bluuebunny/crossref_metadata_2025 huggingface dataset:
Cyclotetrapeptide Mimics Based on a 13‐Membered, Partially Modified Retro‐Inverso Structure
Authors: Gentilucci Luca , Cardillo Giuliana , Tolomelli Alessandra , Spampinato Santi , Sparta Antonino , Squassabia Federico
Published: November 2007

Cyclic tetrapeptides (CTP) incorporating a distinct β‐amino acid represent realistic conformationally homogeneous CTP analogs, and they can find application in medicinal chemistry as turn mimics and scaffolds. In this respect, we synthesized a small library of CTP‐mimics based on a 13‐membered, partially modified retro‐inverso (PMRI) structure containing a 1,2‐diamine as a β‐amino acid mimetic and malonic acid as a glycine surrogate. Conformational analysis revealed that the PMRI–CTP models containing an unsubstituted diamine (1, 2) exhibited a certain flexibility. On the contrary, the introduction of a chiral, substituted 1,2‐diamine rendered the backbone more rigid (3, 4) and induced type I β‐turn structures. The comparison with a β‐amino acid containing CTP revealed that the PMRI–CTPs can be regarded as alternative β‐turn scaffolds. To validate the structural deductions based on conformational analysis, we synthesized a couple of diastereomeric RGD analogs (5, 6) as integrin inhibitors, and we found a clear relationship between the 3D display of the pharmacophores and biological activity. In particular, 6 showed good efficacy in inhibiting fibronectin adhesion to the αvβ3 integrin‐expressing human melanoma cells SK‐MEL‐24 (EC50 = 3.7 × 10–7). (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008)
Predictors of treatment in patients with chronic hepatitis C infection—Role of patient versus nonpatient factors
Authors: Kanwal Fasiha , Hoang Tuyen , Spiegel Brennan M.R. , Eisen Seth , Dominitz Jason A. , Gifford Allen , Goetz Mathew , Asch Steven M.
Published: November 2007

Treatment with interferon and ribavirin is effective in patients with chronic infection with hepatitis C virus (HCV). Previous data indicate that treatment rates are suboptimal. We sought to identify patient and provider-level predictors of treatment receipt in HCV by conducting a retrospective cohort study of 5701 HCV patients in a large regional Veteran's Administration (VA) healthcare network. We also determined the degree of variation in treatment rates attributable to patient, provider, and facility factors. Three thousand seven hundred forty-three patients (65%) were seen by a specialist and 894 (15.7%) received treatment. Treatment rates varied from 6% to 29% across the 5 facilities included in the analysis. Patients were less likely to receive treatment if they were older [RR, 0.55; 95% CI, 0.45, 0.67), single (RR, 0.77; 95%CI, 0.67, 0.88), had hepatic dysfunction (RR, 0.73; 95%CI, 0.66, 0.89), had normal alanine aminotransferase (ALT) (RR, 0.73; 95%CI, 0.59, 0.89), had HCV genotype 1 (RR, 0.78; 95%CI, 0.71, 0.86), were African American with genotype 1 (RR, 0.78; 95% CI, 0.71, 0.86), or were anemic (RR, 0.70; CI, 0.60, 0.89). In addition, patients evaluated by less experienced providers were 77% less likely to receive treatment than those evaluated by more experienced providers. The patient, provider, and facility factors explained 23%, 25%, and 7% of variation in treatment rates, respectively.

Conclusion:

These data suggest that although patient characteristics are important predictors of treatment in HCV, a significant proportion of variation in treatment rates is explained by provider factors. These potentially modifiable provider-level factors may serve as high-yield targets for future quality improvement initiatives in HCV. (Hepatology 2007;46:1741–1749.)
Identification of resident hepatic stem cell populations
Authors: Shackel Nicholas A , Warner Fiona J , Kowdley Kris , McCaughan Geoffrey , Trautwein Christian
Published: November 2007

Human hepatic stem cells (hHpSCs), which are pluripotent precursors of hepatoblasts and thence of hepatocytic and biliary epithelia, are located in ductal plates in fetal livers and in Canals of Hering in adult livers. They can be isolated by immunoselection for epithelial cell adhesion molecule-positive (EpCAM+) cells, and they constitute approximately 0.5–2.5% of liver parenchyma of all donor ages. The self-renewal capacity of hHpSCs is indicated by phenotypic stability after expansion for >150 population doublings in a serum-free, defined medium and with a doubling time of approximately 36 h. Survival and proliferation of hHpSCs require paracrine signaling by hepatic stellate cells and/or angioblasts that coisolate with them. The hHpSCs are approximately 9 microm in diameter, express cytokeratins 8, 18, and 19, CD133/1, telomerase, CD44H, claudin 3, and albumin (weakly). They are negative for alpha-fetoprotein (AFP), intercellular adhesion molecule (ICAM) 1, and for markers of adult liver cells (cytochrome P450s), hemopoietic cells (CD45), and mesenchymal cells (vascular endothelial growth factor receptor and desmin). If transferred to STO feeders, hHpSCs give rise to hepatoblasts, which are recognizable by cordlike colony morphology and up-regulation of AFP, P4503A7, and ICAM1. Transplantation of freshly isolated EpCAM+ cells or of hHpSCs expanded in culture into NOD/SCID mice results in mature liver tissue expressing human-specific proteins. The hHpSCs are candidates for liver cell therapies.

