bluuebunny/crossref_metadata_2025 huggingface dataset:
pH replica‐exchange method based on discrete protonation states
Authors: Itoh Satoru G. , Damjanović Ana , Brooks Bernard R.
Published: September 2011

We propose a new algorithm for obtaining proton titration curves of ionizable residues. The algorithm is a pH replica‐exchange method (PHREM), which is based on the constant pH algorithm of Monganet al. (J Comput Chem 2004;25:2038–2048). In the original replica‐exchange method, simulations of different replicas are performed at different temperatures, and the temperatures are exchanged between the replicas. In our PHREM, simulations of different replicas are performed at different pH values, and the pHs are exchanged between the replicas. The PHREM was applied to a blocked amino acid and to two protein systems (snake cardiotoxin and turkey ovomucoid third domain), in conjunction with a generalized Born implicit solvent. The performance and accuracy of this algorithm and the original constant pH method (PHMD) were compared. For a single set of simulations at different pHs, the use of PHREM yields more accurate Hill coefficients of titratable residues. By performing multiple sets of constant pH simulations started with different initial states, the accuracy of predicted pKavalues and Hill coefficients obtained with PHREM and PHMD methods becomes comparable. However, the PHREM algorithm exhibits better samplings of the protonation states of titratable residues and less scatter of the titration points and thus better precision of measured pKavalues and Hill coefficients. In addition, PHREM exhibits faster convergence of individual simulations than the original constant pH algorithm. Proteins 2011; © 2011 Wiley‐Liss, Inc.
Assessment of template based protein structure predictions in CASP9
Authors: Mariani Valerio , Kiefer Florian , Schmidt Tobias , Haas Juergen , Schwede Torsten
Published: September 2011

In the Ninth Edition of the Critical Assessment of Techniques for Protein Structure Prediction (CASP9), 61,665 models submitted by 176 groups were assessed for their accuracy in the template based modeling category. The models were evaluated numerically in comparison to their experimental control structures using two global measures (GDT and GDC), and a novel local score evaluating the correct modeling of local interactions (lDDT). Overall, the state of the art of template based modeling in CASP9 is high, with many groups performing well. Among the methods registered as prediction “servers”, six independent groups are performing on average better than the rest. The submissions by “human” groups are dominated by meta‐predictors, with one group performing noticeably better than the others. Most of the participating groups failed to assign realistic confidence estimates to their predictions, and only a very small fraction of the assessed methods have provided highly accurate models and realistic error estimates at the same time. Also, the accuracy of predictions for homo‐oligomeric assemblies was overall poor, and only one group performed better than a naïve control predictor. Here, we present the results of our assessment of the CASP9 predictions in the category of template based modeling, documenting the state of the art and highlighting areas for future developments. Proteins 2011; © 2011 Wiley‐Liss, Inc.
CASP9 assessment of free modeling target predictions
Authors: Kinch Lisa , Yong Shi Shuo , Cong Qian , Cheng Hua , Liao Yuxing , Grishin Nick V.
Published: September 2011

We present an overview of the ninth round of Critical Assessment of Protein Structure Prediction (CASP9) “Template free modeling” category (FM). Prediction models were evaluated using a combination of established structural and sequence comparison measures and a novel automated method designed to mimic manual inspection by capturing both global and local structural features. These scores were compared to those assigned manually over a diverse subset of target domains. Scores were combined to compare overall performance of participating groups and to estimate rank significance. Moreover, we discuss a few examples of free modeling targets to highlight the progress and bottlenecks of current prediction methods. Notably, a server prediction model for a single target (T0581) improved significantly over the closest structure template (44% GDT increase). This accomplishment represents the “winner” of the CASP9 FM category. A number of human expert groups submitted slight variations of this model, highlighting a trend for human experts to act as “meta predictors” by correctly selecting among models produced by the top‐performing automated servers. The details of evaluation are available at http://prodata.swmed.edu/CASP9/. © Proteins 2011; © 2011 Wiley‐Liss, Inc.
CASP9 results compared to those of previous casp experiments
Authors: Kryshtafovych Andriy , Fidelis Krzysztof , Moult John
Published: September 2011

The quality of structure models submitted to CASP9 is analyzed in the context of previous CASPs. Comparison methods are similar to those used in previous articles in this series, with the addition of new methods looking at model quality in regions not covered by a single best structural template, alignment accuracy, and progress for template‐free models. Progress in this CASP was again modest and statistically hard to validate. Nevertheless, there are several positive trends. There is an indication of improvement in overall model quality for the midrange of template‐based modeling difficulty, methods for identifying the best model from a set generated have improved, and there are strong indications of progress in the quality of template‐free models of short proteins. In addition, the new examination of a model quality in regions of model not covered by the best available template reveals better performance than had previously been apparent. © Proteins 2011; © 2011 Wiley‐Liss, Inc.
Molecular dynamics simulation of conformational heterogeneity in transportin 1
Authors: Wang Xia , Xu Xue , Zhu Shanna , Xiao Zhengtao , Ma Zhi , Li Yan , Wang Yonghua
Published: September 2011

