bluuebunny/crossref_metadata_2025 huggingface dataset:
Mitochondrial ATP‐Synthase in the Entorhinal Cortex Is a Target of Oxidative Stress at Stages I/II of Alzheimer's Disease Pathology
Authors: Terni Beatrice , Boada Jordi , Portero‐Otin Manuel , Pamplona Reinald , Ferrer Isidro
Published: February 2009

Oxidative stress has been implicated in the pathogenesis of several neurodegenerative diseases including Alzheimer's disease (AD). Several proteins have been identified as targets of oxidative damage in AD dementia (usually stages V/VI of Braak) and in subjects with mild cognitive impairment associated with middle stages of AD pathology (stage IV of Braak). In this study, we investigate whether brain proteins are locally modified by oxidative stress at the first stages of AD‐related pathology when morphological lesions are restricted to the entorhinal and transentorhinal cortices of neurofibrillary pathology (stages I/II of Braak). Using a proteomic approach, we show that the α subunit of the mitochondrial adenosine triphosphate (ATP)‐synthase is distinctly lipoxidized in the entorhinal cortex at Braak stages I/II compared with age‐matched controls. In addition, ATP‐synthase activity is significantly lower in Braak stages I/II than age‐matched control, while electron transport chain, expressed by the mitochondrial complex I activity, remains not affected. This is the first study showing oxidative damage in the first stage, and clinically silent period, of AD‐related pathology characterized by entorhinal and transentorhinal tauopathy.
Eastern Asian endemic seed plant genera and their paleogeographic history throughout the Northern Hemisphere
Authors: MANCHESTER Steven R. , CHEN Zhi‐Duan , LU An‐Ming , UEMURA Kazuhiko
Published: February 2009

We review the fossil history of seed plant genera that are now endemic to eastern Asia. Although the majority of eastern Asian endemic genera have no known fossil record at all, 54 genera, or about 9%, are reliably known from the fossil record. Most of these are woody (with two exceptions), and most are today either broadly East Asian, or more specifically confined to Sino‐Japanese subcategory rather than being endemic to the Sino‐Himalayan area. Of the “eastern Asian endemic” genera so far known from the fossil record, the majority formerly occurred in Europe and/or North America, indicating that eastern Asia served as a late Tertiary or Quaternary refugium for taxa. Hence, many of these genera may have originated in other parts of the Northern Hemisphere and expanded their ranges across continents and former sea barriers when tectonic and climatic conditions allowed, leading to their arrival in eastern Asia. Although clear evidence for paleoendemism is provided by the gymnosperms Amentotaxus, Cathaya, Cephalotaxus, Cunninghamia, Cryptomeria, Glyptostrobus, Ginkgo, Keteleeria, Metasequoia, Nothotsuga, Pseudolarix, Sciadopitys, and Taiwania, and the angiosperms Cercidiphyllum, Choerospondias, Corylopsis, Craigia, Cyclocarya, Davidia, Dipelta, Decaisnea, Diplopanax, Dipteronia, Emmenopterys, Eucommia, Euscaphis, Hemiptelea, Hovenia, Koelreuteria, Paulownia, Phellodendron, Platycarya, Pteroceltis, Rehderodendron, Sargentodoxa, Schizophragma, Sinomenium, Tapiscia, Tetracentron, Toricellia, Trapella, and Trochodendron, we cannot rule out the possibility that neoendemism plays an important role especially for herbaceous taxa in the present‐day flora of Asia, particularly in the Sino‐Himalayan region. In addition to reviewing paleobotanical occurrences from the literature, we document newly recognized fossil occurrences that expand the geographic and stratigraphic ranges previously known for Dipelta, Pteroceltis, and Toricellia.
Measurement of cardiac output and pulmonary transit time for assessment of pulmonary vascular resistance in domestic piglets
Authors: Müller Helmut M. , Rehak Peter H. , Puchinger Markus , Wagner Doris , Marte Wolfgang , Tscheliessnigg Karl‐Heinz
Published: February 2009

The degree of elevated pulmonary vascular resistance (PVR) is a crucial clinical parameter. Cardiac output (CO) and pulmonary transit time (PTT) can be ascertained by a number of radiological methods. A close functional relationship between CO, PTT and PVR would facilitate non‐invasive PVR measurements. One‐hundred and fifty‐one measurements were made in six piglets. Pressures in the pulmonary and systemic circulation were measured invasively. Cardic output was determined by the use of a Doppler flow probe around the truncus pulmonalis. Temperature sensors were placed in the pulmonary truncus and left atrium. Elevated PVR was produced by repeated air embolism. After injection of ice‐cold saline, the time span between the minimal temperature in the truncus pulmonalis and the left atrium was taken as PTT. The CO and PTT were inserted into a new formula derived from the Hagen–Poiseuille law for the calculation of the PVR model. Numerical constants of the formula were calculated by the robust method of minimization. The PVR values, as calculated from invasively measured mean pulmonary artery pressure, mean left atrial pressure and CO, served as reference. In the six piglets, the PVR model and PVR reference showed a strong linear correlation with r= 0.923. The Bland–Altman plot revealed a standard deviation of −0.64/+0.67 Wood units. Cardiac output, PTT and PVR showed a close functional relationship. With a correction for blood viscosity and body size, this relationship could be used for non‐invasive clinical measurements of PVR.
Strong relationships exist between muscle volume, joint power and whole‐body external mechanical power in adults and children
Authors: O’Brien Thomas D. , Reeves Neil D. , Baltzopoulos Vasilios , Jones David A. , Maganaris Constantinos N.
Published: February 2009

