bluuebunny/crossref_metadata_2025 huggingface dataset:
Baicalin and Scutellarin Are Proteasome Inhibitors that Specifically Target Chymotrypsin‐like Catalytic Activity
Authors: Wu Yi‐Xin , Sato Eiji , Kimura Wataru , Miura Naoyuki
Published: November 2012

Baicalin and scutellarin are the major active principal flavonoids extracted from the Chinese herbal medicines Scutellaria baicalensis and Erigeron breviscapus (Vant.) Hand‐Mazz. It has recently been reported that baicalin and scutellarin have antitumor activity. However, the mechanisms of action are unknown. We previously reported that some flavonoids have a specific role in the inhibition of the activity of proteasome subunits and induced apoptosis in tumor cells. To further investigate these pharmacological effects, we examined the inhibitory activity of baicalin and scutellarin on the extracted proteasomes from mice and cancer cells. Using fluorogenic substrates for proteasome catalytic subunits, we found that baicalin and scutellarin specifically inhibited chymotrypsin‐like activity but did not inhibit trypsin‐like and peptidyl‐glutamyl peptide hydrolyzing activities. These data suggested that baicalin and scutellarin specifically inhibit chymotrypsin‐like catalytic activity in the proteasome. Copyright © 2012 John Wiley & Sons, Ltd.
Architecting methodology for spatially and temporally distributed resource extraction systems
Authors: Aliakbargolkar Alessandro , Crawley Edward F.
Published: November 2012

This paper presents a framework aimed at supporting the decision‐making process for the preliminary design of system architectures for the extraction of spatially and temporally distributed resources. The goal of the research is to provide a tool to identify “global best” architectures for resource extraction “systems of systems,” which usually differ from the sum of “local best” systems. The framework presented in this paper consists of an integrated model where both the architecture of the system of systems and the design of the individual systems are considered simultaneously. Using this approach, designers are able to gain insights by generating a selection of top‐performing concepts. Subsequently, they can analyze those concepts using more sophisticated, albeit more resource‐expensive design processes. The implementation of the proposed framework is a complementary tool to existing design practices. It features several advantages such as enabling the analysis of large‐scale problems, for which exhaustive enumeration of architectures of systems of systems is not a viable option. The paper first presents an application of the methodology to the architecture of offshore oil and gas production fields. It then shows how to use the methodology for the development of scenario analyses. ©2012 Wiley Periodicals, Inc. Syst Eng 16
Q‐Chem: an engine for innovation
Authors: Krylov Anna I. , Gill Peter M.W.
Published: November 2012

Q‐Chem is a general‐purpose electronic structure package featuring a variety of established and new methods implemented using innovative algorithms that enable fast calculations of large systems on regular laboratory workstations using density functional and wave‐function‐based approaches. It features an integrated graphical interface and input generator, a large selection of functionals and correlation approaches including methods for electronically excited states and open‐shell systems. In addition to serving the computational chemistry community, Q‐Chem also provides an excellent development platform. © 2012 John Wiley & Sons, Ltd.

This article is categorized under:

Software > Quantum Chemistry
Safe abstractions of data encodings in formal security protocol models
Authors: Pironti Alfredo , Sisto Riccardo
Published: November 2012

When using formal methods, security protocols are usually modeled at a high level of abstraction. In particular, data encoding and decoding transformations are often abstracted away. However, if no assumptions at all are made on the behavior of such transformations, they could trivially lead to security faults, for example leaking secrets or breaking freshness by collapsing nonces into constants.

In order to address this issue this paper formally states sufficient conditions, checkable on sequential code, such that if an abstract protocol model is secure under a Dolev–Yao adversary, then a refined model, which takes into account a wide class of possible implementations of the encoding/decoding operations, is implied to be secure too under the same adversary model. The paper also indicates possible exploitations of this result in the context of methods based on formal model extraction from implementation code and of methods based on automated code generation from formally verified models.
Density related plasticity in stand‐level spatial distribution of the ambrosia beetle, Platypus koryoensis (Coleoptera: Curculionidae)
Authors: Nam Youngwoo , Choi Won Il , Won Dae‐Sung , Kim Jong‐Kuk
Published: November 2012

We tested the hypothesis that the population density of ambrosia beetles at the stand level influences the spatial distribution of infested trees. We evaluated the spatial distribution of the ambrosia beetle, Platypus koryoensis (Murayama) in three oak forest stands that varied in beetle population density using a multi‐year trapping survey. We used these data to inform a clustering analysis based on aggregation indices using the SADIE software. Four important findings emerged: (1) the spatial distribution pattern of P. koryoensis at the stand level changed as the population density of the beetle varied; (2) at low population densities, beetle distribution was contagious at the stand level; (3) as beetle population densities increased, the spatial distribution of infested trees became random, potentially due to beetle avoidance of mass attacked trees; and (4) at high beetle population densities, the spatial distribution of infested trees became contagious, possibly due to temporal changes in location of the attack epicenter within the stand. Our results support the hypothesis that beetle population density has consequences for the spatial distribution of infested trees at the within‐stand scale. We conclude that the spatial distribution of infested trees is flexible in response to beetle population density, suggesting that beetle attack behaviors are mediated by one or more density‐dependent effects.
Apoptosis-induced anticancer effect of transferrin-conjugated solid lipid nanoparticles of curcumin
Authors: Mulik Rohit S. , Mönkkönen Jukka , Juvonen Risto O. , Mahadik Kakasaheb R. , Paradkar Anant R.
Published: November 2012