Transportin 1 (Trn1), as a typical transport receptor of the karyopherin‐β family, mediates numerous RNA binding proteins into the nucleus by recognizing proline‐tyrosine nuclear localization signals (PY‐NLSs). Such process is regulated by RanGTP through its nucleotide cycle, which is associated with ligand dissociation. Yet a proper description including dynamic properties of Trn1 and its response on ligand/Ran binding has not been accessible so far. Here, we use molecular dynamics simulations to probe the conformational dynamics of the apo‐Trn1 and Trn1 in complex with ligand and Ran. The results reveal a strikingly intrinsic flexibility and conformational heterogeneity of Trn1, identified as generally segmental architecture. The segments rotate relative to each other about a flexible hinge and thereby force Trn1 to adopt a conformation compatible with the binding of Ran or substrates. Such binding significantly suppresses the flexibility and conformational heterogeneity of Trn1 and results in a disorder‐to‐order transition of HR8 loop, which facilitates this loop to allosterically communicate with the C‐terminal arch of Trn1. These results give insights into the disassembly and recycling of the Trn1, which has important implications for the regulation of the nuclear transport cycle and for the ligand selectivity. Proteins 2012. © 2011 Wiley Periodicals, Inc.
Predicting extreme pKa shifts in staphylococcal nuclease mutants with constant pH molecular dynamics
Authors: Arthur Evan J. , Yesselman Joseph D. , Brooks Charles L.
Published: September 2011

Accurate computational methods of determining protein and nucleic acid pKa values are vital to understanding pH‐dependent processes in biological systems. In this article, we use the recently developed method constant pH molecular dynamics (CPHMD) to explore the calculation of highly perturbed pKa values in variants of staphylococcal nuclease (SNase). Simulations were performed using the replica exchange (REX) protocol for improved conformational sampling with eight temperature windows, and yielded converged proton populations in a total sampling time of 4 ns. Our REX‐CPHMD simulations resulted in calculated pKa values with an average unsigned error (AUE) of 0.75 pK units for the acidic residues in Δ + PHS, a hyperstable variant of SNase. For highly pKa‐perturbed SNase mutants with known crystal structures, our calculations yielded an AUE of 1.5 pK units and for those mutants based on modeled structures an AUE of 1.4 pK units was found. Although a systematic underestimate of pK shifts was observed in most of the cases for the highly perturbed pK mutants, correlations between conformational rearrangement and plasticity associated with the mutation and error in pKa prediction was not evident in the data. This study further extends the scope of electrostatic environments explored using the REX‐CPHMD methodology and suggests that it is a reliable tool for rapidly characterizing ionizable amino acids within proteins even when modeled structures are employed. Proteins 2011; © 2011 Wiley‐Liss, Inc.
High resolution TEM study of WS2 nanotubes
Authors: Krause Matthias , Mücklich Arndt , Zak Alla , Seifert Gotthard , Gemming Sibylle
Published: September 2011

Closed capped WS2 nanotubes with diameters from 30 to 110 nm are studied by high resolution transmission electron microscopy (HRTEM). The tubes exhibit preferentially a hexagonal stacking order. Atomic resolution images of a 30 nm diameter tube reveal a zigzag chirality. A lattice expansion in c‐axis direction of ≤11% is found within the outermost triple layers. The tube caps often display regular polygon angles. Structural defects like grain boundaries, non‐planar triple layers, dislocations, platelet‐like fragments, terraces, and amorphous precipitates are identified.
Editor's perspective‐‐‐Shale gas development: Environmental issues and opportunities
Authors: Simon John A. , Fleming Martha E.
Published: September 2011

Many professionals in the environmental industry have questioned whether the rapid expansion in shale gas development, particularly in the Marcellus Shale Play, is providing business opportunities. While gas production is a routine practice, the development of shale gas requires a process (fracturing, or, more commonly, “fracing'') that uses chemicals and is far more intrusive to the subsurface environment than traditional gas production. In this Editor's Perspective, we evaluate the environmental issues surrounding shale gas development, with a specific focus on the Marcellus Shale Play because it is currently the most active play in the United States, from both the drilling and political perspectives. In addition, we examine where the business opportunities are likely to be for environmental professionals relative to shale gas development. © 2011 Wiley Periodicals, Inc.
Sustainable remediation: Quo vadis?
Authors: Nathanail Paul
Published: September 2011

Sustainable remediation is at a crossroads. In a few short years it has become a mainstream topic while simultaneously maintaining its chimeral status. Sustainable remediation is a term claimed by many yet a concept apparently understood by few. Its characterization has necessitated the development of a plethora of metrics and tools yet its essence readily emerges. U.S.‐led initiatives have been adopted around the globe. Relative sustainability appraisal is easy to carry out and potentially sufficient for most site circumstances. The need to adequately protect human health and the environment has been recognized. Now the industry needs to focus our attention on protection and restoration that itself has a reasonably maximized net benefit. © 2011 Wiley Periodicals, Inc.
Two‐dimensional transport of lactate‐modified nanoscale iron particles in porous media
Authors: Darko‐Kagya Kenneth , Reddy Krishna R.
Published: September 2011

