bluuebunny/crossref_metadata_2025 huggingface dataset:
A generalized Reynolds analogy for compressible wall-bounded turbulent flows
Authors: Zhang You-Sheng , Bi Wei-Tao , Hussain Fazle , She Zhen-Su
Published: December 2013

A generalized Reynolds analogy (GRA) is proposed for compressible wall-bounded turbulent flows (CWTFs) and validated by direct numerical simulations. By introducing a general recovery factor, a similarity between the Reynolds-averaged momentum and energy equations is established for the canonical CWTFs (i.e. pipes, channels, and flat-plate boundary layers that meet the quasi-one-dimensional flow approximation), independent of Prandtl number, wall temperature, Mach number, Reynolds number, and pressure gradient. This similarity and the relationships between temperature and velocity fields constitute the GRA. The GRA relationship between the mean temperature and the mean velocity takes the same quadratic form as Walz’s equation, with the adiabatic recovery factor replaced by the general recovery factor, and extends the validity of the latter to diabatic compressible turbulent boundary layers and channel/pipe flows. It also derives Duan & Martín’s (J. Fluid Mech., vol. 684, 2011, pp. 25–59) empirical relation for flows at different physical conditions (wall temperature, Mach number, enthalpy condition, surface catalysis, etc.). Several key parameters besides the general recovery factor emerge in the GRA. An effective turbulent Prandtl number is shown to be the reason for the parabolic profile of mean temperature versus mean velocity, and it approximates unity in the fully turbulent region. A dimensionless wall temperature, that we call the diabatic parameter, characterizes the wall-temperature effects in diabatic flows. The GRA also extends the analysis to the fluctuation fields. It recovers the modified strong Reynolds analogy proposed by Huang, Coleman & Bradshaw (J. Fluid Mech., vol. 305, 1995, pp. 185–218) and explains the variation of the temperature–velocity correlation coefficient with wall temperature. Thus, the GRA unveils a generalized similarity principle behind the complex nonlinear coupling between the thermal and velocity fields of CWTFs.
Lateral migration of a capsule in plane shear near a wall
Authors: Singh Rajesh Kumar , Li Xiaoyi , Sarkar Kausik
Published: December 2013

The migration of a capsule enclosed by an elastic membrane in a wall-bounded linear shear is investigated using a front-tracking method. A detailed comparison with the migration of a viscous drop is presented varying the capillary number (in the case of a capsule, the elastic capillary number) and the viscosity ratio. In both cases, the deformation breaks the flow reversal symmetry and makes them migrate away from the wall. They quickly go through a transient evolution to eventually reach a quasi-steady state where the dynamics becomes independent of the initial position and only depends on the wall distance. Previous analytical theories predicted that for a viscous drop, in the quasi-steady state, the migration and slip velocities scale approximately with the square of the inverse of the drop–wall separation, whereas the drop deformation scales as the inverse cube of the separation. These power law relations are shown to hold for a capsule as well. The deformation and inclination angle of the capsule and the drop at the same wall separation show a crossover in their variation with the capillary number: the capsule shows a steeper variation than that of the drop for smaller capillary numbers and slower variation than the drop for larger capillary numbers. Using the Green’s function of Stokes flow, a semi-analytic theory is presented to show that the far-field stresslet that causes the migration has two distinct contributions from the interfacial stresses and the viscosity ratio, with competing effects between the two defining the dynamics. It predicts the scaling of the migration velocity with the capsule–wall separation, however, matching with the simulated result very well only away from the wall. A phenomenological correlation for the migration velocity as a function of elastic capillary number, wall distance and viscosity ratio is developed using the simulation results. The effects of different membrane hyperelastic constitutive equations – neo-Hookean, Evans–Skalak, and Skalak – are briefly investigated to show that the behaviour remains similar for different equations.
Linking hypotheses underlying Class A and Class B methods
Authors: MORGAN M.J. , MELMOTH D. , SOLOMON J.A.
Published: December 2013

Class A psychophysical observations are based on the linking hypothesis that perceptually distinguishable stimuli must correspond to different brain events. Class B observations are related to the appearance of stimuli not their discriminability. There is no clear linking hypothesis underlying Class B observations, but they are necessary for studying the effects of context on appearance, including a large class of phenomena known as “illusions.” Class B observations are necessarily measures of observer bias (Fechner’s “constant error”) as opposed to Class A measures of sensitivity (Fechner’s “variable error”). It is therefore important that Class B observations distinguish between response biases, decisional biases, and perceptual biases. This review argues that the commonly used method of single stimuli fails to do this, and that multiple-alternative forced choice (mAFC) methods can do a better job, particularly if combined with a roving pedestal.
Post-natal oogenesis: a concept for controversy that intensified during the last decade
Authors: Esmaeilian Yashar , Atalay Arzu , Erdemli Esra
Published: December 2013

