bluuebunny/crossref_metadata_2025 huggingface dataset:
Fluctuation induced conductivity in (Cu0.5Tl0.5−xKx)Ba2Ca3Cu4O12−δ superconductor
Authors: Mumtaz M. , Hasnain S. M. , Khurram A. A. , Khan Nawazish A.
Published: January 2011

The fluctuation induced conductivity (FIC) of (Cu0.5Tl0.5−xKx)Ba2Ca3Cu4O12−y (x=0,0.25) superconductor has been studied after potassium substitution at thallium site in the charge reservoir layer (Cu0.5Tl0.5Ba2O4−y). The samples were also post-annealed in oxygen to change the carrier density in CuO2 planes. The zero resistivity critical temperature Tc(0) was found to increase after K+1 substitution at Tl+3 sites in the Cu0.5Tl0.5Ba2O4−y charge reservoir layer. However, Tc(0) has been suppressed after post-annealing the samples in oxygen. The FIC analysis was performed in the frame work of Aslamasov–Larkin theory. The results of FIC analysis have shown three-dimensional (3D), two dimensional (2D) and short wavelength fluctuations (SWFs) in the order parameter. It has been also observed that there is an increase in the 3D-2D and 2D-SWF cross-over temperatures after potassium substitution along with an increase in Tc(0). However, after post-annealing in oxygen, the dimensional cross-over has been shifted to lower temperatures. A direct correlation between the cross-over temperatures, the Tc(0) as well as carrier doping level has been observed.
Aging- and annealing-induced variations in Nb/Al–AlOx/Nb tunnel junction properties
Authors: Pavolotsky Alexey B. , Dochev Dimitar , Belitsky Victor
Published: January 2011

In this paper, we present studies of room temperature aging and annealing of Nb/Al–AlOx/Nb tunnel junctions with the size of 2–3 μm2. We observed a noticeable drop of junction normal resistance Rn unusually combined with increase in subgap resistance Rj as a result of aging. Variation in both Rn and Rj are subject to the junction size effect. An effect of aging history on the junction degradation after consequent annealing was discovered. Discussion and interpretation of the observed phenomena are presented in terms of structural ordering and reconstruction in the AlOx layer, driven by diffusion flows enhanced due to stress relaxation processes in the Al layer interfacing the AlOx layer.
Strain relief at the GaSb/GaAs interface versus substrate surface treatment and AlSb interlayers thickness
Authors: Wang Y. , Ruterana P. , Desplanque L. , El Kazzi S. , Wallart X.
Published: January 2011

Using transmission electron microscopy we investigate the influence of AlSb monolayers and substrate surface preparation on the microstructure of GaSb grown on GaAs (001) by molecular beam epitaxy. The geometric phase analysis method is used to analyze the interface dislocation type and the residual strain, as well as the dislocation core behavior versus the thickness of the AlSb interface layer. A quantitative measurement of the local Burgers vectors shows that the misfit dislocations at the GaSb/GaAs interface are always 60° dislocations. They are arranged in pairs which are more or less distant. For the samples with the lower threading dislocation density, the average distance between the 60° pairs is smaller, the interface is flatter and the local strain is more relieved. These results show that understanding the atomic structure of interfaces may be of great help in improving the quality of GaSb grown on GaAs substrates.
Optical and structural characterization of GaN thin films at different N to Ga flux ratios
Authors: El-Naggar Ahmed M.
Published: January 2011

GaN films were grown on Si(111) substrates under various beam equivalent pressure (BEP) ratios by plasma-assisted molecular beam epitaxy. The optical properties for the grown samples were studied over a wide spectral range from 200 to 3300 nm using the reflectance spectrum only. It was found that increasing the N/Ga BEP ratio from 17.9 to 46.1 increases the refractive index (n) from 2.05 to 2.38 at wavelength 630 nm (for example), while the optical energy gap (Eg) were found to be in the range between 3.325 to 3.35 eV with no specific trend. The structural properties for the grown films were studied through two types of rocking curve measurements; normal rocking curve (ω-scan) and triple axis rocking curve (ω/2θ-scan). It was found that with decreasing the N/Ga ratio from 46.1 to 17.9 the full width at half maximum decreases from 0.62° to 0.58° for ω-scan and from 0.022° to 0.021° for ω/2θ-scan. Thus, our results showed a clear correlation between the optical-structural parameters and the BEP ratios of N and Ga.
Temperature dependence of carrier injection across organic heterojunctions
Authors: Tsang S. W. , Tao Y. , Lu Z. H.
Published: January 2011

We present a theoretical and experimental study of carrier injection across organic heterojunctions of various barrier heights (0.4–1.0 eV) over a wide range of temperatures. An injection model with proposed escape probability function wesc is formulated to include the total hopping frequencies at both sides of the heterojunction. The model predicts that the injection current at low temperature can be dramatically modified by an extremely small amount of deep trap states. More importantly, the temperature dependence of the injection current is found to decrease with increasing the barrier height. This suggests that extracting the barrier height from the J versus 1/T plot, as commonly employed in literature, is problematic. Experimentally, hole-only heterojunction devices with injection barrier from 0.4 to 1.0 eV were fabricated by using various organic materials. 4,4′,4″-tris(N-3-methylphenyl-N-phenyl-amino) triphenylamine was chosen as the injecting layer. The accepting layer was N,N′-diphenyl-N,N′-bis(1-naphthyl)(1,1′-biphenyl)-4,4′-diamine, tris(8-hydroxyquinoline) aluminum (Alq), 4,4′,4″-tris(N-carbazolyl)-triphenylamine, or 2,2′,2″-(1,3,5-phenylene) tris(1-phenyl-1H-benzimidazole). The measured electric field and temperature dependence of the injection currents of the heterojunction devices were in good agreement with the calculation results.
A semiquantitative approach to the impurity-band-related transport properties of GaMnAs nanolayers
Authors: de Oliveira E. J. R. , Lima I. C. da Cunha , Cabral E. Dias , Boselli M. A.
Published: January 2011