Broad spectrum therapeutic potential of curcumin is usually hampered by its photodegradation and low bioavailability. Present investigation was designed with an objective to develop transferrin-mediated solid lipid nanoparticles (Tf-C-SLN) resistant to the photostability and capable of enhancing the bioavailability by targeted drug delivery to elicit anticancer activity against SH-SY5Y neuroblastoma cells in vitro. Hot homogenization method was used for the formulation of Tf-C-SLN and evaluated physicochemically using parameters such as, size, zeta potential, entrapment efficiency and photostability, transmission electron microscopy (TEM), nuclear magnetic resonance (NMR), differential scanning colorimetry (DSC), and in vitro release study. In vitro cytotoxicity and apoptosis investigations were performed using microplate analysis and flow cytometry techniques. The physicochemical characterization confirmed the suitability of formulation method and various parameters therein. TEM investigation revealed the spherical morphology while NMR and DSC study confirmed the entrapment of curcumin inside the nanoparticles. The cytotoxicity, reactive oxygen species, and cell uptake were found to be increased considerably with Tf-C-SLN compared with curcumin-solubilized surfactant solution, and curcumin-loaded SLN (C-SLN) suggesting the targeting effect. AnnexinV-FITC/PI double staining, DNA analysis, caspase detection, and reduced mitochondrial potential confirmed the induction of apoptosis with nanoparticle treatment. Enhanced anticancer activity with Tf-C-SLN compared with curcumin-solubilized surfactant solution and C-SLN was observed from flow cytometry investigations with apoptosis being the major underlying mechanism. The in vitro observations of our investigation are very compelling and concrete to advocate the potential of Tf-C-SLN in enhancing the anticancer effect of curcumin against neuroblastoma in vivo and possible clinical applications.
Criteria of validity in experimental psychopathology: application to models of anxiety and depression
Authors: Vervliet B. , Raes F.
Published: November 2012

The modeling of abnormal behavior in ‘normal’ subjects (often animals) has a long history in pharmacological research for the screening of novel drug compounds. Systematic criteria have been outlined in that literature to estimate the external validity of a model, that is to estimate how closely the model is linked to the disorder of interest. Experimental psychopathology (EPP) also uses behavioral models to study the psychological processes that underlie abnormal behavior. Although EPP researchers may occasionally feel uneasy about the validity of the model that they use, the issue has not received direct attention in this literature. Here, we review the criteria of validity as set out in pharmacology research (face, predictive and construct validity) and discuss their relevance for EPP research. Furthermore, we propose diagnostic validity as an additional criterion of external validity that is relevant to EPP research. We evaluate two models for the study of anxiety and depression, and show that they have good face, diagnostic and construct validity. However, EPP research generally lacks direct tests of predictive validity. We conclude that combined evaluations of predictive, diagnostic and construct validity provide a sound basis to infer the external validity of behavioral models in EPP research.
Reasons for Joy and Reflection: Engaging with Shakespeare at the Craiova Festival
Authors: Shevtsova Maria
Published: November 2012

The Craiova International Shakespeare Festival has been a major touchstone in Europe for theatre artists, theatregoers, and scholars for nearly two decades. This overview briefly situates the Festival historically, indicating the ideals and perspectives developed for it by its founder Emil Boroghina, former director of the National Theatre of Craiova. It identifies as well a number of the Festival's many highlights over the years, Romanian as well as international, and focuses on examples from the 2012 programme, including Silviu Purcarte's The Tempest and Robert Wilson's Shakespeare's Sonnets performed by the Berliner Ensemble. Attention is drawn to the presence at the successive editions of the Festival of productions directed by Purcarete, who established his career at the National Theatre of Craiova, to which Boroghina had invited him, and who won international fame after performances of his Ubu Rex with Scenes from Macbeth at the 1991 Edinburgh Festival. Maria Shevtsova holds the Chair in Drama and Theatre Arts at Goldsmiths, University of London, and is co-editor of New Theatre Quarterly.
The Case against World Theatre History
Authors: Tillis Steve
Published: November 2012

A strong case can be made against world theatre history as a subject of scholarly study. This paper analyzes seven arguments that can be levelled against world theatre history as an academic subject. It then offers rebuttals to each of these arguments. In so doing, it seeks not only to establish the legitimacy of world theatre history as a subject of study, but also to clarify the methodologies and the goals of such study. Steve Tillis received his PhD from the University of California, Berkeley, and currently teaches at St Mary's College of California. He has previously published articles on world theatre history in Asian Theatre Journal, TDR, Theatre Topics, and Theatre Survey.
ON THE RECOVERABILITY OF FORECASTERS’ PREFERENCES
Authors: Lieli Robert P. , Stinchcombe Maxwell B.
Published: November 2012

