bluuebunny/crossref_metadata_2025 huggingface dataset:
Vertical integration of an InGaAsP/InP heterojunction bipolar transistor and a double heterostructure laser
Authors: Chen T. R. , Utaka K. , Zhuang Y. H. , Liu Y. Y. , Yariv A.
Published: July 2002

A double heterostructure InGaAsP/InP mesa laser and a mass transport laser were integrated vertically with an InGaAsP/InP double heterojunction bipolar transistor, resulting in the first realization of laser operation in a vertical integration. Laser thresholds as low as 17 mA and an output laser power of over 30 mW were observed. A new type of bistable laser and electro-optical switching were demonstrated.
Negative ion formation at a barium surface in contact with a hydrogen plasma
Authors: van Os C. F. A. , Heeren R. M. A. , van Amersfoort P. W.
Published: July 2002

Measurements on the production of negative hydrogen ions at a barium surface, in contact with a hydrogen plasma, are presented and discussed. In spite of the high work function of barium compared to more conventional cesiated converter surfaces, considerable yields of negative ions were produced. Conversion efficiencies up to 4% were achieved. No negative barium ions were observed.
Infrared laser scanning microscopy in transmission: A new high-resolution technique for the study of inhomogeneities in bulk GaAs
Authors: Kidd P. , Booker G. R. , Stirland D. J.
Published: July 2002

This letter describes the use of the infrared laser scanning microscope in transmission to observe inhomogeneities in bulk GaAs. The results show that the technique achieves a high lateral resolution of ≂2 μm, and is able to detect low contrast intensity fluctuations down to 0.2%. The images obtained show contrast due to both particle scattering and EL2 absorption. The method is nondestructive, is suitable for bulk specimens, and enables three-dimensional defect distributions to be determined. As examples we show results from both In-doped and undoped liquid encapsulated Czochralski GaAs specimens.
Reduction of surface defects in GaAs grown by molecular beam epitaxy
Authors: Salokatve A. , Varrio J. , Lammasniemi J. , Asonen H. , Pessa M.
Published: July 2002

A method to reduce the density of oval defects originating from pregrowth surface particulates and other contaminants for GaAs layers grown by molecular beam epitaxy (MBE) is presented. It appears that if a thin GaAs buffer layer is deposited by alternately supplying Ga atoms and As4 molecules to a GaAs substrate, prior to further growth by MBE, the density of the oval defects in the final layer is reduced reproducibly by a factor of 7, from about 490 to 70 cm−2, when compared with that obtained using MBE alone under closely similar conditions. The improved surface morphology produced by the pulsed beam method is thought to be related to initial film growth which proceeds likely in a two-dimensional layer-by-layer fashion.
Residual defect center in GaInAs/InP films grown by molecular beam epitaxy
Authors: Loualiche S. , Gauneau A. , Le Corre A. , Lecrosnier D. , L’Haridon H.
Published: July 2002

Schottky contact with apparent barrier height of near 0.65 eV has been fabricated and used to perform capacitance-voltage and deep level transient spectroscopy characterizations on n-type molecular beam epitaxy grown GaInAs layers matched to InP substrates. The experimental results show the existence of a residual defect center located at 0.33 eV below the conduction band which is here described for the first time. This defect center is localized close to the surface and the interface of the grown layers. The origin of the center is not clearly understood, but it seems to be a residual defect in which oxygen atom can be involved.
Electrical activity of defects in molecular beam epitaxially grown GaAs on Si and its reduction by rapid thermal annealing
Authors: Chand N. , Fischer R. , Sergent A. M. , Lang D. V. , Pearton S. J. , Cho A. Y.
Published: July 2002

The electrical activity of defects in GaAs grown on Si by molecular beam epitaxy (MBE) has been examined by studying the diode characteristics and deep level transient spectroscopy (DLTS) of Schottky barriers. The defects are not apparent from the forward bias diode characteristics but they are indicated by large leakage current and early breakdown under reverse-biased conditions. Post-growth rapid thermal annealing (RTA) has been found to significantly improve the diode behavior making it almost comparable to GaAs-on-GaAs. The reverse current in the as-grown material shows a very weak temperature dependence, indicating that its origin is not thermionic emission or carrier generation. It is speculated that a large part of this current is due to defect-assisted tunneling, which is reduced by RTA. DLTS indicated only a modest increase in the concentrations of the well-known electron traps typical of MBE GaAs with no evidence for new levels in the upper half of the band gap.
Aerosol jet etching of fine patterns
Authors: Chen Y. L. , Brock J. R. , Trachtenberg I.
Published: July 2002

