bluuebunny/crossref_metadata_2025 huggingface dataset:
In situ studies of the effect of various gaseous species and ultraviolet illumination on the dark currents of HgMnCdTe and HgCdTe short-wavelength infrared diodes
Authors: Cheung J. T. , Shin S. H. , Pasko J. G. , DeWames R. E.
Published: July 2002

This study deals with the effects of perturbing the surfaces of unpassivated HgMnCdTe and HgCdTe short-wavelength infrared photodiodes to further our understanding of these effects on dark currents. Perturbations include illuminating ultraviolet (UV) radiation in high vacuum and in various gaseous species. The change in dark current at 0.8 V reverse bias and its evolution with time was monitored in situ. By correlating the amount of excess dark current generated by UV radiation to the vacuum conditions, we conclude that it is a surface-related problem. A drastic improvement in device performance was found by illuminating its surface with UV radiation in high vacuum. This simple treatment prevents the generation of excess and persistent dark current and stabilizes the leakage current at low reverse bias. This can be understood in terms of photodesorption of surface contaminants which induce deep level surface states, giving rise to the persistent dark current generation. By studying the effects of various gaseous species, we identified water molecules as the key surface contaminants. We also discovered an anomalous degradation in HgCdTe diodes when they were exposed to hydrogen and UV radiation simultaneously. This anomalous degradation can be interpreted as UV-catalyzed chemical reduction of HgCdTe by hydrogen or the diffusion of hydrogen atoms into the bulk to change the junction characteristics.
Selective low pressure chemical vapor deposition of copper and platinum
Authors: Lecohier B. , Philippoz J.-M. , van den Bergh H.
Published: July 2002

The low pressure chemical vapor deposition of copper and platinum is studied on SiO2 substrates which have been locally prenucleated with ultrathin metal layers of Pt, Cu, Pd, Au, and W. These layers were between 0.1 and 30 Å thick and were produced by vacuum evaporation. Copper metal is deposited selectively on top of the prenucleation layers from the gaseous bis-hexafluoroacetylacetonate {Cu(hfa)2} diluted in hydrogen. High quality copper could be grown at temperatures in the range of 300–400 °C with electrical resistivities as low as 2.5 times the bulk copper value. In contrast, platinum deposited from gaseous Pt(hfa)2 in H2 grows selectively on the clean oxide surface rather than on the areas prenucleated with vacuum evaporated platinum.
Planarization of aluminum films by a technique with the combination of molecular beam deposition and annealing for ultralarge-scale integration metallization
Authors: Mukai R. , Ozawa S.
Published: July 2002

Planarization of aluminum films has been achieved by using the combination of molecular beam deposition (MBD) and annealing for ultralarge-scale integration metallization. The resulting via holes for multilevel interconnection in the metallization are found to be filled by a plug of aluminum. This MBD is an effective deposition method for producing a desired aluminum film; the aluminum is fully deposited on the sidewall and bottom of vias without an overhang occurring. This desired aluminum film is realized because the direction of incoming aluminum vapor is controlled. The direction control is performed with an angle definition and scattering prevention of the vapor. A mass transport of aluminum is created during this annealing procedure. This desired aluminum film is needed in order to perform the via filling and planarization because the mass transport is attributed to the surface tension forces generated by the three-dimensional geometry of the heated aluminum. The resulting condition includes an undesired void in via hole if the aluminum is not fully deposited on the sidewall and bottom of vias. This technique has been shown to allow excellent via filling with the annealing at low temperature (300 °C), and is applicable to filling submicrometer-diameter vias having a diameter of 0.58 μm with a 1.1-μm depth (aspect ratio ∼1.9). The resulting surface of aluminum films is planarized.
In situ sputter cleaning of vias using a getter electrode
Authors: Bauer H. J.
Published: July 2002

An aluminum electrode is rf powered before sputter cleaning of wafers to reduce the partial pressure water vapor in an evaporator. Prolonged sputter cleaning times are thereby avoided because regrowth of the aluminum oxide during sputter cleaning is practically nil. Wafers with temperature sensitive resists, for example, with a polyimide or photoresist lift off mask for fabrication of the conductor lines can be sputter cleaned and low via resistance obtained without mask damage. Histograms of the via resistance as a function of the sputter cleaning time in the range from 15 to 60 s are presented for the as-deposited and sintered metallization. The tooling and the process to obtain low via resistance are described. The author believes, that the principle method and electrode design may be useful for similar applications where a low partial pressure water vapor in a vacuum apparatus is required.
Scanning tunneling microscope observation on the surface of iron meteorite
Authors: Zhang L. P. , Hu J. , Xu L. , Yao X. W. , Zhang G. G. , Zhang Y. , Xu Y. L. , Li M. Q. , Li Z. H. , Xie X. D. , Xu Y. F. , Zhang D. T.
Published: July 2002

The surface of iron meteorite consisting of FeNi–FeS has been studied with scanning tunneling microscope. Fairly good topographic maps for a large area (−3 μm) are obtained showing strong ridge structures with 200–700 nm in spacing, 100–400 nm in valley depth. The top of the ridges has also been observed in more detail. Structures like parallel ridges, promontorylike with faceted surfaces can be seen clearly, which possess some characters as in process of crystallite growth pattern on the earth.
Structure of oxygen-doped silicon grown by chemical-vapor deposition at low temperature
Authors: Liliental-Weber Zuzanna , Schwartz P. V. , Wu C. C. , Sturm J. C.
Published: July 2002