We study the problem of identifying a forecaster’s loss function from observations on forecasts, realizations, and the forecaster’s information set. Essentially different loss functions can lead to the same forecasts in all situations, though within the class of all continuous loss functions, this is strongly nongeneric. With the small set of exceptional cases ruled out, generic nonparametric preference recovery is theoretically possible, but identification depends critically on the amount of variation in the conditional distributions of the process being forecast. There exist processes with sufficient variability to guarantee identification, and much of this variation is also necessary for a process to have universal identifying power. We also briefly address the case in which the econometrician does not fully observe the conditional distributions used by the forecaster, and in this context we provide a practically useful set identification result for loss functions used in forecasting binary variables.
ON THE ORDER OF MAGNITUDE OF SUMS OF NEGATIVE POWERS OF INTEGRATED PROCESSES
Authors: Pötscher Benedikt M.
Published: November 2012

Upper and lower bounds on the order of magnitude of $\sum\nolimits_{t = 1}^n {\lefttnq#x007C; {x_t } \righttnq#x007C;^{ - \alpha } } $, where xt is an integrated process, are obtained. Furthermore, upper bounds for the order of magnitude of the related quantity $\sum\nolimits_{t = 1}^n {v_t } \lefttnq#x007C; {x_t } \righttnq#x007C;^{ - \alpha } $, where vt are random variables satisfying certain conditions, are also derived.
An overview of current ontology meta-matching solutions
Authors: Martinez-Gil Jorge , Aldana-Montes José F.
Published: November 2012

Nowadays, there are a lot of techniques and tools for addressing the ontology matching problem; however, the complex nature of this problem means that the existing solutions are unsatisfactory. This work intends to shed some light on a more flexible way of matching ontologies using ontology meta-matching. This emerging technique selects appropriate algorithms and their associated weights and thresholds in scenarios where accurate ontology matching is necessary. We think that an overview of the problem and an analysis of the existing state-of-the-art solutions will help researchers and practitioners to identify the most appropriate specific features and global strategies in order to build more accurate and dynamic systems following this paradigm.
An overview of the phrase-based statistical machine translation techniques
Authors: Costa-jussà Marta Ruiz
Published: November 2012

This work provides a general overview of the statistical machine translation (SMT) scientific field, which is a subfield of machine translation (MT). Specifically, this paper focuses on one of the most popular SMT approaches, that is, the phrase-based system.

The phrase-based translation units are typically extracted using statistical criteria, and they are weighted using different models. These models are log-linearly combined in the decoding, which is in charge of choosing the most probable translation. Significant quality improvements have been produced from original phrase-based SMT systems. Among others, the main challenges are reordering, domain adaptation and evaluation.
Single Atom Microscopy
Authors: Zhou Wu , Oxley Mark P. , Lupini Andrew R. , Krivanek Ondrej L. , Pennycook Stephen J. , Idrobo Juan-Carlos
Published: November 2012

We show that aberration-corrected scanning transmission electron microscopy operating at low accelerating voltages is able to analyze, simultaneously and with single atom resolution and sensitivity, the local atomic configuration, chemical identities, and optical response at point defect sites in monolayer graphene. Sequential fast-scan annular dark-field (ADF) imaging provides direct visualization of point defect diffusion within the graphene lattice, with all atoms clearly resolved and identified via quantitative image analysis. Summing multiple ADF frames of stationary defects produce images with minimized statistical noise and reduced distortions of atomic positions. Electron energy-loss spectrum imaging of single atoms allows the delocalization of inelastic scattering to be quantified, and full quantum mechanical calculations are able to describe the delocalization effect with good accuracy. These capabilities open new opportunities to probe the defect structure, defect dynamics, and local optical properties in 2D materials with single atom sensitivity.
A Method for Directly Correlating Site-Specific Cross-Sectional and Plan-View Transmission Electron Microscopy of Individual Nanostructures
Authors: Schreiber Daniel K. , Adusumilli Praneet , Hemesath Eric R. , Seidman David N. , Petford-Long Amanda K. , Lauhon Lincoln J.
Published: November 2012

A sample preparation method is described for enabling direct correlation of site-specific plan-view and cross-sectional transmission electron microscopy (TEM) analysis of individual nanostructures by employing a dual-beam focused-ion beam (FIB) microscope. This technique is demonstrated using Si nanowires dispersed on a TEM sample support (lacey carbon or Si-nitride). Individual nanowires are first imaged in the plan-view orientation to identify a region of interest; in this case, impurity atoms distributed at crystalline defects that require further investigation in the cross-sectional orientation. Subsequently, the region of interest is capped with a series of ex situ and in situ deposited layers to protect the nanowire and facilitate site-specific lift-out and cross-sectioning using a dual-beam FIB microscope. The lift-out specimen is thinned to electron transparency with site-specific positioning to within ∼200 nm of a target position along the length of the nanowire. Using the described technique, it is possible to produce correlated plan-view and cross-sectional view lattice-resolved TEM images that enable a quasi-3D analysis of crystalline defect structures in a specific nanowire. While the current study is focused on nanowires, the procedure described herein is general for any electron-transparent sample and is broadly applicable for many nanostructures, such as nanowires, nanoparticles, patterned thin films, and devices.
Basalts erupted along the Tongan fore arc during subduction initiation: Evidence from geochronology of dredged rocks from the Tonga fore arc and trench
Authors: Meffre Sebastian , Falloon Trevor J. , Crawford Tony J. , Hoernle Kaj , Hauff Folkmar , Duncan Robert A. , Bloomer Sherman H. , Wright Dawn J.
Published: November 2012

