bluuebunny/crossref_metadata_2025 huggingface dataset:
Association between STAT1 activity and BRAF mutations in papillary thyroid carcinomas
Authors: Yim Ji Hye , Kim Eun Sook , Choi Hyun‐Jung , Jeon Min Ji , Han Ji Min , Kim Won Gu , Kim Tae Yong , Gong Gyungub , Kim Sang Yoon , Kim Won Bae , Shong Young Kee
Published: April 2012

Background

Signal transducer and activator of transcription‐1 (STAT1) plays a critical role in tumorigenesis by controlling several functions in both tumor cells and the immune system, and is considered to be a tumor suppressor. The present study evaluated the activity of STAT1 in human papillary thyroid carcinomas (PTC).

Methods

STAT1 activity was measured in nuclear extracts of tumor tissues from 35 PTC patients using an ELISA‐based kit.

Results

STAT1 activity was significantly lower in tumors than in the surrounding normal thyroid tissues (P < 0.01). The association between STAT1 activity and clinicopathologic factors was analyzed in PTC tissues. STAT1 activity was significantly lower in tumors that measured 2 cm or more than in tumors that measured 2 cm or less (P = 0.044). Moreover, tumor size was inversely correlated with STAT1 activity (Spearman's rank correlation coefficient (rho) = −0.34, P = 0.048). In addition, tumors with BRAF mutations showed lower STAT1 activity than wild‐type BRAF tumors [0.064 (0.056–0.124) vs. 0.108 (0.073–0.153) arbitrary units, P = 0.048].

Conclusion

STAT1 activity is suppressed in PTCs (as measured by DNA‐binding activities). The tumor with T1799A BRAF mutation and tumor sizes of 2 cm or more were clinicopathologic parameters associated with lower STAT1 activity. STAT1 activity of tumor might be one of potential biomarkers for PTC's. J. Surg. Oncol. 2012; 106:719–723. © 2012 Wiley Periodicals, Inc.
D1 versus D2 lymphadenectomy for gastric cancer
Authors: Schmidt Benjamin , Yoon Sam S.
Published: April 2012

Significant variability exists throughout the world in the extent of lymphadenectomy that is performed for gastric adenocarcinoma. D2 lymphadenectomy is the standard lymphadenectomy performed in high incidence countries such as Japan and South Korea, and less extensive lymphadenectomies are often performed in lower incidence countries such as the Unites States. This article reviews the evidence on the extent of lymphadenectomy that should be performed for gastric adenocarcinoma. J. Surg. Oncol. 2013;107:259–264. © 2012 Wiley Periodicals, Inc.
Contrast-enhanced ultrasound diagnosis of splenic artery steal syndrome after orthotopic liver transplantation
Authors: Zhu Xian-Sheng , Gao Yun-Hua , Wang Sha-Sha , Cheng Qi , Ling Yin , Fan Li , Huo Feng , Pu Miao-Shui , Li Peng
Published: April 2012

The aim of this study was to investigate the use of contrast-enhanced ultrasound (CEUS) for the detection of splenic artery steal syndrome (SASS) after orthotopic liver transplantation (OLT). Two hundred forty-seven patients underwent OLT. Blood tests and color Doppler flow imaging (CDFI) were performed at various time points after the operation. CEUS and celiac angiography were used for patients suspected of having SASS. If the diagnosis of SASS was confirmed, splenic artery embolization was performed to enhance hepatic artery flow. CEUS and angiography were performed for the assessment of postinterventional clinical outcomes. Three of the 247 patients died postoperatively, and 8 patients were suspected of having SASS because of elevated liver enzyme levels and slim or undetectable hepatic artery blood signals by CDFI at various points after the operation. In these 8 patients, CEUS showed a delayed and weak contrast-enhanced blood signal in the hepatic artery associated with a rapid and intense enhancement of the portal vein blood. No narrowing of the hyperintense signal was observed in the hepatic artery by CEUS. The 8 diagnoses of SASS were proven by celiac angiography, which showed delayed perfusion of the hepatic artery and rapid filling of the splenic artery. Immediately after the interventional procedure, CEUS demonstrated a significantly enlarged hyperintense blood signal in the hepatic artery. In conclusion, approximately 3.27% of SASS cases occur after OLT. SASS can be identified as a sluggish and weak hyperintense blood signal in the hepatic artery without the narrowing and interruption of the hypointense signal in CEUS imaging. CEUS is an effective imaging modality for the detection of SASS after OLT. Liver Transpl, 2012. © 2012 AASLD.
Imaginaries in Boolean algebras
Authors: Wencel Roman
Published: April 2012

Given an infinite Boolean algebraB, we find a natural class of\documentclass{article}\usepackage{amssymb}\begin{document}\pagestyle{empty}$\varnothing$\end{document}‐definable equivalence relations\documentclass{article}\usepackage{amssymb}\begin{document}\pagestyle{empty}$\mathcal {E}_{B}$\end{document}such that every imaginary element fromBeqis interdefinable with an element from a sort determined by some equivalence relation from\documentclass{article}\usepackage{amssymb}\begin{document}\pagestyle{empty}$\mathcal {E}_{B}$\end{document}. It follows thatBtogether with the family of sorts determined by\documentclass{article}\usepackage{amssymb}\begin{document}\pagestyle{empty}$\mathcal {E}_{B}$\end{document}admits elimination of imaginaries in a suitable multisorted language. The paper generalizes author's earlier results concerning definable equivalence relations and weak elimination of imaginaries for Boolean algebras, obtained in10.
Preexcisional artery reconstruction: A new strategy in multiple hepatic artery reconstruction for reducing ischemic injury of the liver
Authors: Iida Takuya , Mihara Makoto , Narushima Mitsunaga , Yoshimatsu Hidehiko , Hara Hisako , Koshima Isao
Published: April 2012