We investigate the spin-polarized transport of GaMnAs nanolayers in which a ferromagnetic order exists below a certain transition temperature. Our calculation for the self-averaged resistivity takes into account the existence of an impurity band determining the extended (“metallic” transport) or localized (hopping by thermal excitation) nature of the states at and near the Fermi level. Magnetic order and resistivity are inter-related due to the influence of the spin polarization of the impurity band and the effect of the Zeeman splitting on the mobility edge. We obtain, for a given range of Mn concentration and carrier density, a “metallic” behavior in which the transport by extended carriers dominates at low temperature, and is dominated by the thermally excited localized carriers near and above the transition temperature. This gives rise to a conspicuous hump of the resistivity which has been experimentally observed and brings light onto the relationship between transport and magnetic properties of this material.
Epiphytic diatoms and water quality in shallow lakes: the neutral substrate hypothesis revisited
Authors: Cejudo-Figueiras Cristina , Álvarez-Blanco Irene , Bécares Eloy , Blanco Saúl
Published: January 2011

For bioassessment of freshwaters, diatom indices have been mainly used in streams although their applicability in shallow lakes has been demonstrated in several studies. However, the influence of sampling substrata on periphytic diatom communities and on the ecological quality inferred from them has been paid little attention. In this paper, we test the ‘neutral substrate hypothesis’, which predicts no relevant influence of host plant type on their epiphytic community. Nineteen shallow permanent lakes from north-west Spain were studied and classified into three trophic levels. Epiphytic diatom communities growing on three different macrophytes for each trophic level were sampled and analysed. We assess: (1) which of the most common diatom indices provides a reliable water quality assessment, (2) how different plant substrata influence the diatom communities growing on them and (3) how these differences affect water quality assessment. Similarity tests showed significant differences in the composition of diatom assemblages among nutrient concentrations and host macrophytes. In contrast, ANOVA results for selected diatom-based metrics showed significant differences among trophic levels but not between different plant substrata. This supports the use of epiphytic diatoms as biological indicators for shallow lakes irrespective of the dominant macrophyte.
Site fidelity and movements of sharks associated with ocean-farming cages in Hawaii
Authors: Papastamatiou Yannis P. , Itano David G. , Dale Jonathan J. , Meyer Carl G. , Holland Kim N.
Published: January 2011

Sharks are found in association with main Hawaiian Island ocean fish farms more frequently and at higher densities than is typical for coastal Hawaiian waters. Sharks attracted to fish farms could potentially threaten human water users, interact negatively with other fisheries, and seasonal migrations could be disrupted if individuals become entrained around farms throughout the year. We hypothesised that smaller coastal species would reside near farms, whereas more wide-ranging species would associate with farms only for short periods. We utilised passive acoustic telemetry to monitor the movements and behaviour of sandbar (Carcharhinus plumbeus) and tiger (Galeocerdo cuvier) sharks adjacent to two open ocean fish farms in Hawaii. Approximately half the tagged sandbar sharks showed site fidelity to the farms, with some individuals being detected repeatedly for 2.5 years. Sandbar sharks moved seasonally to the west coast of Oahu, suggesting that fish farms are not disrupting natural seasonal cycles in this species. Tiger sharks tagged near the cages were more transient, and showed much shorter residence times although some individuals returned sporadically to the cages over the 3-year period. Ocean fish cages appear to aggregate sandbar sharks, but are only ‘visited’ by tiger sharks. Although threats to public safety are probably minimal, the ecological effects of aggregating top-predators are still unknown.
Noncontact estimation of intercellular breaking force using a femtosecond laser impulse quantified by atomic force microscopy
Authors: Hosokawa Yoichiroh , Hagiyama Man , Iino Takanori , Murakami Yoshinori , Ito Akihiko
Published: January 2011

When a femtosecond laser pulse (fsLP) is focused through an objective lens into a culture medium, an impulsive force (fsLP-IF) is generated that propagates from the laser focal point (
O

f

) in a micron-sized space. This force can detach individual adherent cells without causing considerable cell damage. In this study, an fsLP-IF was reflected in the vibratory movement of an atomic force microscopy (AFM) cantilever. Based on the magnitude of the vibration and the geometrical relationship between
O

f

and the cantilever, the fsLP-IF generated at
O

f

was calculated as a unit of impulse [N-s]. This impulsive force broke adhesion molecule-mediated intercellular interactions in a manner that depended on the adhesion strength that was estimated by the cell aggregation assay. The force also broke the interactions between streptavidin-coated microspheres and a biotin-coated substrate with a measurement error of approximately 7%. These results suggest that fsLP-IF can be used to break intermolecular and intercellular interactions and estimate the adhesion strength. The fsLP-IF was used to break intercellular contacts in two biologically relevant cultures: a coculture of leukocytes seeded over on an endothelial cell monolayer, and a polarized monolayer culture of epithelial cells. The impulses needed to break leukocyte–endothelial and interepithelial interactions, which were calculated based on the geometrical relationship between
O

f

and the adhesive interface, were on the order of 10
-13
and 10
-12
 N-s, respectively. When the total impulse at
O

f

is well-defined, fsLP-IF can be used to estimate the force required to break intercellular adhesions in a noncontact manner under biologically relevant conditions.
Climate and population density drive changes in cod body size throughout a century on the Norwegian coast
Authors: Rogers Lauren A. , Stige Leif C. , Olsen Esben M. , Knutsen Halvor , Chan Kung-Sik , Stenseth Nils Chr.
Published: January 2011

