bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of pH on the structure and stability of Bacillus circulans ssp. alkalophilus phosphoserine aminotransferase: Thermodynamic and crystallographic studies
Authors: Kapetaniou Evangelia G. , Thanassoulas Angelos , Dubnovitsky Anatoly P. , Nounesis George , Papageorgiou Anastassios C.
Published: March 2006

pH is one of the key parameters that affect the stability and function of proteins. We have studied the effect of pH on the pyridoxal‐5′‐phosphate‐dependent enzyme phosphoserine aminotransferase produced by the facultative alkaliphile Bacillus circulans ssp. alkalophilus using thermodynamic and crystallographic analysis. Enzymatic activity assay showed that the enzyme has maximum activity at pH 9.0 and relative activity less than 10% at pH 7.0. Differential scanning calorimetry and circular dichroism experiments revealed variations in the stability and denaturation profiles of the enzyme at different pHs. Most importantly, release of pyridoxal‐5′‐phosphate and protein thermal denaturation were found to occur simultaneously at pH 6.0 in contrast to pH 8.5 where denaturation preceded cofactor's release by approximately 3°C. To correlate the observed differences in thermal denaturation with structural features, the crystal structure of phosphoserine aminotransferase was determined at 1.2 and 1.5 Å resolution at two different pHs (8.5 and 4.6, respectively). Analysis of the two structures revealed changes in the vicinity of the active site and in surface residues. A conformational change in a loop involved in substrate binding at the entrance of the active site has been identified upon pH change. Moreover, the number of intramolecular ion pairs was found reduced in the pH 4.6 structure. Taken together, the presented kinetics, thermal denaturation, and crystallographic data demonstrate a potential role of the active site in unfolding and suggest that subtle but structurally significant conformational rearrangements are involved in the stability and integrity of phosphoserine aminotransferase in response to pH changes. Proteins 2006. © 2006 Wiley‐Liss, Inc.
D‐Trehalose/D‐maltose‐binding protein from the hyperthermophilic archaeon Thermococcus litoralis: The binding of trehalose and maltose results in different protein conformational states
Authors: Herman Petr , Staiano Maria , Marabotti Anna , Varriale Antonio , Scirè Andrea , Tanfani Fabio , Vecer Jaroslav , Rossi Mose' , D'Auria Sabato
Published: March 2006

In this work, we used fluorescence spectroscopy, molecular dynamics simulation, and Fourier transform infrared spectroscopy for investigating the effect of trehalose binding and maltose binding on the structural properties and the physical parameters of the recombinant D‐trehalose/D‐maltose binding protein (TMBP) from the hyperthermophilic archaeon Thermococcus litoralis. The binding of the two sugars to TMBP was studied in the temperature range 20°–100°C. The results show that TMBP possesses remarkable temperature stability and its secondary structure does not melt up to 90°C. Although both the secondary structure itself and the sequence of melting events were not significantly affected by the sugar binding, the protein assumes different conformations with different physical properties depending whether maltose or trehalose is bound to the protein. At low and moderate temperatures, TMBP possesses a structure that is highly compact both in the absence and in the presence of two sugars. At about 90°C, the structure of the unliganded TMBP partially relaxes whereas both the TMBP/maltose and the TMBP/trehalose complexes remain in the compact state. In addition, Fourier transform infrared results show that the population of α‐helices exposed to the solvent was smaller in the absence than in the presence of the two sugars. The spectroscopic results are supported by molecular dynamics simulations. Our data on dynamics and stability of TMBP can contribute to a better understanding of transport‐related functions of TMBP and constitute ground for targeted modifications of this protein for potential biotechnological applications. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Detection of planar motion objects using Radon transform and one‐dimensional phase‐only matched filtering
Authors: Tsuboi Tatsuhiko , Hirai Shinichi
Published: March 2006

We describe an algorithm to detect the position and orientation of multiple objects in planar motion using the Radon transform and 1D phase‐only matched filtering (POMF). The proposed vision algorithm performs pattern matching between a template and input image to detect the position and orientation of the objects. First, the Radon transform is applied to the two images to separate the rotation and translation of the objects. Next, 1D POMF along the distance of the Radon transform is applied to the transformed images so as to detect the separated position and orientation. Since it uses 1D POMF to detect both position and orientation, the proposed algorithm can detect the position and orientation of multiple objects. © 2006 Wiley Periodicals, Inc. Syst Comp Jpn, 37(5): 56–66, 2006; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/scj.20398
Disease‐related gene search by association analysis based on link structure
Authors: Matsunaga Tsutomu
Published: March 2006

A method is proposed in the present paper for analyzing associations based on a link structure. By means of this method, the effect that disabled target information in a linked information group has on the other information is calculated and the mutual association is quantified. An approach that is well known to biological experimentation is the knockout study whereby a specific gene is knocked out, that is, deleted, and symptoms are observed in an attempt to estimate gene function. The method proposed here can be regarded as one in which the basic concept of this knockout study is introduced as an information processing technique, with the state transition model being used to obtain the observation results. Also discussed is the application of this method to disease‐related gene search in the field of life sciences, where knowledge discovery is very important. In the present paper, the well‐known OMIM (Online Mendelian Inheritance in Man) was used as the database related to hereditary diseases in humans, and the effectiveness of the association analysis was proven through the results of experiments involving hypertension and other lifestyle‐related diseases in which multiple genes play a complex role. © 2006 Wiley Periodicals, Inc. Syst Comp Jpn, 37(5): 46–55, 2006; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/scj.20404
Trace reduction for performance improvement assessment of message passing parallel programs
Authors: Ino Fumihiko , Kanbe Yuki , Okita Masao , Hagihara Kenichi
Published: March 2006

