bluuebunny/crossref_metadata_2025 huggingface dataset:
Protonation and pK changes in protein–ligand binding
Authors: Onufriev Alexey V. , Alexov Emil
Published: July 2013

Formation of protein–ligand complexes causes various changes in both the receptor and the ligand. This review focuses on changes in pK and protonation states of ionizable groups that accompany protein–ligand binding. Physical origins of these effects are outlined, followed by a brief overview of the computational methods to predict them and the associated corrections to receptor–ligand binding affinities. Statistical prevalence, magnitude and spatial distribution of the pK and protonation state changes in protein–ligand binding are discussed in detail, based on both experimental and theoretical studies. While there is no doubt that these changes occur, they do not occur all the time; the estimated prevalence varies, both between individual complexes and by method. The changes occur not only in the immediate vicinity of the interface but also sometimes far away. When receptor–ligand binding is associated with protonation state change at particular pH, the binding becomes pH dependent: we review the interplay between sub-cellular characteristic pH and optimum pH of receptor–ligand binding. It is pointed out that there is a tendency for protonation state changes upon binding to be minimal at physiologically relevant pH for each complex (no net proton uptake/release), suggesting that native receptor–ligand interactions have evolved to reduce the energy cost associated with ionization changes. As a result, previously reported statistical prevalence of these changes – typically computed at the same pH for all complexes – may be higher than what may be expected at optimum pH specific to each complex. We also discuss whether proper account of protonation state changes appears to improve practical docking and scoring outcomes relevant to structure-based drug design. An overview of some of the existing challenges in the field is provided in conclusion.
Distinct synaptic mechanisms create parallel S-ON and S-OFF color opponent pathways in the primate retina
Authors: DACEY DENNIS M. , CROOK JOANNA D. , PACKER ORIN S.
Published: July 2013

Anatomical and physiological approaches are beginning to reveal the synaptic origins of parallel ON- and OFF-pathway retinal circuits for the transmission of short (S-) wavelength sensitive cone signals in the primate retina. Anatomical data suggest that synaptic output from S-cones is largely segregated; central elements of synaptic triads arise almost exclusively from the “blue-cone” bipolar cell, a presumed ON bipolar, whereas triad-associated contacts derive primarily from the “flat” midget bipolar cell, a hyperpolarizing, OFF bipolar. Similarly, horizontal cell connectivity is also segregated, with only the H2 cell-type receiving numerous contacts from S-cones. Negative feedback from long (L-) and middle (M-) wavelength sensitive cones via the H2 horizontal cells elicits an antagonistic surround in S-cones demonstrating that S versus L + M or “blue-yellow” opponency is first established in the S-cone. However, the S-cone output utilizes distinct synaptic mechanisms to create color opponency at the ganglion cell level. The blue-cone bipolar cell is presynaptic to the small bistratified, “blue-ON” ganglion cell. S versus L + M cone opponency arises postsynaptically by converging S-ON and LM-OFF excitatory bipolar inputs to the ganglion cell’s bistratified dendritic tree. The common L + M cone surrounds of the parallel S-ON and LM-OFF cone bipolar inputs appear to cancel resulting in “blue-yellow” antagonism without center-surround spatial opponency. By contrast, in midget ganglion cells, opponency arises by the differential weighting of cone inputs to the receptive field center versus surround. In the macula, the “private-line” connection from a midget ganglion cell to a single cone predicts that S versus L + M opponency is transmitted from the S-cone to the S-OFF midget bipolar and ganglion cell. Beyond the macula, OFF-midget ganglion cell dendritic trees enlarge and collect additional input from multiple L and M cones. Thus S-OFF opponency via the midget pathway would be expected to become more complex in the near retinal periphery as L and/or M and S cone inputs sum to the receptive field center. An important goal for further investigation will be to explore the hypothesis that distinct bistratified S-ON versus midget S-OFF retinal circuits are the substrates for human psychophysical detection mechanisms attributed to S-ON versus S-OFF perceptual channels.
S cones: Evolution, retinal distribution, development, and spectral sensitivity
Authors: HUNT DAVID M. , PEICHL LEO
Published: July 2013

S cones expressing the short wavelength-sensitive type 1 (SWS1) class of visual pigment generally form only a minority type of cone photoreceptor within the vertebrate duplex retina. Hence, their primary role is in color vision, not in high acuity vision. In mammals, S cones may be present as a constant fraction of the cones across the retina, may be restricted to certain regions of the retina or may form a gradient across the retina, and in some species, there is coexpression of SWS1 and the long wavelength-sensitive (LWS) class of pigment in many cones. During retinal development, SWS1 opsin expression generally precedes that of LWS opsin, and evidence from genetic studies indicates that the S cone pathway may be the default pathway for cone development. With the notable exception of the cartilaginous fishes, where S cones appear to be absent, they are present in representative species from all other vertebrate classes. S cone loss is not, however, uncommon; they are absent from most aquatic mammals and from some but not all nocturnal terrestrial species. The peak spectral sensitivity of S cones depends on the spectral characteristics of the pigment present. Evidence from the study of agnathans and teleost fishes indicates that the ancestral vertebrate SWS1 pigment was ultraviolet (UV) sensitive with a peak around 360 nm, but this has shifted into the violet region of the spectrum (>380 nm) on many separate occasions during vertebrate evolution. In all cases, the shift was generated by just one or a few replacements in tuning-relevant residues. Only in the avian lineage has tuning moved in the opposite direction, with the reinvention of UV-sensitive pigments.
Private needs, public space: public toilets provision in the Anglo-Atlantic patriarchal city: London, Dublin, Toronto and Chicago
Authors: FLANAGAN MAUREEN
Published: July 2013