A wide variety of different rock types were dredged from the Tonga fore arc and trench between 8000 and 3000 m water depths by the 1996 Boomerang voyage. 40Ar‐39Ar whole rock and U‐Pb zircon dating suggest that these fore arc rocks were erupted episodically from the Cretaceous to the Pliocene (102 to 2 Ma). The geochemistry suggests that MOR‐type basalts and dolerites were erupted in the Cretaceous, that island arc tholeiites were erupted in the Eocene and that back arc basin and island arc tholeiite and boninite were erupted episodically after this time. The ages generally become younger northward suggesting that fore arc crust was created in the south at around 48–52 Ma and was extended northward between 35 and 28 Ma, between 9 and 15 Ma and continuing to the present‐day. The episodic formation of the fore arc crust suggested by this data is very different to existing models for fore arc formation based on the Bonin‐Marianas arc. The Bonin‐Marianas based models postulate that the basaltic fore arc rocks were created between 52 and 49 Ma at the beginning of subduction above a rapidly foundering west‐dipping slab. Instead a model where the 52 Ma basalts that are presently in a fore arc position were created in the arc‐back arc transition behind the 57–35 Ma Loyalty‐Three Kings arc and placed into a fore arc setting after arc reversal following the start of collision with New Caledonia is proposed for the oldest rocks in Tonga. This is followed by growth of the fore arc northward with continued eruption of back arc and boninitic magmas after that time.
Do Climate Forecast System (CFSv2) forecasts improve seasonal soil moisture prediction?
Authors: Mo Kingtse C. , Shukla Shraddhanand , Lettenmaier Dennis P. , Chen Li‐Chuan
Published: November 2012

We investigated whether seasonal soil moisture forecasts derived from a land surface model forced by seasonal climate forecast model outputs are more skillful than benchmark forecasts derived from the same land surface model but with forcings taken from resampled climatological precipitation, temperature and low level winds. For most forecast leads and over the western United States, soil moisture forecasts based on seasonal climate forecasts are no more skillful than the benchmark. For relatively short (one month) leads, the climate model‐based forecasts are more skillful than the benchmark along a swath from the Gulf States to the Tennessee and Ohio Valleys and the Southwest monsoon region, where the climate model has skillful precipitation forecasts.
A scaling law for impact force of a granular avalanche flowing past a wall
Authors: Faug T. , Caccamo P. , Chanut B.
Published: November 2012

A scaling law is proposed to describe the force experienced by a wall‐like obstacle overflowed by a granular avalanche‐flow when a stagnant zone is formed upstream from the wall and co‐exists with an inertial zone above without granular jump. It relates the force on the wall relative to the force due to the kinetic energy of the undisturbed incident flow to (i) the Froude number, (ii) the wall height relative to the flow thickness, (iii) the slope angle and (iv) the various parameters associated with the properties of the flowing granular material. The scaling law is compared to small‐scale discrete numerical simulations in two dimensions and data from granular laboratory tests. Finally, we discuss on the applicability of the new model to the full‐scale granular flows.
Variability in the Deep Western Boundary Current: Local versus remote forcing
Authors: Peña‐Molino B. , Joyce T. M. , Toole J. M.
Published: November 2012

Horizontal velocity, temperature and salinity measurements from the Line W array for the period 2004–2008 show large changes in the water mass structure and circulation of the Deep Western Boundary Current (DWBC). Fluctuations in the flow with periods from 10 to 60 days are bottom intensified: signals most likely associated with topographic Rossby waves (TRW). A fraction (∼15%) of the DWBC transport variability is caused by Gulf Stream rings and meanders. These flow anomalies are surface intensified and fluctuate at frequencies lower than the TRW. Interannual variability in the velocity field appears to be related to changes in the hydrographic properties. The dominant mode of variability is characterized by an overall freshening, cooling, a potential vorticity (PV) increase in the deep Labrador Sea Water (dLSW) and a PV decrease in the Overflow Water (OW). The variability in the flow associated with these property changes is not spatially homogeneous. Offshore (water depths larger than 3500 m) changes in the velocity are in phase with PV changes in the OW: a decrease in the OW PV is accompanied by an increase in the southward (negative) transport. Conversely, variations of the inshore flow are in phase with changes in the dLSW PV (increasing PV and decreasing transport). This trend, true for most of the record, reverses after the winter of 2007–2008. A sudden decrease of the dLSW PV is observed, with a corresponding intensification of the flow in the inner DWBC as well as a northward shift in the Gulf Stream axis.
Effect of Training Frequency on Maximum Expiratory Pressure
Authors: Anand Supraja , El-Bashiti Nour , Sapienza Christine
Published: November 2012

Purpose

To determine the effects of expiratory muscle strength training (EMST) frequency on maximum expiratory pressure (MEP).