The present study investigated whether differences between adults and children in mechanical power during single‐joint knee extension tasks and the complex multijoint task of jumping could be explained by differences in the quadriceps femoris muscle volume. Peak power was calculated during squat jumps, from the integral of the vertical force measured by a force plate, and during concentric knee extensions at 30, 90, 120, 180 and 240 deg·s−1, and muscle volume was measured from magnetic resonance images for 10 men, 10 women, 10 prepubertal boys and 10 prepubertal girls. Peak power during jumping and isokinetic knee extension was significantly higher in men than in women, and in both adult groups compared with children (P < 0.01), although there were no differences between boys and girls. When power was normalized to muscle volume, the intergroup differences ceased to exist for both tasks. Peak power correlated significantly with quadriceps volume (P < 0.01), with r2 values of 0.8, 0.86, 0.81, 0.78 and 0.81 from isokinetic knee extension at angular velocities of 30, 90, 120, 180 and 240 deg·s−1, respectively, and with an r2 value of 0.9 from squat jumps. These results indicate that the quadriceps femoris muscle volume accounts largely for the increase in power that occurs with maturation in the two genders not only in kinematically constrained knee extensions but also in multijoint tasks. Future studies should examine the role of other factors relating to the generation and transmission of contractile power, such as muscle architecture, tendon stiffness and external mechanical leverage.
Prenatal and perinatal zinc restriction: effects on body composition, glucose tolerance and insulin response in rat offspring
Authors: Padmavathi Inagadapa J. N. , Kishore Yedla Durga , Venu Lagishetty , Ganeshan Manisha , Harishankar Nemani , Giridharan N. V. , Raghunath Manchala
Published: February 2009

Maternal undernutrition increases the risk of adult chronic diseases, such as obesity and type 2 diabetes. This study evaluated the effect of maternal zinc restriction in predisposing the offspring to adiposity and altered insulin response in later life. Seventy‐day‐old female Wistar/NIN rats received a control (ZnC) or zinc‐restricted (ZnR) diet for 2 weeks. Following mating with control males, a subgroup of the ZnR dams were rehabilitated with ZnC diet from parturition. Half the offspring born to the remaining ZnR dams were weaned onto the ZnC diet and the other half continued on the ZnR diet throughout their life. Body composition, glucose tolerance, insulin response and plasma lipid profile were assessed in male and female offspring at 3 and 6 months of age. The ZnR offspring weighed less than control offspring at birth and weaning and continued so until 6 months of age. Rehabilitation regimens corrected the body weights of male but not female offspring. Maternal zinc restriction increased the percentage of body fat and decreased lean mass, fat‐free mass and fasting plasma insulin levels in both male and female offspring at 6 months of age. Also, glucose‐induced insulin secretion was decreased in female but not male offspring. Despite the differences in fasting insulin and the area under the curve for insulin, the fasting glucose and the area under the curve for glucose were in general comparable among offspring of different groups. Rehabilitation from parturition or weaning partly corrected the changes in the percentage of body fat but had no such effect on other parameters. Changes in plasma lipid profile were inconsistent among the offspring of different groups. Thus chronic maternal zinc restriction altered the body composition and impaired the glucose‐induced insulin secretion in the offspring.
Chronic absence of baroreceptor inputs prevents training‐induced cardiovascular adjustments in normotensive and spontaneously hypertensive rats
Authors: Ceroni Alexandre , Chaar Laiali J. , Bombein Rafael L. , Michelini Lisete C.
Published: February 2009

We investigate whether arterial baroreceptors mediate the training‐induced blood pressure fall and resting bradycardia in hypertensive (SHR) and normotensive rats (WKY). Male SHR and WKY rats, submitted to sino‐aortic denervation (SAD) or sham surgery (SHAM group), were allocated to training (T; 55% of maximal exercise capacity) or sedentary (S) protocols for 3 months. Rats were instrumented with arterial and venous catheters for haemodynamic measurements at rest (power spectral analysis) and baroreceptor testing. Kidney and skeletal muscles were processed for morphometric analysis of arterioles. Elevated mean arterial pressure (MAP) and heart rate (HR) in SHAM SHRS were accompanied by increased sympathetic variability and arteriolar wall/lumen ratio [+3.4‐fold on low‐frequency (LF) power and +70%, respectively, versus WKYS, P < 0.05]. Training caused significant HR (∼9% in WKY and SHR) and MAP reductions (−8% in the SHR), simultaneously with improvement of baroreceptor reflex control of HR (SHR and WKY), LF reduction (with a positive correlation between LF power and MAP levels in the SHR) and normalization of wall/lumen ratio of the skeletal muscle arterioles (SHR only). In contrast, SAD increased pressure variability in both strains of rats, causing reductions in MAP (−13%) and arteriolar wall/lumen ratio (−35%) only in the SHRS. Training effects were completely blocked by SAD in both strains; in addition, after SAD the resting MAP and HR and the wall/lumen ratio of skeletal muscle arterioles were higher in SHRT versus SHRS and similar to those of SHAM SHRS. The lack of training‐induced effects in the chronic absence of baroreceptor inputs strongly suggests that baroreceptor signalling plays a decisive role in driving beneficial training‐induced cardiovascular adjustments.
Relatively low temperature synthesis of hexagonal tungsten carbide films by N doping and its effect on the preferred orientation, phase transition, and mechanical properties
Authors: Su Y. D. , Hu C. Q. , Wang C. , Wen M. , Zheng W. T.
Published: February 2009