Reproduced from Journal of Experimental Medicine, 2007, 204:1973–1987. Copyright 2007 Rockefeller University Press.
Calcium‐ and pH‐dependent localization of annexin A6 isoforms in Balb/3T3 fibroblasts reflecting their potential participation in vesicular transport
Authors: Strzelecka‐Kiliszek Agnieszka , Buszewska Malgorzata E. , Podszywalow‐Bartnicka Paulina , Pikula Slawomir , Otulak Katarzyna , Buchet Rene , Bandorowicz‐Pikula Joanna
Published: November 2007

Annexin A6 (AnxA6), calcium‐ and membrane‐binding protein, is involved in membrane dynamics. It exists in the cell in two isoforms, AnxA6‐1 and AnxA6‐2, varying only by the VAAEIL sequence. In most cells, AnxA6‐1 predominates. A limited number of observations suggests that both isoforms differ from each other functionally. The EGF‐dependent Ca2+influx in A431 cells is inhibited only by AnxA6‐1. Moreover, AnxA6‐2 was found to exhibit higher affinity for Ca2+. In this report we addressed the potential significance of the VAAEIL deletion in AnxA6‐2. For this purpose, we expressed AnxA6 isoform cDNAs in bacteria or mouse Balb/3T3 fibroblasts. The recombinant AnxA6‐2 was characterized by a less extended molecular shape than that of AnxA6‐1 and required a narrower [Ca2+] range to bind liposomes. Upon lowering pH in the presence of EGTA recombinant AnxA6‐2 became less hydrophobic than AnxA6‐1 as revealed by the Triton X‐114 partition. Furthermore, AnxA6‐2 revealed stronger F‐actin binding than that of AnxA6‐1. Immunofluorescence microscopy showed that the EGFP‐tagged AnxA6 isoforms expressed in Balb/3T3 fibroblasts relocate in a Ca2+‐ and H+‐sensitive manner to the vesicular structures in a perinuclear region or in cytosol. Cell fractionation showed that in resting conditions AnxA6‐1 is associated with early endosomes and AnxA6‐2 with late endosomes, and an increase in [Ca2+] and/or [H+] induced their opposite distribution. These findings suggest a potentially independent regulation, localization, and function of AnxA6 isoforms in Balb/3T3 fibroblasts. More generally, our findings suggest distinct functions of AnxA6 isoforms in membrane dynamics. J. Cell. Biochem. 104: 418–434, 2008. © 2007 Wiley‐Liss, Inc.
The hardness kernel as the basis for global and local reactivity indices
Authors: Torrent‐Sucarrat Miquel , Salvador Pedro , Solà Miquel , Geerlings Paul
Published: November 2007

In a very recent article (Torrent‐Sucarrat et al., J Comput Chem 2007, 28, 574), we have shown how to evaluate the global hardness for polyatomic molecules using a hardness kernel approximation. We present here an extension of this previous work by improving the model used to evaluate the hardness kernel and the Fukui function. In addition, the concept of the local hardness is analyzed in detail, and for the first time, profiles of local hardness with kinetic and exchange‐correlation contributions for polyatomic molecules are reported. Finally, the concept of condensed atomic hardness is introduced and its usefulness as chemical reactivity descriptor is examined. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008
Relaxation of the mouse pubic symphysis during late pregnancy is not accompanied by the influx of granulocytes
Authors: Rosa Renata Giardini , Tarsitano Christiane Aparecida Badin , Hyslop Stephen , Yamada Áureo Tatsumi , Toledo Olga Maria S. , Joazeiro Paulo Pinto
Published: November 2007

In some animals, such as mice and guinea pigs, a hormonally controlled mechanism increases the flexibility of the pubic symphysis and enhances the cervical remodeling necessary for safe delivery. Cervical ripening during pregnancy is associated with a paradoxical influx of leukocytes. However, the changes in cell metabolism during relaxation of the mouse pubic symphysis for delivery have not been extensively studied. In this work, we used light microscopy and transmission and scanning electron microcopy, as well as immunohistochemistry and Western blotting for MMP‐8, to investigate the involvement of granulocytes or resident stromal cells in the relaxation of the virgin pubic symphysis during late pregnancy (days 18 and 19, before delivery) in vivo and in explanted joints. MMP‐8 was studied because this collagenase is a hallmark for cervical ripening associated with the influx of granulocytes during late pregnancy. Extensive dissolution and disorganization of the extracellular matrix was seen around fibroblastic‐like cells in late pregnancy. In contrast to the cervix (positive control), morphological and immunohistochemical analyses revealed that there was no characteristic cellular inflammatory response in the interpubic tissue. Staining for MMP‐8 was observed in chondroid and fibroblastic‐like cells of virgin and relaxed interpubic ligament, respectively. However, no granulocytes were seen during the extensive remodeling of the pubic joint in late pregnancy. These results indicate that constitutive stromal cells may have an important role in tissue relaxation during remodeling of the pubic symphysis in pregnancy. Microsc. Res. Tech., 2008. © 2007 Wiley‐Liss, Inc.
The Impact of Acute Alcoholic Hepatitis in the Explanted Recipient Liver on Outcome After Liver Transplantation
Authors: Wells Jennifer T. , Said Adnan , Agni Rashmi , Tome Santiago , Hughes Sarah , Dureja Parul , Lucey Michael R.
Published: November 2007

