bluuebunny/crossref_metadata_2025 huggingface dataset:
Tumor–stroma interactions influence cytokine expression and matrix metalloproteinase activities in paired primary and metastatic head and neck cancer cells
Authors: Koontongkaew Sittichai , Amornphimoltham Panomwat , Yapong Bunjird
Published: December 2008

This study evaluates the effects of gingival fibroblasts, type I collagen and autocrine/paracrine elements on cytokine expression in paired primary and metastatic human squamous cell carcinoma (HNSCC) cell lines. Additionally, the effects of IL‐1α, IL‐1β, IL‐6, TNF‐α, TGF‐β and HGF on MMPs and cell invasion were investigated. RT‐PCR results indicated the presence of mRNAs for IL‐1α, IL‐1β, IL‐6, TNF‐α, and TGF‐β in primary and metastatic HNSCC cell lines but high expression of cytokines was not a prerequisite for metastatic cancer cells. HGF mRNA was not detected in the cancer cell lines. Co‐culturing of HNSCC cells with fibroblasts caused increases in cytokine expression. Type I collagen and conditioned media derived from HNSCC cells or fibroblasts enhanced cytokine expression in the cancer cells. Cytokines also enhanced MMP‐2 and MMP‐9 enzymatic activities as well as HNSCC cell invasion. Our findings suggest that the interactions between cancer cells, the extracellular matrix and fibroblasts, as mediated by cytokines, play important roles in the progression of HNSCC.
Cuba's new relationship with foreign capital: economic policy-making since 1990
Authors: MORRIS EMILY
Published: December 2008

This article attempts to analyse the nature of Cuban policymaking during the period of economic ‘adjustment’ since the collapse of the Soviet bloc by focusing on one aspect: the opening to foreign capital. It outlines the widely-accepted characterisation of policy as a cyclical process and identifies the assumptions about the policy-making process that underlie it. Citing data on the changes in economic conditions and the sequencing of policy towards foreign capital in the post-1990 period, it suggests that policy-making can be better understood as an evolutionary process. This conclusion has implications for the way in which we understand the renewed wave of reforms launched in March 2008.
Oxaloacetate-to-malate conversion by mineral photoelectrochemistry: implications for the viability of the reductive tricarboxylic acid cycle in prebiotic chemistry
Authors: Guzman Marcelo I. , Martin Scot T.
Published: December 2008

The carboxylic acids produced by the reductive tricarboxylic acid (rTCA) cycle are possibly a biosynthetic core of initial life, although several steps such as the reductive kinetics of oxaloacetate (OAA) to malate (MA) are problematic by conventional chemical routes. In this context, we studied the kinetics of this reaction as promoted by ZnS mineral photoelectrochemistry. The quantum efficiency φMAof MA production from the photoelectrochemical reduction of OAA followed φMA=0.13 [OAA] (2.1×10−3+[OAA])−1and was independent of temperature (5 to 50°C). To evaluate the importance of this forward rate under a prebiotic scenario, we also studied the temperature-dependent rate of the backward thermal decarboxylation of OAA to pyruvate (PA), which followed an Arrhenius behavior as log (k−2)=11.74–4956/T, wherek−2is in units of s−1. These measured rates were employed in conjunction with the indirectly estimated carboxylation rate of PA to OAA to assess the possible importance of mineral photoelectrochemistry in the conversion of OAA to MA under several scenarios of prebiotic conditions on early Earth. As an example, our analysis shows that there is 90% efficiency with a forward velocity of 3 yr/cycle for the OAA→MA step of the rTCA cycle at 280 K. Efficiency and velocity both decrease for increasing temperature. These results suggest high viability for mineral photoelectrochemistry as an enzyme-free engine to drive the rTCA cycle through the early aeons of early Earth, at least for the investigated OAA→MA step.
Treatment of pain-related fear in chronic (persistent) pain: the role of safety-seeking behaviour and imagery
Authors: Jamani Nicole , Clyde Zoe
Published: December 2008

It is widely recognized that psychological factors play a central role in the adjustment process and subsequent management of chronic pain. The role of anxiety, and specifically pain-related fear, has received particular attention. Paralleling developments in the anxiety disorders literature, psychological models of pain-related fear now highlight the importance of cognitive processes in its maintenance and treatment. However, theoretical and treatment advances in the anxiety disorders literature have not been widely applied to the pain field. In particular, certain cognitive processes, specifically safety-seeking behaviours and imagery, which appear to be involved in the maintenance of pain-related fear. This paper explores how these concepts may apply to pain-related fear and demonstrates how they may aid conceptualization and be used to guide a more cognitively orientated and efficacious treatment.
Under-identification of personality disorder among in-patient mental health service users: implications for CBT therapists
Authors: Kennedy Fiona C. , Thomas Sara
Published: December 2008