Multiple reconstructions of the hepatic arteries (HA) after cancer resection presents a surgical challenge, not only because it is technically demanding, but also because attention must be paid to potential ischemic injury to the liver caused by the prolonged ischemia. We present a novel “preexcisional artery reconstruction” method for minimizing ischemic injury of the liver. A 65‐year‐old woman presented with cholangiocarcinoma invading the HA. Pancreatoduodenectomy, resection, and multiple reconstruction of the HA were performed. First, the left hepatic artery (LHA) was reconstructed prior to the tumor resection. During this procedure, blood supply was maintained to most of the liver via the right hepatic artery (RHA). Then, resection of the tumor en bloc with the HA was performed, followed by reconstruction of the RHA. During this procedure, blood supply was maintained via the already‐reconstructed LHA, thereby limiting the ischemic area. Use of this method allowed the ischemia time and region to be divided and minimized, thereby leading to a reduced risk of ischemia‐related complications. We believe that this method may be one of the useful approaches in multiple HA reconstruction. © 2012 Wiley Periodicals, Inc. Microsurgery, 2012.
Composite vascularized fibular epiphyseo‐osteo‐periosteal transfer for hip reconstruction after proximal femoral tumoral resection in a 4‐year‐old child
Authors: Soldado Francisco , Fontecha Cesar Garcia , Haddad Sleiman , Corona Pablo , Collado Diego , Llusá Manel , Rego Paulo
Published: April 2012

Literature on the reconstruction of the proximal femur in skeletally immature patients with the use of an epiphyseal transplant is scarce and with variable results depending on the indication. We report successful outcomes using a modified vascularized fibular epiphyseal transplant in a 4‐year‐old boy with an oncologic lesion. We discuss the advantages of supplementing the standard graft with a vascularized fibular periosteal tissue.

The vascularized fibular epiphyseal transplant (VFET) is an effective option in the reconstruction of the epiphysis in skeletally immature patients, owing to the advantage of restoring both the joint function and the growth potential in a single surgical operation.1

Multiple reported cases demonstrate the effectiveness of this complex technique in upper extremity reconstruction.1,2 However, literature is scarce regarding its use for the reconstruction of the proximal femur and hip joint.3‐5

Through this article, we report the use of a VFET in the reconstruction of a proximal femur in a 4‐year‐old boy after an intra‐articular wide excision of an epithelioid hemangioendotelioma. We also discuss the advantages of designing the flap as a composite vascularized epiphyseo‐osteo‐periosteal flap.6 © 2012 Wiley Periodicals, Inc. Microsurgery, 2012.
Double‐wall carbon nanotube‐reinforced polyester nanocomposites: Improved dispersion and mechanical properties
Authors: Jacob Muthu S.D. , Paskaramoorthy Ratnam
Published: April 2012

Double‐walled carbon nanotube (DWCNT)‐reinforced polyester nanocomposites were prepared and tested to characterize their mechanical properties. The DWCNTs were functionalized to improve their dispersion within the polyester matrix. The improvement in the mechanical properties shows that the functionalized DWCNTs have better distribution within, and good adhesion with, the polyester matrix. A comparison of the mechanical properties of nanocomposites reinforced by functionalized and nonfunctionalized DWCNTs confirms that the functionalization leads to substantially improved composites. POLYM. COMPOS., 2012. © 2012 Society of Plastics Engineers
Preparation of expandable graphite via H2O2‐hydrothermal process and its effect on properties of high‐density polyethylene composites
Authors: Kuan Chen‐Feng , Tsai Kuang‐Chung , Chen Chia‐Hsun , Kuan Hsu‐Chiang , Liu Tai‐Ying , Chiang Chin‐Lung
Published: April 2012

This study presented a new way to prepare expandable graphite (EG), which is one kind of halogen‐free flame retardant using the H2O2‐hydrothermal process. Natural graphite was immersed in H2O2 and then put in autoclave to proceed the hydrothermal process. The EG was called as H2O2‐HEG from the H2O2‐hydrothermal process. The results showed that the expanded volume of EG using the H2O2‐hydrothermal process was higher than that compared with convectional liquid phase synthesis, ultrasound irradiation, and hydrothermal method. Fourier transform infrared spectroscopy, X‐ray diffraction patterns, scanning electron microscope, and X‐ray photoelectron spectroscopy were used to analyze the structure and confirm that the EG had been prepared. Thermogravimetric analysis presents that H2O2‐HEG can improve the thermal stability of composites. The cone calorimeter show that the peak heat release rate (HRR) values of composites decrease dramatically. Limiting oxygen index (LOI) value of H2O2‐HEG composites is higher than that of high‐density polyethylene (HDPE)/natural flake graphite. HDPE composites are capable of passing the V‐0 classification and have antidripping behavior. LOI, UL‐94, and the cone calorimeter results show that the HDPE/H2O2‐HEG composite possess excellent flame retardant property. POLYM. COMPOS., 2012. © 2012 Society of Plastics Engineers
Preparation and characterization of thermoplastic starch–kaolinite nanocomposite films
Authors: Lu Panfang , Zhang Min , Qian Ping , Zhu Qiang
Published: April 2012