As part of the reconstruction of their built environments at the beginning of the twentieth century, London, Dublin, Toronto and Chicago confronted the question of whether to provide public toilets. In comparing the arguments and decisions over this question, this article demonstrates how the male leadership of each city sought to preserve the centuries-old patriarchal tradition of separate public and private spheres and limit women's access to public spaces. It also reveals the gendered dimension of ideas and experiences of the city that underlay the rhetoric surrounding this question.
Left ventricular rotation and right–left ventricular interaction in congenital heart disease: the acute effects of interventional closure of patent arterial ducts and atrial septal defects
Authors: Laser Kai T. , Haas Nikolaus A. , Fischer Markus , Habash Sheeraz , Degener Franziska , Prinz Christian , Körperich Hermann , Sandica Eugen , Kececioglu Deniz
Published: July 2013

Background

Left ventricular rotation is physiologically affected by acute changes in preload. We investigated the acute effect of preload changes in chronically underloaded and overloaded left ventricles in children with shunt lesions.

Methods

A total of 15 patients with atrial septal defects (Group A: 7.4 ± 4.7 years, 11 females) and 14 patients with patent arterial ducts (Group B: 2.7 ± 3.1 years, 10 females) were investigated using 2D speckle-tracking echocardiography before and after interventional catheterisation. The rotational parameters of the patient group were compared with those of 29 matched healthy children (Group C).

Results

Maximal torsion (A: 2.45 ± 0.9°/cm versus C: 1.8 ± 0.8°/cm, p < 0.05), apical peak systolic rotation (A: 12.6 ± 5.7° versus C: 8.7 ± 3.5°, p < 0.05), and the peak diastolic torsion rate (A: −147 ± 48°/second versus C: −110 ± 31°/second, p < 0.05) were elevated in Group A and dropped immediately to normal values after intervention (maximal torsion 1.5 ± 1.1°/cm, p < 0.05, apical peak systolic rotation 7.2 ± 4.1°, p < 0.05, and peak diastolic torsion rate −106 ± 35°/second, p < 0.05). Patients in Group B had decreased maximal torsion (B: 1.8 ± 1.1°/cm versus C: 3.8 ± 1.4°/cm, p < 0.05) and apical peak systolic rotation (B: 8.3 ± 6.1° versus C: 13.9 ± 4.3°, p < 0.05). Defect closure was followed by an increase in maximal torsion (B: 2.7 ± 1.4°/cm, p < 0.05) and the peak diastolic torsion rate (B: −133 ± 66°/second versus −176 ± 84°/second, p < 0.05).

Conclusions

Patients with chronically underloaded left ventricles compensate with an enhanced apical peak systolic rotation, maximal torsion, and quicker diastolic untwisting to facilitate diastolic filling. In patients with left ventricular dilatation by volume overload, the peak systolic apical rotation and the maximal torsion are decreased. After normalisation of the preload, they immediately return to normal and diastolic untwisting rebounds. These mechanisms are important for understanding the remodelling processes.
Coup d'état, Coronation and Conversion: Some Reflections on the Adoption of Judaism by the Khazar Khaganate
Authors: OLSSON J. T.
Published: July 2013

“The Turks will take control of Kūfa in southern Iraq and the Khazars the province of al-Jazīra in northern Iraq” runs a popular ḥadīth of the early ‘Abbāsid Caliphate. The patently false attribution to the Prophet notwithstanding, this ḥadīth suggests that the Khazars, a militarised semi-nomadic Turkic people securely established in their Khaganate north of the Caucasus Mountains, loomed menacing and large in the imagination – and fears – of their settled neighbours. This is hardly a surprise. The Khazars, who had emerged as the hegemonic regional power after the fragmentation of the Gök Turk Empire, had grown rich as intermediaries in a north-south trading network, and from the tributes derived from their 25 subject peoples. They employed a centralised fiscal administration which allowed them to maintain a standing army of at least ten thousand, whose ranks could probably swell two-or-three-fold with the retinues of their notables and contributions from their subject tribes, and were ensconced within a network of fortifications that provided them with a degree of internal stability and potential for aggressive campaigning highly unusual within other steppe polities.
BILINEAR OPTIMAL CONTROL OF THE VELOCITY TERM IN A VON KÁRMÁN PLATE EQUATION
Authors: PARK JONG YEOUL , PARK SUN HYE , KANG YONG HAN
Published: July 2013

We consider a bilinear optimal control problem for a von Kármán plate equation. The control is a function of the spatial variables and acts as a multiplier of the velocity term. We first state the existence of solutions for the von Kármán equation and then derive optimality conditions for a given objective functional. Finally, we show the uniqueness of the optimal control.
Surface Structure Dependent Electrocatalytic Activity of Co3O4 Anchored on Graphene Sheets toward Oxygen Reduction Reaction
Authors: Xiao Junwu , Kuang Qin , Yang Shihe , Xiao Fei , Wang Shuai , Guo Lin
Published: July 2013