This paper proposes a trace reduction method for assessing the improvability of the performance of message passing parallel programs. This assessment is based on a what‐if prediction approach that forecasts future program performance, for example, the execution time if the target program is modified according to typical tuning techniques. Our method reduces the size of trace files by aggregating records of communications that do not change the predicted execution time. In order to avoid recording such useless information, our method automatically identifies them during program execution by comparing the occurrence time of sends and receives. In case studies, our method reduces the analysis time for what‐if predictions as well as the size of trace files roughly by half. We also discuss the usability of our method. © 2006 Wiley Periodicals, Inc. Syst Comp Jpn, 37(5): 1–13, 2006; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/scj.20521
The effect of patch demography on the community structure of forest trees
Authors: Kohyama Takashi
Published: March 2006

The effect of patch demography on the structure of forest tree communities was examined using a patch‐age and tree‐size structured model of forest dynamics. Changes in abundance of species of different types (four different maximum tree‐size classes each in two or three shade‐tolerance classes) were numerically modeled in response to changes in the duration of the gap‐formation‐free lag phase. Average patch mortality was identical in all simulations. Tolerant species were more abundant without a lag phase due to larger variation in patch longevity, while subtolerant or intolerant species were successful when patch longevity was fixed with a long duration of lag phase. Variation in patch‐age distribution facilitated species coexistence. Increasing ‘advance regeneration’, or surviving fraction at gap formation, brought about the exclusive dominance of the tolerant species. Results suggest that patch demography plays a significant role in the community organization of forest trees. In species‐rich systems like tropical rain forests, longevity or canopy duration of large trees can differ among species, which brings about the variation in patch longevity, thus promoting further coexistence of species.
Tang–Song or Song–Ming: The Significance of a Perspective Shift in Chinese Cultural and Intellectual History
Authors: Zhaoguang Ge
Published: March 2006

Discussions on the contrast between the Tang and Song dynasties are common in Chinese cultural and intellectual history. Will it make more sense if the continuity between Song and Ming are emphasized instead? This shift in research perspective will have multiple effects. Instead of paying exclusive attention to the elites and classics, we will focus on common knowledge, thoughts, and beliefs. As a result of this shift in the core of our research interests, the process by which ideas and cultural novelties are institutionalized, popularized, and “conventionalized” will become an important focus of historical research. Shifting our concern from the “original thinking” of the Tang and Song to the “compromise thinking” of the Song and Ming will cause an increase in the kinds of documents about cultural and intellectual history. Such changes in periodization and research perspective can stimulate fundamental changes in the study of Chinese cultural and intellectual history
A Historical and Jurisprudential Analysis of Suzerain–Vassal State Relationships in the Qing Dynasty
Authors: Shiming Zhang
Published: March 2006

Studies of suzerain–vassal state relationships in the Qing dynasty have been a focus of domestic and overseas academic circles. This paper examines the origins, semiotics, and legal principles of suzerain–vassal state relationships in the Qing dynasty with some innovative viewpoints.
The Characteristics of the Theory of History in Ancient China
Authors: Lindong Qu
Published: March 2006

Historical studies in ancient China have left us many bountiful legacies. One of them is the theory of (objective) history, whose major characteristics can be loosely divided into the following categories: (1) a wide variety of literary forms, including theoretical remarks affixed to historical narratives and even special chapters and books on historical criticism; (2) continuity of research at many levels of historiographic theory; (3) reasoning through facts (i.e., basing theory on facts and offering arguments by following historical evidence); and (4) a wealth of masterpieces.
Tuberculosis of the Hand
Authors: Leung P. C.
Published: March 2006

Eleven cases of tuberculous infection affecting the hand are presented. The age incidence, clinical presentations and investigations are discussed.

Treatment includes chemotherapy, radical synovectomy and early mobilisation.

Hand function after surgery in the follow up period of three to twenty-one months was very satisfactory with the exception of three cases which presented at a very late stage with secondary involvement of the wrists.

The confusion that exists while using such terms as “Tuberculous Dactylitis” and “Tuberculous Tenosynovitis” is discussed. An alternative suggestion is made that “Tuberculosis of the Hand” be used.
MANAGING AN AGRICULTURAL RESEARCH PROGRAMME FOR POVERTY ALLEVIATION IN DEVELOPING COUNTRIES: AN INSTITUTE WITHOUT WALLS
Authors: STIRLING C. M. , HARRIS D. , WITCOMBE J. R.
Published: March 2006