For decades, scientists have considered that female mammals are born with a lifetime reserve of oocytes in the ovary, irrevocably fated to decline after birth. However, controversy in the matter of the possible presence of oocytes and granulosa cells that originate from stem cells in the adult mammalian ovaries has been expanded. The restricted supply of oocytes in adult female mammals has been disputed in recent years by supporters of neo-oogenesis, who claim that germline stem cells (GSCs) exist in the ovarian surface epithelium (OSE) or the bone marrow (BM). Differentiation of ovarian stem cells (OSCs) into oocytes, fibroblast-like cells, granulosa phenotype, neural and mesenchymal type cells and generation of germ cells from OSCs under the contribution of an OSC niche that consists of immune system-related cells and hormonal signalling has been claimed. Although these arguments have met with intense suspicion, their confirmation would necessitate the revision of the current classic knowledge of female reproductive biology.
Microstructure and Ultrastructure of Implant-Bone and Tendon-Bone Interfaces
Authors: Hobbs L.W. , Wang H. , Reese W.M. , Tomerlin B.M. , Lim T.Y.C. , Porter A.E. , Walton M. , Cotton N.J.
Published: December 2013

Extended abstract of a paper presented at Microscopy and Microanalysis 2013 in Indianapolis, Indiana, USA, August 4 – August 8, 2013.
Polyphenols, tannins and caffeine content and antioxidant activity of green teas coming from organic and non-organic production
Authors: Kazimierczak Renata , Hallmann Ewelina , Rusaczonek Anna , Rembiałkowska Ewa
Published: December 2013

Among infusions of green teabags and leafy green teas from organic and non-organic production systems we measured and compared the content of phenolic acids, flavonols and total polyphenols by spectrophotometry, the content of tannins by titration and the content of caffeine by high-performance liquid chromatography (HPLC). In addition, the antioxidant activity of the infusions was determined by spectrophotometry. The results obtained have shown that organic teas contained significantly more flavonols and tannins. However, the content of phenolic acids was higher in non-organic teas. The teas from organic and non-organic production did not differ in terms of total polyphenol content and antioxidant activity. There were no differences in leaf teas in relation to the teabags in contents of phenolic acids, tannins and total polyphenols. Organic teas had higher content of catechin C than the non-organic ones, but at the same time non-organic teas had more epigallocatechin 3-gallate (EGCG) in comparison to organic teas. Epigallocatechin (EGC) and epicatechin (EC) were not found to be different between the two groups of tea. Catechin was found to be significantly higher in teabags, while the EGCG was higher in leaf teas. The reason for this may be the oxidation of teabags, which have a greater exposed surface area. There was no appreciable effect of the form of tea on the content of tannins, caffeine, flavonols, phenolic acids, total polyphenols, EGC and EC as well as the antioxidant activity of the tea infusions examined.
How to Satisfy and Retain Personnel Despite Job-Market Shortage
Authors: Roulin Nicolas , Mayor Eric , Bangerter Adrian
Published: December 2013

Retaining valuable employees is a major issue for organizations, especially for professions characterized by shortage (e.g., nursing). It is thus important for organizations to determine which factors predict personnel satisfaction and intent to leave at various levels (i.e., organization, group, and individual). Nevertheless, few studies on satisfaction in nursing have analyzed a comprehensive set of factors and taken multiple organizational levels into account using appropriate statistical analysis techniques. We conducted a study with 1,547 nurses working in 17 hospitals in Switzerland. Results from multilevel analyses suggest that job satisfaction is predicted by both individual-level (burnout and work-family conflict) and group-level (group cohesion and unit effectiveness) factors, while organizational-level factors (e.g., autonomy) have less impact. Moreover, intent to leave the job is predicted by job satisfaction, whereas the relationship is moderated by perceived differences in priorities between nurses and their employer. When developing strategies to satisfy and retain key personnel, administrators should consider both individual-level and group-level factors as well as how to align priorities and how to best communicate what they have done.
Computational Assay of H7N9 Influenza Neuraminidase Reveals R292K Mutation Reduces Drug Binding Affinity
Authors: Woods Christopher J. , Malaisree Maturos , Long Ben , McIntosh-Smith Simon , Mulholland Adrian J.
Published: December 2013

The emergence of a novel H7N9 avian influenza that infects humans is a serious cause for concern. Of the genome sequences of H7N9 neuraminidase available, one contains a substitution of arginine to lysine at position 292, suggesting a potential for reduced drug binding efficacy. We have performed molecular dynamics simulations of oseltamivir, zanamivir and peramivir bound to H7N9, H7N9-R292K and a structurally related H11N9 neuraminidase. They show that H7N9 neuraminidase is structurally homologous to H11N9, binding the drugs in identical modes. The simulations reveal that the R292K mutation disrupts drug binding in H7N9 in a comparable manner to that observed experimentally for H11N9-R292K. Absolute binding free energy calculations with the WaterSwap method confirm a reduction in binding affinity. This indicates that the efficacy of antiviral drugs against H7N9-R292K will be reduced. Simulations can assist in predicting disruption of binding caused by mutations in neuraminidase, thereby providing a computational ‘assay.’
Centred nine-metal rings of lanthanides
Authors: Zangana Karzan H. , Pineda Eufemio Moreno , McInnes Eric J. L. , Schnack Jürgen , Winpenny Richard E. P.
Published: December 2013