The identification of personality disorder among mental health service users is problematic but important because it is associated with high levels of comorbidity and possibly ineffective service delivery. This study assessed the prevalence of personality disorder using the Millon Clinical Multiaxial Inventory – 3rd edition (MCMI-III) compared with prevalence using frequency of assignment of diagnosis in people referred to an in-patient CBT clinical psychology service. Prevalence rates differed from 85% (MCMI-III) to 16% (diagnosis) using these different measures. Reasons for this difference and implications for CBT therapists' practice are discussed.
Hematite spherules at Meridiani: Results from MI, Mini‐TES, and Pancam
Authors: Calvin W. M. , Shoffner J. D. , Johnson J. R. , Knoll A. H. , Pocock J. M. , Squyres S. W. , Weitz C. M. , Arvidson R. E. , Bell J. F. , Christensen P. R. , de Souza P. A. , Farrand W. H. , Glotch T. D. , Herkenhoff K. E. , Jolliff B. L. , Knudson A. T. , McLennan S. M. , Rogers A. D. , Thompson S. D.
Published: December 2008

We report on observations of hematite‐bearing spherules at Meridiani Planum made using the Microscopic Imager (MI), Mini‐Thermal Emission Spectrometer (Mini‐TES), and Panoramic Camera (Pancam) instruments on the Mars Exploration Rover Opportunity. Spherules were observed on soil surfaces and in outcrop rocks, both on undisturbed surfaces and in abraded surfaces ground using the Rock Abrasion Tool (RAT). Spherule size and shape change little along the 850 m eastward traverse from Eagle Crater to Endurance Crater, but spherules decrease and then slightly increase in size along the 6 km traverse from Endurance south to Victoria Crater. Local populations range from submillimeters to several millimeters in diameter. An additional small diameter (100 μm) size population is possible. An increase in irregular shapes is found near Victoria Crater. This, combined with the size decrease south of Endurance, suggests either a changing depositional environment, or variation in the duration and timing of diagenetic events. The dominant smaller size population observed early in the mission in aeolian areas and ripple crests is observed as the primary size population in abraded outcrop farther south. This suggests that successively younger beds are exposed at the surface along the southward traverse. Stratigraphically higher units removed by erosion could be recorded by the present surface lag deposit. Coordinated systematic observations are used to determine optical and infrared hematite indices of the surface soils in Pancam and Mini‐TES. In spite of the systematic variation seen in MI, both Pancam and Mini‐TES indices are highly variable based on the local surface, and neither show systematic trends south of Endurance. The lack of a 390 cm−1 feature in Mini‐TES spectra suggests concentric or radial interior structure within the spherules at scales too fine for MI to observe. Mini‐TES does not detect any silicate component in the spherules. A bound water component in soils or in exchange with the atmosphere is observed. These spherules have been previously interpreted as concretions formed within what were once water‐saturated, diagenetically altered “dirty evaporate” sandstone sediments. Our observations support this interpretation; however, no single terrestrial analog provides a model that can account for all attributes of the spherules on Mars.
Atmospheric brown cloud report
Authors: Showstack Randy
Published: December 2008

The combined effects of human‐ made atmospheric brown clouds (ABCs) and greenhouse gases in the atmosphere are having broad‐based impacts, including causing some cities to get darker, contributing to faster melting of some glaciers, masking the effects of climate change, and having negative effects on agriculture and air quality, according to a 13 November report released by the United Nations Environment Programme (UNEP). “We believe today's report brings ever more clarity to the ABC phenomena and in doing so must trigger an international response, one that tackles the twin threats of greenhouse gases and brown clouds and the unsustainable development that underpins both,” said Veerabhadran Ramanathan, head of the UNEP scientific panel carrying out the research and a professor at the Scripps Institution of Oceanography, La Jolla, Calif. The report, “Atmospheric brown clouds: Regional assessment report with focus on Asia,” can be found at http://www.unep.org.
Secular evolution of the continental crust: Implications for crust evolution models
Authors: Rollinson Hugh
Published: December 2008

The present‐day flux from mantle to crust is basaltic and yet the average composition of the continental crust is andesitic. This is the crust composition paradox. A new solution to this paradox is proposed whereby the secular evolution in the composition of the continental crust reflects a changing flux from mantle to crust over time. Thus it is proposed that the present‐day composition of the continental crust is a time‐integrated average. Crustal growth curves show that 48–54% of the continental crust was formed by the end of the Archaean. A mass balance model based upon a tonalite‐trondhjemite‐granodiorite compositional model for the Archaean continental crust shows that the post‐Archaean mantle to crust flux was predominantly basaltic and likely a mix of arc‐plume basalts. Trace element modeling, however, reveals that additional processes also contributed to the average crust composition. Balancing Y, Ho, and Yb concentrations requires a garnetiferous mafic granulite lower Archaean crust, which in turn drives the post‐Archaean flux toward a high mg # andesite. This suggests that there was a slab melt contribution to the continents, in addition to basalt. An excess of fluid mobile elements in the continental crust can be explained either by the addition of a slab melt or small fraction melts. A deficiency in Sr requires that the post‐Archaean crustal composition has been modified by erosion. Both Archaean and post‐Archaean continental crust contain contributions from basalt and a slab melt. In the Archaean crust the slab melt contribution is dominant. In the post‐Archaean crust the basaltic contribution is dominant.
Could negative ion production explain the polar mesosphere winter echo (PMWE) modulation in active HF heating experiments?
Authors: Kero A. , Enell C.‐F. , Kavanagh A. J. , Vierinen J. , Virtanen I. , Turunen E.
Published: December 2008