Patients with clinical acute alcoholic hepatitis (AAH) are not considered suitable candidates for orthotopic liver transplantation (OLT). The histological correlates of AAH are often seen in the explanted liver at the time of transplantation. The importance of these findings remains inconclusive regarding their role as a prognostic marker for patient or allograft health. Our aim was to examine the explanted liver of patients with purely alcoholic liver disease (ALD) for findings of histologic AAH and to correlate these to patient and graft outcomes. We compared patients with and without histological AAH with patients transplanted for non-ALD. Of 1,097 liver transplant recipients, 148 had ALD and 125 were non-ALD control patients with similar demographics. Thirty-two of 148 ALD patients had histologic AAH, and 116 had bland alcoholic cirrhosis (BAC). Twenty-eight percent of the ALD patients reported <6 months abstinence, and 54% reported <12 months abstinence. There was a statistically significant relationship between the presence of histologic AAH and abstinence durations <12 months (P = 0.009), but not <6 months. Overall, posttransplantation patient and graft survival between the ALD and non-ALD groups was not significantly different (P = 0.53). Furthermore, patient and graft survival between ALD patients with histologic AAH and BAC were similar (P = 0.13 and P = 0.11, respectively). The rate of posttransplantation relapse among ALD patients was 16%; however, there was no increase in graft loss, nor was there decreased survival compared with controls. The patients with histologic AAH and those with BAC had no differences in posttransplantation relapse (P = 0.13). In multivariate analysis, patient and graft survival was not influenced by pretransplantation abstinence or posttransplantation relapse. In conclusion, histological alcoholic hepatitis in the explant did not predict worse outcome regarding relapse, and allograft or patient survival for liver transplant recipients. Caution should be exercised when liver histology is used to discriminate among suitable candidates for OLT concerning alcoholic patients. Liver Transpl 13: 1728–1735, 2007. © 2007 AASLD.
Macromol. Rapid Commun. 23/2007
Authors: Maity Arjun , Ray Suprakas Sinha , Pillai Sreejarani K.
Published: November 2007

Cover: The cover picture shows SEM pictures displaying the homogeneous wrapping of the outer surface of multi‐walled carbon nanotubes (MWCNTs) with poly(N‐vinylcarbazole)(PNVC‐nanocomposite) in comparison with pure MWCNTs and PNVC extracted from the nanocomposite. This wrapping occurred during polymerization and precipitation from solution. Further details can be found in the article by A. Maity, S. S. Ray,* and S. K. Pillai on page 2224.
Cortical evoked potentials from pallidal stimulation in patients with primary generalized dystonia
Authors: Tisch Stephen , Rothwell John C. , Zrinzo Ludvic , Bhatia Kailash P. , Hariz Marwan , Limousin Patricia
Published: November 2007

Deep brain stimulation (DBS) of globus pallidus internus (GPi) has emerged as an effective treatment for primary generalized dystonia. However, the physiological mechanisms of improvement are not fully understood. Cortical activity in response to pallidal stimulation was recorded in 6 patients with primary generalized dystonia >6 months after bilateral GPi DBS. Scalp electroencephalogram was recorded using 60 surface electrodes during 10 Hz bipolar pallidal DBS at each electrode contact pair. Anatomical position of the electrode contacts in relation to the GPi, medial medullary lamina and globus pallidus externus (GPe) was determined from the postoperative stereotactic MRI. In all six patients an evoked potential (EP) was observed with average onset latency of 10.9 ms ± 0.77, peak latency 26.6 ms ± 1.6, distributed mainly over the ipsilateral hemisphere, maximal centrally. The mean amplitude of this potential was larger with stimulation in posteroventral GPi than in GPe (3.36 μV vs. 0.50 μV, P < 0.0001). The EP was absent in one patient‐side, ipsilateral to a previous thalamotomy. Low frequency GPi stimulation produces an EP distributed centrally over the ipsilateral hemisphere. The latency and distribution of the EP are consistent with stimulation of pallidothalamic neurons projecting to the sensorimotor cortex. Because the EP is larger and more consistently present with stimulation of posteroventral GPi than GPe, it may provide a physiological tool to identify contacts within the optimal surgical target. © 2007 Movement Disorder Society
Lung MRI using an MR‐compatible active breathing control (MR‐ABC)
Authors: Arnold Johannes F.T. , Mörchel Philipp , Glaser Eckard , Pracht Eberhard D. , Jakob Peter M.
Published: November 2007

This work introduces an MR‐compatible active breathing control device (MR‐ABC) that can be applied to lung imaging. An MR‐ABC consists of a pneumotachograph for respiratory monitoring and an airway‐sealing unit. Using an MR‐ABC, the subjects were forced to suspend breathing for short time intervals, which were used in turn for data acquisition. While the breathing flow was stopped, data acquisition was triggered by ECG to achieve simultaneous cardiac and respiratory synchronization and thus avoid artifacts from blood flow or heart movement. The flow stoppage allowed a prolonged acquisition window of up to 1.5 sec. To evaluate the potential of an MR‐ABC for segmented k‐space acquisition, diaphragm displacement was investigated in five volunteers and compared with images acquired using breath‐holding, a respiratory belt, and free breathing. Respiratory movement was comparatively low using the breath‐hold approach, a respiratory belt or an MR‐ABC. During free‐breathing diaphragm displacement was comparatively large. To demonstrate the potential of an MR‐ABC, lung MRI was performed using whole‐chest 3D gradient‐echo imaging, multislice turbo spin‐echo (TSE) imaging, and short tau inversion recovery TSE (STIR‐TSE). Cardiorespiratory synchronization was used for each sequence. None of the volunteers reported any discomfort or inconvenience when using an MR‐ABC. Flow stoppage of up to 2.5 sec per breathing cycle was well tolerated, therefore allowing for a reduction of the total imaging time as compared to usage of a respiratory belt or MR navigator. Magn Reson Med, 2007. © 2007 Wiley‐Liss, Inc.
Compartmental relaxation and diffusion tensor imaging measurements in vivo in λ‐carrageenan‐induced edema in rat skeletal muscle
Authors: Fan Reuben H. , Does Mark D.
Published: November 2007