Catalytic activity is primarily a surface phenomenon, however, little is known about Co3O4 nanocrystals in terms of the relationship between the oxygen reduction reaction (ORR) catalytic activity and surface structure, especially when dispersed on a highly conducting support to improve the electrical conductivity and so to enhance the catalytic activity. Herein, we report a controllable synthesis of Co3O4 nanorods (NR), nanocubes (NC) and nano-octahedrons (OC) with the different exposed nanocrystalline surfaces ({110}, {100} and {111}), uniformly anchored on graphene sheets, which has allowed us to investigate the effects of the surface structure on the ORR activity. Results show that the catalytically active sites for ORR should be the surface Co2+ ions, whereas the surface Co3+ ions catalyze CO oxidation and the catalytic ability is closely related to the density of the catalytically active sites. These results underscore the importance of morphological control in the design of highly efficient ORR catalysts.
Thymic Stromal Lymphopoietin Induces Migration in Human Airway Smooth Muscle Cells
Authors: Redhu Naresh Singh , Shan Lianyu , Movassagh Hesam , Gounni Abdelilah S.
Published: July 2013

Airway remodeling due to increased airway smooth muscle (ASM) mass, likely due to enhanced migration and proliferation, has been shown to be highly associated with decline in lung function in asthma. Thymic stromal lymphopoietin (TSLP) is an IL-7-like, pro-allergic cytokine that has been shown to be necessary and sufficient for the development of allergic asthma. Human ASM (HASM) cells express TSLP receptor (TSLPR), the activation of which leads to enhanced release of proinflammatory mediators such as IL-6, CCL11/eotaxin-1 and CXCL8/IL-8. We show here that TSLP induces HASM cell migration through STAT3 activation since lentiviral-shRNA inhibition of STAT3 abrogated the TSLP-induced cell migration. Moreover, TSLP induced multiple cytoskeleton changes in HASM cells such as actin polymerization, cell polarization and activation of small GTPase Rac1. Collectively, our data suggest a pro-migratory function of TSLP in ASM remodeling and provides better rationale for targeting TSLP/TSLPR pathway for therapeutic approaches in allergic asthma.
Activation of blood coagulation in cancer: implications for tumour progression
Authors: Lima Luize G. , Monteiro Robson Q.
Published: July 2013

Several studies have suggested a role for blood coagulation proteins in tumour progression. Herein, we discuss (1) the activation of the blood clotting cascade in the tumour microenvironment and its impact on primary tumour growth; (2) the intravascular activation of blood coagulation and its impact on tumour metastasis and cancer-associated thrombosis; and (3) antitumour therapies that target blood-coagulation-associated proteins. Expression levels of the clotting initiator protein TF (tissue factor) have been correlated with tumour cell aggressiveness. Simultaneous TF expression and PS (phosphatidylserine) exposure by tumour cells promote the extravascular activation of blood coagulation. The generation of blood coagulation enzymes in the tumour microenvironment may trigger the activation of PARs (protease-activated receptors). In particular, PAR1 and PAR2 have been associated with many aspects of tumour biology. The procoagulant activity of circulating tumour cells favours metastasis, whereas the release of TF-bearing MVs (microvesicles) into the circulation has been correlated with cancer-associated thrombosis. Given the role of coagulation proteins in tumour progression, it has been proposed that they could be targets for the development of new antitumour therapies.
Increasing Social Interaction Using Prelinguistic Milieu Teaching With Nonverbal School-Age Children With Autism
Authors: Franco Jessica H. , Davis Barbara L. , Davis John L.
Published: July 2013

Purpose

Children with autism display marked deficits in initiating and maintaining social interaction. Intervention using play routines can create a framework for developing and maintaining social interaction between these children and their communication partners.

Method

Six nonverbal 5- to 8-year-olds with autism were taught to engage in social interaction within salient play routines. Prelinguistic milieu teaching (PMT) techniques were used to teach the children to communicate intentionally during these routines. Intervention focused on the children's social interaction with an adult. The effects of intervention were evaluated using a multiple baseline design across participants.

Results

At study onset, the participants demonstrated few consistent interaction with others. With intervention, all of the children improved their ability to sustain social interactions, as evidenced by an increase in the number of communicative interactions during play routines. Participants also increased their overall rate of initiated intentional communication.

Conclusion

Development of intentional prelinguistic communication within salient social routines creates opportunities for an adult to teach social and communication skills to young school-age children with autism who function at a nonverbal level.
A Multidimensional Investigation of Children's /r/ Productions: Perceptual, Ultrasound, and Acoustic Measures
Authors: Klein Harriet B. , McAllister Byun Tara , Davidson Lisa , Grigos Maria I.
Published: July 2013

Purpose

This study explored relationships among perceptual, ultrasound, and acoustic measurements of children's correct and misarticulated /r/ sounds. Longitudinal data documenting changes across these parameters were collected from 2 children who acquired /r/ over a period of intervention and were compared with data from children with typical speech.

Method

Participants were 3 children with typical speech, recorded once, and 2 children with /r/ misarticulation, recorded over 7–8 months. The following data from /r/ produced in nonwords were collected: perceptually rated accuracy, ultrasound measures of tongue shape, and F3 – F2 distance.

Results

Regression models revealed significant associations among perceptual, ultrasound, and acoustic measures of /r/ accuracy. The inclusion of quantitative tongue-shape measurements improved the match between the ultrasound and perceptual/acoustic data. Perceptually incorrect /r/ productions were found to feature posteriorly located peaked tongue shapes. Of the children who were seen longitudinally, 1 developed a bunched /r/ and 1 demonstrated retroflexion. The children with typical speech also differed in their tongue shapes.