There is no one widely accepted method of managing international agricultural research and numerous different models exist. Here we review one in particular, referred to as the ‘institute without walls’, from the perspective of the UK Department for International Development's (DFID) Renewable Natural Resource (RNR) Research Strategy (1990–2006). We begin with a brief history of the RNR Research Strategy from 1990 to 2004. We then draw on nearly 15 years experience of managing one of the programmes within the RNR Research Strategy to assess critically the impact of externally and internally imposed organizational and management changes on the performance of the DFID Plant Sciences Programme (PSP). The current RNR Research Strategy (1995–2006), with its emphasis on demand-led research, has greatly increased the relevance and effectiveness of DFID's natural resources research. A comparison between the PSP in 2004 and the early 1990s inevitably concludes that the programme has been transformed: unlike in 1991, research is now firmly demand-driven, much is based in developing countries and farmers are benefiting from the research. Over time, the outputs of the long-term strategic research have been applied in practical plant breeding and participatory crop improvement programmes. Key to the success of the PSP has been the provision of continuous, long-term funding which has allowed projects time to develop and produce outputs of real value to end users. Alongside this, the ability of the PSP to build long-term, in-country partnerships has ensured the effective adoption of its research outputs. We conclude that the successes of the PSP have largely derived from (i) identification of research that is clearly demand driven, (ii) continuous long-term funding that has allowed research to move from the strategic to adaptive phase, (iii) continuity of management, and (iv) the flexibility to develop a wide range of partnerships, both in-country and overseas, based on their ability to deliver.
EVALUATION OF SIMPLE HAND-HELD MECHANICAL SYSTEMS FOR HARVESTING TEA (CAMELLIA SINENSIS)
Authors: BURGESS P. J. , CARR M. K. V. , MIZAMBWA F. C. S. , NIXON D. J. , LUGUSI J. , KIMAMBO E. I.
Published: March 2006

Over an eight-year period, harvesting methods based on simple mechanical aids (blade and shear) were evaluated against hand harvesting on mature morphologically contrasting tea clones in Southern Tanzania. The effects of shear step height (5–32 mm) and the harvest interval (1.8–4.2 phyllochrons) were also examined. Except in the year following pruning, large annual yields (5.7–7.9 t dry tea ha−1) were obtained by hand harvesting at intervals of two phyllochrons. For clones K35 (large shoots) and T207 (small shoots), the mean harvested shoot weights were equivalent to three unfurled leaves and a terminal bud. The proportions of broken shoots (40–48 %) and coarse material (4–6 %) were both relatively high. Using a blade resulted in similar yields to hand harvesting from K35 but larger yields from T207 (+13 %). The yield increase from clone T207 was associated with the harvest of more shoots and heavier shoots, smaller increases in canopy height, and a higher proportion (7–9 %) of coarse material compared to hand harvesting. On bushes, which had been harvested by hand for two years following pruning, using flat shears (no step) supported on the tea canopy resulted, over a three year period, in yields 8–14 % less than those obtained by hand harvesting and, for clone K35, a reduction in the leaf area index to below 5. The development of a larger leaf area index is made possible by adding a step to the shear. However, since annual yields were reduced by 40–50 kg ha−1 per mm increase in step height, the step should be the minimum necessary to maintain long-term bush productivity. As mean shoot weights following shear harvesting were about 13 % below those obtained by hand harvesting, there is scope, when using shears, to extend the harvest interval from 2 to 2.5 phyllochrons.
SOIL WATER CONSERVATION, GROWTH, YIELD AND WATER USE EFFICIENCY OF SORGHUM AS AFFECTED BY LAND CONFIGURATION AND WOOD-SHAVINGS MULCH IN SEMI-ARID NORTHEAST NIGERIA
Authors: CHIROMA A. M. , FOLORUNSO O. A. , ALHASSAN A. B.
Published: March 2006

Water is perhaps the most important single factor that limits crop production in the semi-arid northeast of Nigeria. A four-year field experiment was therefore initiated in 1999 to evaluate the influence of land configuration practices with or without wood-shavings mulch on water conservation, yield and water use efficiency (WUE) of sorghum. The experimental treatments consisted of flat bed (FB), open ridging (OR), tied ridging (TR), FB + mulch (FBM), OR + mulch (ORM), and TR + mulch (TRM). Ridge heights were 15 to 20 cm and furrows were left open (for OR and ORM) or tied (for TR and TRM). Wood-shavings mulch was used at the rate of 5 t ha−1 in 1999, but this was increased to 10 t ha−1 in subsequent years to ensure adequate soil coverage. Differences in soil water storage at various sampling dates were significant only in some cases in each year, but trends were towards greater soil water storage in the mulched treatments than in the non-mulched treatments, irrespective of tillage method. Growth parameters (plant height and leaf area index) indicated significant differences between treatments on only some measurement dates in each year. Sorghum water use varied significantly between years and treatments. Seasonal water use was greater with FBM, ORM and TRM than with the FB treatment in all cropping seasons. Averaged over the four-year period, mean increases in grain yield relative to the FB treatment were 16 % for OR, 25 % for TR, 77 % for FBM, 50 % for ORM and 57 % for TRM. Pooled across the experimental years, the WUE (ET) of FB, OR, TR, FBM, ORM and TRM were 1.95, 2.12, 2.13, 2.74, 2.36 and 2.48 kg ha−1 mm−1 respectively. The corresponding WUE(R) values for these treatments were 1.26, 1.46, 1.56, 2.22, 1.88 and 1.97 kg ha−1 mm−1 respectively. It is concluded that combining the practice of flat bed cultivation with mulching may eliminate the need for ridging in increasing the productivity of sorghum grain in semi-arid northeast Nigeria.
Small cell neuroendocrine carcinoma of the nasal cavity and paranasal sinuses
Authors: Babin E , Rouleau V , Vedrine P O , Toussaint B , de Raucourt D , Malard O , Cosmidis A , Makaeieff M , Dehesdin D
Published: March 2006

Introduction: Small cell neuroendocrine carcinoma (SNEC) of the sinonasal tract is a rare disease.