The relation between the structural quality of Si:O layers grown by chemical-vapor deposition at low temperatures (700–750 °C) and electrical properties was determined. Transmission electron microscopy (TEM), secondary-ion-mass spectroscopy, and resistivity measurements were used for this study. An oxygen concentration in these layers was in the range of 6×10−19–6×10−20 cm−3. TEM studies have shown that amorphous SiOx precipitates were formed at the lower interface (between the Si buffer and Si:O layer) when silane was used for the layer growth. Slightly smaller precipitates were distributed through the entire layer. In the layers with higher oxygen concentration, high density of stacking faults originated at the same interface and propagated through the entire layer. The Si capping layer grown on top of Si:O was monocrystalline with the density of stacking faults two orders of magnitude lower than in the Si:O layer. For the lower oxygen concentration the stacking faults were not formed and the size of precipitates at the lower interface and in the layer was much smaller. The resistivity of ∼105 and ∼106 Ω cm was measured in the layers with lower and higher oxygen content, respectively. Only for the Si:O layers grown in the same range of temperatures (700 °C) using dichlorosilane oxygen induced stacking faults were formed at the upper interface (between Si:O and the capping layer). Some small precipitates were formed at the lower interface but no visible precipitates were present in the Si:O layer. These layers were not semi-insulating. It was concluded that the mechanism to explain semi-insulating properties might be related to the presence of the SiOx precipitates or structural defects present in these layers.
Real-time scanning microprobe reflection high-energy electron diffraction observations of InGaAs surfaces during molecular-beam epitaxy on InP substrates
Authors: Morishita Y. , Goto S. , Nomura Y. , Tamura M. , Isu T. , Katayama Y.
Published: July 2002

The microscopic surface features were observed during the molecular-beam epitaxy of InxGa1−xAs on InP (100) substrates by scanning microprobe reflection high-energy diffraction in real time as a function of x from 0.41 to 0.96. In the case of In0.41Ga0.59As (the lattice mismatch of the strained layer was f=−0.77%, where the minus sign represents a smaller lattice constant of an epitaxial layer than that of a substrate), three-dimensional island growth was observed from the start of growth. On the other hand, two-dimensional layer-by-layer growth was maintained during growth of InxGa1−xAs with x=0.45–0.75 (f=−0.47 to +1.48%, where the plus sign represents a larger lattice constant of an epilayer than that of a substrate). While the growth of compressive epilayers with f between +0.36% and +1.48% proceeded, a surface crosshatched morphology was observed after the growth of certain film thicknesses, which were dependent on the lattice mismatch. A rough textured morphology was observed instead of a crosshatched morphology for those epilayers with a lattice mismatch greater than +2.29% (In0.87Ga0.13As), where three-dimensional island growth was favored over the layer-by-layer growth mode. Transmission electron microscope observations showed that the presence of a surface crosshatched pattern was correlated with the presence of 60° mixed misfit dislocations. The result indicates that the thickness at which the crosshatched line appears represents the critical layer thickness corresponding to misfit dislocation generation.
Fringe stabilization and depth monitoring during the holographic photoelectrochemical etching of n-InP (100) substrates
Authors: Soltz David , De Paoli Marco-A. , Cescato Lucila
Published: July 2002

The holographic photoelectrochemical etching of n-InP (100) samples in aqueous 1 M HCl was monitored optically using the synchronous detection of two wave mixing from the interfering beams. This signal was employed to operate a negative feedback system which stabilizes the projected interference pattern. The use of the stabilization system permits the recording of high spatial frequency gratings (<0.5 μm), though their depth is limited to the value at which the self-diffracted signal passes through zero. It was shown that in the range where scalar theory may be applied, optical monitoring can be used to determine the absolute depth and the rate of relief development. Using this method the influence of sample orientation on the etching rate was studied, and some aspects of the etching process are discussed.
X-ray lithography: Status, challenges, and outlook for 0.13 μm
Authors: Silverman Jerome P.
Published: July 2002

X-ray lithography (XRL) has been under development since the early 1980s, and has reached a state of relative maturity. Numerous devices, including dense and complex integrated circuits, have been fabricated using XRL for one or more critical levels. While development of XRL technology itself continues, XRL is in use in several locations around the world for process development of advanced DRAM (1 Gb and beyond) and logic (0.18 μm and below) integrated circuits. Most of the tool set in use today comes from commercial vendors. Resolution using XRL has been demonstrated at dimensions down to 70 nm or below. Excellent critical dimension (CD) control results have been achieved in simple, single-layer, commercially available resists; for example, a total CD variation of 22 nm (3σ) has been achieved using a mask with a CD variation of 18 nm (3σ). Because of these capabilities, along with the experience and relative maturity of the technology, we believe that XRL is the technology best positioned to succeed optical lithography and be available for timely insertion into manufacturing for 0.13 μm ground rules, as well as to be extendible to 0.10 μm and below. In order to be accepted for manufacturing, however, significant work remains to be done. In particular, new e-beam mask writers and wafer aligners are needed, along with improved mask inspection and repair tools. Mask fabrication processes must also be advanced. The ability to satisfy these needs is not expected to be limited by fundamental physics, but rather is expected to depend on skilled engineering design and implementation.
A review of ion projection lithography
Authors: Melngailis J. , Mondelli A. A. , Berry Ivan L. , Mohondro R.
Published: July 2002