Understanding how populations respond to changes in climate requires long-term, high-quality datasets, which are rare for marine systems. We estimated the effects of climate warming on cod lengths and length variability using a unique 91-y time series of more than 100,000 individual juvenile cod lengths from surveys that began in 1919 along the Norwegian Skagerrak coast. Using linear mixed-effects models, we accounted for spatial population structure and the nested structure of the survey data to reveal opposite effects of spring and summer warming on juvenile cod lengths. Warm summer temperatures in the coastal Skagerrak have limited juvenile growth. In contrast, warmer springs have resulted in larger juvenile cod, with less variation in lengths within a cohort, possibly because of a temperature-driven contraction in the spring spawning period. A density-dependent reduction in length was evident only at the highest population densities in the time series, which have rarely been observed in the last decade. If temperatures rise because of global warming, nonlinearities in the opposing temperature effects suggest that negative effects of warmer summers will increasingly outweigh positive effects of warmer springs, and the coastal Skagerrak will become ill-suited for Atlantic cod.
Contractility of the cell rear drives invasion of breast tumor cells in 3D Matrigel
Authors: Poincloux Renaud , Collin Olivier , Lizárraga Floria , Romao Maryse , Debray Marcel , Piel Matthieu , Chavrier Philippe
Published: January 2011

Cancer cells use different modes of migration, including integrin-dependent mesenchymal migration of elongated cells along elements of the 3D matrix as opposed to low-adhesion-, contraction-based amoeboid motility of rounded cells. We report that MDA-MB-231 human breast adenocarcinoma cells invade 3D Matrigel with a characteristic rounded morphology and with F-actin and myosin-IIa accumulating at the cell rear in a uropod-like structure. MDA-MB-231 cells display neither lamellipodia nor bleb extensions at the leading edge and do not require Arp2/3 complex activity for 3D invasion in Matrigel. Accumulation of phospho-MLC and blebbing activity were restricted to the uropod as reporters of actomyosin contractility, and velocimetric analysis of fluorescent beads embedded within the 3D matrix showed that pulling forces exerted to the matrix are restricted to the side and rear of cells. Inhibition of actomyosin contractility or β1 integrin function interferes with uropod formation, matrix deformation, and invasion through Matrigel. These findings support a model whereby actomyosin-based uropod contractility generates traction forces on the β1 integrin adhesion system to drive cell propulsion within the 3D matrix, with no contribution of lamellipodia extension or blebbing to movement.
Architecture of the DNA polymerase B-proliferating cell nuclear antigen (PCNA)-DNA ternary complex
Authors: Mayanagi Kouta , Kiyonari Shinichi , Nishida Hirokazu , Saito Mihoko , Kohda Daisuke , Ishino Yoshizumi , Shirai Tsuyoshi , Morikawa Kosuke
Published: January 2011

DNA replication in archaea and eukaryotes is executed by family B DNA polymerases, which exhibit full activity when complexed with the DNA clamp, proliferating cell nuclear antigen (PCNA). This replication enzyme consists of the polymerase and exonuclease moieties responsible for DNA synthesis and editing (proofreading), respectively. Because of the editing activity, this enzyme ensures the high fidelity of DNA replication. However, it remains unclear how the PCNA-complexed enzyme temporally switches between the polymerizing and editing modes. Here, we present the three-dimensional structure of the
Pyrococcus furiosus
DNA polymerase B-PCNA-DNA ternary complex, which is the core component of the replisome, determined by single particle electron microscopy of negatively stained samples. This structural view, representing the complex in the editing mode, revealed the whole domain configuration of the trimeric PCNA ring and the DNA polymerase, including protein–protein and protein–DNA contacts. Notably, besides the authentic DNA polymerase-PCNA interaction through a PCNA-interacting protein (PIP) box, a novel contact was found between DNA polymerase and the PCNA subunit adjacent to that with the PIP contact. This contact appears to be responsible for the configuration of the complex specific for the editing mode. The DNA was located almost at the center of PCNA and exhibited a substantial and particular tilt angle against the PCNA ring plane. The obtained molecular architecture of the complex, including the new contact found in this work, provides clearer insights into the switching mechanism between the two distinct modes, thus highlighting the functional significance of PCNA in the replication process.
SCARECROW-LIKE 3 promotes gibberellin signaling by antagonizing master growth repressor DELLA in Arabidopsis
Authors: Zhang Zhong-Lin , Ogawa Mikihiro , Fleet Christine M. , Zentella Rodolfo , Hu Jianhong , Heo Jung-Ok , Lim Jun , Kamiya Yuji , Yamaguchi Shinjiro , Sun Tai-ping
Published: January 2011