Objective: Report a descriptive study of a relatively large cohort of SNEC of the nasal cavity and paranasal sinuses.

Method: The medical records of 21 patients presenting with nasal and paranasal SNEC to various French hospitals, from 1989 to 2003, were analysed to determine the clinical features and current treatment of the disease.

Results: Patient data were obtained from eight French hospitals. Twelve of the patients were male and nine were female, with a mean age at presentation of 55 years (range: 27 to 79 years). Patients' staging for nasal cavity malignancy was: T1, four; T2, three; T3, one; T4, 13; N0, 18; N2, three; M0, 20; and M1, one. None of the patients suffered from SNEC of the sinonasal tract with ectopic hormone production. Immunohistochemistry proved useful for diagnosis in 20 cases. Twelve cases were positive for cytokeratin, 14 for chromogranin, eight for neuron-specific enolase and 11 for neuron-specific synaptophysin. One patient had an adenocarcinoma and an inverted papilloma associated with neuroendocrine carcinoma. Patients underwent surgery (11 cases), radiotherapy (14 cases) and chemotherapy (12 cases). Recurrence occurred in 10 cases. Five patients had visceral metastases or cervical lymph node involvement. Nine of the patients died within four years of onset of the disease.

Conclusion: Small cell neuroendocrine carcinoma of the sinonasal tract is an uncommon neoplasm with aggressive clinical behaviour. Recurrence is frequent and the prognosis is poor. However, the current treatment of these neuroendocrine neoplasms varies widely.
Endoscopy-aided laser therapy for intractable granular myringitis
Authors: Jang C H , Kim Y H , Cho Y B , Wang P C
Published: March 2006

Objective: We report our technique and results for endoscopy-aided CO2 laser therapy for the treatment of intractable granular myringitis, as an out-patient office procedure.

Materials and methods: A total of 21 patients (14 women and seven men; mean age 32.6 years) were retrospectively reviewed, all of whom suffered from intractable granular myringitis and had undergone endoscopy-aided laser treatment. Granulation tissue was vaporized for one to two seconds with a CO2 laser (spot size 0.5–1 mm with a power setting of 5–10 W in continuous mode). The mean follow-up period was 11 months.

Results: Eighteen of the 21 patients (85 per cent) were cured after a single treatment. Three patients with the diffuse form of the disease required repeat laser treatments coupled with self-irrigation with a diluted vinegar solution. We noted no perforations of patients' tympanic membranes after laser vaporization. We also observed no recurrences over follow-up periods ranging from three months to 2.6 years. Our laser procedure produced no adverse effect on hearing thresholds, nor were any other complications observed.

Conclusion: Our results suggest that endoscopy-aided CO2 laser ablation is a reliable and minimally invasive method associated with low rates of recurrence and a low incidence of complications. It can be conducted as an office procedure.
The Past in Weimar History
Authors: GERWARTH ROBERT
Published: March 2006

This article examines Weimar Germany's public controversy about the Republic's place in German history. In a period that was seen by many contemporaries as a time deprived of historical context, all political parties tried to legitimise their actions and aims through the construction of very different historical traditions. Based on a wide range of primary sources, the article seeks to analyse this ‘battle over the past’ within the broader context of Weimar's political culture and the Republic's struggle for survival.
The Fairytale Witch: Laura Marani Argnani and the Fasci Femminili of Reggio Emilia, 1929–1940
Authors: WILLSON PERRY
Published: March 2006

Laura Marani Argnani was one of the most politically fanatical and dedicated of the leaders of the Fasci Femminili (the women's section of the Italian Fascist Party). She was FF provincial fiduciary in the northern province of Reggio Emilia from 1929 to 1940 and a PNF national inspectress from 1937. Marani Argnani is a particularly interesting figure, since the provincial federation she led was one of the most successful in Italy in terms of levels of membership and activities. This article focuses on her ideology, the reasons for her success and the motivation for her political activism.
Determining ‘People of German Blood’, ‘Jews’ and ‘Mischlinge’: The Reich Kinship Office and the Competing Discourses and Powers of Nazism, 1941–1943
Authors: PEGELOW THOMAS
Published: March 2006

This article conceptualises the dissemination by Nazi party and state institutions of racial categories of Germanness and Jewishness and the imposition of these categories on segments of the population as a form of linguistic violence. Centring on the Reich Kinship Office during the Second World War, the article argues that racial discourses were not static, but were constantly remade in the practices of the office's employees and their interaction with petitioners desperately seeking to escape persecution. The office's practices exemplify the competing discourses of Nazism, as employees saw the Kinship Office's discourses increasingly undermined by SS and police agencies and their growing power and more radical languages.
All Steps Necessary: Danish Nuclear Policy, 1949–1960
Authors: AGGER JONATHAN SØBORG , WOLSGAARD LASSE
Published: March 2006

Danish nuclear policy was decided in the years 1949–60. The policies adopted by the Danish government in this period did not differ essentially from those of the other Western allies. For example, the government did not want the crucial decision of whether and when to use nuclear weapons to be made by the military. It should remain a political decision, in practice to be made by the US president. One distinctive Danish policy, however, was the decision not to allow storage of nuclear warheads on Danish soil ‘under the present circumstances’. The motives for this seemingly irresolute policy are discussed in this article.
Considering Islam from the West
Authors: AMIRAUX VALÉRIE
Published: March 2006

Richard W. Bulliet, The Case for Islamo-Christian Civilization (New York: Columbia University Press, 2004), 192 pp., $24.50 (hb), ISBN 0231127960.