The authors deposited N-doped tungsten carbide thin films on Si(100) substrates at 500°C using direct-current reactive magnetron sputtering in a mixture of CH4∕N2∕Ar discharge and explored the effects of N doping on the preferred orientation, phase transition, and mechanical properties of the films by using x-ray diffraction, x-ray photoelectron spectroscopy, and nanoindentation measurements. They found that N doping significantly influenced the compressive stress, which led to a pronounced change in the preferred orientation, phase structure, and hardness for the tungsten carbide film. A phase transition from β-WC to α-WC occurred when N doping was in the range of 2.9 and 4.7at.%, meaning that α-WC can be obtained at relatively low temperature (500°C). To reveal the relationship between the stress and phase transition, as well as preferred orientation, the density-functional theory based on first principles was used to calculate the elastic constants and shear modulus for tungsten carbide with a structure of β-WC or α-WC. The calculated results showed that the preferred orientation depended on the competition between strain energy and surface energy, as well as the grains competitive growth, and the phase transition can be attributed to a decrease in the strain energy. The hardness of α-WC was harder than β-WC because the shear modulus for α-WC was larger than that of β-WC, whereas the bulk modulus for α-WC was almost equal to that of β-WC.
Thermal-mechanical modeling of nodular defect embedded within multilayer coatings
Authors: Ling Xiulan , Shao Jianda , Fan Zhengxiu
Published: February 2009

The initiation of laser damage within optical coatings can be better understood by thermal-mechanical modeling of coating defects. The result of this modeling shows that a high-temperature rise and thermal stress can be seen just inside the nodular defect compared to surrounding coating layers. The temperature rise and thermal stress tend to increase with seed diameter. Shallower seed tend to cause higher temperature rise and greater thermal stress. There is a critical seed depth at which thermal stress is largest. The composition of the seed resulting from different coating-material emission during evaporation can affect the temperature rise and thermal stress distribution.
Photon emission during fracture of carbon materials
Authors: Yasuda K. , Yamamoto K. , Shiota T. , Matsuo Y.
Published: February 2009

Photon emission (phE) during fracture was investigated on glass-like carbon, pyrolytic graphite, polycrystalline graphite, and carbon fiber reinforced composites (C∕C composites). The C∕C composites were heat treated at 1000, 1500, and 2000°C. The specimen was fractured by three-point bending and the resulting phE was measured at atmospheric pressure, 10−3 and 10−6Pa. The phE was not observed on any samples at atmospheric pressure, whereas it occurred on the glass-like carbon and C∕C composites at 10−3 and 10−6Pa. The phE intensity at 10−3Pa was higher than that at 10−6Pa. This study revealed that the phE on the carbon materials depended on their crystal structure and surrounding gas pressure. The gas pressure dependence suggests that the phE resulted from gas discharge.
Chemistry in long residence time fluorocarbon plasmas
Authors: Sant S. P. , Nelson C. T. , Overzet L. J. , Goeckner M. J.
Published: February 2009

The densities of radicals and neutrals in fluorocarbon (FC) plasmas have been investigated in an inductively coupled plasma system to understand the predominant gain and loss mechanisms of dissociative products and their interaction with chamber surfaces. The input parameters varied in this experiment are the source to chuck gap and the F: C ratio of the feed gas. The densities of F, CF2, CF3, CF4, C2F4, SiF4, COF2, CO, and CO2 are measured and analyzed. In addition, two different forms of C4F8, the standard cyclic c and a radical linear l structures are observed in C4F8 containing plasmas. l-C4F8 is shown to be the primary dissociation product of c-C4F8 and, thus, cannot be neglected from calculations of the loss rate of c-C4F8 to electron collisions. This implies that the typically cited dissociative products of c-C4F8 (primarily C2F4) can have dual production channels: one from l-C4F8 and the other directly from c-C4F8. Furthermore, the measured density of CF4 shows strong correlation to the loss of F to the surfaces, indicating its primary production mechanism is from surface recombination. Similarly, CF3 is mainly produced from deposited FC film on chamber surfaces and lost to electron impact reactions. The etch products resulting from etch of the quartz window are shown, and an overall neutral density model is developed.
Plasma etching of Hf-based high-k thin films. Part I. Effect of complex ions and radicals on the surface reactions
Authors: Martin Ryan M. , Chang Jane P.
Published: February 2009

The effect of ion and radical compositions in BCl3/Cl2 plasmas was assessed in this work with a focus on the formation of etch products in patterning hafnium aluminate, a potential high-k gate oxide material. The plasma composition became increasingly more complex as the percentage of boron trichloride was increased, which led to the formation of a significant amount of boron-containing species including B+, BCl+, BCl2+, BCl3+, B2Cl3+, and B2OCl3+ in the plasma. The BCl2+ ions were found to be the dominant species in BCl3 containing plasmas at most conditions; however, increasing the pressure or decreasing the power led to an increase in the formation of higher mass ions. Several compositions of Hf1−xAlxOy thin films ranging from pure HfO2 to pure Al2O3 were etched in BCl3/Cl2 plasmas as functions of ion energy and plasma composition. The etch product distributions were measured and the dominant metal-containing etch products were HfClx and AlClx in a Cl2 plasma and HfClx, HfBOCl4, and AlxCly in a BCl3 plasma, and their concentrations increased with increasing ion energy. Oxygen was detected removed in the form of ClO in Cl2 and as trichloroboroxin ((BOCl)3) in BCl3. Both the etch rate and the etch product formation are enhanced in BCl3/Cl2 plasmas, as compared to those in Cl2 plasmas, due to the change in the composition and reactivity of the dominant ions and radicals.
Plasma etching of Hf-based high-k thin films. Part II. Ion-enhanced surface reaction mechanisms
Authors: Martin Ryan M. , Blom Hans-Olof , Chang Jane P.
Published: February 2009