Two new decametallic lanthanide complexes are reported, that are large odd-numbered rings with a further central metal site. This type of structure appears to be unprecedented. Magnetic studies show weak exchange interactions between the spin sites for the {Gd10} disc.
Novel regio- and stereoselective phosphonyl radical addition to glycals promoted by Mn(ii)–air: syntheses of 1,2-dideoxy 2-C-diphenylphosphinylglycopyranosides
Authors: Zhang Fuyi , Wang Liming , Zhang Cui , Zhao Yufen
Published: December 2013

The novel Mn(ii)–air promoted radical reaction of diphenylphosphine oxide with various glycals in excellent regio- and stereoselectivities generated 1,2-dideoxy-2-C-diphenylphosphinylglycopyranosides.
Concentration quenching of praseodymium ions Pr3+ in BaGd2(MoO4)4 crystals
Authors: Guan Ying , Tsuboi Taiju , Huang Yanlin , Huang Wei
Published: December 2013

The concentration effect on the photoluminescence (PL) of the praseodymium Pr3+ ion is studied at 298–12 K for barium gadolinium molybdate (BaGd2(MoO4)4, called BGM) crystals with a wide Pr3+ concentration range of 0.05–25.0 mol%.
Solvents for sustainable chemical processes
Authors: Pollet Pamela , Davey Evan A. , Ureña-Benavides Esteban E. , Eckert Charles A. , Liotta Charles L.
Published: December 2013

This review highlights solvent systems that were designed to simultaneously address reaction, separation and recycling challenges.
Alkoxide-functionalized imidazolium betaines for CO2 activation and catalytic transformation
Authors: Wang Yan-Bo , Sun Dong-Sheng , Zhou Hui , Zhang Wen-Zhen , Lu Xiao-Bing
Published: December 2013

Alkoxide-functionalized imidazolium betaines (AFIBs) functioned as organocatalysts for the coupling of CO2 with propargylic alcohols to give valuable cyclic carbonates via AFIB-CO2 adducts.
Design, synthesis and evaluation of N6-substituted 2-aminoadenosine-5′-N-methylcarboxamides as A3 adenosine receptor agonists
Authors: Devine Shane M. , May Lauren T. , Scammells Peter J.
Published: December 2013

A series of N6-substituted 2-aminoadenosine-5′-N-methylcarboxamides were synthesized from the versatile intermediate, O6-(benzotriazol-1-yl)-2-amino-2′,3′-O-isopropylideneinosine-5′-N-methylcarboxamide (1) and evaluated as A3 adenosine receptor agonists.
Photocleavage control of nucleated DNA nanosystems – the influence of surface strand sterics
Authors: Hanna Morcos , Munshi Moorsalin , Kedzierski Nancy A. , Chung Paul N. , Huang Terry , Mok Allen K. , Lukeman Philip S.
Published: December 2013

Surfaces that display sterically hindered, photocleavable strands that initiate a strand-displacement based polymerization are studied for their robustness to a ‘leak’ reaction and time dependence of photocleavage.
Bi2S3microspheres grown on graphene sheets as low-cost counter-electrode materials for dye-sensitized solar cells
Authors: Li Guang , Chen Xiaoshuang , Gao Guandao
Published: December 2013

3D Bi2S3 microspheres compsed of a nanorod assembly grown along the (211) facet on graphene sheets were synthesized with obviously enhanced CEs.
A cascading reaction sequence involving ligand-directed azaelectrocyclization and autooxidation-induced fluorescence recovery enables visualization of target proteins on the surfaces of live cells
Authors: Tanaka Katsunori , Kitadani Masataka , Tsutsui Ayumi , Pradipta Ambara R. , Imamaki Rie , Kitazume Shinobu , Taniguchi Naoyuki , Fukase Koichi
Published: December 2013

A general probe designed to induce a cascading sequence of reactions on a target protein was efficiently synthesized.
Cationic lipophosphoramidates with two different lipid chains: synthesis and evaluation as gene carriers
Authors: Le Corre Stéphanie S. , Berchel Mathieu , Belmadi Nawal , Denis Caroline , Haelters Jean-Pierre , Le Gall Tony , Lehn Pierre , Montier Tristan , Jaffrès Paul-Alain
Published: December 2013

The synthesis of a series of new cationic lipids possessing two different lipid chains is detailed. The transfection efficacies have shown the interest to associate a phytanyl chain with either, a lauryl or oleyl chain.
Oxenoids in organic synthesis
Authors: Minko Yury , Marek Ilan
Published: December 2013

Recent advances on the use of oxenoid compounds in organic synthesis are highlighted in this review.
Palladium-catalyzed benzo[d]isoxazole synthesis by C–H activation/[4 + 1] annulation
Authors: Duan Pingping , Yang Yunfang , Ben Rong , Yan Yiyong , Dai Lu , Hong Mei , Wu Yun-Dong , Wang Dongqi , Zhang Xinhao , Zhao Jing
Published: December 2013

A new protocol has been developed for the synthesis of benzo[d]isoxazole through a palladium-catalyzed C–H bond functionalization–[4 + 1] annulation pathway.
Sequestration of the abrin A chain to the nucleus by BASP1 increases the resistance of cells to abrin toxicity
Authors: Gadadhar Sudarshan , Bora Namrata , Tiwari Vinita , Karande Anjali A.
Published: December 2013