This study investigates the two‐dimensional transport of nanoscale iron particles (NIP) and lactate‐modified NIP (LMNIP) in homogeneous and heterogeneous porous media under typical pressurized groundwater flow conditions. A two‐dimensional bench‐scale test setup was developed and a series of experiments was conducted simulating homogeneous sand profile and two‐layer profile with two different sands. NIP and LMNIP at a concentration of 4 g/L were prepared in electrolyte simulating groundwater conditions and were injected at the inlet of the test setup under different pressure gradients (0.5. 0.8, 1, and 2 pounds per square inch). During the testing, effluent was collected and its volume and nanoiron concentrations were measured. At the end of the testing, soil cores were obtained at different distances from the inlet and were used to measure nanoiron concentrations and magnetic susceptibility values. Results showed that the transport of NIP and LMNIP was enhanced by increased pressure gradient. LMNIP transport occurred more uniformly as compared to bare NIP. The iron concentrations decreased with distance from the inlet to the outlet and increased from the top to the bottom of the test cell. The data indicate that, as the particles were transported, they underwent aggregation and sedimentation, which resulted in the observed non‐uniform spatial distribution of iron. The NIP and LMNIP transported through the high‐porosity and high‐permeability soil layer in the heterogeneous soil profile, implying that the transport occurred predominantly along the path of least resistance for the flow. Magnetic susceptibility values are found to have good correlation with the iron content in the soil and are helpful to characterize the transport of NIP and LMNIP. Overall, this study shows that the non‐uniform distribution of NIP and LMNIP occurs under two‐dimensional transport conditions and the soil heterogeneities can significantly impact the transport of NIP and LMNIP. The design of field delivery systems should consider such conditions and optimize the pressurized injection systems. © 2011 Wiley Periodicals, Inc.
Physical impact of waterjet‐based sediment remediation on benthic organisms
Authors: Harper Grace , Elmore Andrew Curtis , Redell Christopher , Risley Gavin , Burken Joel G.
Published: September 2011

Adding activated carbon to sediments has been shown to be an effective means of reducing the bioavailability of certain contaminants. The current state of the practice is to mechanically mix activated carbon to a target concentration of 3 percent at depths of approximately 30 cm using a rotovator or similar construction equipment. Waterjets have been used to cut hard material using a mixture of water and an abrasive. If activated carbon is substituted for the abrasive, waterjets have the potential to use surface injection as a replacement for mechanical mixing during sediment remediation. A perceived benefit of waterjet‐based sediment remediation is that there may be a reduced potential for benthic organism mortality related to amendment delivery. A set of waterjet parameters were identified that have the potential to achieve amendment placement goals, and a series of waterjet tests were conducted to evaluate the potential impact on the benthic community. The tests included mortality testing using a swimming macroinvertebrate and a burrowing invertebrate, benthic artifacts such as shells, and craft foam as a surrogate for living organisms. The results indicated that the immediate survivability was typically greater than 50 percent, and that empirical relationships between two variables (waterjet nozzle diameter and the water column height between the nozzle and the target) and the depth of cut in the foam could be established. Data are not available in the literature for direct comparison of organism survivability immediately after mechanical mixing, but the results of this study provide motivation for the further evaluation of waterjets on the basis of the low observed mortality rates. Future waterjet work may address field‐scale characterization of mixing effectiveness, resuspension potential, technical feasibility, and cost. © 2011 Wiley Periodicals, Inc.
Designing funnel‐and‐gate groundwater remediation systems near property corners
Authors: Hudak Paul F.
Published: September 2011

Numerical models were used to simulate alternative funnel‐and‐gate groundwater remediation structures near property corners in hypothetical homogeneous and heterogeneous unconfined aquifers. Each structure comprised a highly permeable central gate (hydraulic conductivity = 25 m/d) and soil‐bentonite slurry walls (hydraulic conductivity = 0.00009 m/d). Gates were perpendicular to regional groundwater flow and approximately 5 m from a contaminant plume's leading tip. Funnel segments collinear to the central gate reached property boundaries; additional funnel segments followed property boundaries in the most hydraulically upgradient direction. Structures were 1 m thick and anchored into the base of the aquifer. Two structures were simulated for each aquifer: one with a 3.0‐m‐long central gate and funnels on either side; and a second with a 1.5‐m‐long central gate, funnels on either side, and 0.75‐m‐long end gates. Funnels were lengthened in successive simulations, until a structure contained a contaminant plume. Results suggest that, for the same total gate length, one‐gate structures may facilitate more rapid remediation, up to 44 percent less time in trials conducted in this study, than multiple‐gate structures constructed near property corners. However, in order to effectively contain a plume, one‐gate structures were up to 46 percent larger than multiple‐gate structures. © 2011 Wiley Periodicals, Inc.
Effects of the Composition of Residual Materials from Steelwork on the Crushing Strength of DRI
Authors: Chuang Hsin‐Chien , Fu Jian‐Xun , Hwang Weng‐Sing , Liu Shih‐Hsien
Published: September 2011

The goal of this study is to investigate the effects of the composition of residual materials, such as the basicity and (C/Ored)mol, as well as the reduction temperature and time, on the crushing strength of direct reduced iron (DRI) under the carbothermic reduction through the rotary hearth furnace (RHF) process. Laboratory‐ scale experiments were executed to examine the DRI quality in the RHF operation. It is observed that when the composition of residual materials varies or the reduction temperature and time decrease, DRI crushing strength becomes lower than the 60 kg/piece requirement for blast furnace feed stock. Both basicity and (C/Ored)mol of the residual materials would affect the crushing strength of DRI. As B2 increase, the crushing strength of DRI also rises, and the maximum value is when the basicity is 1.4. The result shows that as the value of (C/Ored)mol rose above 1.20, the DRI strength declined.
Malignant mixed Müllerian tumors of the uterus: sonographic spectrum
Authors: Lee E. J. , Joo H. J. , Ryu H. S.
Published: September 2011

Objective

To describe the sonographic findings for malignant mixed Müllerian tumors (MMMTs) of the uterus with particular emphasis on their features on saline contrast sonohysterography (SCSH) and color Doppler sonography, and to determine how they relate to pathological findings.