In this work, the thermoplastic starch–kaolinite (KAO) nanocomposite films were first prepared via solution‐casting method using chitosan‐modified KAO (CKAO) and Na+–KAO (NKAO). The structure was investigated by X‐ray diffraction, scanning electron microscopy, and Fourier transform infrared spectroscopy techniques. The results showed that the well‐dispersed KAO layers were delaminated in the starch matrix attesting to anexfoliated nanocomposite and formed strong interaction with starch molecules. According to thermogravimetric analysis, differential scanning calorimetric study, and water absorption testing, the starch–CKAO–urea nanocomposites have the greatest enhancements compared with those of starch–urea film and starch–NKAO–urea nanocomposites. These results provide the important information with using CKAO to obtain the exfoliated starch nanocomposites with high performance. POLYM. COMPOS., 2012. © 2012 Society of Plastics Engineers
Prenatal diagnosis of atrial restriction in hypoplastic left heart syndrome is associated with decreased 2‐year survival
Authors: Lowenthal Alexander , Kipps Alaina K. , Brook Michael M. , Meadows Jeffery , Azakie Anthony , Moon‐Grady Anita J.
Published: April 2012

Objective

To compare the course of hypoplastic left heart syndrome (HLHS) patients diagnosed prenatally with any degree of atrial restriction with those without evidence of atrial restriction.

Design

Retrospective, cohort.

Methods

Prenatally diagnosed HLHS patients from August 1999 to January 2009 were categorized as nonrestrictive versus restrictive, defined by left atrial hypertension on pulmonary venous Doppler and/or an intact interatrial septum.

Results

Of 73 total fetal patients identified, 49 were live‐born. Survival at 2 years was 29/35 [83% confidence interval (CI): 59.5%–88.9%] for the nonrestrictive group and 6/14 (43% CI: 17.7%–6.0%) for the restrictive group (p < 0.0001). Of those who underwent stage 1 palliation (35 with nonrestrictive and 10 with restrictive atrial septa), both groups had a similar incidence of preoperative acidosis and need for ventilation and inotropic support. Postoperatively, there was no difference between groups in ventilator days, length of stay, or survival to discharge. There was decreased survival at 2 years in the restrictive group, 60% (CI: 26.2%–87.8%) versus 83% (CI: 66.4%–93.4%) in the nonrestrictive group. Furthermore, a disproportionate number of interstage deaths was evident in the restrictive group.

Conclusions

Prenatal presence of any degree of atrial septal restriction in the setting of HLHS confers a significant survival disadvantage, with increases in both early and late mortality. © 2012 John Wiley & Sons, Ltd.
Fabrication of highly transparent self‐cleaning protection films for photovoltaic systems
Authors: Lee Seong‐Hwan , Han Kang‐Soo , Shin Ju‐Hyeon , Hwang Seon‐Yong , Lee Heon
Published: April 2012

A moth‐eye anti‐reflective structure was fabricated by hot‐embossing and UV nanoimprint lithography on a solar cell protective film to suppress the reflection of incident light. Moreover, a superhydrophobic surface was developed by reducing the surface energy by forming a hydrophobic self‐assembled monolayer coating on an anti‐reflective structured resin surface. Therefore, the transmittance of incident light was increased by the anti‐reflective structure. As a result, the solar cell efficiency was enhanced and the total accumulated electrical energy generated by a solar cell with a nano‐patterned polymeric film was increased. The efficiency of each solar cell was evaluated by an analysis of its I‐V characteristics using a solar simulator, and the external quantum efficiency according to the wavelength of incident light was analyzed by using an incident photon‐to‐current conversion efficiency system. Finally, the enhancement of the generated power was confirmed by a field test and a power charging experiment. Copyright © 2012 John Wiley & Sons, Ltd.
Brushless and controlled microphase separation of lamellar polystyrene‐b‐polyethylene oxide thin films for block copolymer nanolithography
Authors: Mokarian‐Tabari Parvaneh , Collins Timothy W. , Holmes Justin D. , Morris Michael A.
Published: April 2012

Creating perpendicular alignment in lamellar block copolymer (BCP) systems has considerable industrial and commercial significance, most importantly for generating nanowire structures in electronic devices. In general, these lamellar systems require careful interface engineering to obtain vertical orientation of the blocks. To avoid the strong preferential adsorption of one block to either the substrate or the polymer/air interface, the surface must be “neutralized” by chemical brushes or external forces, for example, solvent fields. Reported here is a stepwise thermo/solvent annealing process allowing the formation of perpendicular domains of polystyrene‐b‐polyethylene oxide lamellar structures while avoiding brush or other surface modifications. This BCP has a relatively small minimum feature size and can be used to generate substrate patterns for use in fabrication of nanowire electronic device structures. © 2012 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2012
Topical Antiinflammatory Activity of Essential Oil of Lippia sidoides Cham: Possible Mechanism of Action
Authors: Veras Helenicy N. H. , Araruna Mariana K. A. , Costa José G. M. , Coutinho Henrique D. M. , Kerntopf Marta R. , Botelho Marco A. , Menezes Irwin R. A.
Published: April 2012