The mechanism behind the modulation of polar mesospheric winter echoes (PMWE) observed in active HF heating experiments is considered. We propose that negative ion chemistry plays a role in the heater‐induced modulation of the PMWEs. In the mesosphere, an increased electron temperature leads to a higher rate of electron to neutral attachment, and therefore to a decreased electron density. To a first‐order approximation, scattering from Bragg‐scale gradients caused by turbulence can be considered to be proportional to the electron density squared. Under this assumption, the electron density variation calculated by the detailed Sodankylä Ion Chemistry model (SIC) predicts correctly both the magnitude and the timescale of the modulation observed with the EISCAT VHF radar.
Spatial heterogeneity of the mantle wedge structure and interplate coupling in the NE Japan forearc region
Authors: Yamamoto Yojiro , Hino Ryota , Suzuki Kensuke , Ito Yoshihiro , Yamada Tomoaki , Shinohara Masanao , Kanazawa Toshihiko , Aoki Gen , Tanaka Masayuki , Uehira Kenji , Fujie Gou , Kaneda Yoshiyuki , Takanami Tetsuo , Sato Toshinori
Published: December 2008

We performed 3‐D seismic tomography in the forearc region of the northeastern Japan subduction zone using both onshore and offshore seismic station data. We obtained the Vp, Vs, and Vp/Vs structures around the plate boundary with high spatial resolution. The position of the plate boundary as defined by relocated hypocenters coincides with the sharp velocity boundary between the oceanic crust and the mantle wedge. The mantle wedge above the coseismic slip area of the 1978 and 2005 off‐Miyagi interplate earthquakes (M > 7) is characterized by high Vp and Vs, but low Vp/Vs. Off Fukushima, however, where large earthquakes rarely occur, we found a high Vp/Vs anomaly at the tip of the mantle wedge. The spatial distribution of serpentinized mantle wedge limits the spatial extent of the strongly coupled area on the plate boundary, and thus can explain the difference in seismic activity between the off‐Miyagi and off‐Fukushima regions.
Complexities of a 3‐D plasmoid flux rope as shown by an MHD simulation
Authors: Farr N. L. , Baker D. N. , Wiltberger M.
Published: December 2008

The results of a global magnetohydrodynamic (MHD) simulation of a pair of magnetospheric substorms on 11 August 2002 are presented. Comparisons of data with simulation results reveal a good agreement regarding the sequence of events during substorm development. We give particular emphasis to results in the simulation of a flux rope formed during the second substorm. Unlike standard 2‐D depictions of reconnection and plasmoid release during the substorm sequence, the simulation shows a highly complex structure that has considerable winding of both closed and open field lines. Additionally, the simulated flux rope does not move tailward uniformly, but rather it has asymmetric motion in which the dawn flank portion moves tailward prior to the dusk portion of the flux rope. This results in a skewed flux rope structure that runs almost parallel to the tail axis instead of perpendicular to it. The simulation compares well with both prior flux rope simulations as well as satellite observations of flux ropes. We use the global simulation to map flux tube properties to the ionosphere, which allows the complexity of the mapping of the magnetic field structure from the tail to the ionosphere to be seen in a novel manner.
Hurricane storm surge simulations comparing three‐dimensional with two‐dimensional formulations based on an Ivan‐like storm over the Tampa Bay, Florida region
Authors: Weisberg Robert H. , Zheng Lianyuan
Published: December 2008

We provide a dynamics‐based comparison on the results from three‐dimensional and two‐dimensional simulations of hurricane storm surge. We begin with the question, What may have occurred in the Tampa Bay, Florida vicinity had Hurricane Ivan made landfall there instead of at the border between Alabama and Florida? This question is explored using a three‐dimensional, primitive equation, finite volume coastal ocean model. The results show that storm surges are potentially disastrous for the Tampa Bay area, especially for landfalls located to the north of the bay mouth. The worst case among the simulations considered is for landfall at Tarpon Springs, such that the maximum wind is positioned at the bay mouth. Along with such regional aspects of storm surge, we then consider the dynamical balances to assess the importance of using a three‐dimensional model instead of the usual, vertically integrated, two‐dimensional approach to hurricane storm surge simulation. With hurricane storm surge deriving from the vertically integrated pressure gradient force tending to balance the difference between the surface and bottom stresses, we show that three‐dimensional structure is intrinsically important. Two‐dimensional models may overestimate (or underestimate) bottom stress, necessitating physically unrealistic parameterizations of surface stress or other techniques for model calibration. Our examination of the dynamical balances inherent to storm surges over complex coastal topography suggests that three‐dimensional models are preferable over two‐dimensional models for simulating storm surges.
AF10‐dependent transcription is enhanced by its interaction with FLRG
Authors: Forissier Stéphanie , Razanajaona Diane , Ay Anne‐Sophie , Martel Sylvie , Bartholin Laurent , Rimokh Ruth
Published: December 2008

Background information. FLRG (follistatin‐related gene) is a secreted glycoprotein which is very similar to follistatin. As observed for follistatin, FLRG is involved in the regulation of various biological processes through its binding to members of the TGFβ (transforming growth factor β) superfamily, activin, BMPs (bone morphogenetic proteins) and myostatin. Unlike follistatin, FLRG has been found to be both secreted and localized within the nucleus of many FLRG‐producing cells, suggesting the existence of specific intracellular functions of the protein.