Method

We assigned 12 healthy participants to 2 groups of training frequency (3 days per week and 5 days per week). They completed a 4-week training program on an EMST trainer (Aspire Products, LLC). MEP was the primary outcome measure used to determine the effect of training frequency.

Results

Participants who trained 3 days per week produced equivalent amounts of improvement in MEP compared with participants who trained 5 days per week. An overall improvement in MEP over the 4-week training period indicated a 33% increase when the data was collapsed across the 2 training groups.

Conclusion

The effects occurring with respiratory muscle strength training in healthy young adults are likely to be different from those occurring in patient populations. Therefore, the results of the present study suggest exploring the variable of training frequency in patient populations. Such knowledge will be informative for designing clinical protocols that are effective and may result in improved treatment compliance for those suffering from expiratory muscle weakness.
Consonant Production Accuracy in Young Cochlear Implant Recipients: Developmental Sound Classes and Word Position Effects
Authors: Ertmer David J. , Kloiber Diana True , Jung Jongmin , Kirleis Katie Connell , Bradford Denise
Published: November 2012

Purpose

To compare young cochlear implant (CI) recipients' consonant production accuracy with that of age- and gender-matched peers who were typically developing (TD). In addition to examining initial consonants, the authors compiled new data regarding the accuracy of final consonants and the order of consonant acquisition.

Methods

Eleven young CI recipients with 24 months of CI experience and 11 age- and gender-matched TD peers produced target words in short sentences. Consonant production accuracy was examined for total scores, initial and final word positions, and three developmental sound classes: Early, Middle, and Late.

Results

Initial consonants were produced with relatively greater accuracy than were final consonants by the TD and CI groups. Whereas initial consonants appeared to be acquired in a typical order, descriptive data suggest that this might not be the case for final consonants.

Conclusions

Although still delayed compared to age-matched peers, young CI recipients showed substantial progress in consonant acquisition. Their accuracy levels after 2 years of CI experience support the notion that implantation at a young age has added value for phonological development.
Historical and Cultural Influences on Establishing Professional Legitimacy: A Case Example From Lionel Logue
Authors: Duchan Judith Felson
Published: November 2012

Purpose

In the film
The King’s Speech,
the credibility of the king’s speech clinician, Lionel Logue, is challenged. This article examines Logue’s credentials in light of the credentialing standards and attitudes of Logue’s time as well as those affecting today’s practices. The aim is to show how standards of legitimacy change with the times.

Method

Documents related to clinical qualifications and clinical practices are analyzed for the period in the early 20th century, when Logue practiced. They are then compared with how clinicians of today attain professional legitimacy.

Conclusion

Early 20th century clinicians drew their credibility from their home disciplines such as medicine, phonetics, elocution, and education. Some of their therapies originated in the home discipline. Other therapies were commonly used, regardless of one’s disciplinary background. Lionel Logue’s background and methods would not have been suspect in his time. He may have been faulted by some for his lack of scientific perspective, but another likely source for the challenges to his credibility were early 20th century British social biases against Australians and against those using Australian dialects. The comparative analysis revealed that early 20th century clinicians and clinicians of today have certain clinical practices in common, but they differ considerably in how they establish their legitimacy. This indicates that judgments about a clinician’s legitimacy are both historically and culturally determined.
Comment on Revalidating Swallowing Assessments
Authors: Carnaby Giselle
Published: November 2012

Purpose

A letter to the editor is presented regarding the recently published article by González-Fernández, Sein, and Palmer (2011). In this letter, Dr.Giselle Carnaby stipulates that although González-Fernández and colleagues' article reports on the revalidation of a common swallowing assessment tool, it does not, however, fully address issues surrounding (a) the use of retrospective data for revalidation, (b) the impact of missing data on analyses, and (c) the failure to replicate an assessment’s scoring system.

Conclusion

These issues are pertinent for the readership of the
American Journal of Speech-Language Pathology
(AJSLP) and for the interpretation and development of future assessment tools in this area.
Environmental issues associated with coal seam gas recovery: managing the fracking boom
Authors: Batley Graeme E. , Kookana Rai S.
Published: November 2012

Environmental context
Coal seam gas reserves are likely to make a major contribution to future energy needs. However, the new technology for exploiting these reserves, termed hydraulic fracturing, raises several environmental issues. We discuss the research required to assess the ecological risks from gas recovery.

Abstract
Coal seam gas reserves represent a major contribution to energy needs, however, gas recovery by hydraulic fracturing (fracking or fraccing), requires management to minimise any environmental effects. Although the industry is adapting where possible to more benign fracking chemicals, there is still a lack of information on exposure to natural and added chemicals, and their fate and ecotoxicity in both the discharged produced and flow-back waters. Geogenic contaminants mobilised from the coal seams during fracking may add to the mixture of chemicals with the potential to affect both ground and surface water quality. The research needs to better assess the ecological risks from gas recovery are discussed.
The effect of aerobic soil conditions, soil volume and sowing date on the development of four tropical rice varieties grown in the greenhouse
Authors: Clerget Benoit , Bueno Crisanta
Published: November 2012