The mechanism for ion-enhanced chemical etching of hafnium aluminate thin films in Cl2/BCl3 plasmas was investigated in this work, specifically how the film composition, ion energy, and plasma chemistry determine their etch rates. Several compositions of Hf1−xAlxOy thin films ranging from pure HfO2 to pure Al2O3 were etched in BCl3/Cl2 plasmas and their etch rates were found to scale with Eion in both Cl2 and BCl3 plasmas. In Cl2 plasmas, a transition point was observed around 50 eV, where the etch rate was significantly enhanced while the linear dependence to Eion was maintained, corresponding to a change in the removal of fully chlorinated to less chlorinated reaction products. In BCl3 plasma, deposition dominates at ion energies below 50 eV, while etching occurs above that energy with an etch rate of three to seven times that in Cl2. The faster etch rate in BCl3 was attributed to a change in the dominant ion from Cl2+ in Cl2 plasma to BCl2+ in BCl3, which facilitated the formation of more volatile etch products and their removal. The surface chlorination (0–3 at. %) was enhanced with increasing ion energy while the amount of boron on the surface increases with decreasing ion energy, highlighting the effect of different plasma chemistries on the etch rates, etch product formation, and surface termination.
Reaction of a hydrogen-terminated Si(100) surface in UHV with ion-pump generated radicals
Authors: Zikovsky Janik , Dogel Stanislav A. , Dickie Adam J. , Pitters Jason L. , Wolkow Robert A.
Published: February 2009

The authors present scanning tunneling microscopy images and mass spectra that show that dosing gases at pressures in the range of 10−6 Torr in an ion-pumped ultrahigh vacuum (UHV) chamber results in a measurable concentration of reactive molecular radicals and atomic hydrogen ions being created. One source of radicals is the fragmentation of the dosed molecule, while another is atomic hydrogen that is re-emitted from the ion pump itself. The dosing of noble gases such as helium also results in harmful radicals escaping the ion pump. These radicals are able to create new reactive sites on a hydrogen-terminated Si(100) surface; they show that these new dangling bonds result in extra molecular line growth in a 2,3-dimethyl-1,3-butadiene dosing experiment. These results serve as a cautionary note to experimenters working with ion-pumped UHV systems and surfaces that are sensitive to radicals, such as hydrogen-terminated Si.
Practical expressions for the mean escape depth, the information depth, and the effective attenuation length in Auger-electron spectroscopy and x-ray photoelectron spectroscopy
Authors: Jablonski A. , Powell C. J.
Published: February 2009

The authors report new calculations of mean escape depths (MEDs), information depths (IDs), and effective attenuation lengths (EALs) for 16 photoelectron lines and 9 Auger-electron lines of five elemental solids (Si, Cu, Ag, W, and Au) and four inorganic compounds (ZrO2, ZrSiO4, HfO2, and HfSiO4). These calculations were made to update similar previous calculations with improved data for the transport mean free path (TMFP) that are now available. Ratios of averages of the new MEDs, IDs, and EALs to the inelastic mean free path for electron emission angles between 0° and 50° varied linearly with the single-scattering albedo, a simple function of the inelastic mean free path and TMFP. The slopes of the linear relations depend only weakly on the atomic potential used in calculations of differential elastic-scattering cross sections (from which TMFPs are derived). The new linear relations are simple practical expressions for determining the MED, ID, and EAL for any solid in conventional Auger electron spectroscopy and x-ray photoelectron spectroscopy.
Investigation of InP etching mechanisms in a Cl2/H2 inductively coupled plasma by optical emission spectroscopy
Authors: Gatilova L. , Bouchoule S. , Guilet S. , Chabert P.
Published: February 2009

Optical emission spectroscopy (OES) has been used in order to investigate the InP etching mechanisms in a Cl2–H2 inductively coupled plasma. The authors have previously shown that anisotropic etching of InP could be achieved for a H2 percentage in the 35%–45% range where the InP etch rate also presents a local maximum [J. Vac. Sci. Technol. B 24, 2381 (2006)], and that anisotropic etching was due to an enhanced passivation of the etched sidewalls by a silicon oxide layer [J. Vac. Sci. Technol. B 26, 666 (2008)]. In this work, it is shown that this etching behavior is related to a maximum in the H atom concentration in the plasma. The possible enhancement of the sidewall passivation process in the presence of H is investigated by comparing OES measurements and etching results obtained for Cl2–H2 and Cl2–Ar gas mixtures.
Influence of vacuum annealing on the physical properties of ZnO/Al/ZnO multilayer coatings
Authors: Al-Maghrabi M. A. , Al-Kuhaili M. F. , Durrani S. M. A. , Bakhtiari I. A.
Published: February 2009

Multilayer ZnO/Al/ZnO coatings were deposited by thermal evaporation on substrates heated to 300 °C. Subsequently, the coatings were annealed in vacuum in the temperature range of 300–600 °C. The structural properties of the films were investigated using x-ray diffraction and atomic force microscopy. The chemical properties were determined from x-ray photoelectron spectroscopy. The electrical and optical properties of the coatings were studied in order to evaluate their performance as transparent conducting coatings. The best performance was obtained with films annealed at 500 °C, for which the average visible transmittance was about 60% and the resistivity was 6.1×10−3 Ω cm.
Effect of pulse frequency on the ion fluxes during pulsed dc magnetron sputtering
Authors: Rahamathunnisa M. , Cameron D. C.
Published: February 2009