The diterpenoid phytohormone gibberellin (GA) controls diverse developmental processes throughout the plant life cycle. DELLA proteins are master growth repressors that function immediately downstream of the GA receptor to inhibit GA signaling. By doing so, DELLAs also play pivotal roles as integrators of internal developmental signals from multiple hormone pathways and external cues. DELLAs are likely nuclear transcriptional regulators, which interact with other transcription factors to modulate expression of GA-responsive genes. DELLAs are also involved in maintaining GA homeostasis through feedback up-regulating expression of GA biosynthesis and receptor genes. However, the molecular mechanisms by which DELLAs restrict growth and development are largely unknown. This study reveals an important step of the mechanism. Previous microarray studies identified
SCARECROW-LIKE 3
(
SCL3
) as a direct target gene of DELLA in Arabidopsis seedlings.
SCL3
expression is induced by DELLA and repressed by GA. Unexpectedly, a
scl3
null mutant displays reduced GA responses and elevated expression of GA biosynthesis genes during seed germination and seedling growth, indicating that SCL3 functions as a positive regulator of GA signaling. SCL3 seems to act as an attenuator of DELLA proteins. Transient expression, ChIP, and co-IP studies show that SCL3 autoregulates its own transcription by directly interacting with DELLA. Our data further show that SCL3 and DELLA antagonize each other in controlling both downstream GA responses and upstream GA biosynthetic genes. This work is beginning to shed light on how this complex regulatory network achieves GA homeostasis and controls GA-mediated growth and development in the plant.
Structural kinetics of myosin by transient time-resolved FRET
Authors: Nesmelov Yuri E. , Agafonov Roman V. , Negrashov Igor V. , Blakely Sarah E. , Titus Margaret A. , Thomas David D.
Published: January 2011

For many proteins, especially for molecular motors and other enzymes, the functional mechanisms remain unsolved due to a gap between static structural data and kinetics. We have filled this gap by detecting structure and kinetics simultaneously. This structural kinetics experiment is made possible by a new technique, (TR)
2
FRET (transient time-resolved FRET), which resolves protein structural states on the submillisecond timescale during the transient phase of a biochemical reaction. (TR)
2
FRET is accomplished with a fluorescence instrument that uses a pulsed laser and direct waveform recording to acquire an accurate subnanosecond time-resolved fluorescence decay every 0.1 ms after stopped flow. To apply this method to myosin, we labeled the force-generating region site specifically with two probes, mixed rapidly with ATP to initiate the recovery stroke, and measured the interprobe distance by (TR)
2
FRET with high resolution in both space and time. We found that the relay helix bends during the recovery stroke, most of which occurs before ATP is hydrolyzed, and two structural states (relay helix straight and bent) are resolved in each nucleotide-bound biochemical state. Thus the structural transition of the force-generating region of myosin is only loosely coupled to the ATPase reaction, with conformational selection driving the motor mechanism.
Reconciliation of opposing views on membrane–sugar interactions
Authors: Andersen Heidi D. , Wang Chunhua , Arleth Lise , Peters Günther H. , Westh Peter
Published: January 2011

It is well established that small sugars exert different types of stabilization of biomembranes both in vivo and in vitro. However, the essential question of whether sugars are bound to or expelled from membrane surfaces, i.e., the sign and size of the free energy of the interaction, remains unresolved, and this prevents a molecular understanding of the stabilizing mechanism. We have used small-angle neutron scattering and thermodynamic measurements to show that sugars may be either bound or expelled depending on the concentration of sugar. At low concentration, small sugars bind quite strongly to a lipid bilayer, and the accumulation of sugar at the interface makes the membrane thinner and laterally expanded. Above ∼0.2 M the sugars gradually become expelled from the membrane surface, and this repulsive mode of interaction counteracts membrane thinning. The dual nature of sugar–membrane interactions offers a reconciliation of conflicting views in earlier reports on sugar-induced modulations of membrane properties.
Structures of sequential open states in a symmetrical opening transition of the TolC exit duct
Authors: Pei Xue-Yuan , Hinchliffe Philip , Symmons Martyn F. , Koronakis Eva , Benz Roland , Hughes Colin , Koronakis Vassilis
Published: January 2011

In bacterial drug resistance and virulence pumps, an inner membrane (IM) transporter and periplasmic adaptor recruit an outer membrane (OM) trimeric TolC exit duct that projects an α-helical tunnel across the periplasm. The TolC periplasmic entrance is closed by densely packed α-helical coiled coils, inner H7/H8, and outer H3/H4, constrained by a hydrogen bond network. On recruitment, these coiled coils must undergo transition to the open state. We present 2.9 Å resolution crystal structures of two sequential TolC open states in which the network is incrementally disrupted and channel conductances defined in lipid bilayers. Superimposition of TolC
RS
(370 pS) and TolC
YFRS
(1,000 pS) on the TolC
WT
closed state (80 pS) showed that in the initial open-state TolC
RS
, relaxation already causes approximately 14° twisting and expansion of helix H7 at the periplasmic tip, increasing interprotomer distances from 12.2 Å in TolC
WT
to 18.9 Å. However, in the crystal structure, the weakened Asp
374
pore constriction was maintained at the closed state 11.3 Å
2
. In the advanced open-state TolC
YFRS
, there was little further expansion at the tip, to interprotomer 21.3 Å, but substantial movement of inner and outer coiled coils dilated the pore constriction. In particular, upon abolition of the TolC
YFRS
intraprotomer Tyr
362
–Asp
153
link, a redirection of Tyr
362
and “bulge” in H3 allowed a simple movement outward of H8, establishing a 50.3 Å
2
opening. Root mean square deviations (rmsds) over the coiled coils of the three protomers of TolC
RS
and TolC
YFRS
illustrate that, whereas independent movement at the periplasmic tips may feature in the initial stages of opening, full dilation of the pore constriction is entirely symmetrical.
Modulation of cardiac macrophages by phosphatidylserine-presenting liposomes improves infarct repair
Authors: Harel-Adar Tamar , Mordechai Tamar Ben , Amsalem Yoram , Feinberg Micha S. , Leor Jonathan , Cohen Smadar
Published: January 2011