Rice has generally been reported to yield less in aerobic soil conditions than in flooded soil conditions, in association with delayed anthesis and a reduction in height. A greenhouse experiment was conducted and repeated twice with four rice varieties grown in either flooded or nearly-saturated aerobic soil, in either large or small pots. The rate of leaf appearance was recorded weekly until heading time, when plants were harvested for shoot and root biomass. The kinetics of leaf appearance was generally trilinear with longer phyllochrons in the May sowing. Pot size had only a small effect whereas aerobic soil conditions slowed down the rate of leaf initiation, which consequently delayed panicle initiation and heading date and thus increased the duration of the tillering phase and finally the number of tillers. Surprisingly, the four varieties showed a significant response to sowing date, especially IR72, which headed 21 days later and after the expansion of two more leaves in the May sowing. The aerobic soil conditions and sowing date have thus changed the rate of development of rice plants and this trait has appeared to be the initial link of a chain of consequences in a series of traits known to be affected by these factors.
Gaudenz Danuser: The symphony of the cell
Authors: Sedwick Caitlin
Published: November 2012

Danuser studies cytoskeletal dynamics, membrane trafficking, and cell migration.
A flagellar A-kinase anchoring protein with two amphipathic helices forms a structural scaffold in the radial spoke complex
Authors: Sivadas Priyanka , Dienes Jennifer M. , St. Maurice Martin , Meek William D. , Yang Pinfen
Published: November 2012

A-kinase anchoring proteins (AKAPs) contain an amphipathic helix (AH) that binds the dimerization and docking (D/D) domain, RIIa, in cAMP-dependent protein kinase A (PKA). Many AKAPs were discovered solely based on the AH–RIIa interaction in vitro. An RIIa or a similar Dpy-30 domain is also present in numerous diverged molecules that are implicated in critical processes as diverse as flagellar beating, membrane trafficking, histone methylation, and stem cell differentiation, yet these molecules remain poorly characterized. Here we demonstrate that an AKAP, RSP3, forms a dimeric structural scaffold in the flagellar radial spoke complex, anchoring through two distinct AHs, the RIIa and Dpy-30 domains, in four non-PKA spoke proteins involved in the assembly and modulation of the complex. Interestingly, one AH can bind both RIIa and Dpy-30 domains in vitro. Thus, AHs and D/D domains constitute a versatile yet potentially promiscuous system for localizing various effector mechanisms. These results greatly expand the current concept about anchoring mechanisms and AKAPs.
Development of proteasome inhibitors as research tools and cancer drugs
Authors: Goldberg Alfred L.
Published: November 2012

The proteasome is the primary site for protein degradation in mammalian cells, and proteasome inhibitors have been invaluable tools in clarifying its cellular functions. The anticancer agent bortezomib inhibits the major peptidase sites in the proteasome’s 20S core particle. It is a “blockbuster drug” that has led to dramatic improvements in the treatment of multiple myeloma, a cancer of plasma cells. The development of proteasome inhibitors illustrates the unpredictability, frustrations, and potential rewards of drug development but also emphasizes the dependence of medical advances on basic biological research.
Characterization of PSII–LHCII supercomplexes isolated from pea thylakoid membrane by one-step treatment with α- and β-dodecyl-
d
-maltoside
Authors: Barera Simone , Pagliano Cristina , Pape Tillmann , Saracco Guido , Barber James
Published: November 2012

It was the work of Jan Anderson, together with Keith Boardman, that showed it was possible to physically separate photosystem I (PSI) from photosystem II (PSII), and it was Jan Anderson who realized the importance of this work in terms of the fluid-mosaic model as applied to the thylakoid membrane. Since then, there has been a steady progress in the development of biochemical procedures to isolate PSII and PSI both for physical and structural studies. Dodecylmaltoside (DM) has emerged as an effective mild detergent for this purpose. DM is a glucoside-based surfactant with a bulky hydrophilic head group composed of two sugar rings and a non-charged alkyl glycoside chain. Two isomers of this molecule exist, differing only in the configuration of the alkyl chain around the anomeric centre of the carbohydrate head group, axial in α-DM and equatorial in β-DM. We have compared the use of α-DM and β-DM for the isolation of supramolecular complexes of PSII by a single-step solubilization of stacked thylakoid membranes isolated from peas. As a result, we have optimized conditions to obtain homogeneous preparations of the C
2
S
2
M
2
and C
2
S
2
supercomplexes following the nomenclature of Dekker & Boekema (2005
Biochim. Biophys. Acta
1706
, 12–39). These PSII–LHCII supercomplexes were subjected to biochemical and structural analyses.
Lipid functions in cytochrome
bc
complexes: an odd evolutionary transition in a membrane protein structure
Authors: Hasan S. Saif , Cramer William A.
Published: November 2012