Methods

The SCSH and color Doppler findings in 29 histologically proven cases of uterine MMMT were reviewed retrospectively and their relationship to gross and histological findings were investigated.

Results

Of the 29 uterine tumors, 16 were located only in the corpus, nine only in the fundus and four in both the corpus and fundus. Mean tumor size was 5.4 cm. The most common appearance was a polypoid mass projecting into the endometrial cavity, found in 23 cases. Twenty‐eight tumors had an irregular surface, which was papillary in 20 cases and lobulated in eight. Most appeared heterogeneously isoechoic (n = 16) or hypoechoic (n = 12), occasionally with a trabecular appearance, and they often had clefts or fissure‐like cystic areas (n = 10), necrosis (n = 4) or hemorrhagic areas (n = 7). Myometrial invasion was present in 27 cases and dilatation of the endometrial cavity was seen in 11. Color Doppler sonography showed moderate to marked vascularity in 20 out of the 24 cases in which it was performed, with a mean resistance index of 0.41, and appeared as feeding (n = 15) or randomly dispersed (n = 9) vessels.

Conclusions

Uterine MMMTs have distinct sonographic features that are related to pathological findings. Knowledge of the sonographic appearance of MMMTs may facilitate diagnosis. Copyright © 2012 ISUOG. Published by John Wiley & Sons, Ltd.
Microwave‐Assisted Synthesis and Properties of Sodium Glycol Bis‐(Isooctyl)Sulfosuccinate
Authors: Chen Hong , Tang Shi‐bo
Published: September 2011

An anionic gemini surfactant was synthesized under microwave irradiation conditions. The optimum reaction conditions were obtained by the reaction of maleic anhydride, glycol, isooctyl alcohol and sodium sulfite. The first step esterification reaction was carried out at 90 °C and 100 W microwave power for 20 min with a ratio a nmaleic anhydride:nglycol = 2.1:1, and 1.0 wt% of catalyst. The second step esterification reaction was carried out at 80 °C for 25 min and 100 W microwave power. Optimum sulfonation was carried out with nsodium sulfite:nglycol bismaleic anhydride bisester = 2.25:1 and 1.5% catalyst for 25 min at 60 °C. It is found that microwave‐assisted synthesis is an efficient means of preparation of this anionic gemini surfactant with shorter reaction times and higher yields. The title compound structure was confirmed by IR. The critical micelle concentration of the title compound is 6.2 × 10−4 mol L−1, γCMC is 25.7 mN m−1, and benzene emulsion persistence was 2 days.
The Deceleration Capacity - a New Measure of Heart Rate Variability Evaluated in Patients With Schizophrenia and Antipsychotic Treatment
Authors: Birkhofer A. , Geissendoerfer J. , Alger P. , Mueller A. , Rentrop M. , Strubel T. , Leucht S. , Förstl H. , Bär K.-J. , Schmidt G.
Published: September 2011

Background

Schizophrenia is associated with increased cardiac mortality. A disturbed autonomic modulation of heart rate (HR) has been described in patients with schizophrenia in whom antipsychotic medication may represent an additional cardiac risk. The novel measure deceleration capacity (DC) of heart rate predicts cardiac mortality in patients with cardiovascular illnesses. The aim of the present paper was to calculate DC in patients with schizophrenia and to compare this measure with established parameters of heart rate variability (HRV).

Methods

HRV and DC were calculated in 24-hour electrocardiogram (ECG) recordings of 20 unmedicated, 40 medicated patients with schizophrenia and 40 controls. As activity has a major influence on HRV, 4-hour periods of “sleep-” and “wake-” ECG were evaluated as additional parameters. Actigraphy was used to ensure comparable levels of activity in patients and controls.

Results

The DC as well as the other established HRV measures were not significantly different comparing unmedicated patients with schizophrenia to healthy controls. However, medicated patients showed a significant reduction of DC calculated from ECG recordings during 4 hour over night periods.

Conclusion

Calculation of DC might contribute to a better monitoring and identification of an increased risk of cardiac mortality in patients with schizophrenia undergoing antipsychotic treatment.
Post-glacial landscape response to climate variability in the southeastern San Juan Mountains of Colorado, USA
Authors: Johnson Bradley G. , Eppes Martha Cary , Diemer John A. , Jiménez-Moreno Gonzalo , Layzell Anthony L.
Published: September 2011