Successful demonstration of a new etching technique, aerosol jet etching (AJE), is reported. AJE has been used to pattern fine lines with good anisotropy in silicon dioxide surfaces on silicon substrates using a hydrofluoric acid ultrafine aerosol jet.
Ultraviolet-light-induced deposition of gold films
Authors: Ye Yutang , Hunsperger Robert G.
Published: July 2002

Gold film has been deposited by ultaviolet-light-induced photolysis of ammonium tetrachloroaurate/nitrocellulose film. The minimum feature size achieve is about 1 μm, and the film exhibits good adhesion. The effect of temperature on the photolyzing rate has been examined.
Observation of electron quantum interference effects due to virtual states in a double-barrier heterostructure at room temperature
Authors: Potter Robert C. , Lakhani Amir A.
Published: July 2002

Strong electron quantum interference effects have been observed at room temperature in the current-voltage characteristics of a double-barrier, wide-well, lattice-matched In0.52Al0.48As /In0.53Ga0.47As heterostructure tunneling device. A total of 22 oscillations was observed in the differential conductance. A model is proposed which attributes ten of the oscillations to the usual resonant tunneling via the subbands and the rest to the presence of virtual states that exist in the well and second barrier regions.
Metalorganic vapor phase epitaxy of low-resistivity p-type ZnSe
Authors: Yasuda T. , Mitsuishi I. , Kukimoto H.
Published: July 2002

Low-resistivity p-type ZnSe layers have been successfully grown on GaAs substrates by metalorganic vapor phase epitaxy with the use of dimethylzinc and diethylselenide as source materials and lithium nitride as the dopant. The lowest resistivity achieved is 0.2 Ω cm, and the highest carrier concentration is 9×1017 cm−3. ZnSe p-n diodes fabricated by this technique have shown blue emission; the spectral peak is located at 467 nm.
2 ps InGaAs photoconductors and their speed-of-response evaluation by optical pulse mixing at inherent nonlinearities
Authors: Loepfe R. , Schaelin A. , Melchior H. , Blaser M. , Jaeckel H. , Bona G. L.
Published: July 2002

Miniaturized In0.53Ga0.47As/InP photoconductors with nanosecond response times were integrated into broadband coplanar 50 Ω microwave structures and their response times shortened by 14 MeV Be3+-ion implants. Using Carruther’s pulse-mixing technique, which relies on the nonlinearities present in many photoconductors, we determined their speed of response to be of the order of 2 ps. Taking band-to-band recombination as the most probable cause of the slightly nonlinear behavior, we show that the response times determined from the mixing of partially overlapping optical pulses are indeed the intrinsic response times of the photoconductors.
Low-temperature (250 °C) selective epitaxy of GaAs films and p-n junction by laser-assisted metalorganic chemical vapor deposition
Authors: Karam N. H. , Liu H. , Yoshida I. , Bedair S. M.
Published: July 2002

Low-temperature selective epitaxial growth of device quality GaAs has been achieved by laser-assisted chemical vapor deposition (LCVD). GaAs substrates thermally biased to temperatures in the range 250–500 °C were irradiated by an Ar ion laser to induce localized deposition of GaAs. Carefully selected growth conditions resulted in growth rates as low as a monolayer per second at 250 °C. This is the lowest substrate temperature for epitaxial GaAs with optical and structural quality comparable to those achieved in conventionally metalorganic chemical vapor deposition grown GaAs. Also reported is the first p-n junction by LCVD technique using zinc as the p-type dopant. This new low-temperature selective deposition process can lead to maskless fabrication of multicomponent devices on the same wafer.
Al0.3Ga0.7As/GaAs metal-insulator-semiconductor-type field-effect transistor fabricated on an InP substrate
Authors: Agarwala S. , Patil M. B. , Peng C. K. , Morkoç H.
Published: July 2002