Although optical lithography has been extended to far smaller dimensions than was predicted 15 years ago, there are definite physical barriers to extending it to the minimum dimensions of 70 nm that are projected to be required 15 years from now. Both focused, point electron beams and ion beams have been used to write dimensions in resist well below 20 nm, albeit at speeds far too slow for production lithography. Projection systems, which employ a mask and, in effect, produce a large array of beams, can provide both small minimum dimensions and high throughput. Ions are particularly well suited for this because they suffer little or no scattering in the resist, the linewidth is not a strong function of dose (good process latitude), and the resist sensitivity is relatively independent to resist thickness or ion energy. IMS in Vienna, Austria has built two generations of ion projection lithography systems which have demonstrated many of the features needed for high throughput lithography. In these systems a stencil mask is irradiated with a uniform beam of light ions, H+, H2+, or He+, and the transmitted pattern is demagnified (by 10× to 3×) and focused on a resist covered wafer at energies in the 70–150 keV range. So far, minimum dimensions down to 70 nm line-space pairs have been demonstrated, drift has been eliminated with a “pattern lock” servo system, and field distortion of less than 0.15 μm over 8×8 mm has been measured in agreement with calculations. Based on these achievements a new generation ion lithography machine has been designed which uses 3× demagnification and will expose a 20×20 mm field at 0.12 μm minimum dimensions with less than 10 nm of distortion introduced by the ion optics. Global and stochastic space charge effects have been modeled and, in some cases, measured with the existing machines. Stochastic space charge effects will not cause unacceptable blur in the new design if the total ion current is kept below 3 μA. At this total current the time to expose one chip is still of order 0.5 s so that the calculated throughput is about 70 wafers (200 mm) per hour. Ion sources with low energy spread (∼2 eV) have been developed and will provide uniform illumination of the mask. Stencil mask fabrication on membranes of 2.5-μm-thick silicon has been developed. Distortion of the pattern cut in the membrane due to stress relief has been modeled, and with proper mask design can be kept below 20 nm (6.7 nm on the wafer). According to calculations and measurements mask distortion due to ion beam heating can be reduced to a negligible level if a radiation cooling cylinder is used. As a result of the building and evaluation of the existing machines and the design of the next generation, significant progress has been made in ion projection lithography which we will review in this article. The next step in the development of ion projection lithography is being conducted by the MEDEA program in Europe, which will develop a full field processing tool.
Liquid Crystal Alignment on Carbonaceous Surfaces with Orientational Order
Authors: Stöhr J. , Samant M. G. , Lüning J. , Callegari A. C. , Chaudhari P. , Doyle J. P. , Lacey J. A. , Lien S. A. , Purushothaman S. , Speidell J. L.
Published: July 2002

We used near-edge x-ray absorption fine structure (NEXAFS) spectroscopy to link the orientational bond order at three carbonaceous surfaces—rubbed polyimide, ion beam–irradiated polyimide, and ion beam–irradiated diamondlike carbon films—with the direction of liquid crystal (LC) alignment on these surfaces. We show that, in general, LC alignment can be created on any carbonaceous substrate by inducing orientational order at its surface. Our results form the scientific basis for LC alignment layers consisting of amorphous carbon films in which orientational order near the surface is induced by a directional low-energy ion beam.
Carboxyl-Terminal Modulator Protein (CTMP), a Negative Regulator of PKB/Akt and v-Akt at the Plasma Membrane
Authors: Maira Sauveur-Michel , Galetic Ivana , Brazil Derek P. , Kaech Stefanie , Ingley Evan , Thelen Marcus , Hemmings Brian A.
Published: July 2002

The PKB (protein kinase B, also called Akt) family of protein kinases plays a key role in insulin signaling, cellular survival, and transformation. PKB is activated by phosphorylation on residues threonine 308, by the protein kinase PDK1, and Serine 473, by a putative serine 473 kinase. Several protein binding partners for PKB have been identified. Here, we describe a protein partner for PKBα termed CTMP, or carboxyl-terminal modulator protein, that binds specifically to the carboxyl-terminal regulatory domain of PKBα at the plasma membrane. Binding of CTMP reduces the activity of PKBα by inhibiting phosphorylation on serine 473 and threonine 308. Moreover, CTMP expression reverts the phenotype of v-
Akt
–transformed cells examined under a number of criteria including cell morphology, growth rate, and in vivo tumorigenesis. These findings identify CTMP as a negative regulatory component of the pathway controlling PKB activity.
Lattice Effects Observed in Chaotic Dynamics of Experimental Populations
Authors: Henson Shandelle M. , Costantino R. F. , Cushing J. M. , Desharnais Robert A. , Dennis Brian , King Aaron A.
Published: July 2002

Animals and many plants are counted in discrete units. The collection of possible values (state space) of population numbers is thus a nonnegative integer lattice. Despite this fact, many mathematical population models assume a continuum of system states. The complex dynamics, such as chaos, often displayed by such continuous-state models have stimulated much ecological research; yet discrete-state models with bounded population size can display only cyclic behavior. Motivated by data from a population experiment, we compared the predictions of discrete-state and continuous-state population models. Neither the discrete- nor continuous-state models completely account for the data. Rather, the observed dynamics are explained by a stochastic blending of the chaotic dynamics predicted by the continuous-state model and the cyclic dynamics predicted by the discrete-state models. We suggest that such lattice effects could be an important component of natural population fluctuations.
Predictability of North Atlantic Multidecadal Climate Variability
Authors: Griffies Stephen M. , Bryan Kirk
Published: July 2002

Atmospheric weather systems become unpredictable beyond a few weeks, but climate variations can be predictable over much longer periods because of the coupling of the ocean and atmosphere. With the use of a global coupled ocean-atmosphere model, it is shown that the North Atlantic may have climatic predictability on the order of a decade or longer. These results suggest that variations of the dominant multidecadal sea surface temperature patterns in the North Atlantic, which have been associated with changes in climate over Eurasia, can be predicted if an adequate and sustainable system for monitoring the Atlantic Ocean exists.
Manganese Oxide Mesoporous Structures: Mixed-Valent Semiconducting Catalysts
Authors: Tian Zheng-Rong , Tong Wei , Wang Jin-Yun , Duan Nian-Gao , Krishnan Venkatesan V. , Suib Steven L.
Published: July 2002