This work reports the chemical composition of the essential oil of Lippia sidoides (EOLS) and evaluation of the topical effect of EOLS and thymol against different irritant agents in vivo. The essential oil was obtained by hydrodistillation, and gas chromatography/mass spectrometry analysis identified the main constituents: thymol (84.9%) and p‐cymene (5.33%). The antiinflammatory activity was evaluated using the mouse models of acute ear inflammation induced by croton oil, arachidonic acid, phenol or histamine, and chronic inflammation induced by croton oil. The topical application of EOLS or thymol at a dose of 2 mg/ear significantly reduced (p < 0.001) ear edema induced with arachidonic acid by 45.1% and 47.4% and reduced ear edema induced with phenol by 33.2% (p < 0.05) and 54.7% (p < 0.01) in acute ear edema. However, a proinflammatory effect of EOLS and thymol was evidenced when it was applied for more than 1 day. There were no statistical differences in antiedematogenic activity between EOLS and thymol. In conclusion, the results indicate that thymol is the constituent responsible for the topical antiinflammatory activity of EOLS. Thus, these findings could justify the popular use of L. sidoides by alternative medicine, but chronic use has an inflammatory effect. Copyright © 2012 John Wiley & Sons, Ltd.
Macrophage Immunomodulatory Activity of a Purified Polysaccharide Isolated from Ganoderma atrum
Authors: Yu Qiang , Nie Shao‐Ping , Li Wen‐Juan , Zheng Wen‐Ya , Yin Peng‐Fei , Gong De‐Ming , Xie Ming‐Yong
Published: April 2012

The objective of this study was to evaluate the immunomodulatory effects of the purified Ganoderma atrum polysaccharide (PSG‐1) on murine macrophage cell line RAW264.7. Phagocytotic assay by fluorescein isothiocyanate‐dextran internalization showed that PSG‐1 stimulated the phagocytosis of macrophages. G. atrum polysaccharide increased the production of NO, and the level of mRNA expression of inducible nitric oxide synthase in a dose–response manner. G. atrum polysaccharide also dose‐dependently induced the release of TNF‐α and interleukin‐1β. Generation of reactive oxygen species was promoted by PSG‐1, as determined by flow cytometry. Moreover, PSG‐1 induced nuclear factor‐κB activation by elevation of p65 nuclear translocation, suggesting that PSG‐1 probably stimulated macrophage activities by activating the nuclear factor‐κB pathway. Copyright © 2012 John Wiley & Sons, Ltd.
Solvent‐based and solvent‐free characterization of low solubility and low molecular weight polyamides by mass spectrometry: a complementary approach
Authors: Barrère Caroline , Hubert‐Roux Marie , Lange Catherine M. , Rejaibi Majed , Kebir Nasreddine , Désilles Nicolas , Lecamp Laurence , Burel Fabrice , Loutelier‐Bourhis Corinne
Published: April 2012

RATIONALE

Polyamides (PA) belong to the most used classes of polymers because of their attractive chemical and mechanical properties. In order to monitor original PA design, it is essential to develop analytical methods for the characterization of these compounds that are mostly insoluble in usual solvents.

METHODS

A low molecular weight polyamide (PA11), synthesized with a chain limiter, has been used as a model compound and characterized by matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOF‐MS). In the solvent‐based approach, specific solvents for PA, i.e. trifluoroacetic acid (TFA) and hexafluoroisopropanol (HFIP), were tested. Solvent‐based sample preparation methods, dried‐droplet and thin layer, were optimized through the choice of matrix and salt. Solvent‐based (thin layer) and solvent‐free methods were then compared for this low solubility polymer. Ultra‐high‐performance liquid chromatography/electrospray ionization (UHPLC/ESI)‐TOF‐MS analyses were then used to confirm elemental compositions through accurate mass measurement.

RESULTS

Sodium iodide (NaI) and 2,5‐dihydroxybenzoic acid (2,5‐DHB) are, respectively, the best cationizing agent and matrix. The dried‐droplet sample preparation method led to inhomogeneous deposits, but the thin‐layer method could overcome this problem. Moreover, the solvent‐free approach was the easiest and safest sample preparation method giving equivalent results to solvent‐based methods. Linear as well as cyclic oligomers were observed. Although the PA molecular weights obtained by MALDI‐TOF‐MS were lower than those obtained by 1H NMR and acido‐basic titration, this technique allowed us to determine the presence of cyclic and linear species, not differentiated by the other techniques. TFA was shown to induce modification of linear oligomers that permitted cyclic and linear oligomers to be clearly highlighted in spectra.

CONCLUSIONS

Optimal sample preparation conditions were determined for the MALDI‐TOF‐MS analysis of PA11, a model of polyamide analogues. The advantages of the solvent‐free and solvent‐based approaches were shown. Molecular weight determination using MALDI was discussed. Copyright © 2012 John Wiley & Sons, Ltd.
Study on the preparation and multiproperties of the polypyrrole films doped with different ions
Authors: Guanggui Cheng , Jianning Ding , Zhongqiang Zhang , Zhiyong Ling , Huasheng Pu
Published: April 2012