Lipid-binding sites and properties were compared in the hetero-oligomeric cytochrome (cyt)
b
6
f
and the yeast
bc
1
complexes that function, respectively, in photosynthetic and respiratory electron transport. Seven lipid-binding sites in the monomeric unit of the dimeric cyanobacterial
b
6
f
complex overlap four sites in the
Chlamydomonas reinhardtii
algal
b
6
f
complex and four in the yeast
bc
1
complex. The proposed lipid functions include: (i) interfacial–interhelix mediation between (a) the two 8-subunit monomers of the dimeric complex, (b) between the core domain (cyt
b
, subunit IV) and the six trans membrane helices of the peripheral domain (cyt
f
, iron–sulphur protein (ISP), and four small subunits in the boundary ‘picket fence’); (ii) stabilization of the ISP domain-swapped trans-membrane helix; (iii) neutralization of basic residues in the single helix of cyt
f
and of the ISP; (iv) a ‘latch’ to photosystem I provided by the β-carotene chain protruding through the ‘picket fence’; (v) presence of a lipid and chlorophyll
a
chlorin ring in
b
6
f
in place of the eighth helix in the
bc
1
cyt
b
polypeptide. The question is posed of the function of the lipid substitution in relation to the evolutionary change between the eight and seven helix structures of the cyt
b
polypeptide. On the basis of the known n-side activation of light harvesting complex II (LHCII) kinase by the p-side level of plastoquinol, one possibility is that the change was directed by the selective advantage of p- to n-side trans membrane signalling functions in
b
6
f
, with the lipid either mediating this function or substituting for the trans membrane helix of a signalling protein lost in crystallization.
Lateral heterogeneity of plant thylakoid protein complexes: early reminiscences
Authors: Anderson Jan M.
Published: November 2012

The concept that the two photosystems of photosynthesis cooperate in series, immortalized in Hill and Bendall's Z scheme, was still a black box that defined neither the structural nor the molecular organization of the thylakoid membrane network into grana and stroma thylakoids. The differentiation of the continuous thylakoid membrane into stacked grana thylakoids interconnected by single stroma thylakoids is a morphological reflection of the non-random distribution of photosystem II/light-harvesting complex of photosystem II, photosystem I and ATP synthase, which became known as lateral heterogeneity.
Protein kinases and phosphatases involved in the acclimation of the photosynthetic apparatus to a changing light environment
Authors: Rochaix Jean-David , Lemeille Sylvain , Shapiguzov Alexey , Samol Iga , Fucile Geoffrey , Willig Adrian , Goldschmidt-Clermont Michel
Published: November 2012

Photosynthetic organisms are subjected to frequent changes in light quality and quantity and need to respond accordingly. These acclimatory processes are mediated to a large extent through thylakoid protein phosphorylation. Recently, two major thylakoid protein kinases have been identified and characterized. The Stt7/STN7 kinase is mainly involved in the phosphorylation of the LHCII antenna proteins and is required for state transitions. It is firmly associated with the cytochrome
b
6
f
complex, and its activity is regulated by the redox state of the plastoquinone pool. The other kinase, Stl1/STN8, is responsible for the phosphorylation of the PSII core proteins. Using a reverse genetics approach, we have recently identified the chloroplast PPH1/TAP38 and PBPC protein phosphatases, which counteract the activity of STN7 and STN8 kinases, respectively. They belong to the PP2C-type phosphatase family and are conserved in land plants and algae. The picture that emerges from these studies is that of a complex regulatory network of chloroplast protein kinases and phosphatases that is involved in light acclimation, in maintenance of the plastoquinone redox poise under fluctuating light and in the adjustment to metabolic needs.
From ecophysiology to phenomics: some implications of photoprotection and shade–sun acclimation
in situ
for dynamics of thylakoids
in vitro
Authors: Matsubara Shizue , Förster Britta , Waterman Melinda , Robinson Sharon A. , Pogson Barry J. , Gunning Brian , Osmond Barry
Published: November 2012

Half a century of research into the physiology and biochemistry of sun–shade acclimation in diverse plants has provided reality checks for contemporary understanding of thylakoid membrane dynamics. This paper reviews recent insights into photosynthetic efficiency and photoprotection from studies of two xanthophyll cycles in old shade leaves from the inner canopy of the tropical trees
Inga sapindoides
and
Persea americana
(avocado). It then presents new physiological data from avocado on the time frames of the slow coordinated photosynthetic development of sink leaves in sunlight and on the slow renovation of photosynthetic properties in old leaves during sun to shade and shade to sun acclimation. In so doing, it grapples with issues
in vivo
that seem relevant to our increasingly sophisticated understanding of
Δ
pH-dependent, xanthophyll-pigment-stabilized non-photochemical quenching in the antenna of PSII in thylakoid membranes
in vitro
.
A low-temperature polymorph ofm-quinquephenyl
Authors: Gomes Ligia R. , Howie R. Alan , Low John Nicolson , Rodrigues Ana S. M. C. , Santos Luís M. N. B. F.
Published: November 2012