Henry Laurens, Orientales II. La IIIe République et l'Islam (Paris: CNRS éditions, 2004), 376 pp., €29.00, ISBN 2271062071.

William E. Watson, Tricolor and Crescent: France and the Islamic World (London: Praeger, 2003), 295 pp., £31.99 (hb), ISBN 0275974707.

But there is a difference between knowledge of other peoples and other times that is the result of understanding, compassion, careful study and analysis for their own sakes, and knowledge that is part of an overall campaign of self affirmation. There is, after all, a profound difference between the will to understand for purposes of co-existence and enlargement of horizons, and the will to dominate for the purposes of control. It is surely one of the intellectual catastrophes of history that an imperialist war confected by a small group of unelected US officials was waged against a devastated Third World dictatorship on thoroughly ideological grounds having to do with world dominance, security control, and scarce resources, but disguised for its true intent, hastened, and reasoned for by Orientalists who betrayed their calling as scholars.
Back to European Fascism
Authors: PINTO ANTÓNIO COSTA
Published: March 2006

Michael Mann Fascists (Cambridge: Cambridge University Press, 2004), 429 pp., £17.99 (pb), ISBN 052153856.

Robert O. Paxton The Anatomy of Fascism (London: Allen Lane, 2004), 321 pp., £8.99 (pb), ISBN 0141014326.

Nancy Bermeo Ordinary People in Extraordinary Times. The Citizenry and the Breakdown of Democracy (Princeton, NJ: Princeton University Press: 2003), 265 pp., £13.95 (pb), ISBN 0691089701.

Didier Musiedlack Mussolini (Paris: Presses de Sciences PO, 2005), 436 pp., €16.15, ISBN 2724608062.

Paul H. Lewis Latin Fascist Elites. The Mussolini, Franco and Salazar Regimes (Westport, CT: Praeger, 2003), 209 pp., $85.95 (hb), ISBN 027597880X.
Measuring Surface Topography with Scanning Electron Microscopy. I. EZEImage: A Program to Obtain 3D Surface Data
Authors: Ponz Ezequiel , Ladaga Juan Luis , Bonetto Rita Dominga
Published: March 2006

Scanning electron microscopy (SEM) is widely used in the science of materials and different parameters were developed to characterize the surface roughness. In a previous work, we studied the surface topography with fractal dimension at low scale and two parameters at high scale by using the variogram, that is, variance vs. step log–log graph, of a SEM image. Those studies were carried out with the FERImage program, previously developed by us. To verify the previously accepted hypothesis by working with only an image, it is indispensable to have reliable three-dimensional (3D) surface data. In this work, a new program (EZEImage) to characterize 3D surface topography in SEM has been developed. It uses fast cross correlation and dynamic programming to obtain reliable dense height maps in a few seconds which can be displayed as an image where each gray level represents a height value. This image can be used for the FERImage program or any other software to obtain surface topography characteristics. EZEImage also generates anaglyph images as well as characterizes 3D surface topography by means of a parameter set to describe amplitude properties and three functional indices for characterizing bearing and fluid properties.
Imaging Thin Films of Nanoporous Low-k Dielectrics:
Comparison between Ultramicrotomy and Focused Ion Beam Preparations for
Transmission Electron Microscopy
Authors: Thompson Leslie E. , Rice Philip M. , Delenia Eugene , Lee Victor Y. , Brock Phillip J. , Magbitang Teddie P. , Dubois Geraud , Volksen Willi , Miller Robert D. , Kim Ho-Cheol
Published: March 2006

Ultramicrotomy, the technique of cutting nanometers-thin slices of
material using a diamond knife, was applied to prepare transmission
electron microscope (TEM) specimens of nanoporous
poly(methylsilsesquioxane) (PMSSQ) thin films. This technique was compared
to focused ion beam (FIB) cross-section preparation to address possible
artifacts resulting from deformation of nanoporous microstructure during
the sample preparation. It was found that ultramicrotomy is a successful
TEM specimen preparation method for nanoporous PMSSQ thin films when
combined with low-energy ion milling as a final step. A thick, sacrificial
carbon coating was identified as a method of reducing defects from the FIB
process which included film shrinkage and pore deformation.
Examination of Hard Segment and Soft Segment Phase Separation in Polyurethane Medical Materials by Electron Microscopy Techniques
Authors: Taylor Jennifer E. , Laity Peter R. , Wong Steven S. , Norris Keith , Khunkamchoo Peck , Cable Martin , Andrews Geoffrey , Johnson Anthony F. , Cameron Ruth E.
Published: March 2006

A combination of transmission electron microscopy (TEM) andin situtensile testing in an environmental scanning electron microscopy (ESEM) was used to evaluate the static bulk and dynamic surface morphologies of medical polyurethanes. TEM results showed phase-separated hard segment and soft segment structures. Surface morphology as a function of strain was studied using ESEM in conjunction with a tensometer.
Ex SituTransmission Electron Microscopy: A Fixed-Bed Reactor Approach
Authors: Kliewer Chris E. , Kiss Gabor , DeMartin Gregory J.
Published: March 2006