Conducting polypyrrole (PPy) films doped withp‐toluene solfonate (pTS−), perchlorate (ClO4−) and polyphosphate (PP−) were electrochemically synthesized on the stainless steel SS‐304 and the Indium Tin Oxide (ITO) glass substrates successfully. The conducting polymer composite films were studied by Fourier transform infrared spectra, integrated thermal analysis system and scanning electron microscopy, respectively. Four‐point probe measurements andin situnanotribolab system equipped with a nanoscale electrical contact resistance package were employed to analyze their electrical and mechanical properties. Results indicate that the film doped with PP−ion showed the best thermal stability. For the ClO4−ion doped films, the glass transition occurred at 274.8 °C. The pTS−ion doped film on the SS‐304 steel had a good conductivity, and there was a voltage barrier that ranged from −1.25 to 1.9 V according to the current–voltage curves. Nanoindentation tests show that the mechanical properties of the PPy/pTS−film and the PPy/PP−film were better than that of PPy/ClO4−films. Copyright © 2012 John Wiley & Sons, Ltd.
Adsorption of carbon monoxide on Pd (210) and (510) surfaces
Authors: Zhang Jing , Wang Zhen
Published: April 2012

Adsorption of carbon monoxide on Pd (210) and (510) stepped surfaces has been investigated by the extended London‐Eyring‐Polyani‐Sato method constructed using a five‐parameter Morse potential. Pd (210) and (510) stepped surfaces consist of terrace with (100) structure and step with (110) character. These results show that there exist common characteristics of CO adsorption on these two surfaces. At low coverage, CO adsorbs in twofold bridge site of the (100) terrace. The critical characteristics inherit that of CO molecule adsorbed in twofold bridge site of (100) original surface. When the coverage is increased, the top site of (110) step is occupied. The critical characteristics resemble that of CO molecule adsorbed in top site of (110) original surface. A number of new sites are exposed on the boundary regions, for example, the fivefold hollow site (H) of these two surfaces. There are stable adsorption sites at high coverage. Because of the different length of the (100) terrace, the (210) and (510) stepped surfaces have some different characteristics. First, CO is tilted adsorption on bridge site of terrace of (210), but perpendicular on terrace of (510) surface. Second, the bridge site (B1) where one Pd atom at the top of the step and the other at the bottom of the step is a stable adsorption site on (210), but the same type of site on Pd (510) surface is not. Copyright © 2012 John Wiley & Sons, Ltd.
Sputtering of a coarse‐grained benzene and Ag(111) crystals by large Ar clusters – effect of impact angle and cohesive energy
Authors: Rzeznik Lukasz , Paruch Robert , Garrison Barbara J. , Postawa Zbigniew
Published: April 2012

Molecular dynamics computer simulations are employed to investigate the role of the substrate cohesive energy on the impact angle dependence of the sputtering yield for Ar60 and Ar2953 projectiles bombarding a benzene molecular solid and a Ag(111) atomistic sample. A different dependence of the total sputtering yield on the impact angle is observed for small and large projectiles for benzene, while a similar dependence is observed for Ag(111). It is demonstrated that the increase of the cohesive energy leads to a significant decrease of the total ejection signal for both Ar60 and Ar2953 projectiles. The shape of the impact angle dependence, however, is much less sensitive to this parameter. The ‘washing out’ mechanism and the structural differences of the irradiated samples are proposed to be responsible for the different shapes of the impact angle dependence. Copyright © 2012 John Wiley & Sons, Ltd.
Effect of ultrasonic nano‐crystalline surface modification on the microstructural evolution and mechanical properties of Al5052 alloy
Authors: Ahn Deokgi , He Yinsheng , Wan Zhixin , Cho In Shik , Lee Chang Soon , Park In Gyu , Pyoun Young Shik , Dong Jiling , Shin Keesam
Published: April 2012

Surface modification of Al5052 alloy was carried out by an ultrasonic nano‐crystalline surface modification (UNSM) technology at various processing conditions. The effect of UNSM processing parameters (amplitude and ball size) on the evolution of microstructure and mechanical properties was investigated. Analyses using electron microscopy, microhardness and wear test showed an obvious grain refinement up to 200 µm in depth from the surface. The hardness of the UNSM‐treated surface increased by approximately 50%, resulting in approximately 48% increase of wear resistance. The effect of ball size in UNSM was predominant on the grain refinement. Copyright © 2012 John Wiley & Sons, Ltd.
Development of nano‐roughness under SIMS ion sputtering of germanium surfaces
Authors: Iacob E. , Demenev E. , Giubertoni D. , Barozzi M. , Gennaro S. , Bersani M.
Published: April 2012

In this work results, about the formation of topography and roughness induced by secondary ion mass spectrometry ion beam sputtering of single crystal (100) germanium surfaces are reported and related with depth resolution issues and matrix species (74Ge±; 74Ge16O±; 74Ge2±) behavior. In particular, the development of nano‐roughness is studied for both O2+ and Cs+ bombardment at low energy (≤ 3 keV), using a magnetic sector instrument. Analysis was carried out in the sputtering chamber either at ultra‐high vacuum (~10−9 mbar) or at a reduced pressure (~10−6 mbar) by oxygen leak. Zalar rotation was also tested as a method to reduce the formation of topography where observed. The results show that ripples are formed under O2+ sputtering for energies ≤ 1 keV (incidence angle ~60°) without rotation, although their amplitude is very small compared to the crater depth. No relevant roughness is observed in the craters when Cs+ ions are used (inc. angle ~50°), while particles of aggregated Cs are detected. Copyright © 2012 John Wiley & Sons, Ltd.
Comparison of a new dead‐time correction method and conventional models for SIMS analysis
Authors: Takano Akio , Takenaka Hisataka , Ichimaru Satoshi , Nonaka Hidehiko
Published: April 2012