Hexagonal and cubic phases of manganese oxide mesoporous structures (MOMS) have been prepared by means of the oxidation of Mn(OH)
2
. The hexagonal MOMS materials form a hexagonal array of pores with an open porous structure, thick walls (1.7 nanometers), and exceptional thermal stability (1000°C). The walls of the mesopores are composed of microcrystallites of dense phases of Mn
2
O
3
and Mn
3
O
4
, with MnO
6
octahedra as the primary building blocks. The calcined hexagonal MOMS have an electrical conductivity of 8.13 × 10
−6
per ohm·centimeter, an average manganese oxidation state of 3.55, and a band gap of 2.46 electron volts. Catalytic oxidations of cyclohexane and
n
-hexane in aqueous solutions in a batch reactor show conversions of ∼10 and ∼8 percent, respectively. Characterization and catalytic data suggest that MOMS systems show significant enhancement in thermal stability with respect to octahedral molecular sieve materials.
Angiogenic and HIV-Inhibitory Functions of KSHV-Encoded Chemokines
Authors: Boshoff Chris , Endo Yoshio , Collins Paul D. , Takeuchi Yasuhiro , Reeves Jacqueline D. , Schweickart Vicki L. , Siani Michael A. , Sasaki Takuma , Williams Timothy J. , Gray Patrick W. , Moore Patrick S. , Chang Yuan , Weiss Robin A.
Published: July 2002

Unique among known human herpesviruses, Kaposi's sarcoma–associated herpesvirus (KSHV or HHV-8) encodes chemokine-like proteins (vMIP-I and vMIP-II). vMIP-II was shown to block infection of human immunodeficiency virus–type 1 (HIV-1) on a CD4-positive cell line expressing CCR3 and to a lesser extent on one expressing CCR5, whereas both vMIP-I and vMIP-II partially inhibited HIV infection of peripheral blood mononuclear cells. Like eotaxin, vMIP-II activated and chemoattracted human eosinophils by way of CCR3. vMIP-I and vMIP-II, but not cellular MIP-1α or RANTES, were highly angiogenic in the chorioallantoic assay, suggesting a possible pathogenic role in Kaposi's sarcoma.
From Shifting Silt to Solid Stone: The Manufacture of Synthetic Basalt in Ancient Mesopotamia
Authors: Stone E. C. , Lindsley D. H. , Pigott V. , Harbottle G. , Ford M. T.
Published: July 2002

Slabs and fragments of gray-black vesicular “rock,” superficially resembling natural basalt but distinctive in chemistry and mineralogy, were excavated at the second-millennium B.C. Mesopotamian city of Mashkan-shapir, about 80 kilometers south of Baghdad, Iraq. Most of this material appears to have been deliberately manufactured by the melting and slow cooling of local alluvial silts. The high temperatures (about 1200°C) required and the large volume of material processed indicate an industry in which lithic materials were manufactured (“synthetic basalt”) for grinding grain and construction.
Aminoacyl-CoAs as Probes of Condensation Domain Selectivity in Nonribosomal Peptide Synthesis
Authors: Belshaw Peter J. , Walsh Christopher T. , Stachelhaus Torsten
Published: July 2002

In nonribosomal biosynthesis of peptide antibiotics by multimodular synthetases, amino acid monomers are activated by the adenylation domains of the synthetase and loaded onto the adjacent carrier protein domains as thioesters, then the formation of peptide bonds and translocation of the growing chain are effected by the synthetase's condensation domains. Whether the condensation domains have any editing function has been unknown. Synthesis of aminoacyl–coenzyme A (CoA) molecules and direct enzymatic transfer of aminoacyl-phosphopantetheine to the carrier domains allow the adenylation domain editing function to be bypassed. This method was used to demonstrate that the first condensation domain of tyrocidine synthetase shows low selectivity at the donor residue (
d
-phenylalanine) and higher selectivity at the acceptor residue (
l
-proline) in the formation of the chain-initiating
d
-Phe-
l
-Pro dipeptidyl-enzyme intermediate.
Field-Effect Flow Control for Microfabricated Fluidic Networks
Authors: Schasfoort Richard B. M. , Schlautmann Stefan , Hendrikse Jan , van den Berg Albert
Published: July 2002

The magnitude and direction of the electro-osmotic flow (EOF) inside a microfabricated fluid channel can be controlled by a perpendicular electric field of 1.5 megavolts per centimeter generated by a voltage of only 50 volts. A microdevice called a “flowFET,” with functionality comparable to that of a field-effect transistor (FET) in microelectronics, has been realized. Two flowFETs integrated with a channel junction have been used to generate opposite flows inside a single EOF-pumped channel, thus illustrating the potential of the flowFET as a controlling and switching element in microfluidic networks.
Translation of the Edited mRNA for Cytochrome b in Trypanosome Mitochondria
Authors: Horváth Anton , Berry Edward A. , Maslov Dmitri A.
Published: July 2002

