bluuebunny/crossref_metadata_2025 huggingface dataset:
Separate and independent reductions in direct tunneling in oxide/nitride stacks with monolayer interface nitridation associated with the (i) interface nitridation and (ii) increased physical thickness
Authors: Lucovsky G. , Wu Y. , Niimi H. , Yang H. , Keister J. , Rowe J. E.
Published: July 2002

Direct tunneling limits aggressive scaling of thermally grown oxides to about 1.6 nm, a thickness at which the tunneling current density Jg at 1 V is ∼1 A/cm2. This article demonstrates that stacked gate dielectrics prepared by remote plasma processing and including (i) ultrathin nitrided SiO2 interfacial layers and (ii) either silicon nitride or oxynitride bulk dielectrics can extend the equivalent oxide thickness to 1.1–1.0 nm before Jg exceeds 1 A/cm2. Significant reductions in direct tunneling are derived from (i) interface nitridation at the monolayer level and (ii) the increased physical thickness of the nitride or oxynitride alloy layers. The “portability” of the interface contribution is demonstrated by combining the nitrided SiO2 interface layers with transition-metal oxides, e.g., Ta2O5, in stacked gate dielectric structures and obtaining essentially the same reductions in tunneling current on n- and p-type substrates with respect to non-nitrided plasma-grown interface layers.
Demonstration of broadband radio frequency sensing: Empirical polysilicon etch rate estimation in a Lam 9400 etch tool
Authors: Garvin Craig , Grizzle J. W.
Published: July 2002

The sensitivity of a novel broad frequency band (1–2.25 GHz) radio frequency sensing system to plasma etching process conditions is demonstrated. This is accomplished by using the sensing system to estimate polysilicon etch rate in a Lam 9400 etch tool. A designed experiment varying physical and chemical reactive ion etching regimes was performed with five repetitions at each experimental point. A model relating broadband sensor response to etch rate was regressed using four repetitions of the data and validated on the fifth. Two representations of the broadband data were considered separately when regressing the models, with subset selection used in each case to choose the best predictor variables. In one representation, the sensor data was considered as a vector of 402 real numbers corresponding to magnitude and phase of reflection coefficient at each of 201 frequencies, resulting in an R2 of etch rate estimate of 0.997. In the other, the broadband response was parameterized on the basis of a multimodal cavity resonance model. The inferred parameters of natural frequency, quality factor and resistance were then used as the predictor variables for regression, resulting in an R2 of 0.962.
Study on the characteristics of TiN thin film deposited by the atomic layer chemical vapor deposition method
Authors: Jeon Hyeongtag , Lee June-Woo , Kim Young-Do , Kim Deok-Soo , Yi Kyoung-Soo
Published: July 2002

TiN film was deposited on Si substrate by using an atomic layer chemical vapor deposition (CVD) system. In this system, the TiCl4 and NH3 gases were supplied, separately and Ar purge gas was added between the source and reactant gases to suppress the direct reaction. The microstructure of TiN was observed to be the columnar grain structure. The chemical species was analized by Auger electron spectroscopy (AES) and the Cl content in TiN film was detected below the detection limit of AES which was below 0.5%. The density of film grown at 450 °C measured by Rutherford backscattering spectroscopy was 4.85 g/cm3 and decreased as the process temperature decreased. The resistivity of this TiN was about 75 μΩ cm, which was very low compared to TiN film grown by other CVD methods. The step coverage of TiN film showed almost 100% conformality at 450 °C.
Study of the mechanical behavior of plasma-deposited silica films on polycarbonate and steel
Authors: Hofrichter A. , Constantinescu A. , Benayoun S. , Bulkin P. , Drévillon B.
Published: July 2002

In the present study, we deposited amorphous hydrogenated silicon oxide films on polycarbonate, stainless steel, and silicon by plasma enhanced chemical vapor deposition using a low pressure, high density integrated distributed electron cyclotron resonance plasma reactor. Substrate curvature, vibrating slab, and Vickers indentation experiments were used to evaluate the intrinsic stress, the Young modulus of the films, and the composite hardness of the film–substrate system. The indentation experiments were modeled by finite element analysis and the calculated values were compared to experimentally measured hardness values. A reasonable accordance with the experiment was found both for stainless-steel and polycarbonate substrates, indicating that the modeling is valid and may be used to enhance the interpretation of the indentation experiments. The calculations show an important bending of the film in the noncontact region in the case of a Vickers indentation on a coated polycarbonate sample. The analysis of the thus-induced strain distribution in the coating indicates that the measured diagonal might be overestimated and not representative of the real contact area. The calculations indicate that the yield limit of the plasma-deposited silica films is of about 4 GPa.
Effects of dry etching on GaAs
Authors: Pang S. W. , Lincoln G. A. , McClelland R. W. , DeGraff P. D. , Geis M. W. , Piacentini W. J.
Published: July 2002

A number of dry etching techniques have been developed and their ability to produce anisotropic etch profiles has been demonstrated. In addition to etch anisotropy, an important consideration for device and circuit fabrication is whether a sample suffers radiation damage by exposure to ions, electrons, or ultraviolet light during etching. In this study we evaluate the degree of radiation damage induced in GaAs by ion-beam etching with Ar, reactive-ion etching with CF4 and CHF3, and ion-beam-assisted etching with Ar and Cl2. In addition, we propose and demonstrate processing techniques which can be used after dry etching to reduce the effects of radiation damage. GaAs samples were etched under a variety of etching conditions. The degree of radiation damage caused by etching was determined by evaluating Schottky diodes fabricated on the etched surfaces and by using deep level transient spectroscopy to characterize trapping centers. It was found that the barrier heights and breakdown voltages of Schottky diodes were changed after etching. Also, an increase in the density of traps was observed. Variations in the etching conditions had a strong effect on the measured characteristics of the samples.
Variation of n-GaAs (100) interface Fermi level by Ge and Si overlayers
Authors: Grant R. W. , Waldrop J. R.
Published: July 2002