Conclusion

Results support the validity of using qualitative and quantitative ultrasound measures to characterize the accuracy of children's /r/ sounds. Clinically, findings suggest that it is important to encourage pharyngeal constriction while allowing children to find the /r/ tongue shape that best fits their individual vocal tract.
Waveguide slot-excited long racetrack electron cyclotron resonance plasma source for roll-to-roll (scanning) processing
Authors: You H.-J.
Published: July 2013

We present a SLot-excited ANtenna (SLAN) long racetrack ECR plasma source that is utilized for roll-to-roll plasma processing such as thin film encapsulation of large-area OLED (organic light emitting diode) panel or modification of fabric surfaces. This source is designed to be long, and to operate under high density uniform plasma with sub-milli-torr pressures. The above features are accomplished by a slot-excited long racetrack resonator with a toroidal geometry of magnetic field ECR configuration, and reinforced microwave electric distributions along the central region of plasma chamber. Also, a new feature has been added to the source. This is to employ a tail plunger, which allows the microwave electric field and the uniformity of the plasma profile to be easily adjustable. We have successfully generated Ar plasmas operating with the microwave power of 0.5–3 kW in the pressure range of 0.2–10 mTorr. The plasma is uniform (<10%) in the direction of the straight track and has a Gaussian profile in the roll-to-roll (scanning) direction. In addition, it is shown that the tail plunger could adjust the plasma profile in order to obtain plasma uniformity. Furthermore, based on the results, we suggest a newly designed up-scaled racetrack-SLAN source.
Temperature dependence of the training effect in electrodeposited Co/CoO nanotubes
Authors: Proenca M. P. , Ventura J. , Sousa C. T. , Vazquez M. , Araujo J. P.
Published: July 2013

High aspect ratio Co/CoO nanotubes (NTs) were obtained by potentiostatic electrodeposition of Co inside nanoporous alumina templates followed by the natural oxidation of their inner walls. Magnetic measurements performed at low temperatures after field cooling the samples from above its blocking temperature (TB∼220 K), evidenced the existence of exchange bias (EB) coupling between the Co ferromagnetic outer wall and the CoO antiferromagnetic inner wall of the NTs. A decrease in the magnitude of the EB field was measured at T<TB when cycling the Co/CoO NT arrays through consecutive hysteresis loops. This decrease is known as the training effect (TE) and is here studied in the 6 K≤T<TB temperature range. The TE was fitted using the recursive Binek formula, giving small values for the characteristic decay rate of the training behavior, and evidencing a decrease of EB with increasing antiferromagnetic layer thickness. A phenomenological theory for the temperature dependence of the TE in exchange biased systems was applied for the first time to core-shell nanotubular structures. The good agreement obtained between the experimental results and the theoretical data, provided a strong confirmation of the qualitative correctness of the spin configuration relaxation model used in these systems.
Electronic topological transition and semiconductor-to-metal conversion of Bi2Te3 under high pressure
Authors: Zhang Junkai , Liu Cailong , Zhang Xin , Ke Feng , Han Yonghao , Peng Gang , Ma Yanzhang , Gao Chunxiao
Published: July 2013

Accurate high pressure in situ Hall-effect and temperature dependent electrical resistivity measurements have been carried out on Bi2Te3, a topological insulator. The pressure dependent electrical resistivity, Hall coefficient, carrier concentration, and mobility show the abnormal inflection points at 8, 12, and 17.8 GPa, indicating that the pressure-induced structural phase transitions of Bi2Te3 can result in a series of changes in the carrier transport behavior. In addition, the Hall coefficient shows a significant discontinuous change at 4 GPa, which is caused by the electronic topological transition. A sign inversion of Hall coefficient from positive to negative is found around 8 GPa. Furthermore, the temperature dependent electrical resistivity shows that the sample undergoes a semiconductor-to-metal conversion around 9.2 GPa, indicating that the insulating gap of Bi2Te3 becomes closed at this pressure. As the metallization occurs in the sample, the topological property of Bi2Te3 disappears.
Conducting grain boundaries enhancing thermoelectric performance in doped Mg2Si
Authors: Muthiah Saravanan , Pulikkotil Jiji , Srivastava A. K. , Kumar Ashok , Pathak B. D. , Dhar Ajay , Budhani R. C.
Published: July 2013

The thermoelectric properties of Pb doped Mg2Si, synthesized using reactive sintering employing spark plasma sintering, are investigated and are compared with other dopants reported in literature. While a moderate decrease in Seebeck coefficient and thermal conductivity is observed for 2 at. % of Pb doping in Mg2Si, a substantial enhancement in the material's thermoelectric figure-of-merit is observed, which is due to an enormous increase in its electrical conductivity. A brick-layer model is proposed to explain these results, wherein the inter-granular electronic conductivity is facilitated by Pb (or Mg2Pb) phases at grain boundaries, which is supported by microstructural evidences.
Single-shot measurement of a terahertz electric-field waveform using a reflective echelon mirror
Authors: Minami Yasuo , Hayashi Yusuke , Takeda Jun , Katayama Ikufumi
Published: July 2013