Recently, secondary ion mass spectrometry (SIMS) has been used in the analysis of not only impurities but also matrix elements, thus requiring a wide dynamic range for SIMS analysis. However, SIMS detectors, which are mostly used in pulse counting systems, have difficulties with detector saturation. In this paper, we investigate whether a dead‐time model that was developed for X‐ray measurement is applicable for SIMS analysis. We then compare a new correction method with conventional correction methods for detector saturation in SIMS analysis. We report that the new method can better correct the intensity in regions of higher intensity than that achieved by conventional methods. Copyright © 2012 John Wiley & Sons, Ltd.
Synergistic use of NMR and MD simulations to study the structural heterogeneity of proteins
Authors: Esteban‐Martín Santiago , Bryn Fenwick Robert , Salvatella Xavier
Published: April 2012

Nuclear magnetic resonance spectroscopy (NMR) and molecular dynamics (MD) simulations are powerful techniques for the structural characterization of macromolecules. NMR is unique in its ability to provide experimental information at atomic level on the structure as well as on the amplitude and rate of structural fluctuations. MD provides physically sound models and potential mechanisms that connect conformations in time. Nevertheless, none of these techniques allow yet obtaining experimentally validated movies of protein motions at atomic resolution. Instead, it is their complementarity and synergy which offer a unique opportunity toward this end. Here, we overview recent examples that illustrate how much these two techniques benefit from each other, both passively and actively, for the characterization of the structural heterogeneity in proteins. © 2012 John Wiley & Sons, Ltd.

This article is categorized under:

Molecular and Statistical Mechanics > Molecular Dynamics and Monte-Carlo Methods
Hansch analysis 50 years on
Authors: Martin Yvonne Connolly
Published: April 2012

The invention of quantitative structure–activity relationships (QSAR) launched the use of computers to understand the multiple factors that contribute to the relationship between the chemical and biological properties of molecules. The original Hansch–Fujita QSAR continues to be performed to this day, fifty years since its inception. In addition, it has inspired vigorous research that has inspired many related methods: for example, methods that use descriptors such as substructures or three‐dimensional features or methods that are based on mathematical models such as partial least squares or recursive partitioning. The influence of QSAR is felt in the recognition of the value of predictions from such models by regulatory agencies and by the widespread use of octanol–water log P in agricultural, environmental, and medicinal chemistry.

This article is categorized under:

Computer and Information Science > Chemoinformatics
Evolution and development in cave animals: from fish to crustaceans
Authors: Protas Meredith , Jeffery William R.
Published: April 2012

Cave animals are excellent models to study the general principles of evolution as well as the mechanisms of adaptation to a novel environment: the perpetual darkness of caves. In this article, two of the major model systems used to study the evolution and development (evo–devo) of cave animals are described: the teleost fish Astyanax mexicanus and the isopod crustacean Asellus aquaticus. The ways in which these animals match the major attributes expected of an evo–devo cave animal model system are described. For both species, we enumerate the regressive and constructive troglomorphic traits that have evolved during their adaptation to cave life, the developmental and genetic basis of these traits, the possible evolutionary forces responsible for them, and potential new areas in which these model systems could be used for further exploration of the evolution of cave animals. Furthermore, we compare the two model cave animals to investigate the mechanisms of troglomorphic evolution. Finally, we propose a few other cave animal systems that would be suitable for development as additional models to obtain a more comprehensive understanding of the developmental and genetic mechanisms involved in troglomorphic evolution. WIREs Dev Biol 2012. doi: 10.1002/wdev.61

This article is categorized under:

Comparative Development and Evolution > Evolutionary Novelties
Sensitivity of berry productivity to climatic variation in the Cabinet–Yaak grizzly bear recovery zone, Northwest United States, 1989–2010
Authors: Holden Zachary A. , Kasworm Wayne F. , Servheen Christopher , Hahn Beth , Dobrowski Solomon
Published: April 2012

Berry‐producing shrubs are culturally, economically, and ecologically important for both people and animals in the Pacific Northwest of the United States. We examined huckleberry (Vaccinium membranaceum) and serviceberry (Amelanchier alnifolia) productivity across the Cabinet–Yaak grizzly bear recovery zone in Northern Idaho and Western Montana. An index of annual berry productivity was measured at field plots from 1989 to 2010. Temperature, precipitation, and snow indices were derived from nearby Snowpack Telemetry (SNOTEL) stations. Huckleberry production was highest during cool springs with high July diurnal temperature ranges. April–June growing‐degree days and July temperature range explain 70% of the inter‐annual variability in huckleberry productivity. Serviceberry production was correlated with maximum snow‐water equivalent and April–June growing‐degree days, which explained 86% of the variance in annual serviceberry production. These models show potential to forecast annual berry production and to anticipate potential bear–human interactions. Further development of models is essential to better predict the potential changes in important wildlife resources in the context of climate change. Published 2012. This article is a U.S. Government work and is in the public domain in the USA.
Market-based measures for greenhouse gas emissions from ships: a review
Authors: Psaraftis Harilaos N.
Published: April 2012

The purpose of this paper is to review several distinct proposals for market-based measures (MBMs) that are under consideration by the International Maritime Organization (IMO) for greenhouse gases (GHGs). Thus far, some ten distinct MBM proposals have been submitted to the IMO. The paper discusses the general concept of an MBM, the mechanisms used by MBMs, and attempts to discuss the pros and cons of the submitted proposals, according to some specific criteria.
Genomic analysis of ICEVchBan8: An atypical genetic element in Vibrio cholerae
Authors: Taviani Elisa , Spagnoletti Matteo , Ceccarelli Daniela , Haley Bradd J. , Hasan Nur A. , Chen Arlene , Colombo Mauro M. , Huq Anwar , Colwell Rita R.
Published: April 2012