A low-temperature polymorph of 1,1′:3′,1′′:3′′,1′′′:3′′′,1′′′′-quinquephenyl (m-quinquephenyl), C30H22, crystallizes in the space groupP21/cwith two molecules in the asymmetric unit. The crystal is a three-component nonmerohedral twin. A previously reported room-temperature polymorph [Rabideau, Sygula, Dhar & Fronczek (1993).Chem. Commun.pp. 1795–1797] also crystallizes with two molecules in the asymmetric unit in the space groupP\overline{1}. The unit-cell volume for the low-temperature polymorph is 4120.5 (4) Å3, almost twice that of the room-temperature polymorph which is 2102.3 (6) Å3. The molecules in both structures adopt a U-shaped conformation with similar geometric parameters. The structural packing is similar in both compounds, with the molecules lying in layers which stack perpendicular to the longest unit-cell axis. The molecules pack alternately in the layers and in the stacked columns. In both polymorphs, the only interactions between the molecules which can stabilize the packing are very weak C—H...π interactions.
Does microbial stoichiometry modulate eutrophication of aquatic ecosystems?
Authors: Steenbergh A. K. , Bodelier P. L. E. , Heldal M. , Slomp C. P. , Laanbroek H. J.
Published: November 2012

The stoichiometry of prokaryotes (Bacteria and Archaea) can control benthic phosphorus (P) fluxes relative to carbon (C) and nitrogen (N) during organic matter remineralization. This paper presents the first experimental data on benthic microbial stoichiometry. We used X‐ray microanalysis to determine C : N : P ratios of individual prokaryotes from C‐limited Baltic Sea sediments incubated under oxic or anoxic conditions. At approximately 400:1, C : P ratios of prokaryotes from both oxic and anoxic incubations were higher than the Redfield ratio for marine organic matter (106:1), whereas prokaryotic C : N ratios (6.4:1) were close to the Redfield ratio. We conclude that high microbial C : P ratios contribute to the enhanced remineralization of P from organic matter relative to C and N observed in many low oxygen marine settings.
Risk of developmental dysplasia of the hip in breech presentation: the effect of successful external cephalic version
Authors: Lambeek AF , De Hundt M , Vlemmix F , Akerboom BMC , Bais JMJ , Papatsonis DNM , Mol BWJ , Kok M
Published: November 2012

Please cite this paper as: Lambeek A, De Hundt M, Vlemmix F, Akerboom B, Bais J, Papatsonis D, Mol B, Kok M. Risk of developmental dysplasia of the hip in breech presentation: the effect of successful external cephalic version. BJOG 2012; DOI: 10.1111/1471‐0528.12013.

Objective  To evaluate the effect of successful external cephalic version on the incidence of developmental dysplasia of the hip (DDH) requiring treatment in singleton breech presentation at term.

Design  Observational cohort study.

Setting  Three large teaching hospitals in the Netherlands.

Population  Women with a singleton breech presentation of 34 weeks of gestation or more, who underwent an external cephalic version attempt.

Methods  We made a comparison of the incidence of DDH between children born in breech presentation and children born in cephalic presentation after a successful external cephalic version.

Main outcome measure  The incidence of DDH requiring either conservative treatment, with a harness, or surgical treatment.

Results  A total of 498 newborns were included in the study, of which 40 (8%) were diagnosed with DDH and 35 required treatment. Multivariate analysis showed that female gender (OR 2.79, 95% CI 1.23–6.35) and successful external cephalic version (OR 0.29, 95% CI 0.09–0.95) were independently associated with DDH.

Conclusions  A successful external cephalic version is associated with a lower incidence of DDH, although a high percentage of children born after a successful external cephalic version still appear to have DDH. A larger cohort study is needed to establish the definite nature of this relationship. Until then, we recommend the same screening policy for infants born in cephalic position after a successful external cephalic version as for infants born in breech position.
S100A12: A noninvasive marker of inflammation in inflammatory bowel disease
Authors: van de Logt Floor , Day Andrew S
Published: November 2012

Inflammatory bowel diseases are incurable conditions that feature gut inflammation. Standard markers have inadequate sensitivity and specificity. S100A12 is a new fecal marker that has promise as a non‐invasive indicator of gut inflammation. This article reviews recent studies focusing on S100A12 and highlights the current and potential roles of this biomarker.
A quest for indigenous truffle helper prokaryotes
Authors: Gryndler Milan , Soukupová Lucie , Hršelová Hana , Gryndlerová Hana , Borovička Jan , Streiblová Eva , Jansa Jan
Published: November 2012

Tuber aestivum is the most common European truffle with significant commercial exploitation. Its production originates from natural habitats and from artificially inoculated host tree plantations. Formation of Tuber ectomycorrhizae in host seedling roots is often inefficient. One possible reason is the lack of indigenous associative microbes. Here we aimed at metagenetic characterization and cultivation of indigenous prokaryotes associated with T. aestivum in a field transect cutting through the fungus colony margin. Several operational taxonomic units (OTUs) showed close association with the T. aestivum in the ectomycorrhizae and in the soil, but there was no overlap between the associative prokaryotes in the two different habitats. Among those positively associated with the ectomycorrhizae, we identified several bacterial genera belonging to Pseudonocardineae. Extensive isolation efforts yielded many cultures of ectomycorrhizae‐associative bacteria belonging to Rhizobiales and Streptomycineae, but none belonging to the Pseudonocardineae. The specific unculturable Tuber‐associated prokaryotes are likely to play important roles in the biology of these ectomycorrhizal fungi, including modulation of competition with other symbiotic and saprotrophic microbes, facilitation of root penetration and/or accessing mineral nutrients in the soil. However, the ultimate proof of this hypothesis will require isolation of the microbes for metabolic studies, using novel cultivation approaches.