Results. In order to analyse the function of the nuclear form of FLRG, we performed a yeast two‐hybrid screen, in which we identified AF10 [ALL1 (acute lymphoblastic leukaemia) fused gene from chromosome 10], a translocation partner of the MLL (mixed‐lineage leukaemia) oncogene in human leukaemia, as a FLRG‐interacting protein. This interaction was confirmed by far‐Western‐blot analysis and co‐immunoprecipitation with transfected COS‐7 cells. The N‐terminal region of AF10, including the PHD (plant homeodomain), is sufficient to mediate this interaction, and has been shown to be involved in AF10 homo‐oligomerization. By immunoprecipitation experiments, we showed that FLRG enhances the homo‐oligomerization of AF10. Functional studies demonstrated that FLRG enhances the transactivation properties of the AF10 protein fused to Gal4 DNA‐binding domains in transient transfection assays.

Conclusions. Our present study provides novel insights into the function of the nuclear form of the FLRG protein, which is revealed as a novel regulator of transcription. The nuclear isoform of FLRG lacks an intrinsic transactivation domain, but enhances AF10‐mediated transcription, probably through promoting the homo‐oligomerization of AF10, thus facilitating the recruitment of co‐activators.
Long-Term Usage of Modern Signal Processing by Listeners With Severe or Profound Hearing Loss: A Retrospective Survey
Authors: Keidser Gitte , Hartley David , Carter Lyndal
Published: December 2008

Purpose

To investigate the long-term benefit of multichannel wide dynamic range compression (WDRC) alone and in combination with directional microphones and noise reduction/speech enhancement for listeners with severe or profound hearing loss.

Method

At the conclusion of a research project, 39 participants with severe or profound hearing loss were fitted with WDRC in one program and WDRC with directional microphones and speech enhancement enabled in a 2nd program. More than 2 years after the 1st participants exited the project, a retrospective survey was conducted to determine the participants' use of, and satisfaction with, the 2 programs.

Results

From the 30 returned questionnaires, it seems that WDRC is used with a high degree of satisfaction in general everyday listening situations. The reported benefit from the addition of a directional microphone and speech enhancement for listening in noisy environments was lower and varied among the users. This variable was significantly correlated with how much the program was used.

Conclusions

The less frequent and more varied use of the program with directional microphones and speech enhancement activated in combination suggests that these features may be best offered in a 2nd listening program for listeners with severe or profound hearing loss.
Interfacial and wetting properties of a binary point Yukawa fluid
Authors: Hopkins Paul , Archer Andrew J. , Evans Robert
Published: December 2008

We investigate the interfacial phase behavior of a binary fluid mixture composed of repulsive point Yukawa particles. Using a simple approximation for the Helmholtz free energy functional, which yields the random phase approximation for the pair direct correlation functions, we calculate the equilibrium fluid density profiles of the two species of particles adsorbed at a planar wall. We show that for a particular choice (repulsive exponential) of the wall potentials and the fluid pair-potential parameters, the Euler–Lagrange equations for the equilibrium fluid density profiles may be transformed into a single ordinary differential equation and the profiles obtained by a simple quadrature. For certain other choices of the fluid pair-potential parameters fluid-fluid phase separation of the bulk fluid is observed. We find that when such a mixture is exposed to a planar hard wall, the fluid exhibits complete wetting on the species 2 poor side of the binodal, i.e., we observe a thick film of fluid rich in species 2 adsorbed at the hard wall. The thickness of the wetting film grows logarithmically with the concentration difference between the fluid state point and the binodal and is proportional to the bulk correlation length of the intruding (wetting) fluid phase. However, for state points on the binodal that are further from the critical point, we find there is no thick wetting film. We determine the accompanying line of first-order (prewetting) surface phase transitions which separate a thin and thick adsorbed film. We show that for some other choices of repulsive wall potentials the prewetting line is still present, but its location and extent in the phase diagram is strongly dependent on the wall-fluid interaction parameters.
High-field transport and terahertz generation in GaN
Authors: Dyson A. , Ridley B. K.
Published: December 2008

The conduction-band structure of GaN suggests that electron transport at high fields should exhibit a negative differential resistance (NDR) either via the transferred-electron effect or as a consequence of the negative effective mass beyond the inflection point. In order to discuss these possibilities we use a simple model of the band structure and obtain analytical expressions for the density of states and scattering rates due to the interaction with polar-optical phonons. Estimates of the cutoff frequencies for the Gunn effect in GaN and AlN are obtained. The negative-mass NDR is described in terms of a hydrodynamic model and the result is compared with that of Esaki and Tsu [IBM J. Res. Dev. 14, 61 (1970)]. We explore the effect in short diodes of length and transit time on the frequency-dependent NDR associated with quasiballistic motion and conclude with a discussion of transport when the electrons are localized by Bragg reflection.
Plume dynamics and shielding characteristics of nanosecond scale multiple pulse in carbon ablation
Authors: Pathak Kedar , Povitsky Alex
Published: December 2008