Herein we investigated a new strategy for the modulation of cardiac macrophages to a reparative state, at a predetermined time after myocardial infarction (MI), in aim to promote resolution of inflammation and elicit infarct repair. The strategy employed intravenous injections of phosphatidylserine (PS)-presenting liposomes, mimicking the anti-inflammatory effects of apoptotic cells. Following PS-liposome uptake by macrophages in vitro and in vivo, the cells secreted high levels of anti-inflammatory cytokines [transforming growth factor β (TGFβ) and interleukin 10 (IL-10)] and upregulated the expression of the mannose receptor—CD206, concomitant with downregulation of proinflammatory markers, such as tumor necrosis factor α (TNFα) and the surface marker CD86. In a rat model of acute MI, targeting of PS-presenting liposomes to infarct macrophages after injection via the femoral vein was demonstrated by magnetic resonance imaging (MRI). The treatment promoted angiogenesis, the preservation of small scars, and prevented ventricular dilatation and remodeling. This strategy represents a unique and accessible approach for myocardial infarct repair.
Multistage nanoparticle delivery system for deep penetration into tumor tissue
Authors: Wong Cliff , Stylianopoulos Triantafyllos , Cui Jian , Martin John , Chauhan Vikash P. , Jiang Wen , Popović Zoran , Jain Rakesh K. , Bawendi Moungi G. , Fukumura Dai
Published: January 2011

Current Food and Drug Administration-approved cancer nanotherapeutics, which passively accumulate around leaky regions of the tumor vasculature because of an enhanced permeation and retention (EPR) effect, have provided only modest survival benefits. This suboptimal outcome is likely due to physiological barriers that hinder delivery of the nanotherapeutics throughout the tumor. Many of these nanotherapeutics are ≈100 nm in diameter and exhibit enhanced accumulation around the leaky regions of the tumor vasculature, but their large size hinders penetration into the dense collagen matrix. Therefore, we propose a multistage system in which 100-nm nanoparticles “shrink” to 10-nm nanoparticles after they extravasate from leaky regions of the tumor vasculature and are exposed to the tumor microenvironment. The shrunken nanoparticles can more readily diffuse throughout the tumor's interstitial space. This size change is triggered by proteases that are highly expressed in the tumor microenvironment such as MMP-2, which degrade the cores of 100-nm gelatin nanoparticles, releasing smaller 10-nm nanoparticles from their surface. We used quantum dots (QD) as a model system for the 10-nm particles because their fluorescence can be used to demonstrate the validity of our approach. In vitro MMP-2 activation of the multistage nanoparticles revealed that the size change was efficient and effective in the enhancement of diffusive transport. In vivo circulation half-life and intratumoral diffusion measurements indicate that our multistage nanoparticles exhibited both the long circulation half-life necessary for the EPR effect and the deep tumor penetration required for delivery into the tumor's dense collagen matrix.
Crystal structures of complexes containing domains from two viral internal ribosome entry site (IRES) RNAs bound to the 70S ribosome
Authors: Zhu Jianyu , Korostelev Andrei , Costantino David A. , Donohue John P. , Noller Harry F. , Kieft Jeffrey S.
Published: January 2011

Internal ribosome entry site (IRES) RNAs are elements of viral or cellular mRNAs that bypass steps of canonical eukaryotic cap-dependent translation initiation. Understanding of the structural basis of IRES mechanisms is limited, partially due to a lack of high-resolution structures of IRES RNAs bound to their cellular targets. Prompted by the universal phylogenetic conservation of the ribosomal P site, we solved the crystal structures of proposed P site binding domains from two intergenic region IRES RNAs bound to bacterial 70S ribosomes. The structures show that these IRES domains nearly perfectly mimic a tRNA•mRNA interaction. However, there are clear differences in the global shape and position of this IRES domain in the intersubunit space compared to those of tRNA, supporting a mechanism for IRES action that invokes hybrid state mimicry to drive a noncanonical mode of translocation. These structures suggest how relatively small structured RNAs can manipulate complex biological machines.
Kikuchi ultrafast nanodiffraction in four-dimensional electron microscopy
Authors: Yurtsever Aycan , Zewail Ahmed H.
Published: January 2011

Coherent atomic motions in materials can be revealed using time-resolved X-ray and electron Bragg diffraction. Because of the size of the beam used, typically on the micron scale, the detection ofnanoscalepropagating waves in extended structures hitherto has not been reported. For elastic waves of complex motions, Bragg intensities contain all polarizations and they are not straightforward to disentangle. Here, we introduce Kikuchi diffraction dynamics, using convergent-beam geometry in an ultrafast electron microscope, to selectively probe propagating transverse elastic waves with nanoscale resolution. It is shown that Kikuchi band shifts, which are sensitive only to the tilting of atomic planes, reveal the resonance oscillations, unit cell angular amplitudes, and the polarization directions. For silicon, the observed wave packet temporal envelope (resonance frequency of 33 GHz), the out-of-phase temporal behavior of Kikuchi’s edges, and the magnitude of angular amplitude (0.3 mrad) and polarizationelucidate the nature of the motion: one that preserves the mass density (i.e., no compression or expansion) but leads to sliding of planes in the antisymmetric shear eigenmode of the elastic waveguide. As such, the method of Kikuchi diffraction dynamics, which is unique to electron imaging, can be used to characterize the atomic motions of propagating waves and their interactions with interfaces, defects, and grain boundaries at the nanoscale.
Cellulose δ
18
O is an index of leaf-to-air vapor pressure difference (VPD) in tropical plants
Authors: Kahmen Ansgar , Sachse Dirk , Arndt Stefan K. , Tu Kevin P. , Farrington Heraldo , Vitousek Peter M. , Dawson Todd E.
Published: January 2011