A fixed-bed reactor has been designed and constructed for ex situ transmission electron microscopy (TEM) studies of heterogeneous catalysts. Theex situfacility exposes a fully prepared TEM sample on a grid to actual process conditions (e.g., temperature, pressure, gas composition, etc.) by placing the grid at the exit section of a conventional fixed-bed reactor. A unique reactor design allows grid transfer into the electron microscope and back into the reactor again under a controlled (inert) environment, thus allowing time-resolved monitoring of catalyst morphology changes under realistic, well-controlled conditions. This facility stands completely independent of the TEM. Thus, no special TEM modifications are required and long-termex situstudies do not impact microscope utilization. The utility of the facility is demonstratedviathe oxidation of intermediate size (∼20–∼80 nm) supported copper particles.
Imaging Atomic Structure in Metal Nanoparticles Using High-Resolution Cryo-TEM
Authors: Balmes Olivier , Malm Jan-Olle , Pettersson Niklas , Karlsson Gunnel , Bovin Jan-Olov
Published: March 2006

It has been shown, by imaging gold (200) planes, that it is possible to achieve better than 0.20-nm structural resolution in cryo-transmission electron microscopy (cryo-TEM). This has been done using commercially available cryo equipment and using a 300-kV field emission gun (FEG) TEM. The images of 15-nm gold particles embedded in amorphous frozen water clearly show the (111) planes (separated by 0.235 nm) in gold. Fourier transform demonstrates the presence of (200) planes in the image, proving a resolution of better than 0.20 nm. The experimental results are supported by image simulations using the multislice method. These simulations suggest that it should be possible to achieve the same resolution even in smaller particles and particles of lighter elements. The crucial experimental problem to overcome is keeping the thickness of the amorphous film low and to work at low electron dose conditions.
Electron Energy Loss Spectroscopy (EELS) of Iron Fischer–Tropsch Catalysts
Authors: Jin Yaming , Xu Huifang , Datye Abhaya K.
Published: March 2006

Electron energy loss spectroscopy (EELS), X-ray photoelectron spectroscopy (XPS), and transmission electron microscopy have been used to study iron catalysts for Fischer–Tropsch synthesis. When silica-containing iron oxide precursors are activated in flowing CO, the iron phase segregates into iron carbide crystallites, leaving behind some unreduced iron oxide in an amorphous state coexisting with the silica binder. The iron carbide crystallites are found covered by characteristic amorphous carbonaceous surface layers. These amorphous species are difficult to analyze by traditional catalyst characterization techniques, which lack spatial resolution. Even a surface-sensitive technique such as XPS shows only broad carbon or iron peaks in these catalysts. As we show in this work, EELS allows us to distinguish three different carbonaceous species: reactive amorphous carbon, graphitic carbon, and carbidic carbon in the bulk of the iron carbide particles. The carbidic carbon K edge shows an intense “π*” peak with an edge shift of about 1 eV to higher energy loss compared to that of the π* of amorphous carbon film or graphitic carbon. EELS analysis of the oxygen K edge allows us to distinguish the amorphous unreduced iron phase from the silica binder, indicating these are two separate phases. These results shed light onto the complex phase transformations that accompany the activation of iron catalysts for Fischer–Tropsch synthesis.
Acceleration mechanism responsible for the formation of the new radiation belt during the 2003 Halloween solar storm
Authors: Shprits Y. Y. , Thorne R. M. , Horne R. B. , Glauert S. A. , Cartwright M. , Russell C. T. , Baker D. N. , Kanekal S. G.
Published: March 2006

Observations of the relativistic electron flux increases during the first days of November, 2003 are compared to model simulations of two leading mechanisms for electron acceleration. It is demonstrated that radial diffusion driven by ULF waves cannot explain the formation of the new radiation belt in the slot region and instead predicts a decay of fluxes during the recovery phase of the October 31st storm. Compression of the plasmasphere during the main phases of the storm created preferential conditions for local acceleration during interactions with VLF chorus. Local acceleration of electrons at L = 3 is modelled with a 2‐D pitch‐angle, energy diffusion code. We show that the energy diffusion driven by whistler mode waves can explain the gradual build up of fluxes to energies exceeding 3 MeV in a new radiation belt which is formed in the slot region normally devoid of high energy electrons.
Measuring pickup ions to characterize the surfaces and exospheres of planetary bodies: Applications to the Moon
Authors: Hartle Richard E. , Killen Rosemary
Published: March 2006

The composition and structure of neutral exospheres imbedded in the solar wind can be determined by measurements of their pickup ion progeny. Using Earth's Moon as the parent body, we consider transport of pickup ions from their birthplaces to measurement sites on possible spacecraft orbits. An ion observed to have a specific mass and velocity at a spacecraft position can be mapped back to its point of birth on the surface or in the atmosphere. Ion measurements of this type are shown to be a sensitive way to map the composition of surfaces and atmospheres of bodies with surface bound exospheres.
Were extreme waves in the Rockall Trough the largest ever recorded?
Authors: Holliday Naomi P. , Yelland Margaret J. , Pascal Robin , Swail Val R. , Taylor Peter K. , Griffiths Colin R. , Kent Elizabeth
Published: March 2006