The ion fluxes and energies which impinge on the substrate during the deposition of chromium nitride by asymmetric bipolar pulsed dc reactive magnetron sputtering have been analyzed using energy resolved mass spectrometry. It has been found that there is a remarkable increase in ion flux at higher pulse frequencies and that the peak ion energy is directly related to the positive voltage overshoot of the target voltage. The magnitude of the metal flux depositing on the substrate is consistent with a “dead time” of ∼0.7μs at the start of the on period. The variation of the ion flux with pulse frequency has been explained by a simple model in which the ion density during the on period has a large peak which is slightly delayed from the large negative voltage overshoot which occurs at the start of the on pulse due to increased ionization at that time. This is consistent with the previously observed phenomena in pulsed sputtering.
High etching rates of bulk Nb in Ar/Cl2 microwave discharge
Authors: Rašković M. , Popović S. , Upadhyay J. , Vušković L. , Phillips L. , Valente-Feliciano A.-M.
Published: February 2009

Plasma-based Nb surface treatment provides an excellent opportunity to eliminate surface imperfections and increase the cavity quality factor in important applications such as particle accelerators and cavity quantum electrodynamics, as well as Josephson junctions. In this study, plasma etching of bulk Nb is performed on the surface of disk-shaped samples with the goal of eliminating nonsuperconductive pollutants in the penetration depth region and the mechanically damaged surface layer. The authors have demonstrated that in the microwave glow discharge, an etching rate of 1.5 μm/min can be achieved using Cl2 as a reactive gas. The influence of plasma parameters such as input power, pressure, and concentration of the reactive gas on the etching rate is determined. Simultaneously, plasma emission spectroscopy was used to estimate the densities of Cl, Cl+, and Cl2 under various plasma conditions.
A molecular basis for the onset of turbulence
Authors: Muriel A.
Published: February 2009

The authors review the atomic and molecular data to analyze flow experiments on the onset of turbulent flow in gases. They use published and unpublished data from pipe flow experiments and calculate ratios of critical velocities obtained from identical apparatus. In contrast to the use of derived quantities for characterizing the onset of turbulence, such as the Reynolds number, we restrict our data and analysis using observable quantities such as molecular properties and critical velocities. We find a rationale for a molecular origin of turbulence, in contrast to the exclusive use of continuum theory. Several new predictions are made from the molecular theory of turbulence.
Chemical and structural properties of atomic layer deposited La2O3 films capped with a thin Al2O3 layer
Authors: Li X. L. , Tsoutsou D. , Scarel G. , Wiemer C. , Capelli S. C. , Volkos S. N. , Lamagna L. , Fanciulli M.
Published: February 2009

X-ray diffraction and infrared spectroscopy measurements are conducted in order to assess the crystallographic structure and chemical purity of lanthanum oxide (La2O3) films grown by atomic layer deposition (ALD) on Si substrates. In situ capping with thin aluminum oxide (Al2O3) layer is proved to be beneficial in preventing the formation of lanthanum hydroxide phases. The effect of two process parameters, namely, La2O3 film growth temperature (260–500°C range) and postdeposition annealing temperature (600–1100°C range), on the chemical and structural evolutions of Al2O3∕La2O3∕Si stacks is discussed. This study enables the identification of the optimum ALD growth recipe yielding the highest hexagonal La2O3 phase content, which might be suitable for integration into innovative metal oxide semiconductor devices.
Improved optical and electrical properties of rf sputtered Al doped ZnO films on polymer substrates by low-damage processes
Authors: Min Hyung Seob , Yang Min Kyu , Lee Jeon-Kook
Published: February 2009

Three types of low-damage radio-frequency (rf) magnetron sputtering processes—an interruptive process, a rotating cylindrical holder method, and an off-axis sputtering method—were designed and studied to reduce the film surface temperature during deposition. Low-damage sputtering processes were investigated to improve the resistivity and optical transmittance in the visible range of Al doped ZnO (AZO) thin films deposited on polymer substrates. In the case of the polyethersulfone substrate, AZO films with a resistivity of 1.0×10−3 Ω cm and an optical transmittance of 75% were obtained by the rotating repeat holder method during rf sputtering.
Roughening during XeF2 etching of Si(100) through interface layers: H:Si(100) and a-Si∕Si(100)
Authors: Stevens A. A. E. , van de Sanden M. C. M. , Beijerinck H. C. W. , Kessels W. M. M.
Published: February 2009

Real-time spectroscopic ellipsometry has been applied in situ in an Ar+∕XeF2 beam-etching experiment to study the roughening of Si(100) etched by XeF2 at room temperature. The role of initial surface conditions has been examined. For the etching of hydrogen-terminated (H:)Si(100), the roughness evolution as a function of XeF2 dose can be characterized by an initially fast roughening phase followed by a slower, final roughening phase. Similar behavior is observed when etching through an amorphous silicon (a-Si) layer on top of crystalline Si(100) bulk as obtained by sputter cleaning of Si(100) substrates. These observations can be explained as follows. Both H termination and a-Si lead to patch formation on the surface where etching is impeded and hence, high aspect-ratio etch pits develop. The quantitative differences in roughening can then be attributed to the duration and timing of the influence of the H-terminated and a-Si patches on the etch process until H-bonded Si surface atoms or a-Si are totally removed from the surface. Surface area increase due to the roughening can therefore be held responsible for observed trends and differences in etch rates, reaction layer thickness, and composition as a function of etch time.
Carbonitriding of silicon using plasma focus device
Authors: Jabbar S. , Khan I. A. , Ahmad R. , Zakaullah M. , Pan J. S.
Published: February 2009