The behavior of ablated plumes produced by nanosecond scale multiple laser pulses typical for carbon ablation is studied in order to understand the plume expansion dynamics and shielding effect of plume with special interest to ionization of plumes. The patterns of a planar plume (typical for channel cutting) and an axisymmetric plume (typical for hole drilling) appear to be quite different. Ionization in carbon plume is estimated using the Saha equation. An iterative procedure is developed to determine the local equilibrium temperature affected by ionization. It is shown that though shielding due to the presence of ionized particles in carbon plume is small, the effect of ionization on plume temperature can be considerable. Shielding effect is calculated for laser pulses with different time intervals between pulses. The effects of high temperature and low density of plume are conflicting and cause shielding behavior to be nonmonotonic. It is shown that the nonmonotonic dependence of the delivered laser energy, the pulse number, and the difference in shielding characteristics between planar and axisymmetric formulations increase with the time duration between two consecutive pulses.
Mechanisms of efficiency enhancement in the doped electroluminescent devices based on a europium complex
Authors: Zhou Liang , Zhang Hongjie , Shi Weidong , Deng Ruiping , Li Zhefeng , Yu Jiangbo , Guo Zhiyong
Published: December 2008

In this study, we investigated the dependence of electroluminescence (EL) efficiency on carrier distribution in the light-emitting layer (EML) of the device based on Eu(TTA)3phen (TTA=thenoyltrifluoroacetone, phen=1,10-phenanthroline) doped 4,4′-N,N′-dicarbazole-biphenyl (CBP) system. We found that EL efficiency increases monotonously with increasing hole injection even when holes are the majority carriers. This phenomenon was attributed to the accumulation of holes in EML, which improves the balance of holes and electrons on Eu(TTA)3phen molecules, thus enhancing the EL efficiency. To further improve the balance of holes and electrons on Eu(TTA)3phen molecules, the injection of electron was gently decreased by modulating the thickness of Al and LiF layers. Interestingly, EL efficiency increases gradually to a maximum and then decreases rapidly with decreasing electron injection. As a result, the device with 80 nm Al and 1.2 nm LiF obtained the maximal current efficiency of 9.53 cd/A, power efficiency of 5.35 lm/W, and external quantum efficiency of 5.15%. Our experimental results demonstrated that the balance of holes and electrons on dye molecules is the precondition for the doped device to obtain high EL efficiency, when carrier trapping is the dominant EL mechanism.
Temperature dependence of the current conduction mechanisms in LaAlO3 thin films
Authors: Chang Ingram Yin-Ku , Lee Joseph Ya-Min
Published: December 2008

Metal-oxide-semiconductor capacitors and transistors with LaAlO3 dielectric films were fabricated and the current conduction mechanisms were studied. The LaAlO3 films remained amorphous with postdeposition annealing up to 1000 °C. The leakage current density was 8.3×10−5 A/cm2 at −1 V. The low leakage current was attributed to the high barrier height of Al/LaAlO3 interface. The Al/LaAlO3 barrier height and the effective electronic mass calculated from Schottky emission and Fowler–Nordheim tunneling were 1.12 eV and 0.27m0, respectively. The dominant conduction mechanism in the temperature range of 300 K<T<420 K was space-charge-limited current, and the trapping depth was determined to be 0.36±0.1 eV.
Recent origins and genetic fragmentation of Simulium (Hebridosimulium) laciniatum (Diptera), the endemic Fijian simuliid
Authors: Gaudreau Christine , LaRue Bernard , Charbonneau Valérie , Charpentier Guy , Craig Douglas A.
Published: December 2008

Simulium laciniatum Edwards, 1924 is endemic to Fiji and is also the only known black fly species in the Fiji archipelago, a most unusual situation since neighbouring Vanuatu harbours fourteen precinctive species from the same subgenus, Hebridosimulium Grenier & Rageau, 1961. Morphology indicates that S. (H.) laciniatum is monospecific throughout the Fiji archipelago, so the species was further scrutinised from a molecular standpoint. Samples taken from five islands of Fiji show a major lack of heterogeneity in the mitochondrial COII gene and a probable date around 105 years has been inferred for the S. (H.) laciniatum ancestor, a likely migrant from Vanuatu. COII homogeneity may also reflect the dispersal abilities of blood-seeking females of this species, abetted possibly by shortened distances between islands during ice ages concurrent with depressed sea levels. However, the ITS1 spacer between the 18S and 5.8S rDNA genes exhibits six haplotypes, with the two predominant ones clearly arrayed in a north–south distribution. This suggests sufficient distance between suites of islands in recent times to allow precinctive population development.
Effects of gradient encoding and number of signal averages on fractional anisotropy and fiber density index in vivo at 1.5 tesla
Authors: Widjaja E. , Mahmoodabadi S. Z. , Rea D. , Moineddin R. , Vidarsson L. , Nilsson D.
Published: December 2008

Background: Tensor estimation can be improved by increasing the number of gradient directions (NGD) or increasing the number of signal averages (NSA), but at a cost of increased scan time.

Purpose: To evaluate the effects of NGD and NSA on fractional anisotropy (FA) and fiber density index (FDI) in vivo.

Material and Methods: Ten healthy adults were scanned on a 1.5T system using nine different diffusion tensor sequences. Combinations of 7 NGD, 15 NGD, and 25 NGD with 1 NSA, 2 NSA, and 3 NSA were used, with scan times varying from 2 to 18 min. Regions of interest (ROIs) were placed in the internal capsules, middle cerebellar peduncles, and splenium of the corpus callosum, and FA and FDI were calculated. Analysis of variance was used to assess whether there was a difference in FA and FDI of different combinations of NGD and NSA.