The interface Fermi level (EiF) for interfaces that were formed by depositing thin (∼10 Å) layers of Ge and Si onto heated GaAs (100) substrates was studied by x-ray photoelectron spectroscopy. The value of EiF for Ge overlayers (relative to the GaAs valence band maximum) could be varied from ∼0.5 eV to ∼1.2 eV by depositing the Ge in vacuum or by depositing it in an As4 or P2 background pressure (∼10−7 Torr). These EiF values roughly correspond to the band edges of Ge at the Ge/GaAs heterojunction interface, which suggests that the dopant type in the Ge overlayer and band alignment play a significant role in determining EiF. A thin Si overlayer with incorporated As also exhibited an EiF of ∼1.2 eV. The results suggest that heterojunction band alignment characteristics for Ge/GaAs and Si/GaAs based electrical contacts are important in determining the range over which EiF can be varied. The large EiF variation could have an application in the design of nonalloyed GaAs ohmic contacts.
Atomic force microscopy of biological samples at low temperature
Authors: Prater C. B. , Wilson M. R. , Garnaes J. , Massie J. , Elings V. B. , Hansma P. K.
Published: July 2002

The atomic force microscope (AFM) has been successful imaging rigid samples with atomic resolution, but this resolution has not been matched on soft biological samples at room temperature. On many biological samples even tracking forces as small as 10−9 N distort the sample during a scan.At low temperatures proteins freeze into a single conformational state and become much more rigid. In this paper we demonstrate that it should be feasible to get atomic resolution on frozen biological samples with a low-temperature AFM. We also show some preliminary low-temperature AFM images of one biological sample, purple membrane.
Palladium clusters on mica: A study by scanning force microscopy
Authors: Colchero J. , Marti O. , Mlynek J. , Humbert A. , Henry C. R. , Chapon C.
Published: July 2002

A compact scanning force microscope with a force sensor based on the light beam deflection method was used to study palladium clusters on mica. The force microscope was equipped to measure topography of the sample surface and the friction force between the sample and the tip. The evaporation of palladium on mica was done under UHV conditions, which were closely monitored to control both the morphology and the size of the clusters. The resulting clusters were characterized by transmission electron microscopy. The samples were then transferred in air and imaged with the scanning force microscope under ambient conditions. The diameter to height ratio near 10 and the truncated triagonal shapes of the palladium clusters agree well with the results obtained by transmission electron microscopy and with the results of a scanning tunneling microscopy study of palladium clusters on graphite. Friction images show, that the interaction between the tip and the clusters does charge them.
Force microscope using a twin-path interferometer
Authors: Watanabe S. , Hane K. , Goto T.
Published: July 2002

In this article, a force microscope using a twin-path (common-path) laser interferometer is presented. The interferometer was developed for the displacement detection of a small cantilever. Since the two interfering beams were very close to each other, the perturbation caused by the environmental disturbances were minimized. The optical path difference between the two beams was easily adjusted by the moire effect of the gratings. The vibrational amplitude of 10−3 nm was measured under the resonance conditions of the tungsten lever. The drift rate of the interference signal was less than 10−3 nm/s. An etched-resist coated with thin gold film was imaged by using electrostatic forces under the conditions of ac mode operation.
Single-layer chemically amplified photoresists for 193-nm lithography
Authors: Wallraff G. M. , Allen R. D. , Hinsberg W. D. , Larson C. F. , Johnson R. D. , DiPietro R. , Breyta G. , Hacker N. , Kunz R. R.
Published: July 2002

Recent advances in ArF excimer laser exposure tools have led to a search for new resist materials for use at 193 nm. To date much of this effort has been directed toward surface imaged or bilayer resist schemes and only recently have there been reports of single layer systems with sufficient transparency for use at this short wavelength. We will describe our approach to a 193 nm single layer resist system based on methacrylate terpolymers. A terpolymer system based on tert-butylmethacrylate, methyl methacrylate and methacrylic acid developed for laser direct imaging applications has been adapted for high resolution imaging by modifying the terpolymer composition and by optimizing the photoacid generator loading. This resist is useful for the characterization of new exposure systems and we will describe imaging results on a prototype 0.50-NA step and scan system. We will also describe the effect photoacid structure has on the imaging properties of the resist and compare the efficiency of deprotection chemistry at 193 and 248 nm. In addition, we will discuss modifications of the aliphatic polymer described above by replacement of the ‘‘inert’’ methyl methacrylate monomer by monomers containing alicyclic substituents to improve the resistance to reactive ion etching.
Structural study of Langmuir–Blodgett films by scanning surface potential microscopy
Authors: Fujihira Masamichi , Kawate Hirosuke
Published: July 2002