Geomorphic mapping in the upper Conejos River Valley of the San Juan Mountains has shown that three distinct periods of aggradation have occurred since the end of the last glacial maximum (LGM). The first occurred during the Pleistocene–Holocene transition (~ 12.5–9.5 ka) and is interpreted as paraglacial landscape response to deglaciation after the LGM. Evidence of the second period of aggradation is limited but indicates a small pulse of sedimentation at ~ 5.5 ka. A third, more broadly identifiable period of sedimentation occurred in the late Holocene (~ 2.2–1 ka). The latest two periods of aggradation are concurrent with increases in the frequency of climate change in the region suggesting that Holocene alpine and sub-alpine landscapes respond more to rapid changes in climate than to large singular climatic swings. Soil development and radiocarbon dating indicate that hillslopes were stable during the Holocene even while aggradation was occurring in valley bottoms. Thus, we can conclude that erosion does not occur equally throughout the landscape but is focused upslope of headwater streams, along tributary channels, or on ridge tops. This is in contrast to some models which assume equal erosion in headwater basins.
Percutaneous upsizing of a Blalock–Taussig shunt
Authors: Tzifa Aphrodite , Rosenthal Eric , Qureshi Shakeel
Published: September 2011

Percutaneous upsizing of surgically placed Blalock–Taussig shunts is an uncommon practice. We report the case of an 8-month-old infant with single-ventricle physiology, who – due to comorbidities – was deemed unsuitable to proceed with Glenn operation. The 3.5-millimetre Blalock–Taussig shunt was stented successfully with a 5-millimetre pre-mounted stent, resulting in an increase in shunt diameter and oxygen saturation by nearly 30% and 10%, respectively.
Hungary's Constitutional Transformation
Authors: Kovács Kriszta , Tóth Gábor Attila
Published: September 2011

Hungary – Democratic state structure – Two-thirds parliamentary majority – First flurry of constitutional amendments of 2010 – Checks and balances – Media – Ex post facto legislation – Hungarian Constitutional Court – Judicial review – Wholesale constitutional review and Basic Law of 2011
Degradation of cyanobacterial biomass in anoxic tidal-flat sediments: a microcosm study of metabolic processes and community changes
Authors: Graue Jutta , Engelen Bert , Cypionka Heribert
Published: September 2011

To follow the anaerobic degradation of organic matter in tidal-flat sediments, a stimulation experiment with 13C-labeled Spirulina biomass (130 mg per 21 g sediment slurry) was conducted over a period of 24 days. A combination of microcalorimetry to record process kinetics, chemical analyses of fermentation products and RNA-based stable-isotope probing (SIP) to follow community changes was applied. Different degradation phases could be identified by microcalorimetry: Within 2 days, heat output reached its maximum (55 μW), while primary fermentation products were formed (in μmol) as follows: acetate 440, ethanol 195, butyrate 128, propionate 112, H2 127 and smaller amounts of valerate, propanol and butanol. Sulfate was depleted within 7 days. Thereafter, methanogenesis was observed and secondary fermentation proceeded. H2 and alcohols disappeared completely, whereas fatty acids decreased in concentration. Three main degraders were identified by RNA-based SIP and denaturant gradient gel electrophoresis. After 12 h, two phylotypes clearly enriched in 13C: (i) Psychrilyobacter atlanticus, a fermenter known to produce hydrogen and acetate and (ii) bacteria distantly related to Propionigenium. A Cytophaga-related bacterium was highly abundant after day 3. Sulfate reduction appeared to be performed by incompletely oxidizing species, as only sulfate-reducing bacteria related to Desulfovibrio were labeled as long as sulfate was available.
Standardized Model for Repeated Social Defeat Stress vs. Sensory Contact Model: similarities and differences, strengths and weaknesses
Authors: Kudryavtseva Natalia N.
Published: September 2011

Of all the models used by behavioral neuroscience the biosocial models are gaining in popularity among the scientists who study the consequences of chronic social conflicts and social stress in animals. One of such models, the Standardized Model for Repeated Social Defeat Stress (SMRSDS) (Golden et al., 2011) has been widely applied to produce important results on the molecular mechanisms of the social defeat stress (Berton et al., 2006). SMRSDS is a modified version of the Sensory Contact Model (SCM) (Kudryavtseva, 1991), which has been used by different laboratories in its original or modified forms for elucidating implications of chronic social conflicts. The basic design and justification of the SCM different stages are described in detail in the latest publication “Sensory contact model: Protocol, control, applications” (Kudryavtseva, 2011). Thus, it is now possible to compare similarities, differences and, as a consequence, strengths and weaknesses of these two behavioral
Phospholipase D1 mediates bFGF-induced Bcl-2 expression leading to neurite outgrowth in H19-7 cells
Authors: Yoon Sung Nyo , Kim Kang Sik , Cho Ju Hwan , Ma Weina , Choi Hye-Jin , Kwon Sung-Joon , Han Joong-Soo
Published: September 2011