Abrin, a type II ribosome-inactivating protein, comprises A and B subunits wherein the A subunit harbours toxin activity and the B subunit has a galactose-specific lectin activity. The entry of the protein inside the cell is through the binding of the B chain to cell surface glycoproteins followed by receptor-mediated endocytosis and retrograde transport. A previous study from our laboratory showed that different cell lines exhibited differences of as great as ~200-fold in abrin toxicity, prompting the present study to compare the trafficking of the toxin within cells. Observations made in this regard revealed that the abrin A chain, after being released into the cytosol, is sequestered into the nucleus through interaction with a cellular protein of ~25 kDa, BASP1 (brain acid-soluble protein 1). The nuclear localization of the A chain is seen predominantly in cells that are less sensitive to abrin toxicity and dependent on the levels of BASP1 in cells. The sequestration by BASP1 renders cells increasingly resistant to the inhibition of protein synthesis by abrin and the nucleus act as a sink to overcome cellular stress induced by the toxin.
Cap-binding complex (CBC)
Authors: Gonatopoulos-Pournatzis Thomas , Cowling Victoria H.
Published: December 2013

The 7mG (7-methylguanosine cap) formed on mRNA is fundamental to eukaryotic gene expression. Protein complexes recruited to 7mG mediate key processing events throughout the lifetime of the transcript. One of the most important mediators of 7mG functions is CBC (cap-binding complex). CBC has a key role in several gene expression mechanisms, including transcription, splicing, transcript export and translation. Gene expression can be regulated by signalling pathways which influence CBC function. The aim of the present review is to discuss the mechanisms by which CBC mediates and co-ordinates multiple gene expression events.
Compact frequency selective surface for polarisation transform
Authors: Morrow I.L. , Thomas P.
Published: December 2013

The polarisation transforming properties of a compact frequency selective surface (FSS) are reported. Although known designs made with meander lines employ several cascaded surfaces with many interconnects, the design methodology presented uses a single planar surface of very closely arrayed metallic meander lines impedance loaded with rectangular metal patches. A simulated axial ratio of ≤ −3 dB was obtained over a 40% bandwidth, from 2.10 to 3.2 GHz and optimised for 2.75 GHz. Simulation of normal and oblique incidence in both planes of polarisation shows a ±30° wide range of angles of incidence for polariser performance. A unit cell of the FSS circular polariser is λo/12 in size at the optimised operating frequency. The FSS circular polariser was manufactured and attached to a horn antenna aperture and measurement confirmed axial ratio performance.
Power amplifier non‐linearity treatment with distorted constellation estimation and demodulation for 60 GHz single‐carrier frequency‐domain equalisation transmission
Authors: Zhang Changming , Xiao Zhenyu , Gao Bo , Su Li , Jin Depeng
Published: December 2013

Power amplifier (PA) non‐linearity is extremely significant for 60 GHz millimetre‐wave communications, which distorts signal constellation seriously. In dealing with this problem, the commonly used digital predistortion (DPD) becomes unaffordable for 60 GHz systems in both power consumption and price. This study proposes to handle PA non‐linearity with distorted constellation (DCS) estimation and demodulation for 60 GHz systems with single‐carrier frequency‐domain equalisation transmission, which has a low implementation cost. Employing the least‐square (LS) algorithm, the DCS is estimated both before and after equalisation, where LS after equalisation has a lower computational complexity than LS before equalisation. Subsequently, the estimated DCS, instead of the standard constellation, is used as a criterion for demodulation, which is shown to achieve a significant improvement on the symbol‐error‐rate (SER) performance, especially when the non‐linear distortion is severe. Moreover, compared with DPD, the proposed method achieves a better SER performance and behaves more robustly in the low range of input power back‐off (IBO), whereas achieving a close SER performance in the high‐IBO range.
Design of a dual‐polarised antenna with high isolation and a metallic cube for beyond 4G small base station applications
Authors: Lee Jung‐Nam , Kwon Heon‐Kook , Kang Byung‐Su , Lee Kwang‐Chun
Published: December 2013

Dual polarised antenna with high isolation for small base‐station applications is proposed. The proposed antenna is composed of two metallic trapezoidal dipole elements, two metallic feed plates, a dielectric substrate, a metallic cube and a radome. The measured −10 dB impedance bandwidth is 2.4 GHz to 2.8 GHz in Port‐1 and 2.5 GHz to 3 GHz in Port‐2. The proposed antenna has an isolation of >45 dB at the centre frequency. The measured average antenna gain is 7.5 dBi, and the cross polarisations are all <30 dB below the co‐polarisation value.
Varactor‐tuned microstrip bandpass filters with different passband characteristics
Authors: Ni Jia , Hong Jiasheng
Published: December 2013

Two novel types of tunable bandpass filters are introduced in this study. The first type is composed of varactor‐loaded parallel‐coupled lines and short‐circuited stubs, which allows for the lower passband edge and two transmission zeros around the lower passband skirt to be reconfigured separately while the corresponding upper ones maintain fixed. The second type of tunable bandpass filter is built by cascading the first type of tunable bandpass and another tunable lowpass filter, which results in a great flexibility to tune both centre frequency and passband bandwidth. The designed prototype tunable filters are implemented using liquid crystal polymer (LCP) bonded multilayer printed circuit board (PCB) technology. The measured results demonstrate very promising performance in terms of wide tunability and high selectivity.
Bayesian passive acoustic tracking of a cooperative moving source in shallow water
Authors: Yang Zhiguo , Zhao Hangfang , Xu Wen
Published: December 2013