In this paper we describe the structural study of Langmuir–Blodgett (LB) films with a scanning surface potential microscope (SSPM) together with an ordinary atomic force microscope (AFM). The SSPM is a new type of high-resolution potentiometry due to electrostatic force microscopy and is a member of the AFM family. Our SSPM is a modified Kelvin probe force microscope, and is based upon the design of a recently developed scanning Maxwell stress microscope (SMM). This microscope can be used to study distribution of the surface potential or the contact potential difference (CPD) with submicrometer spatial resolution. We have applied this microscope to the study of molecular orientation of amphiphilic molecules in LB films. The surface dipole moments due to the terminal CH3 group of the long alkyl chain and the hydrophilic head group are used to study the orientation in the multilayered structures of LB films. In the present work, we focused on reorientation of the amphiphilic molecules in LB films during monolayer transfer and by oxidation of the substrate surface.
Cross-sectional characterization of thin-film transistors with transmission electron microscopy
Authors: Tsuji S. , Tanaka M. , Iwama H. , Tsutsui N. , Kuroda K. , Saka H.
Published: July 2002

The nanometer-scale multilayered structure of hydrogenated amorphous silicon thin-film transistors (a-Si:H TFTs) used as elements for active matrix liquid crystal displays was characterized by means of cross-sectional transmission electron microscopy (TEM). This article describes how an array can be characterized by using a TFT array tester that can detect, accurately locate, and identify pixel faults. Cross-sectional TEM was used to investigate the discrete layer construction of a faulty TFT and the generation of defects during manufacturing processes. Two types of faulty TFTs are examined in this study: (1) those in which gross defects such as contamination are readily detectable and (2) those in which no significant anomalies are detectable under an optical microscope inspection. Cross-sectional results were obtained by TEM for both types of faulty TFTs. Contamination layers composed of silicon oxide were observed in the same location in both cases, with a thickness of 10–30 nm. These layers caused contact failures. This observation led to identification of the fault and analysis of its cause, which in turn led to a marked yield improvement. An a-Si layer was crystallized as an artifact during TEM observation. Electron irradiation damage is also discussed.
Field emission in a microwave field*
Authors: Fursey George N.
Published: July 2002

This article deals with principal peculiarities of field electron emission in a microwave field. The adiabaticity problem in respect to the field emission process, experimental verification of the Fowler–Nordheim theory, and problem of maximum densities of the emission current are analyzed. The new effect of abrupt decreases in the ion bombardment of cathode (more than a factor of 106) in a microwave field and peculiarities in the energy spectrum of an electron beam are discussed. First experiments on the field electron emission from liquid metals in microwave field are described.
Effects of graded superlattice on endpoint detection for low damage heterojunction bipolar transistor etching
Authors: Thomas S. , Chen H. H. , Pang S. W.
Published: July 2002

Endpoint detection for the emitter etch of an AlInAs/GaInAs heterojunction bipolar transistor with a graded nine period AlInAs/GaInAs superlattice was investigated. Ga optical emission at 417.2 nm was detected after ∼10 nm of the superlattice had been etched. Once this occurred, an additional overetch of 30 nm was required to completely remove the superlattice and the lightly doped p-type GaInAs spacer layer. The etch-induced damage was characterized by measuring the contact resistivity (ρc) of the base layer and comparing this to a wet etched sample. Two step etching was studied to minimize surface roughness and reduce damage. This requires etching at high rf power initially to maintain smooth surface morphology and then etching at reduced rf power to remove damage created in the first part of the etch. By etching the first 50% of n-type GaInAs at 160 W rf power and the rest at 30 W rf power, a nearly damage free smooth surface can be achieved. Etching with just 30 W rf power can completely eliminate the damage. Damage to both n-type and p+-GaInAs has been studied. For n-type material, damage decreases ρc and for p+-type material damage increases ρc when compared to the wet etched samples. The effect of annealing on the transmission line measurements was also studied. For the p+-GaInAs, an annealed contact on the sample etched with low rf power had a contact resistivity of 8.1×10−6 Ω cm2. This is lower than the wet etched sample, where ρc was 1.6×10−5 Ω cm2. This could be related to the smoother surface that was obtained from dry etching when compared to wet etching.
Probeless voltage contrast using a focused ion beam for opens and shorts defect isolation of ultralarge scale integration technologies
Authors: Giewont Kenneth J. , Hunt Douglas B. , Hummler Klaus M.
Published: July 2002

Defect isolation in large yield mazes for accurate and timely physical analysis continues to be a critical part of process development for 0.4 and 0.25 μm technologies. Shrinking dimensions have challenged common approaches such as light emission microscopy (LEM), optical beam induced current (OBIC), liquid crystal, and mechanical probing to the point where alternate techniques are needed. This article describes simple but powerful defect isolation techniques using probeless voltage contrast in a focused ion beam (FIB) tool. Fail modes to which the techniques are applicable include deep trench capacitor polysilicon to substrate leakage, gate conductor to self-aligned contact shorts, metal line opens, via chain opens, and metal line to line shorts. When possible, OBIC or LEM are initially used to determine the approximate fail location followed by precise isolation using the FIB. Typical examples of each fail mode will be shown. The basic principle employs the positive focused ion beam to charge floating structures which tend to attenuate the secondary electron image. This provides a suitable potential difference between grounded and ungrounded structures which can be easily observed in the electron imaging mode. Using this phenomenon along with leveraging the ability of the FIB to cut and deposit replaces the need for a probe. In addition, once a defect is isolated it can be precisely marked and then unlayered or cross sectioned in situ. This technique has provided the only practical solution to isolate defects in some situations while reducing the average turn around time for feedback to process engineering.
Scatterometry measurement of sub-0.1 μm linewidth gratings
Authors: Coulombe Stephen A. , Minhas Babar K. , Raymond Christopher J. , Sohail H. Naqvi S. , McNeil John R.
Published: July 2002