Single-shot measurements of terahertz (THz) electric-field waveforms are demonstrated using a reflective echelon mirror, which produces multiple probe pulses with different time-delays. The polarization rotation of the probe pulses, due to the electro-optic effect induced by the THz electric field generated from grating-coupled LiNbO3, was imaged onto a two-dimensional complementary metal-oxide-semiconductor camera. A waveform with a weak peak field strength of 0.6 kV/cm was obtained with a good signal-to-noise ratio, demonstrating precise single-shot detection of the THz electric field waveform.
A-centers in silicon studied with hybrid density functional theory
Authors: Wang H. , Chroneos A. , Londos C. A. , Sgourou E. N. , Schwingenschlögl U.
Published: July 2013

Density functional theory employing hybrid functional is used to gain fundamental insight into the interaction of vacancies with oxygen interstitials to form defects known as A-centers in silicon. We calculate the formation energy of the defect with respect to the Fermi energy for all possible charge states. It is found that the neutral and doubly negatively charged A-centers dominate. The findings are analyzed in terms of the density of states and discussed in view of previous experimental and theoretical studies.
Dislocation distribution across ultrathin silicon-on-insulator with epitaxial SiGe stressor
Authors: Bonera Emiliano , Gatti Riccardo , Isella Giovanni , Norga Gerd , Picco Andrea , Grilli Emanuele , Guzzi Mario , Texier Michaël , Pichaud Bernard , von Känel Hans , Miglio Leo
Published: July 2013

We studied the plastic deformation of an ultrathin silicon-on-insulator with epitaxial Si1−xGex by transmission electron microscopy, Raman spectroscopy, and finite-element method. We analyzed a top Si layer of 10 nm (testing also a 2 nm layer) with epitaxial Si0.64Ge0.36 stressors of 50 and 100 nm. SiGe plastically deforms the top Si layer, and this strain remains even when Si1−xGex is removed. For low dislocation densities, dislocations are gettered close to the Si/SiO2 interface, while the SiGe/Si interface is coherent. Beyond a threshold dislocation density, interactions between dislocations force additional dislocations to position at the Si1−xGex/Si interface.
VIGS technology: an attractive tool for functional genomics studies in legumes
Authors: Pflieger Stéphanie , Richard Manon M. S. , Blanchet Sophie , Meziadi Chouaib , Geffroy Valérie
Published: July 2013

Legume species are among the most important crops worldwide. In recent years, six legume genomes have been completely sequenced, and there is now an urgent need for reverse-genetics tools to validate genes affecting yield and product quality. As most legumes are recalcitrant to stable genetic transformation, virus-induced gene silencing (VIGS) appears to be a powerful alternative technology for determining the function of unknown genes. VIGS technology is based on the property of plant viruses to trigger a defence mechanism related to post-transcriptional gene silencing (PTGS). Infection by a recombinant virus carrying a fragment of a plant target gene will induce homology-dependent silencing of the endogenous target gene. Several VIGS systems have been developed for legume species since 2004, including those based on Bean pod mottle virus, Pea early browning virus, and Apple latent spherical virus, and used in reverse-genetics studies of a wide variety of plant biological processes. In this work, we give an overview of the VIGS systems available for legumes, and present their successful applications in functional genomics studies. We also discuss the limitations of these VIGS systems and the future challenges to be faced in order to use VIGS to its full potential in legume species.
Effects of Temperature on Inorganic Nitrogen Dynamics in Sequencing Batch Reactors using Biofloc Technology to Treat Aquaculture Sludge
Authors: Yao Chen , Tan Hong-Xin , Luo Guo-Zhi , Li Li
Published: July 2013

As a new aquaculture technology, biofloc technology (BFT) makes it possible to minimize water exchange and convert the nitrogen in aquacultural waste into biofloc, which can be a natural fish food within the culture system. In the current study, biofloc bacteria were employed to treat sludge from a recirculating aquaculture system under four different temperatures (15, 20, 25, and 30°C) in three sequencing batch reactors (SBRs) per temperature. Ammonium reduction was seen on days 19, 17, 13, and 17 for the 15, 20, 25, and 30°C groups, respectively, indicating that the biofloc bacteria started to convert ammonium to microbial biomass on that day. The nitrite concentration remained below 6.5 mg/L for each group except the 30°C group, in which the value reached 13.88 mg/L. The nitrate concentration remained below 4.5 mg/L for each group. An ammonia nitrogen removal study revealed that all SBRs could remove a total ammonia nitrogen (TAN) concentration of 10 mg/L in 6 h without increasing the nitrite and nitrate concentrations; the 25°C group needed only 3 h to remove the TAN. The protein content of the biofloc at the end of the study was 27.81 ± 1.99% (mean ± SD) for the 15°C group, 28.6 ± 3.14% for the 20°C group, 36.80 ± 3.31% for the 25°C group, and 35.06 ± 3.94% for the 30°C group, indicating that the bacteria could be harvested as biological protein for feeding the cultured species.
The Palestinians – lessons from the Arab Spring
Authors: Ghanem As’ad
Published: July 2013