This study addresses the problem of tracking acoustically a moving source in shallow water, which is challenged by multi‐path sound propagation. A specific source of interest is an autonomous underwater vehicle with periodic sound transmissions. Given a simple horizontal linear receiving array, the authors develop a Bayesian tracking method based on measurements of signal arriving angle and difference of respective sonar transmission and receiving time intervals. To counter the multi‐path effect and thus improve estimation accuracy of time differences, passive time reversal processing is exploited. Further, the unscented Kalman filter is adopted in tracking to handle nonlinearity in measurements. The proposed method is tested in simulations as well as an at‐sea experiment, and the results validate the effectiveness of the developed approach.
Marginal unscented Kalman filter for cross‐correlated process and observation noise at the same epoch
Authors: Chang Guobin
Published: December 2013

The independence of the process and observation noises is the prerequisite of many Kalman‐type filters. However, the fact is that these two noises may be correlated with each other in actual applications. The filtering of the non‐linear systems with cross‐correlated process and observation noises at the same epoch is studied. First, a decorrelated scheme is introduced and a pseudo non‐linear process equation is reconstructed in which the corresponding pseudo process noise is no longer cross‐correlated with the observation noise; so a celebrated non‐linear filter, that is, the unscented Kalman filter (UKF) can be used to filter the non‐linear problem. Second, the (conditionally) linear substructure in the above non‐linear system is exploited and a refined filter called marginal UKF is employed so as to reduce computational load without deteriorating the accuracy. The performance of the standard UKF for the original system equations, the standard and marginal unscented UKFs for the reconstructed system equation are compared in the simulation. From the results of the simulation, the theoretical statements are validated, and some interesting but not surprising phenomena are also founded, that is, the performance of the conventional filter actually does not degenerate, whereas that of the proposed filters become better when cross‐correlation exists and increases. This phenomenon can be due to the fact that the proposed filters exploited the extra information buried in the cross‐correlation, whereas the conventional filter fails to do so.
Persymmetric detectors with enhanced rejection capabilities
Authors: Hao Chengpeng , Orlando Danilo , Ma Xiaochuan , Yan Shefeng , Hou Chaohuan
Published: December 2013

In this study, the authors deal with the problem of adaptive detection of point‐like targets in Gaussian disturbance with unknown but persymmetric structured covariance matrix induced by the space and/or time symmetry of the sensing system. In this framework, they devise and assess two selective receivers exploiting the Rao test and the generalised likelihood ratio test design criteria. The performance assessment, conducted by Monte Carlo simulation, has shown that the proposed receivers can significantly outperform their unstructured counterparts and guarantee enhanced rejection performance of unwanted signals with respect to their natural competitors.
Field operational testing for safety improvement of freight trains using wireless monitoring by sensor network
Authors: Grudén Mathias , Hinnemo Malkolm , Dancila Dragos , Zherdev Filip , Edvinsson Nils , Brunberg Kjell , Andersson Lennart , Byström Roger , Rydberg Anders
Published: December 2013

Today, the majority of wagon failures on railroad systems are because of the poor maintenance of ball bearings, which causes emergent stops and delays. The existing stationary detectors, lack in predicting failures which cause troubles in scheduling maintenance. During the fall of 2011, a trial was performed by applying a wireless sensor network (WSN) aboard a train wagon with the objective to demonstrate a proof of concept for monitoring the temperature of ball bearings aboard the train wagon. This trial investigates several key aspects when applying sensor networks such as radio wave propagation, energy scavenging and performance of the WSN aboard the wagon. Two wireless links were used in the WSN. The aboard network communicates at 2.45 GHz, and the external communication is an 868 MHz radio frequency identification radio link. Since the energy in the WSN node is limited, appropriate energy scavenging devices are also presented and evaluated in a lab environment. Effort has been made to overcome these problems. The energy consumption in the network is still a problem; the most promising energy scavenging technique is piezoelectric harvesting by vibrations, which in the experiments scavenged 2.32 mW.
Defining and redefining monophyly: Haeckel, Hennig, Ashlock, Nelson and the proliferation of definitions
Authors: Vanderlaan Tegan A. , Ebach Malte C. , Williams David M. , Wilkins John S.
Published: December 2013

The various existing definitions of monophyly have resulted in confusion within the systematics community. The divergence in terminology started with the work of Willi Hennig who attempted to introduce a precise definition of phylogenetic relationship in 1950, a term that he had synonymised with monophyly by 1953, thereby creating a new definition. In 1965, Hennig introduced paraphyly to distinguish his version of monophyly from groups based on symplesiomorphies or stem groups. In attempting to resolve the confusion, Ashlock synonymised Hennig’s monophyly as holophyly, resulting in another new term. Ashlock, Mayr and others defended Haeckel’s original use of monophyly, by including holophyly and paraphyly. The result was an unresolved 21-year debate on monophyly and its various uses. A review of the history of monophyly and the origins of its various definitions has resulted in two new terms to distinguish the different versions of monophyly currently in use: diamonophyly, which group definitions based a notion of ancestor-descendant relationships, and synmonophyly, which groups definition based on kinship relationships. The terms ‘reciprocal monophyly’ and ‘oligophyly’ are discussed as being diamonophyletic.
Transfer of Lejeunea huctumalcensis to Physantholejeunea (Lejeuneaceae, Porellales)
Authors: Czumay Aleksandra , Dong Shanshan , Scheben Armin , Schäfer-Verwimp Alfons , Feldberg Kathrin , Heinrichs Jochen
Published: December 2013

