176, 2015. © 2014 Society of Plastics Engineers
Experimental techniques and the underlying device physics
Authors: Tessler Nir
Published: July 2014

This review, which has a very deep tutorial nature to it, aims to collect a range of experimental techniques that are relevant to charge transport and place them all under one device‐physics framework. The types of semiconductors in mind are low mobility ones with an emphasis toward organic semiconductors. As this contribution needs to have a finite length, there are many important methods or techniques not covered in this review. My hope is that by covering methods that are very different in nature, it would make it easier to extend the understanding or intuition collected through this review to methods/techniques not mentioned. © 2014 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2014, 52, 1119–1152
Can a climate model reproduce extreme regional precipitation events over England and Wales?
Authors: Pearson K. J. , Shaffrey L. C. , Methven J. , Hodges K. I.
Published: July 2014

The ability of the High‐Resolution Global Environmental Monitoring (HiGEM) climate model to represent high‐impact, regional precipitation events is investigated in two ways. The first focuses on a case study of extreme regional accumulation of precipitation during the passage of a summer extratropical cyclone across southern England on 20 July 2007 that resulted in a national flooding emergency. The climate model is compared with a global numerical weather prediction (NWP) model and higher‐resolution, nested limited‐area models. While the climate model does not simulate the timing and location of the cyclone and associated precipitation as accurately as the NWP simulations, the total accumulated precipitation in all models is similar to the rain‐gauge estimate across England and Wales. The regional accumulation over the event is insensitive to horizontal resolution for grid spacings ranging from 90–4 km.

Secondly, the free‐running climate model reproduces the statistical distribution of daily precipitation accumulations observed in the England–Wales precipitation record. The model distribution diverges increasingly from the record for longer accumulation periods, with a consistent under‐representation of more intense multiday accumulations. This may indicate a lack of low‐frequency variability associated with weather regime persistence. Despite this, the overall seasonal and annual precipitation totals from the model are still comparable to those from ERA‐Interim.
The Prediction Pioneers
Authors: Macer Tim
Published: July 2014

A world of new opportunities that focuses on ‘what next’
Cost analysis of non-invasive fractional flow reserve derived from coronary computed tomographic angiography in Japan
Authors: Kimura Takeshi , Shiomi Hiroki , Kuribayashi Sachio , Isshiki Takaaki , Kanazawa Susumu , Ito Hiroshi , Ikeda Shunya , Forrest Ben , Zarins Christopher K. , Hlatky Mark A. , Norgaard Bjarne L.
Published: July 2014

Percutaneous coronary intervention (PCI) based on fractional flow reserve (FFRcath) measurement during invasive coronary angiography (CAG) results in improved patient outcome and reduced healthcare costs. FFR can now be computed non-invasively from standard coronary CT angiography (cCTA) scans (FFRCT). The purpose of this study is to determine the potential impact of non-invasive FFRCT on costs and clinical outcomes of patients with suspected coronary artery disease in Japan. Clinical data from 254 patients in the HeartFlowNXT trial, costs of goods and services in Japan, and clinical outcome data from the literature were used to estimate the costs and outcomes of 4 clinical pathways: (1) CAG-visual guided PCI, (2) CAG-FFRcath guided PCI, (3) cCTA followed by CAG-visual guided PCI, (4) cCTA-FFRCT guided PCI. The CAG-visual strategy demonstrated the highest projected cost ($10,360) and highest projected 1-year death/myocardial infarction rate (2.4 %). An assumed price for FFRCT of US $2,000 produced equivalent clinical outcomes (death/MI rate: 1.9 %) and healthcare costs ($7,222) for the cCTA-FFRCT strategy and the CAG-FFRcath guided PCI strategy. Use of the cCTA-FFRCT strategy to select patients for PCI would result in 32 % lower costs and 19 % fewer cardiac events at 1 year compared to the most commonly used CAG-visual strategy. Use of cCTA-FFRCT to select patients for CAG and PCI may reduce costs and improve clinical outcome in patients with suspected coronary artery disease in Japan.
Ship security challenges in high-risk areas: manageable or insurmountable?
Authors: Liwång Hans , Sörenson Karl , Österman Cecilia
Published: July 2014