Carbonitride thin films have been deposited on silicon substrate by the irradiation of energetic nitrogen ions emanated from dense plasma focus device. The carbon ions are ablated by the irradiation of relativistic electrons from the insert material (graphite) placed at the anode tip. The x-ray diffraction analysis demonstrates that a polycrystalline thin film consisting of various compounds such as Si3N4, SiC, and C3N4 is formed on the silicon (100) substrate. Crystallinity of different compounds decreases with the increase in angular positions (0°, 10°, and 20°). Raman spectroscopy shows the appearance of graphitic and disordered bands with silicon nitride and silicon carbide indicating the formation of carbonitride. Raman spectra also indicate that broadening of bands increases with the increase in focus deposition shots, leading to the amorphization of the thin film. The amorphization of the thin films depends on the ion energy flux as well as on the sample angular position. The scanning electron microscopy exhibits the damaging of the substrate surface at 0° angular position. The microstructure shows the tubular shape for higher ion dose (40 focus shots). At 10° angular position, a two phase phenomenon is observed with the ordered phase in the solid solution. A smooth and uniform surface morphology showing a small cluster is observed for the 20° angular position.
Surface chemistry and surface electronic properties of ZnO single crystals and nanorods
Authors: Uhlrich J. J. , Olson D. C. , Hsu J. W. P. , Kuech T. F.
Published: February 2009

The surface chemistry of ZnO single crystals of (0001) and (101¯0) orientations and ZnO nanorods was studied using x-ray and ultraviolet photoelectron spectroscopies. Air drying and UV-ozone preparations were studied in particular as chemical treatments that could be applied to poly(3-hexylthiophene) (P3HT)-ZnO solar cells to enhance performance. The UV-ozone treatment showed negligible effect by photoelectron spectroscopy on the ZnO single crystal surfaces, but brought about electronic shifts consistent with increased upward band bending by ∼0.25eV on the ZnO nanorod surface. Modest interface dipoles of ∼0.15 and ∼0.25eV were measured between P3HT and the (101¯0) and (0001) single crystal orientations, respectively, with the dipole moment pointing from ZnO to the P3HT layer. The sol-gel films showed evidence of forming a small interface dipole in the opposite direction, which illustrates the difference in surface chemistry between the solution-grown ZnO and the ZnO single crystals.
Gas jet assisted vapor deposition of yttria stabilized zirconia
Authors: Hass D. D. , Wadley H. N. G.
Published: February 2009

A gas jet assisted electron beam evaporation process for synthesizing yttria stabilized zirconia (YSZ) coatings has recently been reported. The process uses a rarefied inert gas jet to entrain and transport vapor to a substrate. The gas jet enables the lateral spreading of the flux to be controlled and large fractions of the vapor to be deposited on samples of relatively small size. When the gas pressure is high, coatings grown at 1050°C and below have a columnar structure and a high pore fraction. The total pore volume fraction, the morphology of the inter- and intracolumn pores and the coating texture are all observed to be a strong function of the gas pressure in the chamber with increasing chamber pressure leading to larger intercolumnar pore spacings, wider pores, a higher total pore volume fraction, and a reduction in the coating texture. A direct simulation Monte Carlo simulation approach has been used to investigate vapor transport for the various gas pressures explored in this study. The simulation indicates that as the gas pressure increases, binary scattering events between the vapor and background gas broaden the vapor molecule incidence angle distribution. This intensifies flux shadowing and results in the incorporation of voids in the coating. Increasing the gas pressure also results in a rapid increase in the vapor phase nucleation of YSZ clusters. This observation coincides with a transition from a [200] textured columnar morphology at moderate pressures to a nanogranular structure with no texture and a very high nanoscopic pore volume fraction at high pressures.
Antibody Recognition of a Highly Conserved Influenza Virus Epitope
Authors: Ekiert Damian C. , Bhabha Gira , Elsliger Marc-André , Friesen Robert H. E. , Jongeneelen Mandy , Throsby Mark , Goudsmit Jaap , Wilson Ian A.
Published: February 2009

Influenza virus presents an important and persistent threat to public health worldwide, and current vaccines provide immunity to viral isolates similar to the vaccine strain. High-affinity antibodies against a conserved epitope could provide immunity to the diverse influenza subtypes and protection against future pandemic viruses. Cocrystal structures were determined at 2.2 and 2.7 angstrom resolutions for broadly neutralizing human antibody CR6261 Fab in complexes with the major surface antigen (hemagglutinin, HA) from viruses responsible for the 1918 H1N1 influenza pandemic and a recent lethal case of H5N1 avian influenza. In contrast to other structurally characterized influenza antibodies, CR6261 recognizes a highly conserved helical region in the membrane-proximal stem of HA1 and HA2. The antibody neutralizes the virus by blocking conformational rearrangements associated with membrane fusion. The CR6261 epitope identified here should accelerate the design and implementation of improved vaccines that can elicit CR6261-like antibodies, as well as antibody-based therapies for the treatment of influenza.
Catalase Overexpression Reduces Lactic Acid-Induced Oxidative Stress in
Saccharomyces cerevisiae
Authors: Abbott Derek A. , Suir Erwin , Duong Giang-Huong , de Hulster Erik , Pronk Jack T. , van Maris Antonius J. A.
Published: February 2009