In February 2000 those onboard a British oceanographic research vessel near Rockall, west of Scotland experienced the largest waves ever recorded by scientific instruments in the open ocean. Under severe gale force conditions with wind speeds averaging 21 ms−1 a shipborne wave recorder measured individual waves up to 29.1 m from crest to trough, and a maximum significant wave height of 18.5 m. The fully formed sea developed in unusual conditions as westerly winds blew across the North Atlantic for two days, during which time a frontal system propagated at a speed close to the group velocity of the peak waves. The measurements are compared to a wave hindcast (AES40, Swail and Cox, 2000) which successfully simulated the arrival of the wave group but underestimated the most extreme waves.
Coseismic deformation of the 2002 Denali Fault earthquake: Insights from GPS measurements
Authors: Hreinsdóttir Sigrún , Freymueller Jeffrey T. , Bürgmann Roland , Mitchell Jim
Published: March 2006

We estimate coseismic displacements from the 2002Mw7.9 Denali Fault earthquake at 232 GPS sites in Alaska and Canada. Displacements along a N‐S profile crossing the fault indicate right‐lateral slip on a near‐vertical fault with a significant component of vertical motion, north‐side up. We invert both GPS displacements and geologic surface offsets for slip on a three‐dimensional (3‐D) fault model in an elastic half‐space. We restrict the motion to right‐lateral slip and north‐side‐up dip slip. Allowing for oblique slip along the Denali and Totschunda faults improves the model fit to the GPS data by about 30%. We see mostly right‐lateral strike‐slip motion on the Denali and Totschunda faults, but in a few areas we see a significant component of dip slip. The slip model shows increasing slip from west to east along the Denali Fault, with four localized higher‐slip patches, three near the Trans‐Alaska pipeline crossing and a large slip patch corresponding to aMw7.5 subevent about 40 km west of the Denali‐Totschunda junction. Slip of 1–3 m was estimated along the Totschunda Fault with the majority of slip being at shallower than 9 km depth. We have limited resolution on the Susitna Glacier Fault, but the estimated slip along the fault is consistent with aMw7.2 thrust subevent. Total estimated moment in the Denali Fault earthquake is equivalent toMw7.89. The estimated slip distribution along the surface is in very good agreement with geological surface offsets, but we find that surface offsets measured on glaciers are biased toward lower values.
Microwave radiative transfer model validation
Authors: Rosenkranz Philip W. , Barnet Christopher D.
Published: March 2006

Within the geophysical retrieval algorithm for AIRS/AMSU/HSB, a forward radiative transfer model is used to calculate microwave brightness temperatures. Components of the microwave forward model include a surface emissivity model, the influence of surface scattering characteristics on reflected downwelling emission from the atmosphere, and an atmospheric transmittance model. Over the ocean, the surface model parameters are shown to be related to near‐surface wind speed. Calculations using the atmospheric transmittance model with profiles from dedicated radiosondes launched underneath the Aqua satellite show good agreement with HSB measurements.
Global distribution pattern of anthropogenic nitrogen oxide emissions: Correlation analysis of satellite measurements and model calculations
Authors: Toenges‐Schuller N. , Stein O. , Rohrer F. , Wahner A. , Richter A. , Burrows J. P. , Beirle S. , Wagner T. , Platt U. , Elvidge C. D.
Published: March 2006

Nitrogen oxides play a key role in tropospheric chemistry; to study the distribution patterns of the corresponding anthropogenic emissions (fossil, industrial, waste), we use three independent data sources: GOME measurements of the tropospheric NO2 column density fields, the EDGAR 3 emission inventory as an estimation of the anthropogenic NOx emissions and nighttime images of worldwide human settlements seen by the DMSP OLS satellite instrument as a proxy for these emission patterns. The uncertainties are not known precisely for any of the fields. Using the MOZART‐2 CTM, tropospheric column density fields are calculated from the emission estimates, and transformations are developed to turn the GOME columns into anthropogenic emission fields. Assuming the errors of the three data sources (GOME, EDGAR, lights) to be independent, we are able to determine ranges for the pattern errors of the column density fields and values for the pattern errors of the source fields by a correlation analysis that connects relative error (co)variances and correlation coefficients. That method was developed for this investigation but can generally be used to calculate relative error variances of data sets, if the errors of at least three of them can be assumed to be independent. We estimate the pattern error of the EDGAR 3 anthropogenic NOx emission field as (27 ± 5)%, which can be reduced by combining all fields to (15 ± 3)%. By determining outliers, we identify locations with high uncertainty that need further examination.
Lightning, radar reflectivity, infrared brightness temperature, and surface rainfall during the 2–4 July 2004 severe convective system over Taiwan area
Authors: Wang Kuo‐Ying , Liao Shun‐An
Published: March 2006

On 2–4 July 2004, unusually severe convective systems developed over Taiwan area, following the passage of Typhoon Mindulle (10W, T0407). During the lifetime of these storms, total lightning was detected by the TPC SAFIR total lightning detection system, infrared cloud‐top temperatures were measured by the NOAA GOES‐9 satellite, radar reflectivity was observed by the CWB Doppler network, and hourly surface rainfall was measured by a network of high‐density raingauge stations. Using these data, we find that proxies published in previous research are useful for studying the evolution of convection in the July 2004 storm. This paper focuses on a 6‐hour portion of the “oceanic” storm's lifetime. Our study shows the following: (1) Middle‐level (at 6 km altitude) 40‐dBZ radar reflectivity and high‐level (at 12 km altitude) 20‐dBZ radar reflectivity are good indicators for tracking deep convective cells and total lightning. (2) Areas with infrared cloud‐top temperatures lower than −77°C, areas covered by 6‐km 40‐dBZ contours and 12‐km 20‐dBZ contours, and areas with intense surface rainfall are closely related to each other. (3) Column maximum radar reflectivities are good indicators for surface rainfall. The motion of the rain fields can be tracked by following the leading portion of areas defined by infrared cloud‐top temperatures lower than −72°C. The correlation between lightning, radar reflectivity, infrared cloud‐top temperatures, and heavy surface rainfall found in this work will be a critical test for models of storm processes.
On maintaining pressure equilibrium between a soil CO2 flux chamber and the ambient air
Authors: Xu Liukang , Furtaw Michael D. , Madsen Rodney A. , Garcia Richard L. , Anderson Daniel J. , McDermitt Dayle K.
Published: March 2006