The purpose of the present study was to investigate the role of PLD (phospholipase D) in bFGF (basic fibroblast growth factor)-induced Bcl-2 expression and to examine whether overexpressed Bcl-2 influences neurite outgrowth in immortalized hippocampal progenitor cells (H19-7 cells). We found that Bcl-2 expression was maximally induced by bFGF within 24 h, and that this effect was reduced by inhibiting PLD1 expression with PLD1 small interfering RNA or by overexpressing DN (dominant-negative)-PLD1, whereas PLD1 overexpression markedly induced Bcl-2 expression. bFGF treatment activated Ras, Src, PI3K (phosphoinositide 3-kinase), PLCγ (phospholipase Cγ) and PKCα (protein kinase Cα). Among these molecules, Src and PKCα were not required for Bcl-2 expression. PLD activity was decreased by Ras, PI3K or PLCγ inhibitor, suggesting that PLD1 activation occurred through Ras, PI3K or PLCγ. We found that Ras was the most upstream molecule among these proteins, followed by the PI3K/PLCγ pathway, indicating that bFGF-induced PLD activation took place through the Ras/PI3K/PLCγ pathway. Furthermore, PLD1 was required for activation of JNK (c-Jun N-terminal kinase), which led to activation of STAT3 (signal transducer and activator of transcription 3) and finally Bcl-2 expression. When Bcl-2 was overexpressed, neurite outgrowth was stimulated along with induction of neurotrophic factors such as brain-derived neurotrophic factor and neurotrophin 4/5. In conclusion, PLD1 acts as a downstream effector of bFGF/Ras/PI3K/PLCγ signalling and regulates Bcl-2 expression through JNK/STAT3, which leads to neurite outgrowth in H19-7 cells.
Identification of cancer stem cells from human glioblastomas: growth and differentiation capabilities and CD133/prominin‐1 expression
Authors: Gambelli Federica , Sasdelli Federica , Manini Ivana , Gambarana Carla , Oliveri Giuseppe , Miracco Clelia , Sorrentino Vincenzo
Published: September 2011

CD133 can be a marker of tumorigenic CSCs (cancer stem cells) in human GBM (glioblastoma multiforme), although tumorigenic CD133‐negative CSCs have been also isolated. Additional evidence indicates that CSCs from GBM exhibit different phenotypes, with increasing interest in the potential significance of the different CSCs with respect to diagnosis, prognosis and the development of novel targets for treatment. We have analysed the expression of CD133 in freshly isolated cells from 15 human GBM specimens. Only 4 of them contained cells positive for AC133 by FACS analysis, and all of them yielded distinct CSC lines, whereas only 6 CSC lines were obtained from the other 11 GBMs. Of these 10 CSCs lines, we further characterized 6 CSC lines. Three CSCs grew as fast‐growing neurospheres with higher clonogenic ability, whereas the remaining 3 grew as slow‐growing semi‐adherent spheres of lower clonogenicity. In addition, the former CSC lines displayed better differentiation capabilities than the latter ones. PCR and Western blot analysis showed that all 6 GBM CSC lines expressed CD133/prominin‐1, suggesting that cells negative by FACS analysis may actually represent cells expressing low levels of CD133 undetected by FACS. Nevertheless, all the 6 CSC lines were tumorigenic in nude mice. In conclusion, CSCs from human primary GBMs show different phenotypes and variable levels of CD133 expression, but these parameters did not directly correlate with the tumorigenic potential.
Normal and inverse magnetocaloric effects in ferromagnetic Sm0.6−xLaxSr0.4MnO3
Authors: Naik V. B. , Mahendiran R.
Published: September 2011

We report magnetic and magnetocaloric properties of Sm0.6−xLaxSr0.4MnO3 (x = 0–0.6). A rapid increase around TC and an anomalous peak at a temperature T* ≪ TC occur in magnetization, which lead to normal and inverse magnetocaloric effects (MCE), respectively. While TC increases with increasing x (TC = 118 K for x = 0 and TC = 363 K for x = 0.6), T* increases from 30 K (x = 0) to 120 K (x = 0.4) and then decreases to 105 K (x = 0.5). The ΔSm is negative around TC and it decreases from ΔSm = −6.2 Jkg−1K−1 for x = 0 to −4.2 Jkg−1K−1 for x = 0.6 for ΔH = 5 T. The inverse MCE occurs below T* and shows a maximum value of ΔSm = +1.07 Jkg−1K−1 at T = 10 K for ΔH = 5 T at x = 0.4. This composition also shows a significant normal MCE (ΔSm = −4 Jkg−1K−1) around TC = 320 K, along with a high refrigeration capacity of 214 Jkg−1, which makes it an interesting compound for room temperature magnetic refrigeration. The inverse MCE has been suggested to be caused by the antiferromagnetic coupling between Sm 4f and Mn 3d moments. The coexistence of normal and inverse MCEs in a single material is interesting because the sample can be cooled by adiabatic magnetization and demagnetization in different temperature regions, which will enhance the refrigeration capacity.
The ZrO/W(100) Schottky cathode: Morphological modification and its effect on long term operation
Authors: Bahm Alan , Schwind Greg , Swanson Lyn
Published: September 2011

An investigation of the change in various geometric and emission parameters over the life cycle of nine ZrO/W(100) Schottky cathodes was performed. The initial shape for all emitters was “Stage 1,” i.e., a large square, low work function (100) facet intersected by four (112) and (110) facets. The ending shape for all emitters was “Stage 0,” i.e., a round central (100) facet with four side (110) planes. Change in geometric parameters such as emitter apex radius r, cone angle α, central (100) facet size f, and neck size L were measured at the beginning and after 10 000 to 18 000 h of cathode operation. For a particular end form (or Stage), f scaled linearly with emitter radius r. In addition, emission parameters such as the axial angular current density I′, total current It, work function ϕ, electric field F, and extraction voltage Ve were monitored continuously. Of the nine sources investigated four experienced collapsing net planes (ring collapse) on the central (100) crystal facet. The emitters with ring collapse events had the largest increase in r and a corresponding reduction in the field factor β = F/Ve. For the most part β, ϕ, and r remained unchanged for those emitters not having ring collapse events. The ending I′ values mostly decreased at a constant Ve, but less so for those emitters with no ring collapse. Experimental results showed that for I′ ≤ 0.3 mA/sr and T = 1800 K ring collapse occurs. In contrast, for I′ ≥ 0.3 mA/sr ring collapse does not occur. For all emitters investigated, the parameters exhibiting the largest increase over the course of the life test were L and It, whereas α was typically unchanged.
Using swarm intelligence for finding transition states and reaction paths
Authors: Fournier René , Bulusu Satya , Chen Stephen , Tung Jamie
Published: September 2011