The effort discussed here addresses the use of shorter incident wavelengths for characterizing sub-0.1 μm linewidths and the corresponding influence on scatterometry measurement sensitivity to linewidth variations. A sensitivity metric, based on the variance statistic, was developed using well-characterized, large-pitch (0.80 μm) photoresist grating structures on Si illuminated at 633 and 442 nm. The same metric was applied to short-pitch (0.20 μm), etched gratings on InP, with the result that appreciable scatterometry sensitivity was measured, even at the 633 nm incident wavelength. Modeling was used to estimate scatterometry sensitivity at three wavelengths for photoresist critical dimensions of 100 and 70 nm on Si. A significant increase in sensitivity was not found until the incident wavelength was reduced to 325 nm. We are presently investigating techniques to improve measurement sensitivity for short-pitch structures using the 633 nm incident wavelength.
Reactive ion etching of Pb(ZrxTi1−x)O3 thin films in an inductively coupled plasma
Authors: Chung Chee Won
Published: July 2002

Reactive ion etching of PbZrxTi1−xO3 (PZT) thin films was studied by using Cl2/C2F6/Ar gas chemistry in an inductively coupled plasma (ICP). PZT films were deposited on Pt/Ti/SiO2/Si substrates by the sol–gel process. PZT films were etched by varying the etching parameters including coil rf power, dc-bias voltage to the substrate, and gas pressure. Etching characteristics of PZT films were investigated in terms of etch rate, etch selectivity, etch profile and etching mechanism. Etch profile along with etch anisotropy was observed as a function of etching parameter by field emission scanning electron microscopy. For understanding of the etching mechanism, x-ray photoelectron spectroscopy and ICP analysis for film composition were utilized. Finally, the pattern transfer of PZT films with fine geometry was successfully achieved at the optimum etching condition.
High emission current double-gated field emitter arrays
Authors: Hosono Akihiko , Kawabuchi Shinji , Horibata Shinji , Okuda Soichiro , Harada Hiroshi , Takai Mikio
Published: July 2002

To realize a high current under focusing operation we investigated the structure of double-gated field emitter arrays (FEAs) and tried to anodize the tip of the silicon emitters. It was found from these investigations that the FEAs with the thick extraction gate could maintain high emission current during focusing operation. Furthermore, the anodized Si FEAs with thick extraction gate achieved a high emission current per tip of about 300 nA under focusing operation.
Characterization of low-temperature wafer bonding by infrared spectroscopy
Authors: Milekhin A. , Friedrich M. , Hiller K. , Wiemer M. , Gessner T. , Zahn D. R. T.
Published: July 2002

We present the results of an infrared (IR) spectroscopic investigation of interfaces between two hydrophilic Si wafers bonded at low temperature. Multiple internal transmission IR spectra were recorded of the bonds, with different chemical pretreatments of Si surfaces employed before bonding. The analysis of IR spectra shows that the number of O–H and H–Si–Ox species at the interface depends strongly on the chemical pretreatment type, which determines the bonding energy. The annealing procedure used in the bonding process leads to dissociation of water molecules, oxidation of silicon at the interfaces, and diffusion of hydrogen into silicon oxide layer formed at the interface. The difference in bonding processes is discussed.
LaCoO3 Nanopowders by XPS
Authors: Armelao Lidia , Bettinelli Marco , Bottaro Gregorio , Barreca Davide , Tondello Eugenio
Published: July 2002

Mixed oxide materials belonging to the perovskite family (ABO3, LaCoO3) have come under intense scrutiny for their possible applications in different scientific and technological fields, such as heterogeneous catalysis, oxygen sensors, solid oxide fuel cells and magnetic media. The growing interest in such mixed oxide systems relies on a detailed investigation of structure-properties relationships that can lead to the optimization of their performances with respect to different applications, e.g., catalysis, sensors, etc. Similar solid state devices would require high surface area thin films in order to optimize the full potential of these oxide materials; specifically, nanostructured systems with a high defect content (oxygen vacancies and local lattice disorder) are expected to show superior properties with respect to the conventional ones. The possibility to tailor these features as a function of the surface area and grain size appears thus as a powerful tool in order to optimize the material properties for functional applications. In particular the present investigation is focused on x-ray photoelectron spectroscopy (XPS) and x-ray excited Auger electron spectroscopy (XE-AES) analysis of the main core levels (O 1s, Co 2p, Co LMM, La 3d, and La 4d) of LaCoO3 nanophasic powders obtained by combustion synthesis. The formation of LaCoO3 was ascertained by the position and shape of La 3d and Co 2p photopeaks.
Interference by Huntingtin and Atrophin-1 with CBP-Mediated Transcription Leading to Cellular Toxicity
Authors: Nucifora Frederick C. , Sasaki Masayuki , Peters Matthew F. , Huang Hui , Cooper Jillian K. , Yamada Mitsunori , Takahashi Hitoshi , Tsuji Shoji , Troncoso Juan , Dawson Valina L. , Dawson Ted M. , Ross Christopher A.
Published: July 2002