This paper examines the implications of the Arab Spring for the Palestinians. The aim is to point out the basic lessons and implications of the transformations occurring in the Arab world for the Palestinians as an exceptional case, due to their situation under occupation and exile. Cause for optimism is discerned in the anticipated increase in broad and practical Arab support for the Palestinians. However, the contention here is that Palestinians themselves have derived too limited a lesson from the Arab revolutions by focusing only on the call for unity between the competing Palestinian factions. Their reconciliation is only about their self-preservation and that of the system which has served them hitherto. The recommendations posited here are for the Palestinians to embrace the full message of the Arab Spring and make peaceful protest en masse and across the whole Palestinian people their path to liberation.
Bridgeland stability conditions on threefolds I: Bogomolov-Gieseker type inequalities
Authors: Bayer Arend , Macrì Emanuele , Toda Yukinobu
Published: July 2013

We construct new t-structures on the derived category of coherent sheaves on smooth projective threefolds. We conjecture that they give Bridgeland stability conditions near the large volume limit. We show that this conjecture is equivalent to a Bogomolov-Gieseker type inequality for the third Chern character of certain stable complexes. We also conjecture a stronger inequality, and prove it in the case of projective space, and for various examples.

Finally, we prove a version of the classical Bogomolov-Gieseker inequality, not involving the third Chern character, for stable complexes.
Claude Lévi-Strauss
Authors: Harkin Michael
Published: July 2013

Claude Lévi-Strauss (b. 1908–d. 2009) was the preeminent French anthropologist of the twentieth century and one of the most influential thinkers on the subjects of myth, culture, religion, and social organization. He is the originator of the best-known version of “structuralism,” a theoretical framework that examines elementary units of cultural systems, such as myth, and the principles by which they are organized at a systemic level. His work has been highly influential within and outside anthropology, especially in fields such as literary studies and philosophy. Indeed, a generation of “post-structuralist” French philosophers, such as Michel Foucault, Jacques Derrida, and Jean Baudrillard, arose to modify and contest structuralism, and thus to affirm its importance.
Max Gluckman
Authors: Marx Emanuel
Published: July 2013

Max (Herman) Gluckman (b. 1911–d. 1975) was a South African who became a pathbreaking British social anthropologist. In his studies of South and Central African societies he realized how deeply the colonial regimes and the global economy affected every aspect of peoples’ lives. As director of the Rhodes-Livingstone Institute in Northern Rhodesia and later as professor of social anthropology at the University of Manchester in the United Kingdom, he made long-term plans to study this modernity in urbanization, industrialization, and labor migration. While seeking to implement the research programs according to plan, he never prevented his colleagues and students from following their own inclinations and ideas. In the 1950s and 1960s the Manchester department assimilated and contributed to a constant flow of innovative ideas, such as the social field, social networks, the extended case study, and the analysis of social situations. It also engaged in several new areas and fields of study, such as rural and urban communities and industrial organizations in England and Wales, and the adaptation of new immigrants to various social formations in Israel. The lively and sometimes even aggressive propagation of the new ideas of the Manchester network induced anthropologists in other departments to refer, jokingly at first, to a Manchester School of Anthropology. Discussions about whether such a school ever existed continue to this day.
Historical Archaeology
Authors: Orser, Jr. Charles E.
Published: July 2013

Historical archaeology is a relatively new field, having been professionalized only since the 1960s. Some historical archaeology was practiced before this date but generally not by professionally trained scholars. Archaeologists use “historical archaeology” in two ways. They use the term in a general sense to refer to any archaeological research that employs both archaeological materials and historical (textual, oral, visual, architectural) sources of information. They also use the term in a more restricted way to refer to the archaeological and historical study of sites, properties, and issues related specifically to post-Columbian history (dating after approximately 1492). Both definitions are correct, but archaeologists generally mean the second definition when they use the term. This usage means that while classical archaeology is technically historical archaeology (because of its method), classical archaeologists usually do not think of themselves as historical archaeologists per se. The close association of historical archaeology with the discipline of history has meant that the profession has had some difficulty defining itself. Historical archaeology is today practiced throughout the globe, with historical archaeologists examining many kinds of sites (e.g., missions, indigenous villages, fortifications, abandoned towns, mining camps, and even still-occupied sites). The recent date of many sites means that historical archaeologists often interact with a site’s descendants or past actual residents.
Cargo Cults
Authors: Lindstrom Lamont
Published: July 2013

When the Second World War ended in 1945, anthropologists resumed their studies of Pacific Island societies with new interest in social change and social unrest that had been sparked by wartime turmoil and the impending collapse of colonial empires. Defiant social movements were impossible to ignore. In the Melanesian islands of the southwestern Pacific, anthropologists labeled these political and religious movements, cargo cults, and eventually they would describe several hundred of these political/religious organizations that erupted across New Guinea (today, Papua New Guinea and the Indonesian province of Papua), Solomon Islands, Vanuatu, New Caledonia, and Fiji. Cargo cult proved remarkably popular as a descriptive term, and ethnographers used it promiscuously also to relabel prewar social disturbances as well as movements elsewhere in the Pacific and beyond. Islanders, in a classic cargo cult, embraced new prophecies and innovative ritual practices that promised the arrival or return of “cargo” (or kago in the Pidgin Englishes of Melanesia). Cult rituals typically included new forms of dance, marching, and drilling, imaginative strategies to contact spirits and ancestors, and new moral codes to secure group unity and harmony. Community ancestors or, in the postwar period, the American military would reward the faithful with shipments of cargo. Cargo, as object of organized community desire, is semantically complex. Sometimes, cargo meant money or Western manufactured goods shipped into the islands in massive amounts particularly during the Pacific War. Anthropologists also interpreted cargo to represent the return of dead ancestors, achievement of balanced exchange relations with Europeans, assertion of a sense of honor and self-worth, desire for political sovereignty, or the transformation and transcendence of everyday reality. Many cults flared up quickly but then burned themselves out when no cargo arrived. Others, however, have been institutionalized and survive today as churches, political parties, and business organizations. Some anthropologists have argued that Melanesian cultures embrace a constant background of imminent cargoism, or expectation of sudden, episodic change. The energy and desire that once sparked cargo culting, however, currently animates island enthusiasm for evangelical and Pentecostal Christianity alongside economic development projects both genuine and spurious.
Early Disruption of Maternal–Zygotic Interaction and Activation of Defense-Like Responses inArabidopsisInterspecific Crosses
Authors: Burkart-Waco Diana , Ngo Kathie , Dilkes Brian , Josefsson Caroline , Comai Luca
Published: July 2013