The type of RNA editing found in the kinetoplast-mitochondria of trypanosomes and related protozoa, involving uridylate insertions and deletions, creates translatable messenger RNAs (mRNAs) out of nonsense pre-edited RNAs by correcting encoded defects that vary from simple frameshifts to large “cryptic” regions. However, any evidence for translation of these mRNAs in the kinetoplast has been missing for decades. We identified a kinetoplast-encoded protein, apocytochrome b, whose mRNA is edited in the 5′ region. The determined amino-terminal sequence of the protein coincides with the predicted sequence derived from the edited region, demonstrating that the cognate apocytochrome b mRNA is translated into a functional protein. This finding represents the first direct evidence for a functional translation system in the kinetoplasts.
IB-367, a Protegrin Peptide with In Vitro and In Vivo Activities against the Microflora Associated with Oral Mucositis
Authors: Mosca Deborah A. , Hurst Malinda A. , So Wendy , Viajar Beverly S. C. , Fujii Craig A. , Falla Timothy J.
Published: July 2002

Although the microflora associated with oral mucositis initiated by cytotoxic therapy is not well characterized, several studies suggest that reduction of the microbial load in the oral cavity has some clinical benefit. The MICs of IB-367, a synthetic protegrin analog, ranged from 0.13 to 64 μg/ml for gram-positive bacteria (
Streptococcus mitis
,
Streptococcus sanguis
,
Streptococcus salivarius
, and
Staphylococcus aureus
) and from 0.06 to 8 μg/ml for gram-negative species (
Klebsiella
,
Escherichia
, and
Pseudomonas
). IB-367 exhibited rapid, microbicidal activity against both log- and stationary-phase cultures of methicillin-resistant
Staphylococcus aureus
(MRSA) and
Pseudomonas aeruginosa
. At concentrations near the MICs for these two organisms (4 and 2 μg/ml, respectively), IB-367 reduced viability by more than 3 logs in less than 16 min. Similarly, IB-367 effected a 4-log reduction of the endogenous microflora in pooled human saliva within 2 min at 250 μg/ml, a concentration readily attained by local delivery. After nine serial transfers at 0.5× the MIC, the MIC of IB-367 for MRSA and
P. aeruginosa
increased only two to four times. In a phase I clinical study with healthy volunteers, IB-367 was well tolerated, with no detectable systemic absorption. One hour after treatment with 9 mg of IB-367, the prevalence of gram-negative bacteria and yeast was reduced, and the density of the predominant gram-positive oral flora was decreased 1,000 times. IB-367's properties (speed of killing, breadth of spectrum, and lack of resistance) make the compound a strong candidate for the prophylaxis of oral mucositis. Phase II clinical trials with IB-367 are under way for this indication in immunocompromised subjects.
Activities of Several Antimicrobials against
Mycobacterium ulcerans
Infection in Mice
Authors: Dega Herve , Robert Jerome , Bonnafous Pascale , Jarlier Vincent , Grosset Jacques
Published: July 2002

Mycobacterium ulcerans
inoculated into the footpads of mice at 6 × 10
3
CFU was shown to have a generation time of 6.5 days when estimated from weekly changes in microscopic counts of acid-fast bacilli (AFB) and 7.5 days when calculated from actual CFU enumerated on Lowenstein-Jensen egg medium incubated at 32°C. Footpads became swollen at week 10 (W10) after infection, and all infected control mice were dead at W15 after infection. Daily (5 days/week) treatment with 100 mg of clarithromycin (CLR)/kg of body weight beginning the day after infection prevented swelling of footpads at W10. When initiation of treatment was delayed until obvious footpad swelling was observed, there was a reduction in both the increase in AFB counts and deterioration of swollen footpads and also a prolonged survival of the mice to W18. Mice infected in the hind footpads with 5 × 10
5
CFU of
M. ulcerans
were divided into an untreated control group and six treatment groups that received one of the following therapies for 8 weeks: 100 mg of CLR/kg, 25 mg of minocycline (MIN)/kg, 50 mg of sparfloxacin (SPX)/kg, 10 mg of rifampin (RIF)/kg, 10 mg of rifabutin (RBT)/kg, or 100 mg of amikacin (AMK)/kg. After completion of therapy, treated animals were observed for an additional 17 weeks. All control mice and mice treated with CLR, MIN, or SPX exhibited swollen footpads during the observation period. In contrast, of those animals treated with RIF, RBT, or AMK, none had footpad swelling and all inoculated cultures done after the W17 observation remained negative. These results suggest that RIF, RBT, and AMK may be effective in the treatment of human infection with
M. ulcerans
.
Characterization of a Genetic Element Carrying the Macrolide Efflux Gene
mef
(A) in
Streptococcus pneumoniae
Authors: Santagati Maria , Iannelli Francesco , Oggioni Marco R. , Stefani Stefania , Pozzi Gianni
Published: July 2002

The
mef
(A) gene from a clinical isolate of
Streptococcus pneumoniae
exhibiting the M-type resistance to macrolides was found to be part of the 7,244-bp chromosomal element Tn
1207.1
, which contained 8 open reading frames.
orf2
encodes a resolvase/invertase, and
orf5
is a homolog of the macrolide-streptogramin B resistance gene
msr
(SA).
Correlation of In Vitro Susceptibilities to Newer Quinolones of Naturally Occurring Quinolone-Resistant
Neisseria gonorrhoeae
Strains with Changes in GyrA and ParC
Authors: Shultz Tiffany R. , Tapsall John W. , White Peter A.
Published: July 2002