Cellulose in plants contains oxygen that derives in most cases from precipitation. Because the stable oxygen isotope composition, δ
18
O, of precipitation is associated with environmental conditions, cellulose δ
18
O should be as well. However, plant physiological models using δ
18
O suggest that cellulose δ
18
O is influenced by a complex mix of both climatic and physiological drivers. This influence complicates the interpretation of cellulose δ
18
O values in a paleo-context. Here, we combined empirical data analyses with mechanistic model simulations to
i
) quantify the impacts that the primary climatic drivers humidity (
e
a
) and air temperature (
T
air
) have on cellulose δ
18
O values in different tropical ecosystems and
ii
) determine which environmental signal is dominating cellulose δ
18
O values. Our results revealed that
e
a
and
T
air
equally influence cellulose δ
18
O values and that distinguishing which of these factors dominates the δ
18
O values of cellulose cannot be accomplished in the absence of additional environmental information. However, the individual impacts of
e
a
and
T
air
on the δ
18
O values of cellulose can be integrated into a single index of plant-experienced atmospheric vapor demand: the leaf-to-air vapor pressure difference (VPD). We found a robust relationship between VPD and cellulose δ
18
O values in both empirical and modeled data in all ecosystems that we investigated. Our analysis revealed therefore that δ
18
O values in plant cellulose can be used as a proxy for VPD in tropical ecosystems. As VPD is an essential variable that determines the biogeochemical dynamics of ecosystems, our study has applications in ecological-, climate-, or forensic-sciences.
PDGF-BB and TGF-β1 on cross-talk between endothelial and smooth muscle cells in vascular remodeling induced by low shear stress
Authors: Qi Ying-Xin , Jiang Jun , Jiang Xiao-Hua , Wang Xiao-Dong , Ji Su-Ying , Han Yue , Long Ding-Kun , Shen Bao-Rong , Yan Zhi-Qiang , Chien Shu , Jiang Zong-Lai
Published: January 2011

Shear stress, especially low shear stress (LowSS), plays an important role in vascular remodeling during atherosclerosis. Endothelial cells (ECs), which are directly exposed to shear stress, convert mechanical stimuli into intracellular signals and interact with the underlying vascular smooth muscle cells (VSMCs). The interactions between ECs and VSMCs modulate the LowSS-induced vascular remodeling. With the use of proteomic analysis, the protein profiles of rat aorta cultured under LowSS (5 dyn/cm
2
) and normal shear stress (15 dyn/cm
2
) were compared. By using Ingenuity Pathway Analysis to identify protein–protein association, a network was disclosed that involves two secretary molecules, PDGF-BB and TGF-β1, and three other linked proteins, lamin A, lysyl oxidase, and ERK 1/2. The roles of this network in cellular communication, migration, and proliferation were further studied in vitro by a cocultured parallel-plate flow chamber system. LowSS up-regulated migration and proliferation of ECs and VSMCs, increased productions of PDGF-BB and TGF-β1, enhanced expressions of lysyl oxidase and phospho-ERK1/2, and decreased Lamin A in ECs and VSMCs. These changes induced by LowSS were confirmed by using PDGF-BB recombinant protein, siRNA, and neutralizing antibody. TGF-β1 had similar influences on ECs as PDGF-BB, but not on VSMCs. Our results suggest that ECs convert the LowSS stimuli into up-regulations of PDGF-BB and TGF-β1, but these two factors play different roles in LowSS-induced vascular remodeling. PDGF-BB is involved in the paracrine control of VSMCs by ECs, whereas TGF-β1 participates in the feedback control from VSMCs to ECs.
Signal integration by DegS and RseB governs the σ
E
-mediated envelope stress response in
Escherichia coli
Authors: Chaba Rachna , Alba Benjamin M. , Guo Monica S. , Sohn Jungsan , Ahuja Nidhi , Sauer Robert T. , Gross Carol A.
Published: January 2011

In
Escherichia coli
, the σ
E
transcription factor monitors and maintains outer membrane (OM) integrity by activating genes required for assembly of its two key components, outer membrane proteins (OMPs) and lipopolysaccharide (LPS) and by transcribing small RNAs to down-regulate excess unassembled OMPs. σ
E
activity is governed by the rate of degradation of its membrane-spanning anti-σ factor, RseA. Importantly, the DegS protease can initiate RseA cleavage only when activated by binding to unassembled OMPs. The prevalent paradigm has been that the σ
E
response is controlled by the amount of activated DegS. Here we demonstrate that inactivation of a second negative regulator, the periplasmic protein RseB, is also required for σ
E
induction in vivo. Moreover, OMPs, previously known only to activate DegS, also generate a signal to antagonize RseB inhibition. This signal may be lipid related, as RseB is structurally similar to proteins that bind lipids. We propose that the use of an AND gate enables σ
E
to sense and integrate multivariate signals from the envelope.
Wild-type LRP6 inhibits, whereas atherosclerosis-linked LRP6
R611C
increases PDGF-dependent vascular smooth muscle cell proliferation
Authors: Keramati Ali R. , Singh Rajvir , Lin Aiping , Faramarzi Saeed , Ye Zhi-jia , Mane Shrikant , Tellides George , Lifton Richard P. , Mani Arya
Published: January 2011