Seed death resulting from hybridization between Arabidopsis thaliana and Arabidopsis arenosa has complex genetic determination and involves deregulation 5 to 8 d after pollination (DAP) of AGAMOUS-LIKE genes and retroelements. To identify causal mechanisms, we compared transcriptomes of compatible and incompatible hybrids and parents at 3 DAP. Hybrids misexpressed endosperm and seed coat regulators and hyperactivated genes encoding ribosomal, photosynthetic, stress-related, and immune response proteins. Regulatory disruption was more severe in Columbia-0 hybrids than in C24 hybrids, consistent with the degree of incompatibility. Maternal loss-of-function alleles for endosperm growth factor TRANSPARENT TESTA GLABRA2 and HAIKU1 and defense response regulators NON-EXPRESSOR OF PATHOGENESIS RELATED1 and SALICYLIC ACID INDUCTION-DEFICIENT2 increased hybrid seed survival. The activation of presumed POLYCOMB REPRESSIVE COMPLEX (PRC) targets, together with a 20-fold reduction in expression of FERTILIZATION INDEPENDENT SEED2, indicated a PRC role. Proximity to transposable elements affected natural variation for gene regulation, but transposon activation did not differ from controls. Collectively, this investigation provides candidates for multigenic orchestration of the incompatibility response through disruption of endosperm development, a novel role for communication between endosperm and maternal tissues and for pathways previously connected to immunity, but, surprisingly, does not identify a role for transposons.
The Receptor-Like Protein ReMAX of Arabidopsis Detects the Microbe-Associated Molecular Pattern eMax from Xanthomonas
Authors: Jehle Anna Kristina , Lipschis Martin , Albert Markus , Fallahzadeh-Mamaghani Vahid , Fürst Ursula , Mueller Katharina , Felix Georg
Published: July 2013

As part of their immune system, plants have pattern recognition receptors (PRRs) that can detect a broad range of microbe-associated molecular patterns (MAMPs). Here, we identified a PRR of Arabidopsis thaliana with specificity for the bacterial MAMP eMax from xanthomonads. Response to eMax seems to be restricted to the Brassicaceae family and also varied among different accessions of Arabidopsis. In crosses between sensitive accessions and the insensitive accession Shakhdara, eMax perception mapped to RECEPTOR-LIKE PROTEIN1 (RLP1). Functional complementation of rlp1 mutants required gene constructs that code for a longer version of RLP1 that we termed ReMAX (for receptor of eMax). ReMAX/RLP1 is a typical RLP with structural similarity to the tomato (Solanum lycopersicum) RLP Eix2, which detects fungal xylanase as a MAMP. Attempts to demonstrate receptor function by interfamily transfer of ReMAX to Nicotiana benthamiana were successful after using hybrid receptors with the C-terminal part of ReMAX replaced by that of Eix2. These results show that ReMAX determines specificity for eMax. They also demonstrate hybrid receptor technology as a promising tool to overcome problems that impede interfamily transfer of PRRs to enhance pathogen detection in crop plants.
The Caspase-Related Protease Separase (EXTRA SPINDLE POLES) Regulates Cell Polarity and Cytokinesis inArabidopsis
Authors: Moschou Panagiotis N. , Smertenko Andrei P. , Minina Elena A. , Fukada Kazutake , Savenkov Eugene I. , Robert Stephanie , Hussey Patrick J. , Bozhkov Peter V.
Published: July 2013

Vesicle trafficking plays an important role in cell division, establishment of cell polarity, and translation of environmental cues to developmental responses. However, the molecular mechanisms regulating vesicle trafficking remain poorly understood. Here, we report that the evolutionarily conserved caspase-related protease separase (EXTRA SPINDLE POLES [ESP]) is required for the establishment of cell polarity and cytokinesis in Arabidopsis  thaliana. At the cellular level, separase colocalizes with microtubules and RabA2a (for RAS GENES FROM RAT BRAINA2a) GTPase-positive structures. Separase facilitates polar targeting of the auxin efflux carrier PIN-FORMED2 (PIN2) to the rootward side of the root cortex cells. Plants with the radially swollen4 (rsw4) allele with compromised separase activity, in addition to mitotic failure, display isotropic cell growth, perturbation of auxin gradient formation, slower gravitropic response in roots, and cytokinetic failure. Measurements of the dynamics of vesicle markers on the cell plate revealed an overall reduction of the delivery rates of KNOLLE and RabA2a GTPase in separase-deficient roots. Furthermore, dissociation of the clathrin light chain, a protein that plays major role in the formation of coated vesicles, was slower in rsw4 than in the control. Our results demonstrate that separase is a key regulator of vesicle trafficking, which is indispensable for cytokinesis and the establishment of cell polarity.
Metabolic ecology
Authors: Humphries Murray M. , McCann Kevin S.
Published: July 2013

Ecological theory that is grounded in metabolic currencies and constraints offers the potential to link ecological outcomes to biophysical processes across multiple scales of organization.