Piracy can lead to risks so high that they, according to the International Maritime Organization, are tolerable only if risk reduction is not practicable or is disproportionate to the benefits achieved. Therefore, there is a need for reducing ship security risks in relation to antagonistic threats such as piracy. The aim of this study is to identify challenges for ship operators when developing their ship security management. Furthermore, this study also investigates two central aspects in the analysis: understanding the threat and understanding how a security threat affects the crew and operation of the ship. It is clear from the analysis that the importance of subjective aspects beyond a ship operators’ direct control is high. This seems to be the fact for all aspects of the risk management process. The situation is also dynamic as the security risk, as well as the risk perception, can change dramatically even though there are no actual operational changes. As a result, the ship security management process is highly iterative and depends on situations on board as well as conditions out of the ship operator’s control. In order to make ship security manageable, the risk management has to put particular focus on methodological understanding, relevant system understanding and well-defined risk acceptance criteria as well as on including all levels of the organization in the risk reduction implementation and on a continuous monitoring.
The planar X-junction flow: stability analysis and control
Authors: Lashgari Iman , Tammisola Outi , Citro Vincenzo , Juniper Matthew P. , Brandt Luca
Published: July 2014

The bifurcations and control of the flow in a planar X-junction are studied via linear stability analysis and direct numerical simulations. This study reveals the instability mechanisms in a symmetric channel junction and shows how these can be stabilized or destabilized by boundary modification. We observe two bifurcations as the Reynolds number increases. They both scale with the inlet speed of the two side channels and are almost independent of the inlet speed of the main channel. Equivalently, both bifurcations appear when the recirculation zones reach a critical length. A two-dimensional stationary global mode becomes unstable first, changing the flow from a steady symmetric state to a steady asymmetric state via a pitchfork bifurcation. The core of this instability, whether defined by the structural sensitivity or by the disturbance energy production, is at the edges of the recirculation bubbles, which are located symmetrically along the walls of the downstream channel. The energy analysis shows that the first bifurcation is due to a lift-up mechanism. We develop an adjustable control strategy for the first bifurcation with distributed suction or blowing at the walls. The linearly optimal wall-normal velocity distribution is computed through a sensitivity analysis and is shown to delay the first bifurcation from $\def \xmlpi #1{}\def \mathsfbi #1{\boldsymbol {\mathsf {#1}}}\let \le =\leqslant \let \leq =\leqslant \let \ge =\geqslant \let \geq =\geqslant \def \Pr {\mathit {Pr}}\def \Fr {\mathit {Fr}}\def \Rey {\mathit {Re}}\mathit{Re}=82.5$ to $\mathit{Re}=150$. This stabilizing effect arises because blowing at the walls weakens the wall-normal gradient of the streamwise velocity around the recirculation zone and hinders the lift-up. At the second bifurcation, a three-dimensional stationary global mode with a spanwise wavenumber of order unity becomes unstable around the asymmetric steady state. Nonlinear three-dimensional simulations at the second bifurcation display transition to a nonlinear cycle involving growth of a three-dimensional steady structure, time-periodic secondary instability and nonlinear breakdown restoring a two-dimensional flow. Finally, we show that the sensitivity to wall suction at the second bifurcation is as large as it is at the first bifurcation, providing a possible mechanism for destabilization.
The State, Relational Governance, and Nomad Sedentarization: Land Reform in Inner Mongolia, 1900–1911
Authors: Wang Liping
Published: July 2014

This article is a study of the Inner Mongolian land reform undertaken by the Qing government in the last decade of its rule. Instead of portraying land reform as a state process of taming and transforming nomads, I examine the metamorphosis of the multi-ethnic governing relationships enabled by the reform. The frontier governance system on which I focus consisted of coalitions and conflicts among four key players: Mongol banners, neighboring Han Chinese provinces, the Court of Dependencies, and frontier military governors. By elucidating the changing relationships that bound these players together, I pinpoint the most significant agendas of land reform, how the Mongols' position vis-à-vis state agencies changed throughout the reform process, and to what extent these changes resulted in state centralization. My study illuminates a variety of topics, including nomad sedentarization, frontier politics, and modern state expansion.
Identification of tissue-specific gene clusters and orthologues of nodulation-related genes in Vigna angularis
Authors: Kang Yang Jae , Lee Jayern , Kim Yong Hwan , Lee Suk-Ha
Published: July 2014