Expanded polyglutamine repeats have been proposed to cause neuronal degeneration in Huntington's disease (HD) and related disorders, through abnormal interactions with other proteins containing short polyglutamine tracts such as the transcriptional coactivator CREB binding protein, CBP. We found that CBP was depleted from its normal nuclear location and was present in polyglutamine aggregates in HD cell culture models, HD transgenic mice, and human HD postmortem brain. Expanded polyglutamine repeats specifically interfere with CBP-activated gene transcription, and overexpression of CBP rescued polyglutamine-induced neuronal toxicity. Thus, polyglutamine-mediated interference with CBP-regulated gene transcription may constitute a genetic gain of function, underlying the pathogenesis of polyglutamine disorders.
Control of Nitrogen Export from Watersheds by Headwater Streams
Authors: Peterson Bruce J. , Wollheim Wilfred M. , Mulholland Patrick J. , Webster Jackson R. , Meyer Judy L. , Tank Jennifer L. , Martí Eugènia , Bowden William B. , Valett H. Maurice , Hershey Anne E. , McDowell William H. , Dodds Walter K. , Hamilton Stephen K. , Gregory Stanley , Morrall Donna D.
Published: July 2002

A comparative
15
N-tracer study of nitrogen dynamics in headwater streams from biomes throughout North America demonstrates that streams exert control over nutrient exports to rivers, lakes, and estuaries. The most rapid uptake and transformation of inorganic nitrogen occurred in the smallest streams. Ammonium entering these streams was removed from the water within a few tens to hundreds of meters. Nitrate was also removed from stream water but traveled a distance 5 to 10 times as long, on average, as ammonium. Despite low ammonium concentration in stream water, nitrification rates were high, indicating that small streams are potentially important sources of atmospheric nitrous oxide. During seasons of high biological activity, the reaches of headwater streams typically export downstream less than half of the input of dissolved inorganic nitrogen from their watersheds.
The Indian Ocean Experiment: Widespread Air Pollution from South and Southeast Asia
Authors: Lelieveld J. , Crutzen P. J. , Ramanathan V. , Andreae M. O. , Brenninkmeijer C. A. M. , Campos T. , Cass G. R. , Dickerson R. R. , Fischer H. , de Gouw J. A. , Hansel A. , Jefferson A. , Kley D. , de Laat A. T. J. , Lal S. , Lawrence M. G. , Lobert J. M. , Mayol-Bracero O. L. , Mitra A. P. , Novakov T. , Oltmans S. J. , Prather K. A. , Reiner T. , Rodhe H. , Scheeren H. A. , Sikka D. , Williams J.
Published: July 2002

The Indian Ocean Experiment (INDOEX) was an international, multiplatform field campaign to measure long-range transport of air pollution from South and Southeast Asia toward the Indian Ocean during the dry monsoon season in January to March 1999. Surprisingly high pollution levels were observed over the entire northern Indian Ocean toward the Intertropical Convergence Zone at about 6°S. We show that agricultural burning and especially biofuel use enhance carbon monoxide concentrations. Fossil fuel combustion and biomass burning cause a high aerosol loading. The growing pollution in this region gives rise to extensive air quality degradation with local, regional, and global implications, including a reduction of the oxidizing power of the atmosphere.
Stimulation of RNA Polymerase II Elongation by Hepatitis Delta Antigen
Authors: Yamaguchi Yuki , Filipovska Julija , Yano Keiichi , Furuya Akiko , Inukai Naoto , Narita Takashi , Wada Tadashi , Sugimoto Seiji , Konarska Maria M. , Handa Hiroshi
Published: July 2002

Transcription elongation by RNA polymerase II (RNAPII) is negatively regulated by the human factors DRB-sensitivity inducing factor (DSIF) and negative elongation factor (NELF). A 66-kilodalton subunit of NELF (NELF-A) shows limited sequence similarity to hepatitis delta antigen (HDAg), the viral protein required for replication of hepatitis delta virus (HDV). The host RNAPII has been implicated in HDV replication, but the detailed mechanism and the role of HDAg in this process are not understood. We show that HDAg binds RNAPII directly and stimulates transcription by displacing NELF and promoting RNAPII elongation. These results suggest that HDAg may regulate RNAPII elongation during both cellular messenger RNA synthesis and HDV RNA replication.
The Epidemic Behavior of the Hepatitis C Virus
Authors: Pybus Oliver G. , Charleston Michael A. , Gupta Sunetra , Rambaut Andrew , Holmes Edward C. , Harvey Paul H.
Published: July 2002

Hepatitis C virus (HCV) is a leading worldwide cause of liver disease. Here, we use a new model of HCV spread to investigate the epidemic behavior of the virus and to estimate its basic reproductive number from gene sequence data. We find significant differences in epidemic behavior among HCV subtypes and suggest that these differences are largely the result of subtype-specific transmission patterns. Our model builds a bridge between the disciplines of population genetics and mathematical epidemiology by using pathogen gene sequences to infer the population dynamic history of an infectious disease.
Density Fluctuations Under Confinement: When Is a Fluid Not a Fluid?
Authors: Heuberger M. , Zäch M. , Spencer N. D.
Published: July 2002