Phylogenetic analyses of a three-marker dataset of Lejeuneaceae (chloroplast genome rbcL gene and trnL–trnF region, and nuclear ribosomal ITS1–5.8S-ITS2 region) resolve Lejeunea huctumalcensis (synonym Ceratolejeunea dussiana) in a well supported lineage with Physantholejeunea portoricensis. Representatives of Lejeunea and Ceratolejeunea form independent lineages. Physantholejeunea and L. huctumalcensis share the presence of ocelli, pycnolejeuneoid innovations and keeled perianths, with keels forming horn-like projections. On the basis of the molecular phylogenetic and morphological evidence, we transfer L. huctumalcensis to Physantholejeunea.
Carbon sequestration under subtropical perennial pastures II: Carbon dynamics
Authors: Sanderman Jonathan , Fillery I. R. P. , Jongepier R. , Massalsky A. , Roper M. M. , Macdonald L. M. , Maddern T. , Murphy D. V. , Baldock J. A.
Published: December 2013

Here we take advantage of the stable carbon isotope shift that occurs when a C4 plant is sown into a soil previously dominated by C3 vegetation, to explore the movement and fate of newly sequestered soil organic carbon (SOC) following establishment of subtropical perennial pastures in temperate regions of Australia. In kikuyu-based pastures up to 33 years of age, SOC accumulated exclusively in the coarse size fraction (>50 μm) in the sandy soils of southern Western Australia. In South Australian loams, regardless of pasture age, new SOC was found to accumulate in both the coarse and fine (<50 μm) size fractions. These differential results suggest that in soils with low clay content, new SOC remains in an unprotected form that is highly vulnerable to loss through decomposition and erosion. The Rothamsted Carbon Model, modified to track changes in stable isotopes, was able to represent the changes in total SOC stocks in both regions; however, the model over-predicted the incorporation of the new C4-SOC into the soil. This difference between data and model output could be reconciled if a greater proportion of new SOC is rapidly mineralised without being incorporated into any sort of stabilised pool.
Relationship between environmental and land-use variables on soil carbon levels at the regional scale in central New South Wales, Australia
Authors: Badgery Warwick B. , Simmons Aaron T. , Murphy Brian M. , Rawson Andrew , Andersson Karl O. , Lonergan Vanessa E. , van de Ven Remy
Published: December 2013

The potential to change agricultural land use to increase soil carbon stocks has been proposed as a mechanism to offset greenhouse gas emissions. To estimate the potential carbon storage in the soil from regional surveys it is important to understand the influence of environmental variables (climate, soil type, and landscape) before land management can be assessed. A survey was done of 354 sites to determine soil organic carbon stock (SOC stock; Mg C/ha) across the Lachlan and Macquarie catchments of New South Wales, Australia. The influences of climate, soil physical and chemical properties, landscape position, and 10 years of land management information were assessed. The environmental variables described most of the regional variation compared with management. The strongest influence on SOC stock at 0–10 cm was from climatic variables, particularly 30-year average annual rainfall. At a soil depth of 20–30 cm, the proportion of silica (SiO2) determined by mid-infrared spectra (SiMIR) had a negative relationship with SOC stock, and sand and clay measured by particle size analysis also showed strong relationships at sites where measured. Of the difference in SOC stock explained by land use, cropping had lower soil carbon than pasture in rotation or permanent pasture at 0–10 cm. This relationship was consistent across a rainfall gradient, but once soil carbon was standardised per mm of average annual rainfall, there was a greater difference between cropping and permanent pasture with increasing SiMIR in soils. Land use is also regulated by climate, topography, and soil type, and the effect on SOC stock is better assessed in smaller land-management units to remove some variability due to climate and soil.
Capacity for increasing soil organic carbon stocks in dryland agricultural systems
Authors: Hoyle F. C. , D'Antuono M. , Overheu T. , Murphy D. V.
Published: December 2013