Integrated diffusion tensor T2 measurements were made on normal and edematous rat muscle, and the data were fitted with one‐ and two‐compartment models, respectively. Edematous muscle exhibited a short‐lived component (T2 = 28 ± 6 ms), with diffusion characteristics similar to that of normal muscle, and a long‐lived component (T2 = 96 ± 27 ms), with greater mean apparent diffusion coefficient (ADC) and lower fractional anisotropy (FA). With this two‐component description of diffusion and relaxation, values of ADC and FA estimated with a conventional pulsed‐gradient spin‐echo sequence will depend on the echo time, relative fraction of short‐lived and long‐lived water signals, and the intrinsic ADC and FA values within the tissue. On the basis of the relative differences in water diffusion properties between long‐lived and short‐lived water signals, as well as the similarities between the short‐lived component and normal tissue, it is postulated that these two signal components largely reflect intracellular and extracellular water. Copyright © 2007 John Wiley & Sons, Ltd.
Solving the hub location problem in a star–star network
Authors: Labbé Martine , Yaman Hande
Published: November 2007

We consider the problem of locating hubs and assigning terminals to hubs for a telecommunication network. The hubs are directly connected to a central node and each terminal node is directly connected to a hub node. The aim is to minimize the cost of locating hubs, assigning terminals and routing the traffic between hubs and the central node. We present two formulations and show that the constraints are facet‐defining inequalities in both cases. We test the formulations on a set of instances. Finally, we present a heuristic based on Lagrangian relaxation. © 2007 Wiley Periodicals, Inc. NETWORKS, 2008
Polynomial algorithms for partitioning a tree into single‐center subtrees to minimize flat service costs
Authors: Apollonio N. , Lari I. , Ricca F. , Simeone B. , Puerto J.
Published: November 2007

This paper deals with the following graph partitioning problem. Consider a connected graph with n nodes, p of which are centers, while the remaining ones are units. For each unit‐center pair there is a fixed service cost and the goal is to find a partition into connected components such that each component contains only one center and the total service cost is minimum. This problem is known to be NP‐hard on general graphs, and here we show that it remains such even if the service cost is monotone and the graph is bipartite. However, in this paper we derive some polynomial time algorithms for trees. For this class of graphs we provide several reformulations of the problem as integer linear programs proving the integrality of the corresponding polyhedra. As a consequence, the tree partitioning problem can be solved in polynomial time either by linear programming or by suitable convex nondifferentiable optimization algorithms. Moreover, we develop a dynamic programming algorithm, whose recursion is based on sequences of minimum weight closure problems, which solves the problem on trees in O(np) time. © 2007 Wiley Periodicals, Inc. NETWORKS, 2008
Prostate‐specific antigen levels in relation to cadmium exposure and zinc intake: results from the 2001–2002 national health and nutrition examination survey
Authors: van Wijngaarden Edwin , Singer Eric A. , Palapattu Ganesh S.
Published: November 2007

BACKGROUND

Cadmium exposure has been suggested as a risk factor for prostate cancer, and experimental literature suggests that the carcinogenic effect of cadmium is modified by the presence of zinc. We evaluated total prostate‐specific antigen (PSA) levels in relation to urinary cadmium concentrations and dietary zinc intake.

METHODS

PSA levels were determined in 1,320 men over the age of 40 in the 2001–2002 National Health and Nutrition Examination Survey (NHANES). Urinary cadmium concentrations were measured in about one‐third of the sample population, whereas dietary zinc intake was based on participants' 24‐hr recall. Information on all three variables was available for 422 men in the 2001–2002 NHANES survey. We performed linear regressions to evaluate the relationships these factors after accounting for age and other covariates.

RESULTS

Little evidence for an association between cadmium and elevated PSA level was observed. However, the data provide suggestive evidence for an interaction between zinc intake and cadmium exposure (P for interaction = 0.09). Among men with zinc intake less than the median level of 12.67 mg/day, an increase in 1 µg/g creatinine cadmium exposure was associated with a 35% increase in PSA level. In contrast, among men with greater than median zinc intake, little evidence for an association between cadmium and PSA was found.

CONCLUSIONS

These findings suggest a protective effect of zinc intake on cadmium‐induced prostatic injury, and may provide further rationale for investigating the impact of these factors individually and jointly on the etiology of prostate cancer. Prostate 68: 122–128, 2008. © 2007 Wiley‐Liss, Inc.
Return immigration: the chronic migration of Canadian immigrants, 1991, 1996 and 2001
Authors: King Karen M. , Newbold K. Bruce
Published: November 2007

Recognizing that immigration is not a one‐time event, the international migration literature has acknowledged return emigration as one option. Typically, international return migrations are evaluated as returns to a country of birth, although they may also involve returns to the host country following a brief sojourn or period outside. However, this form of ‘return’ immigration has received limited attention. Using data drawn from the 1991, 1996 and 2001 Canadian censuses, we examine return immigration, defined here as the immigration act of foreign‐born residents of Canada who have temporarily emigrated from Canada and who subsequently return to Canada. Firstly, we describe the volume and characteristics of Canadian immigrants who undertake return immigration. Secondly, we examine the likelihood of immigrants to undertake a return immigration given their socio‐economic and demographic characteristics. Understanding such return immigrations is one way to an understanding of Canada's attractiveness and ability to retain immigrants. In general, we found the characteristics of return immigrants conformed to general migration theories and the domestic return migration literature. Copyright © 2007 John Wiley & Sons, Ltd.
Adaptive Flüssigkeitstilger für Vertikalschwingungen von Ingenieurstrukturen – Teil 1 – Laborversuche
Authors: Wendner Roman , Reiterer Michael , Hoffmann Simon , Strauss Alfred , Bergmeister Konrad
Published: November 2007