A metal-insulator-semiconductor-type Al0.3Ga0.7As/GaAs field-effect transistor with 1-μm-long by 145-μm-wide gates and intrinsic transconductance of 180 mS/mm has been demonstrated on an InP substrate. The dislocation propagation is minimized by incorporating a superlattice on InP, and a 1.5 μm undoped GaAs buffer layer is grown prior to the actual channel to ensure good quality of the 250 Å active layer. A channel mobility of 1920 cm2/(V s) and a carrier concentration of 1.28×1018 cm−3 have been measured at 300 K. The device exhibits excellent pinch-off, and the gate-to-source reverse breakdown voltage is greater than 5 V. The low output conductance of 2.5 mS/mm indicated small parallel conduction in the undoped GaAs buffer layer. Also, very little hysteresis was found in the current-voltage characteristics, implying few traps in the epilayer.
Sulfhydryl modification of V449C in the glutamate transporter EAAT1 abolishes substrate transport but not the substrate-gated anion conductance
Authors: Seal Rebecca P. , Shigeri Yasushi , Eliasof Scott , Leighton Barbara H. , Amara Susan G.
Published: July 2002

Excitatory amino acid transporters (EAATs) buffer and remove
synaptically released
l
-glutamate and maintain its
concentrations below neurotoxic levels. EAATs also mediate a
thermodynamically uncoupled substrate-gated anion conductance that may
modulate cell excitability. Here, we demonstrate that modification of a
cysteine substituted within a C-terminal domain of EAAT1 abolishes
transport in both the forward and reverse directions without affecting
activation of the anion conductance. EC
50
s for
l
-glutamate and sodium are significantly lower after
modification, consistent with kinetic models of the transport cycle
that link anion channel gating to an early step in substrate
translocation. Also, decreasing the pH from 7.5 to 6.5 decreases the
EC
50
for
l
-glutamate to activate the anion
conductance, without affecting the EC
50
for the entire
transport cycle. These findings demonstrate for the first time a
structural separation of transport and the uncoupled anion flux.
Moreover, they shed light on some controversial aspects of the EAAT
transport cycle, including the kinetics of proton binding and anion
conductance activation.
Reevaluation of the accepted allosteric mechanism of phosphofructokinase from
Bacillus stearothermophilus
Authors: Kimmel Jennifer L. , Reinhart Gregory D.
Published: July 2002

The binding of phospho
enol
pyruvate (PEP) to the single allosteric site on phosphofructokinase (EC
2.7.1.11
) from
Bacillus stearothermophilus
(BsPFK) diminishes the ability of the enzyme to bind the substrate fructose 6-phosphate (Fru-6-P). Comparisons of crystal structures with either Fru-6-P or phosphoglycolate, an analog of PEP, bound have shown that Arg-162 interacts with the negatively charged Fru-6-P. Upon the binding of phosphoglycolate, Arg-162 is virtually replaced by Glu-161, which introduces a potential coulombic repulsion between enzyme and substrate [Schirmer, T. & Evans, P. R. (1990)
Nature (London)
343, 140–145]. It has previously been proposed that this structural transition explains the allosteric inhibition in BsPFK, and this explanation has appeared in textbooks to illustrate how an allosteric ligand can influence substrate binding at a distance. Site-directed mutagenesis has been employed to create three mutants of BsPFK that substitute an alanine residue for Glu-161, Arg-162, or both. The E161A mutation does not affect the inhibition of BsPFK by PEP at 25°C, and while the R162A mutation decreases BsPFK's affinity for Fru-6-P by approximately 30-fold, R162A diminishes the effectiveness of PEP inhibition by only 1/3. Combining E161A and R162A produces behavior comparable to R162A alone. These and other data suggest that the movement of Glu-161 and Arg-162 does not play the central role in producing the allosteric inhibition by PEP as originally envisioned in the Schirmer and Evans mechanism.
The structure of aspartyl dipeptidase reveals a unique fold with a Ser-His-Glu catalytic triad
Authors: Håkansson Kjell , Wang Andrew H.-J. , Miller Charles G.
Published: July 2002