Industrial production of lactic acid with the current pyruvate decarboxylase-negative
Saccharomyces cerevisiae
strains requires aeration to allow for respiratory generation of ATP to facilitate growth and, even under nongrowing conditions, cellular maintenance. In the current study, we observed an inhibition of aerobic growth in the presence of lactic acid. Unexpectedly, the
cyb2
Δ reference strain, used to avoid aerobic consumption of lactic acid, had a specific growth rate of 0.25 h
−1
in anaerobic batch cultures containing lactic acid but only 0.16 h
−1
in identical aerobic cultures. Measurements of aerobic cultures of
S. cerevisiae
showed that the addition of lactic acid to the growth medium resulted in elevated levels of reactive oxygen species (ROS). To reduce the accumulation of lactic acid-induced ROS, cytosolic catalase (
CTT1
) was overexpressed by replacing the native promoter with the strong constitutive
TPI1
promoter. Increased activity of catalase was confirmed and later correlated with decreased levels of ROS and increased specific growth rates in the presence of high lactic acid concentrations. The increased fitness of this genetically modified strain demonstrates the successful attenuation of additional stress that is derived from aerobic metabolism and may provide the basis for enhanced (micro)aerobic production of organic acids in
S. cerevisiae
.
TaqMan Probe-Based Real-Time PCR Assay for Detection and Discrimination of Class I, II, and III
tfdA
Genes in Soils Treated with Phenoxy Acid Herbicides
Authors: Bælum Jacob , Jacobsen Carsten S.
Published: February 2009

Separate quantification of three classes of
tfdA
genes was performed using TaqMan quantitative real-time PCR for 13 different soils subsequent to mineralization of three phenoxy acids. Class III
tfdA
genes were found to be involved in mineralization more often than class I and II
tfdA
genes.
Empirical Testing of 16S rRNA Gene PCR Primer Pairs Reveals Variance in Target Specificity and Efficacy Not Suggested by In Silico Analysis
Authors: Morales Sergio E. , Holben William E.
Published: February 2009

Phylogenetic and “fingerprinting” analyses of the 16S rRNA genes of prokaryotes have been a mainstay of microbial ecology during the last two decades. However, many methods and results from studies that rely on the 16S rRNA gene for detection and quantification of specific microbial taxa have seemingly received only cursory or even no validation. To directly examine the efficacy and specificity of 16S rRNA gene-based primers for phylum-, class-, and operational taxonomic unit-specific target amplification in quantitative PCR, we created a collection of primers based solely on an extensive soil bacterial 16S rRNA gene clone library containing ∼5,000 sequences from a single soil sample (i.e., a closed site-specific library was used to create PCR primers for use at this site). These primers were initially tested in silico prior to empirical testing by PCR amplification of known target sequences and of controls based on disparate phylogenetic groups. Although all primers were highly specific according to the in silico analysis, the empirical analyses clearly exhibited a high degree of nonspecificity for many of the phyla or classes, while other primers proved to be highly specific. These findings suggest that significant care must be taken when interpreting studies whose results were obtained with target specific primers that were not adequately validated, especially where population densities or dynamics have been inferred from the data. Further, we suggest that the reliability of quantification of specific target abundance using 16S rRNA-based quantitative PCR is case specific and must be determined through rigorous empirical testing rather than solely in silico.
Pathway and Evolutionary Implications of Diphenylamine Biodegradation by
Burkholderia
sp. Strain JS667
Authors: Shin Kwanghee A. , Spain Jim C.
Published: February 2009

Diphenylamine (DPA) is a common contaminant at munitions-contaminated sites as well as at aniline manufacturing sites. Little is known about the biodegradation of the compound, and bacteria able to use DPA as the growth substrate have not been reported.
Burkholderia
sp. strain JS667 and
Ralstonia
sp. strain JS668 were isolated by selective enrichment from DPA-contaminated sediment. The isolates grew aerobically with DPA as the sole carbon, nitrogen, and energy source. During induction of DPA degradation, stoichiometric amounts of aniline accumulated and then disappeared, which suggested that aniline is on the DPA degradation pathway. Genes encoding the enzymes that catalyze the initial steps in DPA degradation were cloned from the genomic DNA of strain JS667. The
Escherichia coli
clone catalyzed stoichiometric transformation of DPA to aniline and catechol. Transposon mutagenesis, the sequence similarity of putative open reading frames to those of well-characterized dioxygenases, and
18
O
2
experiments support the conclusion that the initial reaction in DPA degradation is catalyzed by a multicomponent ring-hydroxylating dioxygenase. DPA is converted to aniline and catechol via dioxygenation at the 1,2 position of the aromatic ring and spontaneous rearomatization. Aniline and catechol are further biodegraded by the well-established aniline degradation pathway. Genes that encode the complete aniline degradation pathway were found 12 kb downstream of the genes that encode the initial dioxygenase. Expression of the relevant dioxygenases was confirmed by reverse transcription-PCR analysis. Both the sequence similarity and the gene organization suggest that the DPA degradation pathway evolved recently by the recruitment of two gene clusters that encode the DPA dioxygenase and aniline degradation pathway.
Chimeric Genomes of Natural Hybrids of
Saccharomyces cerevisiae
and
Saccharomyces kudriavzevii
Authors: Belloch Carmela , Pérez-Torrado Roberto , González Sara S. , Pérez-Ortín José E. , García-Martínez José , Querol Amparo , Barrio Eladio
Published: February 2009