Das Schwingungsverhalten von Ingenieurkonstruktionen aus Stahl, Stahlbeton‐ und Spannbeton führt bei Anregung durch Wind, Verkehr, Personen oder Erdbeben trotz statisch ausreichender Bemessung oftmals zu gebrauchstauglichkeitskritischen Zuständen. Dies ist zum einen durch den Trend zu immer schlankeren Bauwerken begründet, zum anderen auch durch Schwierigkeiten bei der Abschätzung des dynamischen Verhaltens in der Planungsphase. Treten kritische Schwingungszustände nach Fertigstellung der Konstruktion auf, so können diese durch den Einsatz von passend abgestimmten Schwingungstilgern effektiv reduziert werden. Der in diesem Aufsatz vorgestellte Flüssigkeitstilger für Vertikalschwingungen stellt eine wirtschaftlich sinnvolle Alternative zum konventionellen Masse‐Feder‐Dämpfer‐Tilger dar. In der Folge werden die theoretischen Grundlagen näher erläutert sowie die Funktionsfähigkeit anhand zahlreicher Laborversuche demonstriert und neue Wege zur aktiven Steuerung und optimalen Abstimmung vorgestellt. Schlussendlich werden Vor‐ und Nachteile des vorgestellten Flüssigkeitstilgers für Vertikalschwingungen von Ingenieurkonstruktionen im Vergleich mit dem klassischen Masse‐Feder‐Dämpfer‐Tilger diskutiert.
The FoxO transcription factors and metabolic regulation
Authors: Nakae Jun , Oki Miyo , Cao Yongheng
Published: November 2007

Forkhead transcription factors FoxOs are conserved beyond species and regulated by insulin signaling pathway. FoxOs have diverse functions on differentiation, proliferation and cell survival. In calorie restriction (CR) or starvation, FoxOs are in nucleus, active transcriptionally, and increase hepatic glucose production, decrease insulin secretion, increase food intake and cause degradation of skeletal muscle for supplying substrates for glucose production. However, even in insulin resistance due to excessive calorie intake, FoxOs are active and causes type 2 diabetes and hyperlipidemia. The understanding of molecular mechanism how FoxOs affect glucose or lipid metabolism will shed light on the novel therapy of type 2 diabetes and the metabolic syndrome.
Pore space reconstruction of vuggy carbonates using microtomography and multiple‐point statistics
Authors: Okabe Hiroshi , Blunt Martin J.
Published: November 2007

To reconstruct complex porous media, such as carbonates, we propose a two‐step approach to combine different types of images: microtomography at the resolution of a few microns to resolve large pores and vugs, with statistically reconstructed high‐resolution images for smaller features. Two‐dimensional (2‐D) thin sections provide multiple‐point statistics which describe the statistical relation between multiple spatial locations that can be used to generate 3‐D images with accurate connectivity. These statistical reconstructions are combined with images directly measured by microtomography. The integrated method is tested on carbonates for which 3‐D images of disconnected vugs are captured, while 2‐D thin sections characterize the small‐scale structure. The integrated images have permeabilities computed using the lattice Boltzmann method that are similar to laboratory‐measured values.
Climatology of a nonhydrostatic global model with explicit cloud processes
Authors: Iga S. , Tomita H. , Tsushima Y. , Satoh M.
Published: November 2007

This is the first study to obtain a statistical climate state under a perpetual July condition using a nonhydrostatic global model with explicit cloud processes. Horizontal grid intervals of approximately 7 and 14 km over the globe marginally allowed for a general representation of meso‐scale circulations associated with deep clouds. The fine‐scale precipitation distribution was similar to satellite observations, particularly in regions of the Intertropical Convergence Zone. Realistic distributions of cloud cover in upper, middle, and lower levels were also obtained, although the geographic locations of lower clouds differed slightly from observations over the eastern Pacific. Sensitivity experiments revealed a decrease in outgoing longwave radiation (OLR) as ice fall speed increased or as mixing in the boundary layer was enhanced. As the horizontal resolution increased, the cloud fraction increased and both the OLR and the total water path decreased, implying that cloud overlap also decreased as the resolution increased.
An Antarctic assessment of IPCC AR4 coupled models
Authors: Connolley William M. , Bracegirdle Thomas J.
Published: November 2007

We assess 19 coupled models from the IPCC fourth assessment report archive from the simulation of the 20th century, based on the calculation of “skill scores.” The models show a wide range of scores when assessed against Antarctic or global measures of large‐scale circulation indices. Except for continental mass balance, the model average proves a more reliable estimate than that for any one model. Individual models show a very wide scatter in simulated Antarctic temperature trends over the past century; the large trend over the Antarctic peninsula in winter is not well represented, which makes it clear that whatever has been driving these trends is not well captured by many GCMs. Trends in temperature are clearly linked to the sea ice simulation, another variable that most models do not simulate well.
Role of fault branches in earthquake rupture dynamics
Authors: Bhat Harsha S. , Olives Marion , Dmowska Renata , Rice James R.
Published: November 2007