Assessment of the potential for soil carbon sequestration based on soil type, land use, and climate scenarios is crucial for determining which agricultural regions can be used to help mitigate increasing atmospheric CO2 concentrations. In semi-arid and Mediterranean-type environments, soil organic carbon (SOC) storage capacity is rarely achieved under dryland agricultural systems. We aimed to assess both actual (measured) and attainable (modelled) SOC stock values for the dryland agricultural production zone of Western Australia. We measured actual SOC storage (0–0.3 m) and known constraints to plant growth for a range of soils types (3–27% clay) and land uses (continuous cropping, mixed cropping, annual and perennial pastures) on the Albany sand plain in Western Australia (n = 261 sites), spanning a rainfall gradient of 421–747 mm. Average actual SOC stocks for land use–soil type combinations ranged from 33 to 128 t C/ha (0–0.3 m). Up to 89% of the variability in actual SOC stock was explained by soil depth, rainfall, land use, and soil type. The scenarios modelled with Roth-C predicted that attainable SOC values of 59–140 t C/ha (0–0.3 m) could be achieved within 100 years. This indicated an additional storage capacity of 5–45% (7–27 t C/ha) depending on the specific land use–soil type combination. However, actual SOC in the surface 0–0.1 m was 95 to >100% of modelled attainable SOC values, suggesting this soil depth was ‘saturated’. Our findings highlight that additional SOC storage capacity in this region is limited to the subsoil below 0.1 m. This has implications for management strategies to increase SOC sequestration in dryland agricultural systems, as current practices tend to concentrate organic matter near the soil surface.
Quantifying the allocation of soil organic carbon to biologically significant fractions
Authors: Baldock J. A. , Sanderman J. , Macdonald L. M. , Puccini A. , Hawke B. , Szarvas S. , McGowan J.
Published: December 2013

Soil organic carbon (OC) exists as a diverse mixture of organic materials with different susceptibilities to biological decomposition. Computer simulation models constructed to predict the dynamics of soil OC have dealt with this diversity using a series of conceptual pools differentiated from one another by the magnitude of their respective decomposition rate constants. Research has now shown that the conceptual pools can be replaced by measureable fractions of soil OC separated on the basis of physical and chemical properties. In this study, an automated protocol for allocating soil OC to coarse (>50 µm) and fine (≤50 µm) fractions was assessed. Automating the size fractionation process was shown to reduce operator dependence and variability between replicate analyses. Solid-state 13C nuclear magnetic resonance spectroscopy was used to quantify the content of biologically resistant poly-aryl carbon in the coarse and fine size fractions. Cross-polarisation analyses were completed for coarse and fine fractions of 312 soils, and direct polarisation analyses were completed for 38 representative fractions. Direct polarisation analyses indicated that the resistant poly-aryl carbon was under-represented in the cross-polarisation analyses, on average, by a factor of ~2. Combining this under-representation with a spectral analysis process allowed the proportion of coarse- and fine-fraction OC existing as resistant poly-aryl C to be defined. The content of resistant OC was calculated as the sum of that found in the coarse and fine fractions. Contents of particulate and humus OC were calculated after subtracting the resistant OC from the coarse and fine fractions, respectively. Across the 312 soils analysed, substantial variations in the contents of humus, particulate, and resistant carbon were noted, with respective average values of 9.4, 4.0, and 4.5 g fraction C/kg soil obtained. When expressed as a proportion of the OC present in each soil, the humus, particulate, and resistant OC accounted for 56, 19, and 26%, respectively. The nuclear magnetic resonance analyses also indicated that the use of a 50-µm sieve to differentiate particulate (>50 µm) from humus (≤50 µm) forms of OC provided an effective separation based on extents of decomposition. The procedures developed in this study provided a means to differentiate three biologically significant forms of soil OC based on size, extent of decomposition, and chemical composition (poly-aryl content).
Soil carbon is only higher in the surface soil under minimum tillage in Vertosols and Chromosols of New South Wales North-West Slopes and Plains, Australia
Authors: McLeod M. K. , Schwenke G. D. , Cowie A. L. , Harden S.
Published: December 2013

Reduced carbon stock levels in Australian soil due to cropping provide a significant opportunity for carbon sequestration, and the recent initiative to consider soil carbon in domestic emissions trading requires a scientific assessment of soil carbon levels under a range of cropping soil management practices. Some of the previous research in southern and western New South Wales (NSW) showed that the rate of carbon decline in cropping soils is slowed under minimum tillage when the stubble is also retained. However, such comparison is rare in the NSW North-West Slopes and Plains region, particularly on the red soils (Chromosols) which are one of the major soil types in the region. We surveyed 50 dryland Chromosols, 72 dryland Vertosols, and 25 irrigated Vertosols on commercial farms across this region to examine the effects of conventional tillage, minimum tillage, and irrigation on total soil organic carbon. Samples of 0.1 m segments to 0.3 m depth were analysed for total organic carbon and other soil properties. Mid-infrared scans were used to predict the particulate, humus, and resistant soil organic carbon fractions. Bulk density was used to calculate total organic carbon stock for each segment, and equivalent soil mass (ESM) for 0–0.3 m. In Vertosols, for 0–0.3 m ESM, total organic carbon and particulate organic carbon were not different between management practices, whereas humic organic carbon and resistant organic carbon were consistently lower under conventional tillage. However, in 0–0.1 m, total organic carbon was greater under minimum tillage (15.2 Mg ha–1) than conventional tillage (11.9 Mg ha–1) or irrigation (12.0 Mg ha–1), reflecting less soil surface disturbance under minimum tillage. In Chromosols, only total organic carbon was higher under minimum tillage than conventional tillage in the 0–0.3 m ESM (39.8 v. 33.5 Mg ha–1) and in 0–0.1 m (19.7 v. 16.9 Mg ha–1). The strong influences of rainfall, temperature, bulk density, texture, and management history on soil carbon stocks suggested that these environmental and management factors require further consideration when gauging soil carbon sequestration potential under current and novel tillage practices in key regional locations.
Impact of carbon farming practices on soil carbon in northern New South Wales
Authors: Cowie Annette L. , Lonergan Vanessa E. , Rabbi S. M. Fazle , Fornasier Flavio , Macdonald Catriona , Harden Steven , Kawasaki Akitomo , Singh Brajesh K.
Published: December 2013