The three-dimensional structure of
Salmonella
typhimurium
aspartyl dipeptidase, peptidase E, was solved
crystallographically and refined to 1.2-Å resolution. The structure of
this 25-kDa enzyme consists of two mixed β-sheets forming a V,
flanked by six α-helices. The active site contains a Ser-His-Glu
catalytic triad and is the first example of a serine
peptidase/protease with a glutamate in the catalytic triad. The
active site Ser is located on a strand–helix motif reminiscent of that
found in α/β-hydrolases, but the polypeptide fold and the
organization of the catalytic triad differ from those of the known
serine proteases. This enzyme is a member of a family of serine
hydrolases and appears to represent a new example of convergent
evolution of peptidase activity.
RbcS
suppressor mutations improve the thermal stability and CO
2
/O
2
specificity of
rbcL
- mutant ribulose-1,5-bisphosphate carboxylase/oxygenase
Authors: Du Yu-Chun , Hong Seokjoo , Spreitzer Robert J.
Published: July 2002

In the green alga
Chlamydomonas reinhardtii
, a
Leu
290
-to-Phe (L290F) substitution in the large subunit of
ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), which is
coded by the chloroplast
rbcL
gene, was previously found
to be suppressed by second-site Ala
222
-to-Thr and
Val
262
-to-Leu substitutions. These substitutions complement
the photosynthesis deficiency of the L290F mutant by restoring the
decreased thermal stability, catalytic efficiency, and
CO
2
/O
2
specificity of the mutant enzyme back
to wild-type values. Because residues 222, 262, and 290 interact with
the loop between
β
strands A and B of the Rubisco
small subunit, which is coded by
RbcS1
and
RbcS2
nuclear genes, it seemed possible that
substitutions in this loop might also suppress L290F. A mutation in a
nuclear gene,
Rbc-1
, was previously found to suppress
the biochemical defects of the L290F enzyme at a posttranslational
step, but the nature of this gene and its product remains unknown. In
the present study, three nuclear-gene suppressors were found to be
linked to each other but not to the
Rbc-1
locus. DNA
sequencing revealed that the
RbcS2
genes of these
suppressor strains have mutations that cause either
Asn
54
-to-Ser or Ala
57
-to-Val substitutions in
the small-subunit
β
A/
β
B loop. When
present in otherwise wild-type cells, with or without the resident
RbcS1
gene, the mutant small subunits improve the
thermal stability of wild-type Rubisco. These results indicate that the
β
A/
β
B loop, which is unique to
eukaryotic Rubisco, contributes to holoenzyme thermal stability,
catalytic efficiency, and CO
2
/O
2
specificity.
The small subunit may be a fruitful target for engineering improved
Rubisco.
Structure and function in rhodopsin: correct folding and misfolding in point mutants at and in proximity to the site of the retinitis pigmentosa mutation Leu-125-->Arg in the transmembrane helix C.
Authors: Garriga P , Liu X , Khorana H G
Published: July 2002

L125R is a mutation in the transmembrane helix C of rhodopsin that is associated with autosomal dominant retinitis pigmentosa. To probe the orientation of the helix and its packing in the transmembrane domain, we have prepared and studied the mutations E122R, I123R, A124R, S127R, L125F, and L125A at, and in proximity to, the above mutation site. Like L125R, the opsin expressed in COS-1 cells from E122R did not bind 11-cis-retinal, whereas those from I123R and S127R formed the rhodopsin chromophore partially. A124R opsin formed the rhodopsin chromophore (lambda max 495 nm) in the dark, but the metarhodopsin II formed on illumination decayed about 6.5 times faster than that of the wild type and was defective in transducin activation. The mutant opsins from L125F and L125A bound 11-cis-retinal only partially, and in both cases, the mixtures of the proteins produced were separated into retinal-binding and non-retinal-binding (misfolded) fractions. The purified mutant rhodopsin from L125F showed lambda max at 500 nm, whereas that from L125A showed lambda max at 503 nm. The mutant rhodopsin L125F showed abnormal bleaching behavior and both mutants on illumination showed destabilized metarhodopsin II species and reduced transducin activation. Because previous results have indicated that misfolding in rhodopsin is due to the formation of a disulfide bond other than the normal disulfide bond between Cys-110 and Cys-187 in the intradiscal domain, we conclude from the misfolding in mutants L125F and L125A that the folding in vivo in the transmembrane domain is coupled to that in the intradiscal domain.
Probing the oligomeric structure of an enzyme by electrospray ionization time-of-flight mass spectrometry.
Authors: Fitzgerald M C , Chernushevich I , Standing K G , Whitman C P , Kent S B
Published: July 2002