Knowing the behavior of a fluid in small volumes is essential for the understanding of a vast array of common problems in science, such as biological interactions, fracture propagation, and molecular tribology and adhesion, as well as pressure solvation and other geophysical processes. When a fluid is confined, its phase behavior is altered and excluded-volume effects become apparent. Pioneering measurements performed with the surface forces apparatus have revealed so-called structural or oscillatory solvation forces as well as the occurrence of a finite shear stress, which was interpreted as a solidification transition. Here, we report measurements obtained with an extended surface forces apparatus, which makes use of fast spectral correlation to gain insight into the behavior of a thin film of cyclohexane confined within attoliter volumes, with simultaneous measurement of film thickness and refractive index. With decreasing pore width, cyclohexane is found to undergo a drastic transition from a three-dimensional bulk fluid to a two-dimensional adsorbate with strikingly different properties. Long-range density fluctuations of unexpected magnitude are observed.
Glycosylation of Nucleocytoplasmic Proteins: Signal Transduction and O-GlcNAc
Authors: Wells Lance , Vosseller Keith , Hart Gerald W.
Published: July 2002

The dynamic glycosylation of serine or threonine residues on nuclear and cytosolic proteins by O-linked β-
N
-acetylglucosamine (O-GlcNAc) is abundant in all multicellular eukaryotes. On several proteins, O-GlcNAc and O-phosphate alternatively occupy the same or adjacent sites, leading to the hypothesis that one function of this saccharide is to transiently block phosphorylation. The diversity of proteins modified by O-GlcNAc implies its importance in many basic cellular and disease processes. Here we systematically examine the current data implicating O-GlcNAc as a regulatory modification important to signal transduction cascades.
Genetic Clues to Dispersal in Human Populations: Retracing the Past from the Present
Authors: Cann Rebecca L.
Published: July 2002

Ongoing debate about proper interpretation of DNA sequence polymorphisms and their ability to reconstruct human population history illustrates a important change in perspective that we have achieved in the past 20 years of population genetics. To what extent does the history of a locus represent the history of a population? Tools originally developed for molecular systematics, where genetic lineages have been separated by speciation events, are routinely applied to the analysis of variation within our species, with conflicting results. Because of automated technologies and linkage analysis, we are poised to harvest a wealth of information about our past, if we are successful in moving beyond a current polarization regarding models of human evolution. Rather than just suggesting that true resolution will only come by considering fossil or archaeological evidence, the realistic and appropriate application of genetic models for analysis of population structure is also necessary. Three examples from different dispersal events are highlighted here.
Collapse of the California Current During Glacial Maxima Linked to Climate Change on Land
Authors: Herbert T. D. , Schuffert J. D. , Andreasen D. , Heusser L. , Lyle M. , Mix A. , Ravelo A. C. , Stott L. D. , Herguera J. C.
Published: July 2002

Time series of alkenone unsaturation indices gathered along the California margin reveal large (4° to 8°C) glacial-interglacial changes in sea surface temperature (SST) over the past 550,000 years. Interglacial times with SSTs equal to or exceeding that of the Holocene contain peak abundances in the pollen of redwood, the distinctive component of the temperate rainforest of the northwest coast of California. In the region now dominated by the California Current, SSTs warmed 10,000 to 15,000 years in advance of deglaciation at each of the past five glacial maxima. SSTs did not rise in advance of deglaciation south of the modern California Current front. Glacial warming along the California margin therefore is a regional signal of the weakening of the California Current during times when large ice sheets reorganized wind systems over the North Pacific. Both the timing and magnitude of the SST estimates suggest that the Devils Hole (Nevada) calcite record represents regional but not global paleotemperatures, and hence does not pose a fundamental challenge to the orbital (“Milankovitch”) theory of the Ice Ages.
G-Protein Signaling Through Tubby Proteins
Authors: Santagata Sandro , Boggon Titus J. , Baird Cheryl L. , Gomez Carlos A. , Zhao Jin , Shan Wei Song , Myszka David G. , Shapiro Lawrence
Published: July 2002

Dysfunction of the tubby protein results in maturity-onset obesity in mice. Tubby has been implicated as a transcription regulator, but details of the molecular mechanism underlying its function remain unclear. Here we show that tubby functions in signal transduction from heterotrimeric GTP-binding protein (G protein)–coupled receptors. Tubby localizes to the plasma membrane by binding phosphatidylinositol 4,5-bisphosphate through its carboxyl terminal “tubby domain.” X-ray crystallography reveals the atomic-level basis of this interaction and implicates tubby domains as phosphorylated-phosphatidyl- inositol binding factors. Receptor-mediated activation of G protein α
q
(Gα
q
) releases tubby from the plasma membrane through the action of phospholipase C–β, triggering translocation of tubby to the cell nucleus. The localization of tubby-like protein 3 (TULP3) is similarly regulated. These data suggest that tubby proteins function as membrane-bound transcription regulators that translocate to the nucleus in response to phosphoinositide hydrolysis, providing a direct link between G-protein signaling and the regulation of gene expression.
An Ultradense Polymorph of Rutile with Seven-Coordinated Titanium from the Ries Crater
Authors: Goresy Ahmed El , Chen Ming , Dubrovinsky Leonid , Gillet Philippe , Graup Günther
Published: July 2002

We report the discovery of an ultradense post-rutile polymorph of titanium dioxide in shocked gneisses of the Ries crater in Germany. The microscopic diagnostic feature is intense blue internal reflections in crossed polarizers in reflected light. X-ray diffraction studies revealed a monoclinic lattice, isostructural with the baddeleyite ZrO2polymorph, and the titanium cation is coordinated with seven oxygen anions. The cell parameters are as follows:a= 4.606(2) angstroms,b= 4.986(3) angstroms,c= 4.933(3) angstroms, β (angle betweencandaaxes) = 99.17(6)°; space groupP21/c; density = 4.72 grams per cubic centimeter, where the numbers in parentheses are standard deviations in the last significant digits. This phase is 11% denser than rutile. The mineral is sensitive to x-ray irradiation and tends to invert to rutile. The presence of baddeleyite-type TiO2in the shocked rocks indicates that the peak shock pressure was between 16 and 20 gigapascals, and the post-shock temperature was much lower than 500°C.
Duration of Nuclear NF-κB Action Regulated by Reversible Acetylation
Authors: Chen Lin-feng , Fischle Wolfgang , Verdin Eric , Greene Warner C.
Published: July 2002