Results: There was no significant difference in FA of different combinations of NGD and NSA of the ROIs ( P>0.005). There was a significant difference in FDI between 7 NGD/1 NSA and 25 NGD/3 NSA in all three ROIs ( P<0.005). There were no significant differences in FDI between 15 NGD/3 NSA, 25 NGD/1 NSA, and 25 NGD/2 NSA and 25 NGD/3 NSA in all ROIs ( P>0.005).

Conclusion: We have not found any significant difference in FA with varying NGD and NSA in vivo in areas with relatively high anisotropy. However, lower NGD resulted in reduced FDI in vivo. With larger NGD, NSA has less influence on FDI. The optimal sequence among the nine sequences tested with the shortest scan time was 25 NGD/1 NSA.
Functional mechanism of lung mosaic CT attenuation: Assessment with deep-inspiration breath-hold perfusion SPECT-CT fusion imaging and non-breath-hold technegas SPECT
Authors: Suga K. , Yasuhiko K. , Iwanaga H. , Tokuda O. , Matsunaga N.
Published: December 2008

Background: The functional mechanism of lung mosaic computed tomography attenuation (MCA) in pulmonary vascular disease (PVD) and obstructive airway disease (OAD) has not yet been fully clarified.

Purpose: To clarify the mechanism of MCA in these diseases by assessing the relationship between regional lung function and CT attenuation change at MCA sites with the use of automated deep-inspiratory breath-hold (DIBrH) perfusion single-photon emission computed tomography (SPECT)-CT fusion images and non-breath-hold Technegas SPECT.

Material and Methods: Subjects were 42 PVD patients (31 pulmonary thromboembolism, four primary/two secondary pulmonary hypertension, and five Takayasu arteritis), 12 OAD patients (five acute asthma, four obliterative bronchiolitis, and three bronchiectasis), and 12 normal controls, all of whom had MCA on DIBrH CT. The relationship between regional lung function and CT attenuation change at the lung slices with MCA was assessed using DIBrH perfusion SPECT-CT fusion images and non-breath-hold Technegas SPECT. The severity of perfusion defects with or without MCA was quantified by regions-of-interest analysis.

Results: On DIBrH CT and perfusion SPECT, in contrast to no noticeable CT attenuation abnormality and fairly uniform perfusion in controls, 60 MCA and 274 perfusion defects in PVD patients, and 18 MCA and 61 defects in OAD patients were identified, with a total of 77 ventilation defects on Technegas SPECT in all patients. SPECT-CT correlation showed that, throughout the 78 MCA sites of all patients, lung perfusion was persistently decreased at low CT attenuation and preserved at intervening high CT attenuation, while lung ventilation was poorly correlated with CT attenuation change. The radioactivity ratios of reduced perfusion and the intervening preserved perfusion at the 78 perfusion defects with MCA were significantly lower than those at the remaining 257 defects without MCA ( P<0.0001).

Conclusion: Although further validation is required, our results indicate that heterogeneous pulmonary arterial perfusion may be a dominant mechanism of MCA in PVD and OAD.
A predictive model for identifying mini-regulatory modules in the mouse genome
Authors: Yaragatti Mahesh , Sandler Ted , Ungar Lyle
Published: December 2008

Motivation: Rapidly advancing genome technology has allowed access to a large number of diverse genomes and annotation data. We have defined a systems model that integrates assembly data, comparative genomics, gene predictions, mRNA and EST alignments and physiological tissue expression. Using these as predictive parameters, we engineered a machine learning approach to decipher putative active regions in the genome.

Results: Analysis of genomic sequences showed nucleosome-free region (NFR) modules containing a higher percentage of conserved regions, RNA-encoding sequences, CpG islands, splice sites and GC-rich areas. In contrast, random in silico fragments revealed higher percentages of DNA repeats and a lower conservation. The larger conserved sequences from the Vista enhancer browser (VEB) showed a greater percentage of short DNA sequence matches and RNA coding regions in multiple species.

Our model can predict small regulatory regions in the genome with >95% prediction accuracy using NFR modules and >85% prediction accuracy with VEB elements. Ultimately, this systems model can be applied to any organism to identify candidate transcriptional modules on a genome scale.

Contact:  myar@seas.upenn.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
The cohesin complex and its roles in chromosome biology
Authors: Peters Jan-Michael , Tedeschi Antonio , Schmitz Julia
Published: December 2008

Cohesin is a chromosome-associated multisubunit protein complex that is highly conserved in eukaryotes and has close homologs in bacteria. Cohesin mediates cohesion between replicated sister chromatids and is therefore essential for chromosome segregation in dividing cells. Cohesin is also required for efficient repair of damaged DNA and has important functions in regulating gene expression in both proliferating and post-mitotic cells. Here we discuss how cohesin associates with DNA, how these interactions are controlled during the cell cycle; how binding of cohesin to DNA may mediate sister chromatid cohesion, DNA repair, and gene regulation; and how defects in these processes can lead to human disease.
Modular control of endothelial sheet migration
Authors: Vitorino Philip , Meyer Tobias
Published: December 2008