Pressure equilibrium between inside a soil CO2 flux chamber and the surrounding air outside the chamber must be maintained during a measurement if measured soil CO2 flux (FCO2) is to accurately represent the rate occurring naturally outside the chamber. In previous studies a simple vent tube connecting to the chamber has often been used to maintain pressure equilibrium. This approach, however, can be effective only under calm conditions. Under windy conditions, negative pressure excursions will occur inside the chamber that are artifacts resulting from wind passing over the vent tube's external open end, a phenomenon known as the Venturi effect. This causes anomalous mass flow of CO2‐rich air from the soil into the chamber, leading to a significant overestimation of FCO2. In this present study, we found that negative chamber pressure excursions due to the Venturi effect cannot be observed unless the differential pressure measurement is made with the chamber resting on an impermeable base. Making pressure measurements with a chamber resting on porous soil can lead to the erroneous conclusion that an anomalous mass flow is not a problem precisely when it is causing serious artifacts. We also present a new vent design for a soil CO2 flux chamber capable of maintaining pressure equilibrium between inside the chamber and the ambient air outside the chamber under both calm and windy conditions. Differential pressure measurements from field experiments show that the pressures inside our newly designed vented chamber equal those outside the chamber when wind speed at a height of 0.5 m is up to 7 m s−1, thus virtually eliminating artifacts due to the Venturi effect. Our field data show that the problem of overestimation in measured FCO2 by a chamber with older vent designs under windy conditions can be avoided with our newly designed vented chamber.
Chemical characterization of the ambient organic aerosol soluble in water: 1. Isolation of hydrophobic and hydrophilic fractions with a XAD‐8 resin
Authors: Sullivan Amy P. , Weber Rodney J.
Published: March 2006

Group separation of the aqueous extract of fine particles bearing water‐soluble organic carbon (WSOC) provides unique insights into the sources of organic carbon (OC). XAD‐8 resin coupled with a Total Organic Carbon analyzer allows for direct quantification. We term the fraction of WSOC not retained by a XAD‐8 resin column at pH 2 as hydrophilic WSOC (WSOCxp); this includes saccharides, amines, and carbonyls and aliphatic monocarboxylic/dicarboxylic/oxocarboxylic acids with less than 4 or 5 carbons. The fraction of WSOC retained by XAD‐8, termed the hydrophobic fraction (WSOCxr), include aromatic acids, phenols, organic nitrates, cyclic acids, and carbonyls and monocarboxylic/dicarboxylic acids with greater than 3 or 4 carbons. However, only aromatic compounds (or aromatic‐like compounds with similar properties) can subsequently be extracted from XAD‐8 with high efficiency. By coupling a Particle‐into‐Liquid Sampler with this technique, online measurements of WSOC, WSOCxp, and WSOCxr are possible. Urban measurements from St. Louis and Atlanta, on a carbon mass basis, show an increase in the mean WSOC fraction from winter (51%) to summer (61%), due to increases in the WSOCxp/OC from 0.25 to 0.35. During a summer Atlanta PM event, WSOC to OC was 0.75, driven largely by increases in the WSOCxp. The results are consistent with the view that in the summer, there are increased amounts of oxygenated polar compounds, possibly from secondary organic aerosol production, and that these compounds account for an even larger fraction of OC during stagnation events. A companion paper describes a method to further group speciate these XAD‐8 isolated fractions.
Molecular correlation functions for uniaxial ellipsoids in the isotropic state
Authors: De Michele Cristiano , Scala Antonio , Schilling Rolf , Sciortino Francesco
Published: March 2006

We perform event-driven molecular dynamics simulations of a system composed by uniaxial hard ellipsoids for different values of the aspect ratio and packing fraction. We compare the molecular orientational-dependent structure factors previously calculated within the Percus-Yevick approximation with the numerical results. The agreement between theoretical and numerical results is rather satisfactory. We also show that, for specific orientational quantities, the molecular structure factors are sensitive to the particle shape and can be used to distinguish prolate from oblate ellipsoids. A first order theoretical expansion around the spherical shape and a geometrical analysis of the configurations confirms and explains such an observation.
Nonintegrability of density perturbations in the Friedmann-Robertson-Walker universe
Authors: Stachowiak Tomasz , Szydłowski Marek , Maciejewski Andrzej J.
Published: March 2006

We investigate the evolution equation of linear density perturbations in the Friedmann-Robertson-Walker universe with matter, radiation, and the cosmological constant. The concept of solvability by quadratures is defined and used to prove that there are no “closed form” solutions except for the known Chernin, Heath, Meszaros and simple degenerate ones. The analysis is performed applying Kovacic’s algorithm. The possibility of the existence of other, more general solutions involving special functions is also investigated.