We analyze earthquake ruptures propagating along a straight “main” fault and encountering a finite‐length branch fault. Such intersections are often observed in natural fault systems. The predicted effects of the interaction with the branch that we report can be remarkable; they can strongly perturb the propagation velocity on the main fault and, in some cases, even arrest that propagation. Earlier work (Kame et al., 2003; Bhat et al., 2004) emphasized the role of the fault pre‐stress state, branch geometry (i.e., branching angle), and the incoming rupture velocity at the branching junction in determining whether the rupture would follow the branch or continue on the main fault or both, through simulations which did not let a rupture on the branch encounter a barrier or a fault end (called ‘infinite’ branch cases henceforth). In this study we look at “finite” branch cases, and study the effect also of branch length, with rupture being blocked from propagation beyond the branch end. It is known that sudden stoppage of a dynamic rupture front leads to the propagation of large dynamic stress perturbations in the medium. These have been known to nucleate or terminate ruptures on adjacent fault segments (Harris et al., 1991; Harris and Day, 1993, 1999; Harris et al., 2002; Fliss et al., 2005, among others). We thus anticipate interaction between the rupture on the main fault and the branched one at two stages, when the rupture is propagating on the branch and when it is suddenly blocked at the branch end. We show that in general rupture termination on a compressional branch little affects propagation on the main fault compared to the infinite branch cases. For branches on the extensional side, we show in some cases, that whereas an infinite' branch would have allowed (or stopped) rupture propagation on the main fault, a finite branch stops (or allows) propagation on the main fault. Such results have a dependence on branch length that we document. We also illustrate branch‐related complexities in rupture velocity evolution which could be one of the sources of the high‐frequency content of strong ground motion record. Complexities in the slip distribution, often associated with a presumed heterogeneous strength distribution along the fault, can also be observed when rupture is terminated on a branch.
Managing hydroclimatological risk to water supply with option contracts and reservoir index insurance
Authors: Brown Casey , Carriquiry Miguel
Published: November 2007

This paper explores the performance of a system of economic instruments designed to facilitate the reduction of hydroclimatologic variability‐induced impacts on stakeholders of shared water supply. The system is composed of bulk water option contracts between urban water suppliers and agricultural users and insurance indexed on reservoir inflows. The insurance is designed to cover the financial needs of the water supplier in situations where the option is likely to be exercised. Insurance provides the irregularly needed funds for exercising the water options. The combined option contract – reservoir index insurance system creates risk sharing between sectors that is currently lacking in many shared water situations. Contracts are designed for a shared agriculture – urban water system in Metro Manila, Philippines, using optimization and Monte Carlo analysis. Observed reservoir inflows are used to simulate contract performance. Results indicate the option – insurance design effectively smooths water supply costs of hydrologic variability for both agriculture and urban water.
Optimization of replica exchange molecular dynamics by fast mimicking
Authors: Hritz Jozef , Oostenbrink Chris
Published: November 2007

We present an approach to mimic replica exchange molecular dynamics simulations (REMD) on a microsecond time scale within a few minutes rather than the years, which would be required for real REMD. The speed of mimicked REMD makes it a useful tool for “testing” the efficiency of different settings for REMD and then to select those settings, that give the highest efficiency. We present an optimization approach with the example of Hamiltonian REMD using soft-core interactions on two model systems, GTP and 8-Br-GTP. The optimization process using REMD mimicking is very fast. Optimization of Hamiltonian-REMD settings of GTP in explicit water took us less than one week. In our study we focus not only on finding the optimal distances between neighboring replicas, but also on finding the proper placement of the highest level of softness. In addition we suggest different REMD simulation settings at this softness level. We allow several replicas to be simulated at the same Hamiltonian simultaneously and reduce the frequency of switching attempts between them. This approach allows for more efficient conversions from one stable conformation to the other.
Sum frequency generation surface spectra of ice, water, and acid solution investigated by an exciton model
Authors: Buch V. , Tarbuck T. , Richmond G. L. , Groenzin H. , Li I. , Shultz M. J.
Published: November 2007

A new computational scheme is presented for calculation of sum frequency generation (SFG) spectra, based on the exciton model for OH bonds. The scheme is applied to unified analysis of the SFG spectra in the OH-stretch region of the surfaces of ice, liquid water, and acid solution. A significant role of intermolecularly coupled collective modes is pointed out. SFG intensity amplification observed for acid solutions in the H-bonded OH-stretch region is reproduced qualitatively and accounted for by enhanced orientational preference “into the surface” of the H2O bisectors within the hydronium solvation shell.
Development of a classical force field for the oxidized Si surface: Application to hydrophilic wafer bonding
Authors: Cole Daniel J. , Payne Mike C. , Csányi Gábor , Mark Spearing S. , Colombi Ciacchi Lucio
Published: November 2007

We have developed a classical two- and three-body interaction potential to simulate the hydroxylated, natively oxidized Si surface in contact with water solutions, based on the combination and extension of the Stillinger-Weber potential and of a potential originally developed to simulate SiO2 polymorphs. The potential parameters are chosen to reproduce the structure, charge distribution, tensile surface stress, and interactions with single water molecules of a natively oxidized Si surface model previously obtained by means of accurate density functional theory simulations. We have applied the potential to the case of hydrophilic silicon wafer bonding at room temperature, revealing maximum room temperature work of adhesion values for natively oxidized and amorphous silica surfaces of 97 and 90mJ∕m2, respectively, at a water adsorption coverage of approximately 1 ML. The difference arises from the stronger interaction of the natively oxidized surface with liquid water, resulting in a higher heat of immersion (203 vs 166mJ∕m2), and may be explained in terms of the more pronounced water structuring close to the surface in alternating layers of larger and smaller densities with respect to the liquid bulk. The computed force-displacement bonding curves may be a useful input for cohesive zone models where both the topographic details of the surfaces and the dependence of the attractive force on the initial surface separation and wetting can be taken into account.
New insights in the formation of thioxophosphine: A quantum chemical study
Authors: Viana Rommel B. , Pimentel André S.
Published: November 2007