Vascular smooth muscle cell (VSMC) proliferation is an important event in atherosclerosis and other vasculopathies. PDGF signaling is a key mediator of SMC proliferation, but the mechanisms that control its activity remain unclear. We previously identified a mutation in LDL receptor-related protein 6 (
LRP6
), LRP6
R611C
, that causes early atherosclerosis. Examination of human atherosclerotic coronary arteries showed markedly increased expression of LRP6 and colocalization with PDGF receptor β (PDGFR-β). Further investigation showed that wild-type LRP6 inhibits but LRP6
R611C
promotes VSMC proliferation in response to PDGF. We found that wild-type LRP6 forms a complex with PDGFR-β and enhances its lysosomal degradation, functions that are severely impaired in LRP6
R611C
. Further, we observed that wild-type and mutant LRP6 regulate cell-cycle activity by triggering differential effects on PDGF-dependent pathways. These findings implicate LRP6 as a critical modulator of PDGF-dependent regulation of cell cycle in smooth muscle and indicate that loss of this function contributes to development of early atherosclerosis in humans.
Methyltransferase Set7/9 regulates p53 activity by interacting with Sirtuin 1 (SIRT1)
Authors: Liu Xiangyu , Wang Donglai , Zhao Ying , Tu Bo , Zheng Zhixing , Wang Lina , Wang Haiying , Gu Wei , Roeder Robert G. , Zhu Wei-Guo
Published: January 2011

Numerous studies indicate that Sirtuin 1 (SIRT1), a mammalian nicotinamide adenine dinucleotide (NAD
+
)-dependent histone deacetylase (HDAC), plays a crucial role in p53-mediated stress responses by deacetylating p53. Nevertheless, the acetylation levels of p53 are dramatically increased upon DNA damage, and it is not well understood how the SIRT1–p53 interaction is regulated during the stress responses. Here, we identified Set7/9 as a unique regulator of SIRT1. SIRT1 interacts with Set7/9 both in vitro and in vivo. In response to DNA damage in human cells, the interaction between Set7/9 and SIRT1 is significantly enhanced and coincident with an increase in p53 acetylation levels. Importantly, the interaction of SIRT1 and p53 is strongly suppressed in the presence of Set7/9. Consequently, SIRT1-mediated deacetylation of p53 is abrogated by Set7/9, and p53-mediated transactivation is increased during the DNA damage response. Of note, whereas SIRT1 can be methylated at multiple sites within its N terminus by Set7/9, a methylation-defective mutant of SIRT1 still retains its ability to inhibit p53 activity. Taken together, our results reveal that Set7/9 is a critical regulator of the SIRT1-p53 interaction and suggest that Set7/9 can modulate p53 function indirectly in addition to acting through a methylation-dependent mechanism.
Community Psychiatry in the Islands Region of New Guinea: 1. Epidemiology
Authors: Hoskin J. O. , Cuthbertson Grace , Cawte J. E.
Published: January 2011

From 1965 to 1967 a regional psychiatric service based on Rabaul was offered to the Islands Region of New Guinea. The results of the first year's work, which included three hundred referred cases were reviewed to provide the guide lines for the second year of the existing project and for possible future developments.
Community Psychiatry in the Islands Region of New Guinea
Authors: Hoskin J. O.
Published: January 2011

The observations of the Islands Region Psychiatry Research Project Team made between 1965 and 1967 and the principles of community psychiatry as presented by Caplan are used as the basis for a design of a psychiatric service in a setting such as New Guinea.
Psychiatric Aspects of Disseminated Lupus Erythematosus in Hong Kong Chinese—Report of Three Cases
Authors: Chiu Edmond
Published: January 2011

The sympomatology of three Hong Kong Chinese developing psychiatric illness in association with disseminated lupus erythematosus is described. The role of steroid therapy is discussed in relationship to cause, aggravation and potentiation of psychiatric symptoms. The attempt to clarify and classify psychiatric symptoms in this disease into ‘functional’ and ‘toxic-confusional’ states is supported. Culture-bound manifestations were not observed.
Personal Networks and the Schizophrenias
Authors: Henderson Scott
Published: January 2011

It is likely that certain elements in the individual's current social environment act causally in the onset of schizophrenia. The construct known as ‘social support’ has recently been invoked as one such element which, when deficient, may be a causal factor. The evidence for this is unsatisfactory and likely to remain so. For clinical purposes, it would be more useful to look at the effect of social relationships in secondary and tertiary prevention.
Predictors of Initial and Final Work Capacity in a Chronic Obstructive Airways Disease Rehabilitation Program
Authors: Singh Bruce S. , Lewin Terry
Published: January 2011

A study was conducted to determine the predictors of initial and final work capacity in men with chronic obstructive airways disease attending an outpatient rehabilitation program in a veterans' hospital. Baseline psychological, ergometric and respiratory physiological data were collected on a sample of 27 patients and ergometric and physiological data were collected again after eight weeks. The study demonstrated that respiratory impairment as measured by vital capacity was predictive of initial work capacity and that knowledge of the patients' psychological state added little to this prediction. In addition, it demonstrated that work capacity could be improved considerably by such a rehabilitation program despite a lack of improvement in respiratory parameters. Such improvement in work capacity as did occur was greatest for those who were less affectively disturbed, had a more positive general psychological state, were less preoccupied with their symptoms and saw their problems as being more under their control.
Effects of the Introduction of the Dexamethasone Suppression Test on Diagnosis and Treatment of Depression by Psychiatrists
Authors: Schrader Geoffrey D. , Durbridge Timothy C.
Published: January 2011