The nuclear expression and action of the nuclear factor kappa B (NF-κB) transcription factor requires signal-coupled phosphorylation and degradation of the IκB inhibitors, which normally bind and sequester this pleiotropically active factor in the cytoplasm. The subsequent molecular events that regulate the termination of nuclear NF-κB action remain poorly defined, although the activation of de novo IκBα gene expression by NF-κB likely plays a key role. Our studies now demonstrate that the RelA subunit of NF-κB is subject to inducible acetylation and that acetylated forms of RelA interact weakly, if at all, with IκBα. Acetylated RelA is subsequently deacetylated through a specific interaction with histone deacetylase 3 (HDAC3). This deacetylation reaction promotes effective binding to IκBα and leads in turn to IκBα-dependent nuclear export of the complex through a chromosomal region maintenance-1 (CRM-1)–dependent pathway. Deacetylation of RelA by HDAC3 thus acts as an intranuclear molecular switch that both controls the duration of the NF-κB transcriptional response and contributes to the replenishment of the depleted cytoplasmic pool of latent NF-κB–IκBα complexes.
Patterns of Gene Expression During
Drosophila
Mesoderm Development
Authors: Furlong Eileen E. M. , Andersen Erik C. , Null Brian , White Kevin P. , Scott Matthew P.
Published: July 2002

The transcription factor Twist initiates
Drosophila
mesoderm development, resulting in the formation of heart, somatic muscle, and other cell types. Using a
Drosophila
embryo sorter, we isolated enough homozygous
twist
mutant embryos to perform DNA microarray experiments. Transcription profiles of
twist
loss-of-function embryos, embryos with ubiquitous
twist
expression, and wild-type embryos were compared at different developmental stages. The results implicate hundreds of genes, many with vertebrate homologs, in stage-specific processes in mesoderm development. One such gene,
gleeful
, related to the vertebrate
Gli
genes, is essential for somatic muscle development and sufficient to cause neural cells to express a muscle marker.
The Centromere Paradox: Stable Inheritance with Rapidly Evolving DNA
Authors: Henikoff Steven , Ahmad Kami , Malik Harmit S.
Published: July 2002

Every eukaryotic chromosome has a centromere, the locus responsible for poleward movement at mitosis and meiosis. Although conventional loci are specified by their DNA sequences, current evidence favors a chromatin-based inheritance mechanism for centromeres. The chromosome segregation machinery is highly conserved across all eukaryotes, but the DNA and protein components specific to centromeric chromatin are evolving rapidly. Incompatibilities between rapidly evolving centromeric components may be responsible for both the organization of centromeric regions and the reproductive isolation of emerging species.
Epigenetic Aspects of X-Chromosome Dosage Compensation
Authors: Park Yongkyu , Kuroda Mitzi I.
Published: July 2002

The X chromosomes of mammals and fruit flies exhibit unusual properties that have evolved to deal with the different dosages of X-linked genes in males (XY) and females (XX). The X chromosome dosage-compensation mechanisms discovered in these species are evolutionarily unrelated, but exhibit surprising parallels in their regulatory strategies. These features include the importance of noncoding RNAs, and epigenetic spreading of chromatin-modifying activities.

Sex chromosomes have posed a fascinating puzzle for biologists. The dissimilar organization, gene content, and regulation of the X and Y chromosomes are thought to reflect selective forces acting on original pairs of identical chromosomes (1–3). The result in many organisms is a male-specific Y chromosome that has lost most of its original genetic content, and a difference in dosage of the X chromosome in males (XY) and females (XX).
Prevention of Scrapie Pathogenesis by Transgenic Expression of Anti-Prion Protein Antibodies
Authors: Heppner Frank L. , Musahl Christine , Arrighi Isabelle , Klein Michael A. , Rülicke Thomas , Oesch Bruno , Zinkernagel Rolf M. , Kalinke Ulrich , Aguzzi Adriano
Published: July 2002

Variant Creutzfeldt-Jakob disease and bovine spongiform encephalopathy are initiated by extracerebral exposure to prions. Although prion transmission from extracerebral sites to the brain represents a potential target for prophylaxis, attempts at vaccination have been limited by the poor immunogenicity of prion proteins. To circumvent this, we expressed an anti-prion protein (anti-PrP) μ chain in
Prnp
o/o
mice. Transgenic mice developed sustained anti-PrP titers, which were not suppressed by introduction of
Prnp
+
alleles. Transgene expression prevented pathogenesis of prions introduced by intraperitoneal injection in the spleen and brain. Expression of endogenous PrP (PrP
C
) in the spleen and brain was unaffected, suggesting that immunity was responsible for protection. This indicates the feasibility of immunological inhibition of prion disease in vivo.
Antarctic Sea Ice--a Habitat for Extremophiles
Authors: Thomas D. N. , Dieckmann G. S.
Published: July 2002