Genomic islands (GIs) and integrative conjugative elements (ICEs) are major players in bacterial evolution since they encode genes involved in adaptive functions of medical or environmental importance. Here we performed the genomic analysis of ICEVchBan8, an unusual ICE found in the genome of a clinical non‐toxigenic Vibrio cholerae O37 isolate. ICEVchBan8 shares most of its genetic structure with SXT/R391 ICEs. However, this ICE codes for a different integration/excision module is located at a different insertion site, and part of its genetic cargo shows homology to other pathogenicity islands of V. cholerae.
Swept-wing boundary-layer receptivity
Authors: Tempelmann David , Hanifi Ardeshir , Henningson Dan S.
Published: April 2012

Adjoint solutions of the linearized incompressible Navier–Stokes equations are presented for a cross-flow-dominated swept-wing boundary layer. For the first time these have been computed in the region upstream of the swept leading edge and may therefore be used to predict receptivity to any disturbances of the incoming free stream as well as to surface roughness. In this paper we present worst-case scenarios, i.e. those external disturbances yielding maximum receptivity amplitudes of a steady cross-flow disturbance. In the free stream, such an ‘optimal’ disturbance takes the form of a streak which, while being convected downstream, penetrates the boundary layer and smoothly turns into a growing cross-flow mode. The ‘worst-case’ surface roughness has a wavy shape and is distributed in the chordwise direction. It is shown that, under such optimal conditions, the boundary layer is more receptive to surface roughness than to incoming free stream disturbances.
Hydraulic control of continuously stratified flow over an obstacle
Authors: Winters Kraig B. , Armi Laurence
Published: April 2012

Motivated by the laboratory experiments of Browand & Winant (Geophys. Fluid Dyn., vol. 4, 1972, pp. 29–53), a series of two-dimensional numerical simulations of flow past a cylinder of diameter $d$ are run for different values of the approach Froude number ${\mathit{Fr}}_{o} = U/ Nd$ between $0. 02$ and $0. 2$ at $\mathit{Re}= O(100)$. The observed flow is characterized by blocking and upstream influence in front of the cylinder and by relatively thin, fast jets over the top and bottom of the cylinder. This continuously stratified flow can be understood in terms of an inviscid non-diffusive integral inertia–buoyancy balance reminiscent of reduced-gravity single-layer hydraulics, but one where the reduced gravity is coupled to the thickness of the jets. The proposed theoretical framework describes the flow upstream of the obstacle and at its crest. The most important elements of the theory are the inclusion of upstream influence in the form of blocked flow within an energetically constrained depth range and the recognition that the flow well above and well below the active, accelerated layers is dynamically uncoupled. These constraints determine, through continuity, the transport in the accelerated layers. Combining these results with the observation that the flow is asymmetric around the cylinder, i.e. hydraulically controlled, allows us to determine the active layer thicknesses, the effective reduced gravity and thus all of the integral flow properties of the fast layers in good agreement with the numerically computed flows.
Cognitive behavioural therapy for occupational trauma: a systematic literature review exploring the effects of occupational trauma and the existing CBT support pathways and interventions for staff working within mental healthcare including allied professions
Authors: Graham Judith
Published: April 2012

This study performed a systematic literature review to examine existing and recommended CBT support for staff working within mental healthcare, who experienced occupational traumatization. The following questions were posed: (1) What are the effects of differing levels of occupational trauma on the individual and/or organization? (2) Are there any current CBT-specific models, or treatment pathways, aimed at supporting those experiencing the effects of occupational trauma? Conclusions showed the effects of occupational trauma are significant, varied and predominantly negative to both employees, and the organizations where they work. There were no CBT-specific models or pathways sourced to address occupational trauma; however, interventions were highlighted which may form parts of a larger pathway. Reviewed evidence suggests that development of a stepped CBT pathway for occupational trauma will be beneficial.
The influence of internal model variability in GEOS‐5 on interhemispheric CO2 exchange
Authors: Allen Melissa , Erickson David , Kendall Wesley , Fu Joshua , Ott Lesley , Pawson Steven
Published: April 2012

An ensemble of eight atmospheric CO2 simulations was completed employing the National Aeronautics and Space Administration (NASA) Goddard Earth Observation System, Version 5 (GEOS‐5) for the years 2000–2001, each with initial meteorological conditions corresponding to different days in January 2000 to examine internal model variability. Globally, the model runs show similar concentrations of CO2 for the two years, but in regions of high CO2 concentrations due to fossil fuel emissions, large differences among different model simulations appear. The phasing and amplitude of the CO2 cycle at Northern Hemisphere locations in all of the ensemble members is similar to that of surface observations. In several southern hemisphere locations, however, some of the GEOS‐5 model CO2 cycles are out of phase by as much as four months, and large variations occur between the ensemble members. This result indicates that there is large sensitivity to transport in these regions. The differences vary by latitude—the most extreme differences in the Tropics and the least at the South Pole. Examples of these differences among the ensemble members with regard to CO2 uptake and respiration of the terrestrial biosphere and CO2 emissions due to fossil fuel emissions are shown at Cape Grim, Tasmania. Integration‐based flow analysis of the atmospheric circulation in the model runs shows widely varying paths of flow into the Tasmania region among the models including sources from North America, South America, South Africa, South Asia and Indonesia. These results suggest that interhemispheric transport can be strongly influenced by internal model variability.
Behind uncertainties in projections of Australian tropical climate: Analysis of 19 CMIP3 models
Authors: Moise A. F. , Colman R. A. , Brown J. R.
Published: April 2012