The metabolic theory of ecology (MTE) has emphasized the potential for metabolism to serve as a unified theory of ecology, while focusing primarily on the size and temperature dependence of whole‐organism metabolic rates.

Generalizing metabolic ecology requires extending beyond prediction and application of standardized metabolic rates to theory focused on how energy moves through ecological systems.

A bibliometric and network analysis of recent metabolic ecology literature reveals a research network characterized by major clusters focused onMTE, foraging theory, bioenergetics, trophic status, and generalized patterns and predictions.

This generalized research network, which we refer to as metabolic ecology, can be considered to include the scaling, temperature and stoichiometric models forming the core ofMTE, as well as bioenergetic equations, foraging theory, life‐history allocation models, consumer–resource equations, food web theory and energy‐based macroecology models that are frequently employed in ecological literature.

We conclude with six points we believe to be important to the advancement and integration of metabolic ecology, including nomination of a second fundamental equation, complementary to the first fundamental equation offered by theMTE.
Survey of high‐dose‐rate prostate brachytherapy practice in Australia and New Zealand, 2010–2011
Authors: van Nieuwenhuysen Jane , Waterhouse David , Bydder Sean , Joseph David , Ebert Martin , Caswell Nikki
Published: July 2013

Introduction

A survey was designed to establish a baseline data set for the current routine practice of high‐dose‐rate prostate brachytherapy (HDR‐PB) in Australia and New Zealand. Existing treatment protocols and clinical implementations are not generally known.

Methods

The survey, for the 2010 and 2011 calendar years, collected data including number of patients treated; equipment used; imaging modalities; applicator verification and correction methods; dose prescriptions and normal tissue dose constraints. The number of HDR‐PB patients treated was compared with the most recently published prostate cancer incidence data in Australia and in New Zealand. Total biologically equivalent doses in 2.0 Gy fractions (EQD2) were calculated for each prescription regime reported.

Results

There were reductions, of 25–60%, in patients treated with HDR‐PB from 2010 to 2011 in four departments. Prostate cancer patients are two to six times more likely to be prescribed HDR‐PB in Western Australia than elsewhere in the region. There were 12 different treatment prescriptions, with EQD2 doses ranging from 73.5 to 97.6 Gy, among the 18 reported by survey respondents. Normal tissue definition methodology and dose constraints varied, and 13 of 15 departments reported that no particular published external guidelines were followed in full.

Conclusion

The high survey response rate, 15 of 17 departments, has provided a representative baseline data set of contemporary HDR‐PB practice in Australia and New Zealand that may assist government and professional bodies, such as the Australasian Brachytherapy Group, in formulating recommendations, setting standards and future planning.
Lifespan extension by dietary intervention in a mouse model of Cockayne Syndrome uncouples early postnatal development from segmental progeria
Authors: Brace Lear E. , Vose Sarah C. , Vargas Dorathy F. , Zhao Shuangyun , Wang Xiu‐Ping , Mitchell James R.
Published: July 2013

Cockayne syndrome (CS) is a rare autosomal recessive segmental progeria characterized by growth failure, lipodystrophy, neurological abnormalities, and photosensitivity, but without skin cancer predisposition. Cockayne syndrome life expectancy ranges from 5 to 16 years for the two most severe forms (types II and I, respectively). Mouse models of CS have thus far been of limited value due to either very mild phenotypes, or premature death during postnatal development prior to weaning. The cause of death in severe CS models is unknown, but has been attributed to extremely rapid aging. Here, we found that providing mutant pups with soft food from as late as postnatal day 14 allowed survival past weaning with high penetrance independent of dietary macronutrient balance in a novel CS model (Csa−/− | Xpa−/−). Survival past weaning revealed a number of CS‐like symptoms including small size, progressive loss of adiposity, and neurological symptoms, with a maximum lifespan of 19 weeks. Our results caution against interpretation of death before weaning as premature aging, and at the same time provide a valuable new tool for understanding mechanisms of progressive CS‐related progeroid symptoms including lipodystrophy and neurodysfunction.
Two new species of Fergusonina Malloch gall fly (Diptera: Fergusoninidae) from leaf bud galls on black sallee (Eucalyptus stellulata) and manna gum (Eucalyptus viminalis)
Authors: Purcell Michaela F , Nelson Leigh A , Thornhill Andrew H , Yeates David K
Published: July 2013

Two new species of Fergusonina flies are described from terminal leaf bud galls on Eucalyptus from south‐eastern Australia. Fergusonina herbaservus Nelson sp. nov. and Fergusonina manchesteri Purcell sp. nov. are the first species of fly from the genus Fergusonina to be described from Eucalyptus stellulata (black sallee) and E. viminalis (manna gum), respectively. The two species can be distinguished from all other described Fergusonina by host specificity, adult colour and setation, morphology of the genitalia, and morphology of the dorsal shield. These records represent the first record of Fergusonina galling for black sallee and a new Fergusonina gall type for manna gum.