This study sought to quantify the influence of ‘carbon farming’ practices on soil carbon stocks, in comparison with conventional grazing and cropping, in northern New South Wales. The study had two components: assessment of impacts of organic amendments on soil carbon and biological indicators in croplands on Vertosols of the Liverpool Plains; and assessment of the impact of grazing management on soil carbon in Chromosols of the Northern Tablelands. The organic amendment sites identified for the survey had been treated with manures, composts, or microbial treatments, while the conventional management sites had received only chemical fertilisers. The rotational grazing sites had been managed so that grazing was restricted to short periods of several days, followed by long rest periods (generally several months) governed by pasture growth. These were compared with sites that were grazed continuously. No differences in total soil carbon stock, or soil carbon fractions, were observed between sites treated with organic amendments and those treated with chemical fertiliser. There was some evidence of increased soil carbon stock under rotational compared with continuous grazing, but the difference was not statistically significant. Similarly, double-stranded DNA (dsDNA) stocks were not significantly different in either of the management contrasts, but tended to show higher values in organic treatments and rotational grazing. The enzymatic activities of β-glucosidase and leucine-aminopeptidase were significantly higher in rotational than continuous grazing but statistically similar for the cropping site treatments. Relative abundance and community structure, measured on a subset of the cropping sites, showed a higher bacteria : fungi ratio and provided evidence that microbial process rates were significantly higher in chemically fertilised sites than organic amendment sites, suggesting enhanced mineralisation of organic matter under conventional management. The higher enzyme activity and indication of greater efficiency of microbial populations on carbon farming sites suggests a greater potential to build soil carbon under these practices. Further research is required to investigate whether the indicative trends observed reflect real effects of management.
Predicting contents of carbon and its component fractions in Australian soils from diffuse reflectance mid-infrared spectra
Authors: Baldock J. A. , Hawke B. , Sanderman J. , Macdonald L. M.
Published: December 2013

Quantifying the content and composition of soil carbon in the laboratory is time-consuming, requires specialised equipment and is therefore expensive. Rapid, simple and low-cost accurate methods of analysis are required to support current interests in carbon accounting. This study was completed to develop national and state-based models capable of predicting soil carbon content and composition by coupling diffuse reflectance mid-infrared (MIR) spectra with partial least-squares regression (PLSR) analyses. Total, organic and inorganic carbon contents were determined and MIR spectra acquired for 20 495 soil samples collected from 4526 locations from soil depths to 1 m within Australia’s agricultural regions. However, all subsequent MIR/PLSR models were developed using soils only collected from the 0–10, 10–20 and 20–30 cm depth layers. The extent of grinding applied to air-dried soil samples was found to be an important determinant of the variability in acquired MIR spectra. After standardisation of the grinding time, national MIR/PLSR models were developed using an independent test-set validation approach to predict the square-root transformed contents of total, organic and inorganic carbon and total nitrogen. Laboratory fractionation of soil organic carbon into particulate, humus and resistant forms was completed on 312 soil samples. Reliable national MIR/PLSR models were developed using cross-validation to predict the contents of these soil organic carbon fractions; however, further work is required to enhance the representation of soils with significant contents of inorganic carbon. Regional MIR/PLSR models developed for total, organic and inorganic carbon and total nitrogen contents were found to produce more reliable and accurate predictions than the national models. The MIR/PLSR approach offers a more rapid and more cost effective method, relative to traditional laboratory methods, to derive estimates of the content and composition of soil carbon and total nitrogen content provided that the soils are well represented by the calibration samples used to build the predictive models.
Mechanisms underlying subunit independence in pyramidal neuron dendrites
Authors: Behabadi Bardia F. , Mel Bartlett W.
Published: December 2013

Significance

Historically, neurons were thought to collect synaptic currents from across their dendritic trees and passively conduct them to the soma where action potentials (APs) are generated. More recent studies have shown that dendrites can generate local spikes and thus may function as independent computational subunits. It remains unknown, however, how dendrites can maintain the integrity and separateness of their local computations, which depend on voltage, despite the repeated synchronization of dendritic potentials by back-propagating somatic APs. This modeling study identifies three biophysical specializations that allow dendrites to remain functionally independent in a firing neuron, one of which is the somatic spiking mechanism itself. Our results suggest that a major class of neurons has been optimized for subunitized computation.
Introduction and background - challenges and limitations of GM plants for animal nutrition.
Authors: Flachowsky G.
Published: December 2013

This chapter presents an overview of the increasing demand and environmental impact of animal and crop production, the role and factors of genetically modified crops as feed for livestock and their effects on the environment and food security.
The fate of transgenic DNA and newly expressed proteins.
Authors: Einspanier R.
Published: December 2013

This chapter summarizes the animal feeding studies published concerning the fate of GM feed DNA and proteins, together with the resulting significance and consequence of a potential GM transfer into animals and their secondary products and the correlating safety aspects.