The pack ice of Earth's polar oceans appears to be frozen white desert, devoid of life. However, beneath the snow lies a unique habitat for a group of bacteria and microscopic plants and animals that are encased in an ice matrix at low temperatures and light levels, with the only liquid being pockets of concentrated brines. Survival in these conditions requires a complex suite of physiological and metabolic adaptations, but sea-ice organisms thrive in the ice, and their prolific growth ensures they play a fundamental role in polar ecosystems. Apart from their ecological importance, the bacterial and algae species found in sea ice have become the focus for novel biotechnology, as well as being considered proxies for possible life forms on ice-covered extraterrestrial bodies.
Distributed and Overlapping Representations of Faces and Objects in Ventral Temporal Cortex
Authors: Haxby James V. , Gobbini M. Ida , Furey Maura L. , Ishai Alumit , Schouten Jennifer L. , Pietrini Pietro
Published: July 2002

The functional architecture of the object vision pathway in the human brain was investigated using functional magnetic resonance imaging to measure patterns of response in ventral temporal cortex while subjects viewed faces, cats, five categories of man-made objects, and nonsense pictures. A distinct pattern of response was found for each stimulus category. The distinctiveness of the response to a given category was not due simply to the regions that responded maximally to that category, because the category being viewed also could be identified on the basis of the pattern of response when those regions were excluded from the analysis. Patterns of response that discriminated among all categories were found even within cortical regions that responded maximally to only one category. These results indicate that the representations of faces and objects in ventral temporal cortex are widely distributed and overlapping.
Biodiversity and Ecosystem Functioning: Current Knowledge and Future Challenges
Authors: Loreau M. , Naeem S. , Inchausti P. , Bengtsson J. , Grime J. P. , Hector A. , Hooper D. U. , Huston M. A. , Raffaelli D. , Schmid B. , Tilman D. , Wardle D. A.
Published: July 2002

The ecological consequences of biodiversity loss have aroused considerable interest and controversy during the past decade. Major advances have been made in describing the relationship between species diversity and ecosystem processes, in identifying functionally important species, and in revealing underlying mechanisms. There is, however, uncertainty as to how results obtained in recent experiments scale up to landscape and regional levels and generalize across ecosystem types and processes. Larger numbers of species are probably needed to reduce temporal variability in ecosystem processes in changing environments. A major future challenge is to determine how biodiversity dynamics, ecosystem processes, and abiotic factors interact.
Ecological Meltdown in Predator-Free Forest Fragments
Authors: Terborgh John , Lopez Lawrence , Nuñez Percy , Rao Madhu , Shahabuddin Ghazala , Orihuela Gabriela , Riveros Mailen , Ascanio Rafael , Adler Greg H. , Lambert Thomas D. , Balbas Luis
Published: July 2002

The manner in which terrestrial ecosystems are regulated is controversial. The “top-down” school holds that predators limit herbivores and thereby prevent them from overexploiting vegetation. “Bottom-up” proponents stress the role of plant chemical defenses in limiting plant depredation by herbivores. A set of predator-free islands created by a hydroelectric impoundment in Venezuela allows a test of these competing world views. Limited area restricts the fauna of small (0.25 to 0.9 hectare) islands to predators of invertebrates (birds, lizards, anurans, and spiders), seed predators (rodents), and herbivores (howler monkeys, iguanas, and leaf-cutter ants). Predators of vertebrates are absent, and densities of rodents, howler monkeys, iguanas, and leaf-cutter ants are 10 to 100 times greater than on the nearby mainland, suggesting that predators normally limit their populations. The densities of seedlings and saplings of canopy trees are severely reduced on herbivore-affected islands, providing evidence of a trophic cascade unleashed in the absence of top-down regulation.
Regulation of Organogenesis by the
Caenorhabditis elegans
FoxA Protein PHA-4
Authors: Gaudet J. , Mango S. E.
Published: July 2002

The
pha
-
4
locus encodes a forkhead box A (FoxA/HNF3) transcription factor homolog that specifies organ identity for
Caenorhabditis elegans
pharyngeal cells. We used microarrays to identify pharyngeal genes and analyzed those genes to determine which were direct PHA-4 targets. Our data suggest that PHA-4 directly activates most or all pharyngeal genes. Furthermore, the relative affinity of PHA-4 for different TRTTKRY (R = A/G, K = T/G, Y = T/C) elements modulates the onset of gene expression, providing a mechanism to activate pharyngeal genes at different developmental stages. We suggest that direct transcriptional regulation of entire gene networks may be a common feature of organ identity genes.
Persistent Solar Influence on North Atlantic Climate During the Holocene
Authors: Bond Gerard , Kromer Bernd , Beer Juerg , Muscheler Raimund , Evans Michael N. , Showers William , Hoffmann Sharon , Lotti-Bond Rusty , Hajdas Irka , Bonani Georges
Published: July 2002

Surface winds and surface ocean hydrography in the subpolar North Atlantic appear to have been influenced by variations in solar output through the entire Holocene. The evidence comes from a close correlation between inferred changes in production rates of the cosmogenic nuclides carbon-14 and beryllium-10 and centennial to millennial time scale changes in proxies of drift ice measured in deep-sea sediment cores. A solar forcing mechanism therefore may underlie at least the Holocene segment of the North Atlantic's “1500-year” cycle. The surface hydrographic changes may have affected production of North Atlantic Deep Water, potentially providing an additional mechanism for amplifying the solar signals and transmitting them globally.