The investigation of the thioxophosphine (PS) formation from different reaction paths is successfully performed and presented in this paper. The PH3+SH1 reaction is likely to yield the intermediates PH22+H2S through an energy barrier of 2.8kcalmol−1. However, the next step is the H2PS2 formation, which has a too high energy barrier, 52.6kcalmol−1. The PH3+S1 reaction path is the likely source of the HPS1 molecule. The other possibilities are the PH1+H2S, PH22+SH1, and PH3+H2S reactions, but they are spin forbidden and energetically unfavorable for the HPS1 and PSH1 formations. On the other hand, the PS2 formation is more likely to happen by the PH1+SH1 reaction. The PH22+S1, PH3+SH1, P2+H2S, and P4+H2S reactions are also favorable in terms of energetics; however, these reactions are spin forbidden. The chemical mechanism for the PS2 formation is now presented in more details, which is of great importance in the atmosphere of Jupiter and Saturn, and in interstellar medium.
Effects of bulk impurity concentration on the reactivity of metal surface: Sticking of hydrogen molecules and atoms to polycrystalline Nb containing oxygen
Authors: Hatano Yuji , Watanabe Kuniaki , Livshits Alexander , Busnyuk Andrei , Alimov Vasily , Nakamura Yukio , Hashizume Ken-ichi
Published: November 2007

Nonmetallic impurities segregated onto metal surfaces are able to drastically decrease the chemical reactivity of metals. In the present paper, effects of bulk impurities on the reactivity of metallic surfaces were investigated in a wide temperature range on an example of the sticking of hydrogen molecules and atoms to Nb [polycrystalline, with mainly (100)] containing solute oxygen. At all the investigated surface temperatures, TS (300–1400K), we found the bulk oxygen concentration CO to have a strong effect on the integral probability, αH2, of dissociative sticking of H2 molecules followed by hydrogen solution in the metal lattice: αH2 monotonically decreased by orders of magnitude with increasing CO from 0.03to1.5at.%. The sticking coefficient αH2 was found to depend on TS but not on the gas temperature. The effect of CO on αH2 is explained by the presence of oxygen-free sites (holes in coverage) serving as active centers of the surface reaction in the oxygen monolayer upon Nb. In contrast to H2 molecules, H atoms were found to stick to, and be dissolved in, oxygen-covered Nb with a probability comparable to 1, depending neither on CO nor on TS. This proves that, unlike H2 molecules, H atoms do stick to be dissolved mainly through regular surface sites covered by oxygen and not through the holes in coverage.
Application of contact theory to metal-metal bonding of silicon wafers
Authors: Leong H. L. , Gan C. L. , Thompson C. V. , Pey K. L. , Li H. Y.
Published: November 2007

A model is presented which relates the applied load and surface roughness to the integrity of metal-metal wafer-level thermocompression bonds. Using contact theory, the true contact area is calculated as a function of the applied load and surface roughness as characterized using atomic force microscopy. The relationship between the nominal and true contact areas quantifies the effects of applied load and surface roughness on the bond integrity of the bonded wafers as indicated by the dicing yield. Experiments on Cu–Cu bonds show that the true contact area provides a better indicator of bond integrity than either the nominal contact area or applied force, taken together or separately.
Analyzer-based x-ray phase-contrast microscopy combining channel-cut and asymmetrically cut crystals
Authors: Hönnicke M. G. , Cusatis C.
Published: November 2007

An analyzer-based x-ray phase-contrast microscopy (ABM) setup combining a standard analyzer-based x-ray phase-contrast imaging (ABI) setup [nondispersive 4-crystal setup (Bonse-Hart setup)] and diffraction by asymmetrically cut crystals is presented here. An attenuation-contrast microscopy setup with conventional x-ray source and asymmetrically cut crystals is first analyzed. Edge-enhanced effects attributed to phase jumps or refraction/total external reflection on the fiber borders were detected. However, the long exposure times and the possibility to achieve high contrast microscopies by using extremely low attenuation-contrast samples motivated us to assemble the ABM setup using a synchrotron source. This setup was found to be useful for low contrast attenuation samples due to the low exposure time, high contrast, and spatial resolution found. Moreover, thanks to the combination with the nondispersive ABI setup, the diffraction-enhanced x-ray imaging algorithm could be applied.
Multistable liquid crystal waveplate
Authors: Wells G. G. , Brown C. V.
Published: November 2007

A multistable liquid crystal waveplate has been produced by confining a roughly disk-shaped nematic liquid crystal droplet of diameter 50μm between two photoresist coated surfaces separated by 15μm. Dimple features occur on opposite sides of the curve-free edge of the droplet, which may indicate the position of nematic disclinations. The diameter that connects these features coincides with an optic axis of the droplet. In-plane ac voltage bursts produce an optic axis rotation, controllable down to 1° steps, to other arbitrary, stable orientations. The rotation angle is proportional to the burst duration and the voltage squared.
Selective area synthesis of magnesium oxide nanowires
Authors: Kim G. , Martens R. L. , Thompson G. B. , Kim B. C. , Gupta A.
Published: November 2007