Electrospray ionization time-of-flight (ESI-TOF) mass spectrometry was used to study the quaternary structure of 4-oxalocrotonate tautomerase (EC 5.3.2; 4OT), and four analogues prepared by total chemical synthesis. Wild-type 4OT is a hexamer of 62 amino acid subunits and contains no cysteine residues. The analogues were: (desPro1)4OT, a truncated construct in which Pro1 was deleted; (Cpc1)4OT in which Pro1 was replaced with cyclopentane carboxylate; a derivative [Met(O)45]4OT in which Met45 was oxidized to the sulfoxide; and an analogue (Nle45)4OT in which Met45 was replaced with norleucine. ESI of (Nle45)4OT, (Cpc1)4OT, and 4OT from solution conditions under which the native enzyme was fully active (5 mM ammonium bicarbonate buffer, pH 7.5) gave the intact hexamer as the major species detected by TOF mass spectrometry. In contrast, analysis of [Met(O)45]4OT and (desPro1)4OT under similar conditions yielded predominantly monomer ions. The ESI-TOF measurements were consistent with structural data obtained from circular dichroism spectroscopy. In the context of kinetic data collected for 4OT and these analogues, ESI-TOF mass spectrometry also provided important evidence for the structural and mechanistic significance of the catalytically important Pro1 residue in 4OT.
Single-amino acid substitutions eliminate lysine inhibition of maize dihydrodipicolinate synthase.
Authors: Shaver J M , Bittel D C , Sellner J M , Frisch D A , Somers D A , Gengenbach B G
Published: July 2002

Dihydrodipicolinate synthase (DHPS; EC 4.2.1.52) catalyzes the first step in biosynthesis of lysine in plants and bacteria. DHPS in plants is highly sensitive to end-product inhibition by lysine and, therefore, has an important role in regulating metabolite flux into lysine. To better understand the feedback inhibition properties of the plant enzyme, we transformed a maize cDNA for lysine-sensitive DHPS into an Escherichia coli strain lacking DHPS activity. Cells were mutagenized with ethylmethanesulfonate, and potential DHPS mutants were selected by growth on minimal medium containing the inhibitory lysine analogue S-2-aminoethyl-L-cysteine. DHPS assays identified surviving colonies expressing lysine-insensitive DHPS activity. Ten single-base-pair mutations were identified in the maize DHPS cDNA sequence; these mutations were specific to one of three amino acid residues (amino acids 157, 162, and 166) localized within a short region of the polypeptide. No other mutations were present in the remaining DHPS cDNA sequence, indicating that altering only one of the three residues suffices to eliminate lysine inhibition of maize DHPS. Identification of these specific mutations that change the highly sensitive maize DHPS to a lysine-insensitive isoform will help resolve the lysine-binding mechanism and the resultant conformational changes involved in inhibition of DHPS activity. The plant-derived mutant DHPS genes may also be used to improve nutritional quality of maize or other cereal grains that have inadequate lysine content when fed to animals such as poultry, swine, or humans.
The NG domain of the prokaryotic signal recognition particle receptor, FtsY, is fully functional when fused to an unrelated integral membrane polypeptide
Authors: Zelazny Adrian , Seluanov Andrei , Cooper Arie , Bibi Eitan
Published: July 2002