Nitrogen fixation in legumes is an important agricultural trait that results from symbiosis between the root and rhizobia. To understand the molecular basis of nodulation, recent research has been focused on the identification of nodulation-related genes by functional analysis using two major model legumes, Medicago truncatula and Lotus japonicus. Thus far, three important processes have been discovered, namely Nod factor (NF) perception, NF signalling and autoregulation of nodulation. Nevertheless, application of the results of these studies is limited for non-model legume crops because a reference genome is unavailable. However, because the cost of whole-transcriptome analysis has dropped dramatically due to the Next generation sequencer (NGS) technology, minor crops for which reference sequences are yet to be constructed can still be studied at the genome level. In this study, we sequenced the leaf and root transcriptomes of Vigna angularis (accession IT213134) and de novo assembled. Our results demonstrate the feasibility of using the transcriptome assembly to effectively identify tissue-specific peptide clusters related to tissue-specific functions and species-specific nodulation-related genes.
Plant genomics in view of plant genetic resources – an introduction
Authors: Phillips Ronald L.
Published: July 2014

Genetic resources form the basis of the new era of global food security. The food crises in many developing countries, reflected by food riots correlated with food prices, have been termed the Silent Tsunami. Plant genetic resources are clearly essential to food security for the future. Fortunately, genetic resources are generally considered a public good and shared internationally. Wild relatives of crop species and their derivatives represent the reservoir of genetic diversity that will help to meet the food demands of nine billion people by 2050. New technologies from genomics bolster conventional plant breeding for enhancing traits to meet these food demands. Genetic diversity is the lifeblood of traditional and modern plant breeding. The dramatic increase in the number of biotech crops reveals the value of new genetic resources. Genetic resources will provide a gateway to a new era of global food security. Although 7.4 million plant accessions are stored in 1750 germplasm banks around the world, only a small portion of the accessions has been used so far to produce commercial varieties. Our challenge is to find better ways to make more efficient use of gene bank materials for meeting food demands in the future.
Improvement of soybean through radiation-induced mutation breeding techniques in Korea
Authors: Ha Bo-Keun , Lee Kyung Jun , Velusamy Vijayanand , Kim Jin-Baek , Kim Sang Hoon , Ahn Joon-Woo , Kang Si-Yong , Kim Dong Sub
Published: July 2014

Mutation breeding techniques have been used to induce new genetic variations and improve agronomic traits in soybean. In Korea, the Korea Atomic Energy Research Institute (KAERI) has unique radiation facilities to induce plant mutations and has been conducting soybean mutation breeding programmes since the mid-1960s. Until now, the KAERI has developed five soybean mutant cultivars exhibiting early maturity, high yield and seed-coat colour change. In this paper, we review these five mutant cultivars in terms of how to successfully induce unique agronomic characteristics through mutation breeding programmes. A number of induced mutants exhibiting null lipoxygenase enzymes, altered protein patterns or Kunitz trypsin inhibitor activity could serve as genetic resources for the genetic analysis of target genes, and one mutant population has been developed for a reverse genetic study.
Genetic diversity analysis using simple sequence repeat markers in soybean
Authors: Hu Zhenbin , Kan Guizhen , Zhang Guozheng , Zhang Dan , Hao Derong , Yu Deyue
Published: July 2014

To evaluate the genetic diversity (GD) of wild and cultivated soybeans and determine the genetic relationships between them, in this study, 127 wild soybean accessions and 219 cultivated soybean accessions were genotyped using 74 simple sequence repeat (SSR) markers. The results of the study revealed that the GD of the wild soybeans exceeded that of the cultivated soybeans. In all, 924 alleles were detected in the 346 soybean accessions using 74 SSRs, with an average of 12.49 alleles per locus. In the 219 cultivated soybean accessions, 687 alleles were detected, with an average of 9.28 alleles per locus; in the 127 wild soybean accessions, 835 alleles were detected, with an average of 11.28 alleles per locus. We identified 237 wild-soybean-specific alleles and 89 cultivated-soybean-specific alleles in the 346 soybean accessions, and these alleles accounted for 35.28% of all the alleles in the sample. Principal coordinates analysis and phylogenetic analysis based on Nei's genetic distance indicated that all the accessions could be classified into two major clusters, corresponding to wild and cultivated soybeans. These results will increase our understanding of the genetic differences and relationships between wild and cultivated soybeans and provide information to develop future breeding strategies to improve soybean yield.
Genetic diversity of mungbean (Vigna radiataL.) germplasm in Indonesia
Authors: Lestari Puji , Kim Sue Kyung , Reflinur  , Kang Yang Jae , Dewi Nurwita , Lee Suk-Ha
Published: July 2014