Recently, a new type of hybrid resulting from the hybridization between
Saccharomyces cerevisiae
and
Saccharomyces kudriavzevii
was described. These strains exhibit physiological properties of potential biotechnological interest. A preliminary characterization of these hybrids showed a trend to reduce the
S. kudriavzevii
fraction of the hybrid genome. We characterized the genomic constitution of several wine
S. cerevisiae
×
S. kudriavzevii
strains by using a combined approach based on the restriction fragment length polymorphism analysis of gene regions, comparative genome hybridizations with
S. cerevisiae
DNA arrays, ploidy analysis, and gene dose determination by quantitative real-time PCR. The high similarity in the genome structures of the
S. cerevisiae
×
S. kudriavzevii
hybrids under study indicates that they originated from a single hybridization event. After hybridization, the hybrid genome underwent extensive chromosomal rearrangements, including chromosome losses and the generation of chimeric chromosomes by the nonreciprocal recombination between homeologous chromosomes. These nonreciprocal recombinations between homeologous chromosomes occurred in highly conserved regions, such as Ty long terminal repeats (LTRs), rRNA regions, and conserved protein-coding genes. This study supports the hypothesis that chimeric chromosomes may have been generated by a mechanism similar to the recombination-mediated chromosome loss acting during meiosis in
Saccharomyces
hybrids. As a result of the selective processes acting during fermentation, hybrid genomes maintained the
S. cerevisiae
genome but reduced the
S. kudriavzevii
fraction.
Microbial Mineral Weathering for Nutrient Acquisition Releases Arsenic
Authors: Mailloux Brian J. , Alexandrova Ekaterina , Keimowitz Alison R. , Wovkulich Karen , Freyer Greg A. , Herron Michael , Stolz John F. , Kenna Timothy C. , Pichler Thomas , Polizzotto Matthew L. , Dong Hailiang , Bishop Michael , Knappett Peter S. K.
Published: February 2009

Tens of millions of people in Southeast Asia drink groundwater contaminated with naturally occurring arsenic. How arsenic is released from the sediment into the water remains poorly understood. Here, we show in laboratory experiments that phosphate-limited cells of
Burkholderia fungorum
mobilize ancillary arsenic from apatite. We hypothesize that arsenic mobilization is a by-product of mineral weathering for nutrient acquisition. The released arsenic does not undergo a redox transformation but appears to be solubilized from the apatite mineral lattice during weathering. Analysis of apatite from the source area in the Himalayan basin indicates the presence of elevated levels of arsenic, with an average concentration of 210 mg/kg. The rate of arsenic release is independent of the initial dissolved arsenic concentration and occurs at phosphate levels observed in Bangladesh aquifers. We also demonstrate the presence of the microbial phenotype that releases arsenic from apatite in Bangladesh aquifer sediments and groundwater. These results suggest that microbial mineral weathering for nutrient acquisition could be an important mechanism for arsenic mobilization.
Cellulase Production from Spent Lignocellulose Hydrolysates by Recombinant
Aspergillus niger
Authors: Alriksson Björn , Rose Shaunita H. , van Zyl Willem H. , Sjöde Anders , Nilvebrant Nils-Olof , Jönsson Leif J.
Published: February 2009

A recombinant
Aspergillus niger
strain expressing the
Hypocrea jecorina
endoglucanase Cel7B was grown on spent hydrolysates (stillage) from sugarcane bagasse and spruce wood. The spent hydrolysates served as excellent growth media for the Cel7B-producing strain,
A. niger
D15[
egI
], which displayed higher endoglucanase activities in the spent hydrolysates than in standard medium with a comparable monosaccharide content (e.g., 2,100 nkat/ml in spent bagasse hydrolysate compared to 480 nkat/ml in standard glucose-based medium). In addition,
A. niger
D15[
egI
] was also able to consume or convert other lignocellulose-derived compounds, such as acetic acid, furan aldehydes, and phenolic compounds, which are recognized as inhibitors of yeast during ethanolic fermentation. The results indicate that enzymes can be produced from the stillage stream as a high-value coproduct in second-generation bioethanol plants in a way that also facilitates recirculation of process water.
Climate and Tick Seasonality Are Predictors of
Borrelia burgdorferi
Genotype Distribution
Authors: Gatewood Anne G. , Liebman Kelly A. , Vourc'h Gwenaël , Bunikis Jonas , Hamer Sarah A. , Cortinas Roberto , Melton Forrest , Cislo Paul , Kitron Uriel , Tsao Jean , Barbour Alan G. , Fish Durland , Diuk-Wasser Maria A.
Published: February 2009

The blacklegged tick,
Ixodes scapularis
, is of significant public health importance as a vector of
Borrelia burgdorferi
, the agent of Lyme borreliosis. The timing of seasonal activity of each immature
I. scapularis
life stage relative to the next is critical for the maintenance of
B. burgdorferi
because larvae must feed after an infected nymph to efficiently acquire the infection from reservoir hosts. Recent studies have shown that some strains of
B. burgdorferi
do not persist in the primary reservoir host for more than a few weeks, thereby shortening the window of opportunity between nymphal and larval feeding that sustains their enzootic maintenance. We tested the hypothesis that climate is predictive of geographic variation in the seasonal activity of
I. scapularis
, which in turn differentially influences the distribution of
B. burgdorferi
genotypes within the geographic range of
I. scapularis
. We analyzed the relationships between climate, seasonal activity of
I. scapularis
, and
B. burgdorferi
genotype frequency in 30 geographically diverse sites in the northeastern and midwestern United States. We found that the magnitude of the difference between summer and winter daily temperature maximums was positively correlated with the degree of seasonal synchrony of the two immature stages of
I. scapularis
. Genotyping revealed an enrichment of 16S-23S rRNA intergenic spacer restriction fragment length polymorphism sequence type 1 strains relative to others at sites with lower seasonal synchrony. We conclude that climate-associated variability in the timing of
I. scapularis
host seeking contributes to geographic heterogeneities in the frequencies of
B. burgdorferi
genotypes, with potential consequences for Lyme borreliosis morbidity.