The in vitro activities of ciprofloxacin, trovafloxacin, moxifloxacin, and grepafloxacin against 174 strains of
Neisseria gonorrhoeae
isolated in Sydney, Australia, were determined. The strains included 84 quinolone-less-sensitive and -resistant
N. gonorrhoeae
(QRNG) strains for which ciprofloxacin MICs were in the range of 0.12 to 16 μg/ml. The QRNG included strains isolated from patients whose infections were acquired in a number of countries, mostly in Southeast Asia. The
gyrA
and
parC
quinolone resistance-determining regions (QRDR) of 18 selected QRNG strains were sequenced, and the amino acid mutations observed were related to the MICs obtained. The activities of moxifloxacin and grepafloxacin against QRNG were comparable to that of ciprofloxacin. Trovafloxacin was more active than the other quinolones against some but not all of the QRNG strains. Increments in ciprofloxacin resistance occurred in a step-wise manner with point mutations initiated in
gyrA
resulting in amino acid alterations Ser91-to-Phe, Ser91-to-Tyr, Asp95-to-Gly, and Asp95-to-Asn. Single
gyrA
changes correlated with ciprofloxacin MICs in the range 0.12 to 1 μg/ml. The Ser91 changes in GyrA were associated with higher MICs and further QRDR changes. QRNG strains for which ciprofloxacin MICs were greater than 1 μg/ml had both
gyrA
and
parC
QRDR point mutations. ParC alterations were seen in these isolates only in the presence of GyrA changes and comprised amino acid changes Asp86-to-Asn, Ser87-to-Asn, Ser87-to-Arg, Ser88-to-Pro, Glu91-to-Lys, and Glu91-to-Gln. QRNG strains for which MICs were in the higher ranges had double GyrA mutations, but again only with accompanying ParC alterations. Not only did the nature and combination of GyrA and ParC changes influence the incremental increases in ciprofloxacin MICs, but they seemingly also altered the differential activity of trovafloxacin. Our findings suggest that the newer quinolones of the type examined are unlikely to be useful replacements for ciprofloxacin in the treatment of gonorrhea, particularly where ciprofloxacin MICs are high or where resistance is widespread.
Peptide Deformylase as an Antibacterial Drug Target: Target Validation and Resistance Development
Authors: Apfel Christian M. , Locher Hans , Evers Stefan , Takács Béla , Hubschwerlen Christian , Pirson Wolfgang , Page Malcolm G. P. , Keck Wolfgang
Published: July 2002

New inhibitors of peptide deformylase (PDF) which are very potent against the isolated enzyme and show a certain degree of antibacterial activity have recently been synthesized by our group. Several lines of experimental evidence indicate that these inhibitors indeed interfere with the target enzyme in the bacterial cell. (i) The inhibition of
Escherichia coli
growth could be counteracted by overexpression of PDF from different organisms, including
E. coli, Streptococcus pneumoniae
, and
Haemophilus influenzae
. Conversely, reduced expression of PDF in
S. pneumoniae
resulted in an increased susceptibility to the inhibitors. (ii) Proteome analysis on two-dimensional gels revealed a shift for many proteins towards lower pI in the presence of PDF inhibitors, as would be expected if the proteins still carry their
N
-formyl-Met terminus. (iii) PDF inhibitors show no antimicrobial activity against
E. coli
under conditions that make growth independent of formylation and deformylation. The antibacterial activity in
E. coli
was characterized as bacteriostatic. Furthermore, the development of resistance in
E. coli
was observed to occur with high frequency (10
−7
). Resistant mutants show a reduced growth rate, and DNA sequence analysis revealed mutations in their formyl transferase gene. Taking all these aspects into account, we conclude that PDF may not be an optimal target for broad-spectrum antibacterial agents.
First Description of
Klebsiella pneumoniae
Harboring CTX-M β-Lactamases (CTX-M-14 and CTX-M-3) in Taiwan
Authors: Yu Wen Liang , Winokur Patricia L. , Von Stein Diana L. , Pfaller Michael A. , Wang Jen Hsien , Jones Ronald N.
Published: July 2002

Klebsiella pneumoniae
isolates from Taiwan medical centers (50 strains; 1998 to 2000) with a CTX-M resistance phenotype (ceftazidime susceptible and ceftriaxone or cefotaxime nonsusceptible) were selected for initial isoelectric focusing analysis. β-Lactamases with pIs of 7.9 (
n
= 22) and 8.4 (
n
= 28) in addition to 5.4 and/or 7.6 were detected. DNA gene sequencing identified the β-lactamases with pIs of 7.9 and 8.4 as CTX-M-14 and CTX-M-3, respectively. Molecular typing suggested inter- and intrahospital clonal dissemination of these Taiwanese CTX-M-producing
Klebsiella
strains.
Streptococcus thermophilus
Cell Wall-Anchored Proteinase: Release, Purification, and Biochemical and Genetic Characterization
Authors: Fernandez-Espla María Dolores , Garault Peggy , Monnet Véronique , Rul Françoise
Published: July 2002

Streptococcus thermophilus
CNRZ 385 expresses a cell envelope proteinase (PrtS), which is characterized in the present work, both at the biochemical and genetic levels. Since PrtS is resistant to most classical methods of extraction from the cell envelopes, we developed a three-step process based on loosening of the cell wall by cultivation of the cells in the presence of glycine (20 mM), mechanical disruption (with alumina powder), and enzymatic treatment (lysozyme). The pure enzyme is a serine proteinase highly activated by Ca
2+
ions. Its activity was optimal at 37°C and pH 7.5 with acetyl-Ala-Ala-Pro-Phe-paranitroanilide as substrate. The study of the hydrolysis of the chromogenic and casein substrates indicated that PrtS presented an intermediate specificity between the most divergent types of cell envelope proteinases from lactococci, known as the PI and PIII types. This result was confirmed by the sequence determination of the regions involved in substrate specificity, which were a mix between those of PI and PIII types, and also had unique residues. Sequence analysis of the PrtS encoding gene revealed that PrtS is a member of the subtilase family. It is a multidomain protein which is maturated and tightly anchored to the cell wall via a mechanism involving an LPXTG motif. PrtS bears similarities to cell envelope proteinases from pyogenic streptococci (C5a peptidase and cell surface proteinase) and lactic acid bacteria (PrtP, PrtH, and PrtB). The highest homologies were found with streptococcal proteinases which lack, as PrtS, one domain (the B domain) present in cell envelope proteinases from all other lactic acid bacteria.
Detection of Human and Animal Rotavirus Sequences in Drinking Water
Authors: Gratacap-Cavallier B. , Genoulaz O. , Brengel-Pesce K. , Soule H. , Innocenti-Francillard P. , Bost M. , Gofti L. , Zmirou D. , Seigneurin J. M.
Published: July 2002