Recent studies have revealed that
Escherichia coli
possesses an essential targeting system for integral membrane proteins, similar to the mammalian signal recognition particle (SRP) machinery. One essential protein in this system is FtsY, a homologue of the α-subunit of the mammalian SRP-receptor (SR-α). However,
E. coli
does not possess a close homologue of the integral membrane protein SR-β, which anchors SR-α to the membrane. Moreover, although FtsY can be found as a peripheral membrane protein, the majority is found soluble in the cytoplasm. In this study, we obtained genetic and biochemical evidence that FtsY must be targeted to the membrane for proper function. We demonstrate that the essential membrane targeting activity of FtsY is mediated by a 198-residue-long acidic N-terminal domain. This domain can be functionally replaced by unrelated integral membrane polypeptides, thus avoiding the need for specific FtsY membrane targeting factors. Therefore, the N terminus of FtsY constitutes an independent domain, which is required only for the targeting of the C-terminal NG domain of FtsY to the membrane.
Inhibition of regulator of G protein signaling function by two mutant RGS4 proteins
Authors: Druey Kirk M. , Kehrl John H.
Published: July 2002

Regulators of G protein signaling (RGS) proteins limit the lifetime of activated (GTP-bound) heterotrimeric G protein α subunits by acting as GTPase-activating proteins (GAPs). Mutation of two residues in RGS4, which, based on the crystal structure of RGS4 complexed with G
iα1
-GDP-AlF
4
−
, directly contact G
iα1
(N88 and L159), essentially abolished RGS4 binding and GAP activity. Mutation of another contact residue (S164) partially inhibited both binding and GAP activity. Two other mutations, one of a contact residue (R167M/A) and the other an adjacent residue (F168A), also significantly reduced RGS4 binding to G
iα1
-GDP-AlF
4
−
, but in addition redirected RGS4 binding toward the GTPγS-bound form. These two mutant proteins had severely impaired GAP activity, but in contrast to the others behaved as RGS antagonists in GAP and
in vivo
signaling assays. Overall, these results are consistent with the hypothesis that the predominant role of RGS proteins is to stabilize the transition state for GTP hydrolysis. In addition, mutant RGS proteins can be created with an altered binding preference for the G
iα
-GTP conformation, suggesting that efficient RGS antagonists can be developed.
Yeast chorismate mutase in the R state: Simulations of the active site
Authors: Ma Jianpeng , Zheng Xiaofeng , Schnappauf Georg , Braus Gerhard , Karplus Martin , Lipscomb William N.
Published: July 2002

The isomerization of chorismate to prephenate by chorismate mutase in the biosynthetic pathway that forms Tyr and Phe involves C5—O (ether) bond cleavage and C1—C9 bond formation in a Claisen rearrangement. Development of negative charge on the ether oxygen, stabilized by Lys-168 and Glu-246, is inferred from the structure of a complex with a transition state analogue (TSA) and from the pH-rate profile of the enzyme and the E246Q mutant. These studies imply a protonated Glu-246 well above pH 7. Here, several 500-ps molecular dynamics simulations test the stability of enzyme–TSA complexes by using a solvated system with stochastic boundary conditions. The simulated systems are (
i
) protonated Glu-246 (stable), (
ii
) deprotonated Glu-246 (unstable), (
iii
) deprotonated Glu-246 plus one H
2
O between Glu-246 and the ether oxygen (unstable), (
iv
) the E246Q mutant (stable), and (
v
) addition of OH
−
between protonated Glu-246 and the ether oxygen. In (
v
), a local conformational change of Lys-168 displaced the OH
−
into the solvent region, suggesting a possible rate-determining step that precedes the catalytic step. In a 500-ps simulation of the enzyme complexed with the reactant chorismate or the product prephenate, no water molecule remained near the oxygen of the ligand. Calculations using the linearized Poisson–Boltzmann equation show that the effective pK
a
of Glu-246 is shifted from 5.8 to 8.1 as the negative charge on the ether oxygen of the TSA is changed from −0.56 electron to −0.9 electron. Altogether, these results support retention of a proton on Glu-246 to high pH and the absence of a water molecule in the catalytic steps.
Separation of inhibition and activation of the allosteric yeast chorismate mutase
Authors: Schnappauf Georg , Lipscomb William N. , Braus Gerhard H.
Published: July 2002