Single crystalline magnesium oxide (MgO) nanowires exhibiting a square cross section have been grown on (001)-oriented MgO and Si substrates using the vapor-liquid-solid growth mechanism. While the nanowires grow vertically aligned on MgO, they display random orientations on the silicon substrate. For growth on MgO substrates, the selective placement and density of the nanowires can be controlled by using electron beam lithography for prepatterning the gold catalyst layer. The nanowire samples have been characterized using field-emission scanning electron microscopy and transmission electron microscopy. The described process for selective placement of the nanowires is attractive for their use as templates for coaxial coatings and also for their manipulation for potential device fabrication.
Simultaneous detection of translational and angular displacements of micromachined elements
Authors: Hwu E.-T. , Hung S.-K. , Yang C.-W. , Hwang I.-S. , Huang K.-Y.
Published: November 2007

An astigmatic detection system is constructed with a modified digital-versatile-disk optical head. This system, with a detecting spot of ∼1μm, can simultaneously measure the vertical displacements and two-dimensional angular tilts of micromachined elements. It can detect thermal vibrations of microfabricated cantilevers with noise levels of 1.3pmHz−1∕2 for the linear displacement and of 3.2nradHz−1∕2 for angular displacements over a frequency range from 1to800kHz. The detecting frequency can even reach beyond 100MHz if high-speed electronic devices are adopted. Further optimization of the system will broaden its applications in diverse technological fields.
Growth of the current modulation in an electron beam propagating through background plasma
Authors: Uhm Han S.
Published: November 2007

Amplitude oscillation of the current modulation in an electron beam propagating through background plasma is investigated. An analytical calculation of the beam current modulation indicates amplitude oscillation at the beginning of propagation due to the perturbed space-charge fluctuation of the beam. It was also found that the mode strength of the beam current modulation further downstream grows exponentially from half, a0∕2, of the initial perturbation instead of its value of a0, in contrast with the conventional understanding of two-stream instability. The analytical results are in good agreement with earlier simulation data.
Noise limited computational speed
Authors: Gammaitoni L.
Published: November 2007

In modern transistor based logic gates, the impact of noise on computation has become increasingly relevant since the voltage scaling strategy aimed at decreasing the dissipated power, has increased the probability of error due to the reduced switching threshold voltages. In this paper, we discuss the role of noise in a two state model that mimic the dynamics of standard logic gates and show that the presence of the noise sets a fundamental limit to the computing speed. An optimal idle time interval that minimizes the error probability is derived.
Integrated epigenomic analyses of neuronal MeCP2 reveal a role for long-range interaction with active genes
Authors: Yasui Dag H. , Peddada Sailaja , Bieda Mark C. , Vallero Roxanne O. , Hogart Amber , Nagarajan Raman P. , Thatcher Karen N. , Farnham Peggy J. , LaSalle Janine M.
Published: November 2007

Mutations in
MECP2
cause the autism-spectrum disorder Rett syndrome. MeCP2 is predicted to bind to methylated promoters and silence transcription. However, the first large-scale mapping of neuronal MeCP2-binding sites on 26.3 Mb of imprinted and nonimprinted loci revealed that 59% of MeCP2-binding sites are outside of genes and that only 6% are in CpG islands. Integrated genome-wide promoter analysis of MeCP2 binding, CpG methylation, and gene expression revealed that 63% of MeCP2-bound promoters are actively expressed and that only 6% are highly methylated. These results indicate that the primary function of MeCP2 is not the silencing of methylated promoters.
Cryo-EM study of the spinach chloroplast ribosome reveals the structural and functional roles of plastid-specific ribosomal proteins
Authors: Sharma Manjuli R. , Wilson Daniel N. , Datta Partha P. , Barat Chandana , Schluenzen Frank , Fucini Paola , Agrawal Rajendra K.
Published: November 2007

Protein synthesis in the chloroplast is carried out by chloroplast ribosomes (chloro-ribosome) and regulated in a light-dependent manner. Chloroplast or plastid ribosomal proteins (PRPs) generally are larger than their bacterial counterparts, and chloro-ribosomes contain additional plastid-specific ribosomal proteins (PSRPs); however, it is unclear to what extent these proteins play structural or regulatory roles during translation. We have obtained a three-dimensional cryo-EM map of the spinach 70S chloro-ribosome, revealing the overall structural organization to be similar to bacterial ribosomes. Fitting of the conserved portions of the x-ray crystallographic structure of the bacterial 70S ribosome into our cryo-EM map of the chloro-ribosome reveals the positions of PRP extensions and the locations of the PSRPs. Surprisingly, PSRP1 binds in the decoding region of the small (30S) ribosomal subunit, in a manner that would preclude the binding of messenger and transfer RNAs to the ribosome, suggesting that PSRP1 is a translation factor rather than a ribosomal protein. PSRP2 and PSRP3 appear to structurally compensate for missing segments of the 16S rRNA within the 30S subunit, whereas PSRP4 occupies a position buried within the head of the 30S subunit. One of the two PSRPs in the large (50S) ribosomal subunit lies near the tRNA exit site. Furthermore, we find a mass of density corresponding to chloro-ribosome recycling factor; domain II of this factor appears to interact with the flexible C-terminal domain of PSRP1. Our study provides evolutionary insights into the structural and functional roles that the PSRPs play during protein synthesis in chloroplasts.