A systematic study is undertaken for projected changes in tropical Australian climate in 19 CMIP3 Coupled Models for the A2 scenario over the 21st century. While equatorial regions to the north of Australia are projected to have increased precipitation during austral summer (December to February) by the end of the 21st century, there is no significant change over northern Australia based on the model ensemble mean. There is a large spread in model simulations of precipitation change, with both large positive and negative anomalies. The ensemble mean change in the seasonal cycle of precipitation over tropical Australia is small, with precipitation increase during March and April, suggesting a prolonged Australian wet season. There is no model consensus on how interannual variability of tropical Australian precipitation will change in future climate, although more models simulate increased variability than decreased. Correlations between full wet season (October to April) precipitation and austral spring (September to November) NINO3.4 sea surface temperature anomalies show a slight weakening. The spread in projected precipitation seasonal cycle changes between simulations from the same model is larger than the inter‐model range, indicating that there is large internal or natural variability in tropical Australian precipitation relative to the climate change signal. Zonal wind changes indicate an intensification of austral summer low level westerlies although combined with a weakening of upper easterlies. Low level westerlies also persist for longer, consistent with a delay in the monsoon retreat. All models simulate an increase in the land‐ocean temperature contrast in austral summer, with a significant correlation between changes in land‐ocean temperature contrast in the pre‐monsoon (austral spring) and summer precipitation changes. Analysis of precipitation changes using regime‐sorting techniques shows offsetting tendencies from thermodynamic changes associated with enhanced atmospheric moisture and dynamic changes associated with a weakened atmospheric circulation.
Campanian‐Maastrichtian intermediate‐ to deep‐water changes in the high latitudes: Benthic foraminiferal evidence
Authors: Koch Mirjam C. , Friedrich Oliver
Published: April 2012

During the latest Cretaceous cooling phase, a positive shift in benthic foraminiferal δ18O values lasting about 1.5 Myr (71.5–70 Ma) can be observed at a global scale (Campanian‐Maastrichtian Boundary Event, CMBE). This δ18O excursion is interpreted as being influenced by a change in intermediate‐ to deep‐water circulation or by temporal build‐up of Antarctic ice sheets. Here we test whether benthic foraminiferal assemblages from a southern high‐latitudinal site near Antarctica (ODP Site 690) are influenced by the CMBE. If the δ18O transition reflects a change in intermediate‐ to deep‐water circulation from low‐latitude to high‐latitude water masses, then this change would result in cooler temperatures, higher oxygen concentration, and possibly lower organic‐matter flux at the seafloor, resulting in a major benthic foraminiferal assemblage change. If, however, the δ18O transition was mainly triggered by ice formation, no considerable compositional difference in benthic foraminiferal assemblages would be expected. Our data show a separation of the studied succession into two parts with distinctly different benthic foraminiferal assemblages. Species dominating the older part (73.0–70.5 Ma) tolerate less bottom water oxygenation and are typical components of low‐latitude assemblages. In contrast, the younger part (70.0–68.0 Ma) is characterized by species that indicate well‐oxygenated bottom waters and species common in high‐latitude assemblages. We interpret the observed change in benthic foraminiferal assemblages toward a well‐oxygenated environment to reflect the onset of a shift from low‐latitude toward high‐latitude dominated intermediate‐ to deep‐water sources. This implies that a change in oceanic circulation was at least a major component of the CMBE.
Simulating the impacts of ionospheric scintillation on L band SAR image formation
Authors: Carrano Charles S. , Groves Keith M. , Caton Ronald G.
Published: April 2012

We develop a phase screen model called the Synthetic Aperture Radar (SAR) Scintillation Simulator (SAR‐SS) for predicting the impacts of ionospheric scintillation on SAR image formation. SAR‐SS consists of a phase screen generator and a propagator. The screen generator creates a 2‐D random realization of spatial phase fluctuations resulting from the traversal of small‐scale field‐aligned irregularities in the ionosphere. It accounts for the motion of the radar platform, the drift of the ionospheric irregularities, and the oblique angle of propagation, all of which determine the scale sizes of the irregularities sampled by the radar beam. The propagator solves the 3‐D parabolic wave equation using the split step technique to compute the ionospheric transfer function for two‐way propagation. This ionospheric transfer function is used to modulate the SAR signal due to terrestrial features in order to assess the ionospheric impact on SAR image formation in the small target approximation. We compare simulated and observed PALSAR imagery over Brazil during disturbed ionospheric conditions. We demonstrate that SAR‐SS can reproduce the field‐aligned streaks in PALSAR imagery caused by irregularities in the equatorial ionosphere that have been observed by previous authors. The field‐aligned streaks exhibited a dominant wavelength larger than the Fresnel break scale, which suggests that refractive scatter was dominant over diffraction as the physical mechanism responsible for the scintillation of the radar signal in this case. The spectral index of phase fluctuations in the screen was quite large (9.0), suggesting that these irregularities were possibly associated with bottomside sinudoidal irregularities rather than equatorial plasma bubbles.