Despite widespread mungbean [Vigna radiata(L.) Wilczek] consumption in Indonesia, few molecular studies have been carried out on accessions and available data are minimal. In this study, we used 30 newly developed simple sequence repeat (SSR) markers designed from the mapped sequence scaffolds of the Korean Sunhwanokdu and Gyeonggijaerae 5 mungbean genomes. These markers were used to examine loci in 83 mungbean accessions collected from diverse geographical areas in Indonesia. A total of 107 alleles were detected among the accessions with 29 polymorphic markers. However, the mean of polymorphic information content (0.33) value and diversity index (0.38) value was indicative of low genetic diversity in this germplasm. The mungbean population structure was not clearly differentiated and the number of subpopulations was unclear. Neighbour-joining tree analysis revealed that the genetic cluster did not reflect the geographical origin of the accessions. Interestingly, the most agriculturally improved varieties were genetically similar to some landraces from one of the main mungbean-producing regions. These newly developed SSR markers could be useful for detecting genetic variability as a basis for establishing a conservation strategy for mungbean germplasm with the aim of enhancing Indonesian breeding programmes.
Identification of quantitative trait loci associated with soybean seed protein content using two populations derived from crosses betweenGlycine maxandGlycine soja
Authors: Yan Long , Xing Li-Li , Yang Chun-Yan , Chang Ru-Zhen , Zhang Meng-Chen , Qiu Li-Juan
Published: July 2014

Seed protein content is one of the most important traits controlled by quantitative trait loci (QTLs) in soybean. In this study, aGlycine sojaaccession (ZYD2738) was crossed with two elite cultivars Jidou 12 and Jidou 9 separately and subsequently the resulting F2:3populations were used to identify QTLs associated with seed protein content. Protein contents in either population appeared to have a normal distribution with transgressive segregation. A total of five QTLs associated with high protein content were identified and mapped to chromosomes 2, 6, 13, 18 and 20, respectively. Of these QTLs, three (qPRO_2_1,qPRO_13_1andqPRO_20_1) were identified in the same region in both the populations, whereas the other two (qPRO_6_1andqPRO_18_1) were mapped in two different regions.qPRO_2_1appears to be a novel protein QTL.qPRO_6_1,qPRO_18_1andqPRO_20_1had additive effects on seed protein content, whileqPRO_13_1had an over-dominant effect on seed protein content. These QTLs and their linked markers could serve as effective tools for marker-assisted selection to increase seed protein content.
Comparative analysis of Cassandra TRIMs in three Brassicaceae genomes
Authors: Sampath Perumal , Yang Tae-Jin
Published: July 2014

Terminal-repeat retrotransposon in miniature (TRIM) elements are a miniature form of retrotransposons and play an important role in genome organization. The Cassandra TRIM family has been identified in over 50 plant species, including both monocots and dicots. Cassandra elements carry an independently transcribed 5S RNA sequence in their terminal repeat regions, which is unique compared with other TRIM families. Although the existence of Cassandra elements has been documented in many plants, much work remains to characterize Cassandra family members and elucidate their distribution. In this study, we comparatively analysed the Cassandra family members in the Brassica oleracea, B. rapa and Arabidopsis thaliana genomes. A total of 602, 451 and 173 members, of which 130, 60 and 9 were relatively intact, were identified from the B. oleracea, B. rapa and A. thaliana genomes, respectively. Most of the Cassandra elements (1120/1226) were found in intergenic spaces, but 106 elements were inserted in genic regions such as introns, exons and untranslated regions. Our comparative analysis of the Cassandra family members in A. thaliana, B. rapa and B. oleracea reveals that some Cassandra elements have been commonly retained during the last 20 million years in three species and some elements have been uniquely evolved in Brassica species. This study promotes our understanding of the role and utility of Cassandra elements in the evolution of the Brassicaceae family.
Evolution, domestication and neo-domestication of the genus Vigna
Authors: Tomooka Norihiko , Naito Ken , Kaga Akito , Sakai Hiroaki , Isemura Takehisa , Ogiso-Tanaka Eri , Iseki Kohtaro , Takahashi Yu
Published: July 2014