We describe an algorithm that explores potential energy surfaces (PES) and finds approximate reaction paths and transition states. A few (≈6) evolving atomic configurations (“climbers”) start near a local minimum M1 of the PES. The climbers seek a shallow ascent, low energy, path toward a saddle point S12, cross over to another valley of the PES, and climb down to a new minimum M2 that was not known beforehand. Climbers use both energy and energy derivatives to make individual decisions, and they use relative fitness to make team-based decisions. In sufficiently long runs, they keep exploring and may go through a sequence M1–S12–M2–S23–M3 … of minima and saddle points without revisiting any of the critical points. We report results on eight small test systems that highlight advantages and disadvantages of the method. We also investigated the PES of Li8, ${\rm Al}_7^+$ Al 7+, Ag7, and Ag2NH3 to illustrate potential applications of this new method.
Defect migration and recombination in nanoindentation of silica glass
Authors: Nomura Ken-ichi , Chen Yi-Chun , Kalia Rajiv K. , Nakano Aiichiro , Vashishta Priya
Published: September 2011

Deformation, plasticity, and flow in silica-based glasses have been studied for decades, and yet important questions remain about the atomistic mechanisms underlying these processes. Our molecular dynamics simulations of nanoindentation indicate that these mechanical processes have a unified underlying atomistic mechanism. The simulations reveal that indentation nucleates under-coordinated silicon and oxygen defects, which migrate by switching bonds in string-like processes. We also observe defect annihilation in the plastic region underneath and the pileup region around the indenter. These defects have also been observed in simulations of nanovoid coalescence under hydrostatic tension and in nanovoid deformation and breakup in shearing silica glass.
Controlled nitrogen incorporation in GaNSb alloys
Authors: Ashwin M. J. , Veal T. D. , Bomphrey J. J. , Dunn I. R. , Walker D. , Thomas P. A. , Jones T. S.
Published: September 2011

The incorporation of N in molecular-beam epitaxy of GaNxSb1−x alloys with x ⩽ 0.022 has been investigated as a function of temperature (325–400°C) and growth rate 0.25–1.6 μmh−1. At fixed growth rate, the incorporated N fraction increases as the temperature is reduced until a maximum N content for the particular growth rate reached. At each temperature, there is a range of growth rates over which the N content is inversely proportional to the growth rate; the results are understood in terms of a kinetic model. The systematic growth rate- and temperature-dependence enables the N content and resulting band gap to be controlled.
Motor pathway convergence predicts syllable repertoire size in oscine birds
Authors: Moore Jordan M. , Székely Tamás , Büki József , DeVoogd Timothy J.
Published: September 2011

Behavioral specializations are frequently associated with expansions of the brain regions controlling them. This principle of proper mass spans sensory, motor, and cognitive abilities and has been observed in a wide variety of vertebrate species. Yet, it is unknown if this concept extrapolates to entire neural pathways or how selection on a behavioral capacity might otherwise shape circuit structure. We investigate these questions by comparing the songs and neuroanatomy of 49 species from 17 families of songbirds, which vary immensely in the number of unique song components they produce and possess a conserved neural network dedicated to this behavior. We find that syllable repertoire size is strongly related to the degree of song motor pathway convergence. Repertoire size is more accurately predicted by the number of neurons in higher motor areas relative to that in their downstream targets than by the overall number of neurons in the song motor pathway. Additionally, the convergence values along serial premotor and primary motor projections account for distinct portions of the behavioral variation. These findings suggest that selection on song has independently shaped different components of this hierarchical pathway, and they elucidate how changes in pathway structure could have underlain elaborations of this learned motor behavior.
The Identities of the Iranian Zūrkhanah
Authors: Rochard Philippe
Published: September 2011

A major ambiguity attaches to the zurkhanah, the traditional gymnasium of Iran. It is celebrated as an abode of chivalry and traditional values such as generosity, forbearance, and fair play, but it also has a reputation of harboring unruly elements on the margins of legality, men who are willing to rent their strong-arm services to whomever pays most. In this article I propose to explore this ambiguity and trace its roots in the social history of the institution. To do this, I shall first provide a quick update on the state of traditional athletics today, then expound on the paradox, and finally attempt to explicate it by discussing the identities of three social types that frequented the zūrkhānah.