Reverse transcription-PCR analysis of drinking water in the homes of 56 children suffering from rotaviral gastroenteritis has shown the presence of the rotavirus genome in four samples. These strains were different from human rotaviruses detected in the children's feces, as determined by sequencing of the VP7-amplified fragments—three of them of animal origin (porcine or bovine) and one of human origin.
Lovastatin Biosynthesis by
Aspergillus terreus
in a Chemically Defined Medium
Authors: Hajjaj Hassan , Niederberger Peter , Duboc Philippe
Published: July 2002

Lovastatin is a secondary metabolite produced by
Aspergillus terreus
. A chemically defined medium was developed in order to investigate the influence of carbon and nitrogen sources on lovastatin biosynthesis. Among several organic and inorganic defined nitrogen sources metabolized by
A. terreus
, glutamate and histidine gave the highest lovastatin biosynthesis level. For cultures on glucose and glutamate, lovastatin synthesis initiated when glucose consumption levelled off. When
A. terreus
was grown on lactose, lovastatin production initiated in the presence of residual lactose. Experimental results showed that carbon source starvation is required in addition to relief of glucose repression, while glutamate did not repress biosynthesis. A threefold-higher specific productivity was found with the defined medium on glucose and glutamate, compared to growth on complex medium with glucose, peptonized milk, and yeast extract.
Expression of the p20 Gene from
Bacillus thuringiensis
H-14 Increases Cry11A Toxin Production and Enhances Mosquito-Larvicidal Activity in Recombinant Gram-Negative Bacteria
Authors: Xu Y. , Nagai M. , Bagdasarian M. , Smith T. W. , Walker E. D.
Published: July 2002

Experimental analyses with recombinant
Escherichia coli
and
Pseudomonas putida
transformed with plasmids bearing genes coding for the Cry11A toxin and P20 protein from
Bacillus thuringiensis
H-14 showed that cells producing both proteins were more toxic when fed to third-instar
Aedes aegypti
larvae than were cells expressing
cry11A
alone; the 50% lethal concentrations were in the range of 10
4
to 10
5
cells/ml. Western blots revealed a higher production of Cry11A when the
p20
gene was coexpressed. Cry11A was detected primarily in insoluble form in recombinant cells. Cry11A was not detected in
P. putida
when P20 was not coproduced, and these recombinants were not toxic to larvae, whereas
P. putida
recombinants producing both proteins were toxic at concentrations similar to those for
E. coli
. A coelution experiment was conducted, in which a
p20
gene construct producing the P20 protein with an extension of six histidines on the C terminus was mixed with the Cry11A protein. The results showed that Cry11A bound to the P20(His
6
) on a nickel chelating column, whereas Cry11A produced without the P20(His
6
) protein was washed through the column, thus indicating that Cry11A and P20 physically interact. Thus, P20 protein either stabilizes Cry11A or helps it attain the folding important for its toxic activity.
Extracellular Polysaccharides of
Rhodococcus rhodochrous
S-2 Stimulate the Degradation of Aromatic Components in Crude Oil by Indigenous Marine Bacteria
Authors: Iwabuchi Noriyuki , Sunairi Michio , Urai Makoto , Itoh Chiaki , Anzai Hiroshi , Nakajima Mutsuyasu , Harayama Shigeaki
Published: July 2002

Rhodococcus rhodochrous
S-2 produces extracellular polysaccharides (S-2 EPS) containing
d
-glucose,
d
-galactose,
d
-mannose,
d
-glucuronic acid, and lipids, which is important to the tolerance of this strain to an aromatic fraction of (AF) Arabian light crude oil (N. Iwabuchi, N. Sunairi, H. Anzai, M. Nakajima, and S. Harayama, Appl. Environ. Microbiol. 66:5073-5077, 2000). In the present study, we examined the effects of S-2 EPS on the growth of indigenous marine bacteria on AF. Indigenous bacteria did not grow significantly in seawater containing AF even when nitrogen, phosphorus, and iron nutrients were supplemented. The addition of S-2 EPS to seawater containing nutrients and AF resulted in the emulsification of AF, promotion of the growth of indigenous bacteria, and enhancement of the degradation of AF by the bacteria. PCR-denaturing gradient gel electrophoresis analyses show that addition of S-2 EPS to the seawater containing nutrients and AF changed the composition of the bacterial populations in the seawater and that bacteria closely related to the genus
Cycloclasticus
became the major population. These results suggest that
Cycloclasticus
was responsible for the degradation of hydrocarbons in AF. The effects of 15 synthetic surfactants on the degradation of AF by indigenous marine bacteria were also examined, but enhancement of the degradation of AF was not significant. S-2 EPS was hence the most effective of the surfactants tested in promoting the biodegradation of AF and may thus be an attractive agent to use in the bioremediation of oil-contaminated marine environments.
Identification, Detection, and Enumeration of Human
Bifidobacterium
Species by PCR Targeting the Transaldolase Gene
Authors: Requena Teresa , Burton Jeremy , Matsuki Takahiro , Munro Karen , Simon Mary Alice , Tanaka Ryuichiro , Watanabe Koichi , Tannock Gerald W.
Published: July 2002