In this paper, we discuss stress-adapted wild Vigna plants and several important Vigna crops. Seeds, young shoots and/or tubers of many wild Vigna species are edible and are eaten by people in some locations where they grow. We propose the concept of ‘neo-domestication’ of stress-adapted wild edible Vigna species. As the causative change of the mutation resulting in a domestication gene is usually ‘loss-of-function’ type, ‘neo-domestication’ could be achieved by conventional mutation breeding together with screening by TILLING. The ‘neo-crops’ could play an important role in areas unsuitable for growing other crops to increase world food production. We also propose that wild Vigna species can be ‘new model plant species’ for the genetic study of natural adaptation to stresses (e.g. salt, acid, alkali, drought, flood, pests and diseases). To facilitate this, the Vigna Genome Project has been initiated. In addition, sustainable cropping systems may be enhanced by analysis of the nitrogen-fixing systems of stress-adapted Vigna species. Stress-adapted symbiotic bacteria produce nodules on stress-adapted Vigna species. Therefore, analyses of the genetic diversity of symbiotic bacteria and the process of symbiosis under stress environments should be conducted.
STAT1 plays a role in TLR signal transduction and inflammatory responses
Authors: Luu Kevin , Greenhill Claire J , Majoros Andrea , Decker Thomas , Jenkins Brendan J , Mansell Ashley
Published: July 2014

Activation of the Toll‐like receptor (TLR) family of innate immune sensors stimulates multiple signal transduction pathways. Previous studies have suggested that TLR2, TLR4 and TLR9 induce serine phosphorylation of Signal Transducers and Activators of Transcription‐1 (STAT1) at residue 727 (S727), although its role in TLR signaling was unclear. We report here that STAT1 rapidly undergoes phosphorylation following TLR4 challenge with lipopolysaccharide (LPS) in a model of LPS hypersensitivity in vivo. Importantly, genetic ablation of STAT1 protected against LPS‐induced lethality suggesting that STAT1 may have a key role in TLR‐induced inflammation. We have found that multiple TLRs induce Ser727 phosphorylation of STAT1, which is dependent on MyD88 and TRIF signaling, but independent of interferon (IFN) regulatory factor (IRF)‐3, IRF7 and the IFN receptor complex, suggesting that activation is a direct TLR response rather than autocrine activation via IFN. Importantly, we found that STAT1 interacts with tumor necrosis factor (TNF) receptor‐associated factor‐6 (TRAF6), a key mediator of TLR signaling after TLR challenge and that following activation, STAT1 translocates to the nucleus. Critically, macrophages generated from mice in which the S727 residue was replaced with alanine (STAT1 S727A mice) display significantly reduced TNFα protein production, but not reduced interleukin‐6 or RANTES protein in response to multiple TLR challenges, as compared with wild‐type macrophages. These results clearly demonstrate cross‐talk between the TLR and JAK/STAT signaling pathways with direct recruitment of STAT1 by TRAF6 and that the direct activation of STAT1 by TLR signaling suggests a crucial role for STAT1 in TLR‐induced inflammation.
Water fleas require microbiota for survival, growth and reproduction
Authors: Sison-Mangus Marilou P , Mushegian Alexandra A , Ebert Dieter
Published: July 2014

Microbiota have diverse roles in the functioning of their hosts; experiments using model organisms have enabled investigations into these functions. In the model crustacean Daphnia, little knowledge exists about the effect of microbiota on host well being. We assessed the effect of microbiota on Daphnia magna by experimentally depriving animals of their microbiota and comparing their growth, survival and fecundity to that of their bacteria-bearing counterparts. We tested Daphnia coming from both lab-reared parthenogenetic eggs of a single genotype and from genetically diverse field-collected resting eggs. We showed that bacteria-free hosts are smaller, less fecund and have higher mortality than those with microbiota. We also manipulated the association by exposing bacteria-free Daphnia to a single bacterial strain of Aeromonas sp., and to laboratory environmental bacteria. These experiments further demonstrated that the Daphnia–microbiota system is amenable to manipulation under various experimental conditions. The results of this study have implications for studies of D. magna in ecotoxicology, ecology and environmental genomics.