Growth factor-induced migration of endothelial cell monolayers enables embryonic development, wound healing, and angiogenesis. Although collective migration is widespread and therapeutically relevant, the underlying mechanism by which cell monolayers respond to growth factor, sense directional signals, induce motility, and coordinate individual cell movements is only partially understood. Here we used RNAi to identify 100 regulatory proteins that enhance or suppress endothelial sheet migration into cell-free space. We measured multiple live-cell migration parameters for all siRNA perturbations and found that each targeted protein primarily regulates one of four functional outputs: cell motility, directed migration, cell–cell coordination, or cell density. We demonstrate that cell motility regulators drive random, growth factor-independent motility in the presence or absence of open space. In contrast, directed migration regulators selectively transduce growth factor signals to direct cells along the monolayer boundary toward open space. Lastly, we found that regulators of cell–cell coordination are growth factor-independent and reorient randomly migrating cells inside the sheet when boundary cells begin to migrate. Thus, cells transition from random to collective migration through a modular control system, whereby growth factor signals convert boundary cells into pioneers, while cells inside the monolayer reorient and follow pioneers through growth factor-independent migration and cell–cell coordination.
Genetic ablation of FLRT3 reveals a novel morphogenetic function for the anterior visceral endoderm in suppressing mesoderm differentiation
Authors: Egea Joaquim , Erlacher Christian , Montanez Eloi , Burtscher Ingo , Yamagishi Satoru , Heß Martin , Hampel Falko , Sanchez Rodrigo , Rodriguez-Manzaneque Maria Teresa , Bösl Michael R. , Fässler Reinhard , Lickert Heiko , Klein Rüdiger
Published: December 2008

During early mouse development, the anterior visceral endoderm (AVE) secretes inhibitor and activator signals that are essential for establishing the anterior–posterior (AP) axis of the embryo and for restricting mesoderm formation to the posterior epiblast in the primitive streak (PS) region. Here we show that AVE cells have an additional morphogenetic function. These cells express the transmembrane protein FLRT3. Genetic ablation of FLRT3 did not affect the signaling functions of the AVE according to the normal expression pattern of Nodal and Wnt and the establishment of a proper AP patterning in the epiblast. However, FLRT3−/− embryos showed a highly disorganized basement membrane (BM) in the AVE region. Subsequently, adjacent anterior epiblast cells displayed an epithelial-to-mesenchymal transition (EMT)-like process characterized by the loss of cell polarity, cell ingression, and the up-regulation of the EMT and the mesodermal marker genes Eomes, Brachyury/T, and FGF8. These results suggest that the AVE acts as a morphogenetic boundary to prevent EMT and mesoderm induction in the anterior epiblast by maintaining the integrity of the BM. We propose that this novel function cooperates with the signaling activities of the AVE to restrict EMT and mesoderm induction to the posterior epiblast.
A note on the description of the kinetics of phosphate sorption
Authors: Barrow N. J. , Hansen H. C. B. , Hansen P. E. , Magid J.
Published: December 2008

Summary Observations on the rate of sorption of phosphate by four samples of Danish soils have been re‐examined. A previously reported lag phase in plots of log concentration against log time could be ascribed to the use of large solution:soil ratios rather than to the inclusion of short periods of reaction.
Economic Growth, Climate Change, Biodiversity Loss: Distributive Justice for the Global North and South
Authors: ROSALES JON
Published: December 2008

Abstract:  Economic growth‐the increase in production and consumption of goods and services‐must be considered within its biophysical context. Economic growth is fueled by biophysical inputs and its outputs degrade ecological processes, such as the global climate system. Economic growth is currently the principal cause of increased climate change, and climate change is a primary mechanism of biodiversity loss. Therefore, economic growth is a prime catalyst of biodiversity loss. Because people desire economic growth for dissimilar reasons‐some for the increased accumulation of wealth, others for basic needs‐how we limit economic growth becomes an ethical problem. Principles of distributive justice can help construct an international climate‐change regime based on principles of equity. An equity‐based framework that caps economic growth in the most polluting economies will lessen human impact on biodiversity. When coupled with a cap‐and‐trade mechanism, the framework can also provide a powerful tool for redistribution of wealth. Such an equity‐based framework promises to be more inclusive and therefore more effective because it accounts for the disparate developmental conditions of the global north and south.
Macroeconomic Policy, Growth, and Biodiversity Conservation
Authors: LAWN PHILIP
Published: December 2008

Abstract:  To successfully achieve biodiversity conservation, the amount of ecosystem structure available for economic production must be determined by, and subject to, conservation needs. As such, the scale of economic systems must remain within the limits imposed by the need to preserve critical ecosystems and the regenerative and waste assimilative capacities of the ecosphere. These limits are determined by biophysical criteria, yet macroeconomics involves the use of economic instruments designed to meet economic criteria that have no capacity to achieve biophysically based targets. Macroeconomic policy cannot, therefore, directly solve the biodiversity erosion crisis. Nevertheless, good macroeconomic policy is still important given that bad macroeconomy policy is likely to reduce human well‐being and increase the likelihood of social upheaval that could undermine conservation efforts.
Insect Herbivory of Ovules and Seeds in Native and Restored Prairies
Authors: Molano‐Flores Brenda
Published: December 2008