A review of case notes before and after the introduction of the DST into clinical psychiatric practice revealed considerable changes in diagnosis and management. Specifically there were increases in the diagnosis of biological depression and treatment with somatic antidepressant therapy. There was no association between DST results and particular management plans. There was a strong association between requesting the DST and management with antidepressants. It is suggested that the introduction of laboratory tests for psychiatric disorders may firm the belief of psychiatrists in the biological basis of some forms of depression and thus alter their diagnostic and treatment practice.
A Malay Cultural Explanation for Epilepsy
Authors: Peng Kok Lee
Published: January 2011

The causal explanation given by a 24-year-old Malay woman from a low socioeconomic class for her epilepsy is described. This case illustrates how cultural explanations can protect an individual from the stigma of illness. The Malay concept of the supernatural and the causation of illness is discussed.
Social Skills Training: An Effective Treatment for Unipolar Non-Psychotic Depression?
Authors: Jackson Henry J. , Moss Jillian D. , Solinski Sylvia
Published: January 2011

In recent times, social skills training (SST) has been used in the treatment of unipolar non-psychotic depression. We outline the rationale for SST in such treatment, provide definitions of SST, and outline the assessment and training procedures. Published studies are reviewed and their shortcomings discussed. We examine four theoretical issues arising from the review, and guidelines for improvements in future studies are suggested.
Early Sensory-Perceptual Changes in Huntington's Disease
Authors: Hayward Linda , Zubrick Stephen R. , Hall Wayne
Published: January 2011

Forty-four patients at risk for Huntington's disease and seventeen diagnosed as having the disease were studied longitudinally over a nine-year period to assess the evolution of cognitive impairment. Results showed that there were measurable changes in sensory-perceptual functions well in advance of the emergence of the movement disorder. Discrimination between patients with Huntington's disease and those at risk for the disease based on tests of sensory-perceptual functioning resulted in a correct classification rate of 95.1%. Subjects who had changed from being at risk to having the disease nearly all had discriminant scores from their first test sequence lying in either the disease range or the pre-symptomatic disease range. The present organic model of Huntington's disease is discussed in light of these findings and implications of the mathematical model underlying prediction are discussed.
Treatment Outlines for the Management of the Somatoform Disorders
Authors: Andrews Gavin
Published: January 2011

The Quality Assurance Project is developing explicit and detailed treatment outlines for each of the major psychiatric disorders. Three sources of information are used: the treatment outcome literature, the opinions of a sample of practising psychiatrists and the views of a panel of nominated experts. The recommendations for the treatment of somatoform disorders were as follows: brief dynamic psychotherapy, family therapy and excellent medical consultation are the basis for the treatment of hypochondriasis. Limited long-term supportive psychotherapy and good medical consultation are important in somatization disorder. Symptom relief, psychotherapeutic support and meticulous collaboration with physicians are the keys to managing psychogenic pain disorder. Physiotherapy to improve physical functioning and patient education to facilitate the distinction between normal symptoms and abnormal illness behaviours are important in all three conditions. Neither the benzodiazepines nor behaviour therapy appear to be of use in these conditions.
Koro Epidemic in North-East India
Authors: Sachdev P. S.
Published: January 2011

Koro is an unusual psychogenic syndrome reported, until recently, predominantly in men of the Chinese race who live in southern China and south-east Asia. Issues concerning its phenomenology, diagnosis and nosology are still controversial. This paper describes an epidemic of koro in north-east India. A psychiatric analysis of thirty-one cases is presented. Probable reasons for the rapid spread of the illness are discussed. The majority of the individuals affected were from the lower socio-economic strata, were poorly educated and in the age group of 20–40 years. Many women were affected. There was no evidence of significant premorbid or sexual psychopathology in most cases. Some patients had a number of episodes but with only minor residual symptoms. The author compares these findings with earlier reports and discusses the implications for its nosology and psychodynamics.
The Treatment of Bulimia Nervosa
Authors: Griffiths Rosalyn A. , Touyz Stephen W. , Mitchell Philip B. , Bacon Wendy
Published: January 2011

We review treatment approaches to bulimia nervosa, with particular emphasis on methodology and research design. The following treatments are considered: behaviour therapy, cognitive behaviour therapy, pharmacological treatment, group therapy, psychoanalytic psychotherapy, self-help and support groups, hypnosis and miscellaneous (family therapy and nutritional approaches). Several directions for future research and methodological recommendations are suggested.
The Place of Crisis Intervention in Psychiatry
Authors: Szmukler George I.
Published: January 2011

This paper examines the concept of crisis intervention and its relevance to psychiatric practice. Crisis theory originated in relation to healthy subjects disturbed by major life hazards. Its application, however, has been widened in an uncritical manner to include patients with psychiatric disorders. To what extent crisis theory and intervention can be applied is discussed and relevant research on the outcome of their use in a variety of settings reviewed. It is concluded that although crisis theory cannot be transplanted in its entirety into psychiatry, modified versions might prove useful. The role of crisis in inducing behaviour change in a variety of psychiatric settings and the ways in which this might be harnessed are of considerable interest and worthy of careful investigation.