Methods that enabled the identification, detection, and enumeration of
Bifidobacterium
species by PCR targeting the transaldolase gene were tested. Bifidobacterial species isolated from the feces of human adults and babies were identified by PCR amplification of a 301-bp transaldolase gene sequence and comparison of the relative migrations of the DNA fragments in denaturing gradient gel electrophoresis (DGGE). Two subtypes of
Bifidobacterium longum
, five subtypes of
Bifidobacterium adolescentis
, and two subtypes of
Bifidobacterium pseudocatenulatum
could be differentiated using PCR-DGGE.
Bifidobacterium angulatum
and
B. catenulatum
type cultures could not be differentiated from each other. Bifidobacterial species were also detected directly in fecal samples by this combination of PCR and DGGE. The number of species detected was less than that detected by PCR using species-specific primers targeting 16S ribosomal DNA (rDNA). Real-time quantitative PCR targeting a 110-bp transaldolase gene sequence was used to enumerate bifidobacteria in fecal samples. Real-time quantitative PCR measurements of bifidobacteria in fecal samples from adults correlated well with results obtained by culture when either a 16S rDNA sequence or the transaldolase gene sequence was targeted. In the case of samples from infants, 16S rDNA-targeted PCR was superior to PCR targeting the transaldolase gene for the quantification of bifidobacterial populations.
Multisite Comparison of CD4 and CD8 T-Lymphocyte Counting by Single- versus Multiple-Platform Methodologies: Evaluation of Beckman Coulter Flow-Count Fluorospheres and the tetraONE System
Authors: Reimann Keith A. , O'Gorman Maurice R. G. , Spritzler John , Wilkening Cynthia L. , Sabath Daniel E. , Helm Karen , Campbell Donald E. ,   The NIAID DAIDS New Technologies Evaluation Group
Published: July 2002

New analytic methods that permit absolute CD4 and CD8 T-cell determinations to be performed entirely on the flow cytometer have the potential for improving assay precision and accuracy. In a multisite trial, we compared two different single-platform assay methods with a predicate two-color assay in which the absolute lymphocyte count was derived by conventional hematology. A two-color method employing lymphocyte light scatter gating and Beckman Coulter Flow-Count fluorospheres for absolute counting produced within-laboratory precision equivalent to that of the two-color predicate method, as measured by coefficient of variation of replicate measurements. The fully automated Beckman Coulter tetraONE System four-color assay employing CD45 lymphocyte gating, automated analysis, and absolute counting by fluorospheres resulted in a small but significant improvement in the within-laboratory precision of CD4 and CD8 cell counts and percentages suggesting that the CD45 lymphocyte gating and automated analysis might have contributed to the improved performance. Both the two-color method employing Flow-Count fluorospheres and the four-color tetraONE System provided significant and substantial improvements in between-laboratory precision of absolute counts. In some laboratories, absolute counts obtained by the single-platform methods showed small but consistent differences relative to the predicate method. Comparison of each laboratory's absolute counts with the five-laboratory median value suggested that these differences resulted from a bias in the absolute lymphocyte count obtained from the hematology instrument in some laboratories. These results demonstrate the potential for single-platform assay methods to improve within-laboratory and between-laboratory precision of CD4 and CD8 T-cell determinations compared with conventional assay methods.
Evaluation of a Capture Screening Enzyme-Linked Immunosorbent Assay for Combined Determination of Immunoglobulin M and G Antibodies Produced during Dengue Infection
Authors: Kit Lam Sai , Lan Ew Cheng , Mitchell Jody L. , Cuzzubbo Andrea J. , Devine Peter L.
Published: July 2002

A commercially available enzyme-linked immunosorbent assay (ELISA) (PanBio Dengue Screening ELISA) that utilized both immunoglobulin M (IgM) and IgG capture in the same microtiter well for the diagnosis of dengue infection was evaluated. Sensitivity in primary and secondary dengue was 95%, while specificity was 94%.
Modified Immunogenicity of a Mucosally Administered Antigen
Authors: Gregory Richard L.
Published: July 2002

Streptococcus mutansis present in the saliva of most individuals and is modified by salivary components bound to the cells. These saliva-boundS. mutansare swallowed, exposed to high levels of acidity in the stomach, and presented to the common mucosal immune system. Much effort has been directed to identifying the specificS. mutansantigens that the mucosal immune responses are directed against. However, little is known about the host-altered antigenic determinants that the mucosal immune system recognizes. The immunogenicity of gastrically intubated untreatedS. mutanscells, cells coated with whole human saliva, cells treated with HCl (pH 2.0), and saliva-coated and acid-treated cells in mice was investigated. Saliva and serum samples were assayed by enzyme linked immunosorbent assay for immunoglobulin A (IgA) and IgG antibodies, respectively, against the untreated or treatedS. mutanscells. In general, the levels of salivary IgA and serum IgG antibodies to the antigen against which the mice were immunized were significantly higher (P≤ 0.05). In addition, human saliva and serum samples from 12 subjects were assayed for naturally occurring antibody against the untreated or treatedS. mutanscells. In every case, significantly higher reactivity was directed against the saliva-coated and acid-treated cells followed by the saliva-coatedS. mutans. These results provide evidence for the altered immunogenicity of swallowedS. mutansin humans by coating nativeS. mutansantigens with salivary components and/or denaturing surfaceS. mutansantigens in the acidic environment of the stomach, which would lead to an immune response to modifiedS. mutansdeterminants and not to nativeS. mutansantigens.