Insect herbivory of ovules and seeds is known to have a negative impact on individual plant reproductive success by reducing overall seed set. Although this seed set reduction has been well documented in plant populations found in native habitats, little work has been done on populations found in restored habitats. In a 4‐year study (2001–2004), I investigated the herbivory of the Gelechiid moth (Coleotechnites eryngiella) of Eryngium yuccifolium populations in native and restored prairies. Data were collected from 20 E. yuccifolium populations (10 native prairies/10 restored prairies) in Illinois. Percent herbivory and percent seed set were determined for each population. From 2001 to 2004, percent herbivory in prairie restorations ranged from 0 to 93 and percent seed set ranged from 2 to 82. In native prairies, percent herbivory ranged from 0 to 98 and percent seed set ranged from 0 to 71. No differences were found between native and restored prairies for percent herbivory or percent seed set. However, significant differences were found among years for percent seed set. This study shows that the antagonistic effects of insect herbivory can reach similar levels in restored and native prairies.
Seed Dispersal Patterns by Large Frugivorous Mammals in a Degraded Mosaic Landscape
Authors: Matías Luis , Zamora Regino , Mendoza Irene , Hódar José A.
Published: December 2008

Seed dispersal by Red fox (Vulpes vulpes), Stone marten (Martes foina), and Wild boar (Sus scrofa) was analyzed in an extensively degraded mosaic landscape in Sierra Nevada (SE Spain). The main objective was to determine whether seed dispersal by mammals was related to habitat degradation within a mosaic of adjacent degraded patches mixed with native forest and thereby to determine the potential role of mammals as seed dispersers in degraded landscape units. For three consecutive years, mammal feces were collected in the fruit production period, extracting all seeds of woody species found therein and analyzing their viability. Feces were collected in three different plots for each of five different landscape units: shrubland, native forest, and dense, cleared, and fenced reforestation stands. Seeds from 16 woody species (which represent more than a half of the total fleshy‐fruited woody species available) were recorded, although some agrarian species are also introduced in a low percentage of the scats. Seeds showed a high viability rate for all dispersed species, irrespective of the mammal disperser. No differences in species composition appeared in the overall landscape units or in the seed density between degraded habitats. Due to the small patch size, the high viability of dispersed seeds, and the large home range of the large mammals, these three animal species act as efficient seed dispersers for a diverse assemblage of woody plant species regardless of the habitat type within this degradation framework. This fact has important consequences for the biodiversity recuperation in these degraded habitats, principally in pine plantations.
Experimental epileptology before 1900
Authors: Eadie Mervyn J.
Published: December 2008

The available English and other major Western European language literature was reviewed to assess the stage of development of experimental epileptology prior to the end of the 19th Century. The relevant investigations had been carried out in animals of various species employing a number of methods of evoking convulsive seizures, mainly mechanical, electrical or chemical stimulation or surgical removal of parts of the cerebral cortex. The studies had produced some conflicting data but (i) allowed the development of a number of reasonably satisfactory experimental models of convulsive epileptic seizures (ii) confirmed that such epileptic seizures arose from the cerebral cortex, and (iii) suggested that for local onset epileptic seizures to become generalised tonic‐clonic ones, the opposite motor cortex and probably a brain stem, possibly pontine, centre needed to be involved. No generally acceptable animal model of chronic epilepsy had been developed, and the non‐motor manifestations of epileptic seizures were still largely unexplored experimentally. Nevertheless, the pre‐1900 investigations not only laid the foundations for the 20th Century expansion of experimental studies on epileptogenesis but also advanced the understanding of epileptic seizure production.
IgM plasma cell myeloma with amyloidosis presenting as mammary microcalcifications
Authors: FERNANDEZ‐AGUILAR SERGIO , SOURTZIS STAUROULA , CHAIKH ALI
Published: December 2008

We report the case of an otherwise healthy 67‐year‐old woman who presented with bilateral breast masses and calcifications. Bilateral mammary biopsies showed infiltration by monoclonal neoplastic plasma cells and diffuse osseous metaplasia. Congo red stains and immunohistochemistry showed amyloid deposits. This case illustrates why multiple myeloma should be kept in mind in the diagnosis of mammary calcifications.
Outpatient care and medical treatment of children and adults with atopic eczema
Authors: Schmitt Jochen , Schmitt Natalie M. , Kirch Wilhelm , Meurer Michael
Published: December 2008

Background: Despite the high prevalence, morbidity and economic burden of atopic eczema (AE), data on outpatient care of affected patients are missing. Methods: Utilizing a population‐based administrative health care database from Saxony, Germany, this study describes outpatient care and medical treatment of AE by different medical disciplines in 2003 and 2004 by means of a representative sample of 11,555 patients with AE.

Results: About 60% of all patients with AE seeking outpatient care were adults. Of the adults 66% and among children 51% consulted a dermatologist at least once within the study period. More than 50% of patients in all age groups received potent topical steroids. Of all patients 8% and 3% received topical pimecrolimus and topical tacrolimus, respectively. More than 10% of patients received systemic steroids, while less than 0.1% was given cyclosporine. The mean annual amount of topical anti‐inflammatory treatment per patient was about 40 grams.

Conclusions: Unexpectedly high proportions of patients with AE received potent topical and systemic steroids. The average total amount of prescribed medications was low. This study suggests insufficient care and medical treatment of patients with AE in routine practice.