The Iranian zūrkhānah, literally “House of Strength,” is the traditional gymnasium in which athletes practice a series of gymnastic and bodybuilding exercises that have been called “ancient sport,“ varzish-i bāstārī, since 1934.
A Political History of Football in Iran
Authors: Chehabi H. E.
Published: September 2011

In late 1997 Iranian football made international headlines. In an article on the Islamic summit held in Iran, The Economist wrote that almost "anything can become a political football in Iran, including football." This attention was precipitated by the political ramifications within Iran of the national team's tie against Australia in Melbourne on November 29th, which secured it a place in the 1998 World Cup in extremis. Since then, major international soccer games have often given rise to massive street demonstrations by young people. That football should cause so much excitement in Iran is not astonishing if one looks at it from a global perspective. Football is a game in which each team works together to try to occupy as much of the "territory" of the other as it can, culminating in attempts symbolically to "conquer" the other side's stronghold by kicking the ball into the goal. The playing field thus becomes a metaphor for the competition between communities, cities, and nations: football focuses group identities.
Interference in Visual Working Memory
Authors: McConnell Jean , Quinn J.G.
Published: September 2011

This paper uses the theoretical distinction that has recently developed between the passive visual store and the active spatial rehearsal mechanism of the visuo-spatial component of working memory (VSSP). It examines the circumstances under which visual fields gain functional access to the passive visual store and seeks to cast light on the circumstances under which irrelevant visual fields interfere with concurrent visual processing. Experiment 1 contrasts a dynamic visual noise field with a static noise field and shows that the static field, in contrast to the dynamic noise field, causes no interference when presented concurrently with a visual task. Experiment 2 investigates the reason for this contrast and concludes that the static field is susceptible to decay and so fails to cause interference. Experiment 3 investigates further the circumstances under which dynamic visual noise causes interference and shows that manipulation of the number of changes within the noise field is also of importance in causing interference. The results allow further consideration of the characteristics of the VSSP.
Interference from Multi-dimensional Objects during Feature and Conjunction Discriminations
Authors: Fournier Lisa R. , Bowd Christopher , Herbert Rhonda J.
Published: September 2011

Feature discrimination performance within an attended object and interference from irrelevant, multi-dimensional objects (distractors) were examined in a two-choice, response compatibility paradigm. Results showed that the amount of interference by multi-dimensional distractors was dependent on three factors: (1) the discriminability of the incompatible, task-relevant distractor features; (2) the number of incompatible, task-relevant distractor features; and (3) whether the task-relevant, incompatible features matched the task goals. The most interesting finding was that additive priming effects were found for multiple, task-relevant features that matched the task goals, whether these features were present in the attended object or in the ignored object. Models that assume that each task-relevant feature primes its corresponding decision/response asynchronously and that this priming is combined to meet a decision/response criterion (at least when attended) can account for distractor interference during conjunction discriminations. Implications of these findings for feature integration models, template models, and a response selection model are discussed.
Hierarchical Knowledge Influences Stimulus-Response Compatibility Effects
Authors: Tlauka Michael , McKenna Frank P.
Published: September 2011

The influence of spatial stimulus grouping on stimulus-response compatibility effects was investigated in three experiments. Stimuli were grouped as part of a superordinate unit BY (1) perceptually organizing them (Experiment 1), (2) organizing them on the basis of semantic links (Experiment 2), or (3) arbitrary links (Experiment 3). In some instances the arrangement of the stimuli resulted in a conflict between two types of spatial relationship: one between stimulus and response and the other between superordinate unit and response. The experiments indicated that it was the latter relationship that mainly determined performance in the experiments. Reaction time analyses showed that responses were fastest if they spatially corresponded to the relative location of the superordinate unit of which the stimulus was part. The results are discussed with reference to hierarchical accounts of coding stimulus information.
Interactions between Exogenous Auditory and Visual Spatial Attention
Authors: Schmitt Michel , Postma Albert , De Haan Edward
Published: September 2011

Six experiments were carried out to investigate the issue of cross-modality between exogenous auditory and visual spatial attention employing Posner's cueing paradigm in detection, localization, and discrimination tasks. Results indicated cueing in detection tasks with visual or auditory cues and visual targets but not with auditory targets (Experiment 1). In the localization tasks, cueing was found with both visual and auditory targets. Inhibition of return was apparent only in the within-modality conditions (Experiment 2). This suggests that it is important whether the attention system is activated directly (within a modality) or indirectly (between modalities). Increasing the cue validity from 50% to 80% influenced performance only in the localization task (Experiment 4). These findings are interpreted as being indicative for modality-specific but interacting attention mechanisms. The results of Experiments 5 and 6 (up/down discrimination tasks) also show cross-modal cueing but not with visual cues and auditory targets. Furthermore, there was no inhibition of return in any condition. This suggests that some cueing effects might be task dependent.
Proprioception and Stimulus-Response Compatibility
Authors: Worringham Charles J. , Kerr Graham K.
Published: September 2011

Sixteen subjects pressed a left or right key in response to lateralized visual stimuli, in uncrossed (left index finger on left key, right finger on right key) and crossed conditions (left finger on right key and vice versa), with varying finger separations. Visual, tactile, or “efference copy” cues about relative finger positions were unavailable. Subjects had to press the key on the same side as (compatible group) or opposite side to the stimulus (incompatible group). Separate proprioceptive judgements of the relative finger positions were obtained. Findings of an overall reaction time (RT) advantage for compatible instructions and for uncrossed hands were replicated. With decreasing finger separation the RT advantage for compatible instructions decreased, and the probability of responding with either hand increased. The compatibility effect disappeared completely at the 6-cm crossed position, not at the position that was hardest to judge proprioceptively. This suggests that two forms of neural activation are summed: automatic activation of the anatomically same-side limb, and an integrated, rule-based activation. The results further demonstrate that independent proprioceptive cues from each limb, unassociated with skin contact between the limbs, can mediate the determination of relative position for response selection in stimulus-response compatibility tasks.