Yeast chorismate mutase (EC
5.4.99.5
) shows homotropic activation by the substrate, allosteric activation by tryptophan, and allosteric inhibition by tyrosine. In this study mutants of chorismate mutase have been found that remain sensitive to one allosteric effector (tryptophan) but insensitive to the other (tyrosine). These mutations are located in the catalytic domain: loop 220s (212–226) and helix 12 (227–251). The first example starts with the Thr-266 → Ile mutant that had previously been shown to be locked in the activated R state. The additional mutation Ile-225 → Thr unlocks the R state and restores the activation by tryptophan but not the inhibition by tyrosine. The second example refers to a molecular trigger for the switch between the T and R state: a hydrogen-bonded system, which stabilizes only the T state, from Tyr-234 to Glu-23 to Arg-157. Various mutants of Tyr-234, especially Tyr-234 → Phe, are unresponsive to tyrosine but are activated by tryptophan. This separation of activation from inhibition may indicate a pathway for activation that is independent of the allosteric transition and may also be consistent with an intermediate structure between T and R states.
Characterization of a 34-kDa soybean binding protein for the syringolide elicitors
Authors: Ji Cheng , Boyd Carol , Slaymaker David , Okinaka Yasushi , Takeuchi Yoji , Midland Sharon L. , Sims James J. , Herman Eliot , Keen Noel
Published: July 2002

Syringolides are water-soluble, low-molecular-weight elicitors that trigger defense responses in soybean cultivars carrying the
Rpg4
disease-resistance gene but not in
rpg
4 cultivars.
125
I-syringolide 1 previously was shown to bind to a soluble protein(s) in extracts from soybean leaves. A 34-kDa protein that accounted for
125
I-syringolide 1 binding activity was isolated with a syringolide affinity-gel column. Partial sequences of internal peptides of the 34-kDa protein were identical to P34, a previously described soybean seed allergen. In soybean seeds, P34 is processed from a 46-kDa precursor protein and was shown to have homology with thiol proteases. P34 is a moderately abundant protein in soybean seeds and cotyledons but its level in leaves is low. cDNAs encoding 46-, 34-, and 32-kDa forms of the soybean protein were cloned into the baculovirus vector, pVL1392, and expressed in insect cells. The resulting 32- and 34-kDa proteins, but not the 46-kDa protein, exhibited ligand-specific
125
I-syringolide binding activity. These results suggest that P34 may be the receptor that mediates syringolide signaling.
Kinetic stability as a mechanism for protease longevity
Authors: Cunningham Erin L. , Jaswal Sheila S. , Sohl Julie L. , Agard David A.
Published: July 2002

The folding of the extracellular serine protease, α-lytic
protease (αLP; EC
3.4.21.12
) reveals a novel mechanism for stability
that appears to lead to a longer functional lifetime for the protease.
For αLP, stability is based not on thermodynamics, but on kinetics.
Whereas this has required the coevolution of a pro region to facilitate
folding, the result has been the optimization of native-state
properties independent of their consequences on thermodynamic
stability. Structural and mutational data lead to a model for catalysis
of folding in which the pro region binds to a conserved β-hairpin in
the αLP C-terminal domain, stabilizing the folding transition state
and the native state. The pro region is then proteolytically degraded,
leaving the active αLP trapped in a metastable conformation. This
metastability appears to be a consequence of pressure to evolve
properties of the native state, including a large, highly cooperative
barrier to unfolding, and extreme rigidity, that reduce susceptibility
to proteolytic degradation. In a test of survival under highly
proteolytic conditions, homologous mammalian proteases that have not
evolved kinetic stability are much more rapidly degraded than αLP.
Kinetic stability as a means to longevity is likely to be a mechanism
conserved among the majority of extracellular bacterial pro-proteases
and may emerge as a general strategy for intracellular eukaryotic
proteases subject to harsh conditions as well.
The labile brain. III. Transients and spatio–temporal receptive fields
Authors: Friston Karl J.
Published: July 2002

In this paper we consider an approach to neuronal transients that is predicated on the information they contain. This perspective is provided by information theory, in particular the principle of maximum information transfer. It is illustrated here in application to visually evoked neuronal transients. The receptive fields that ensue concur with those observed in the real brain, predicting, almost exactly, functional segregation of the sort seen in the visual system. This information theoretical perspective can be reconciled with a selectionist stance by noting that a high mutual information among neuronal systems and the environment has, itself, adaptive value and will be subject to selective pressure, at any level one cares to consider.
Amino acid intrinsic α‐helical propensities III: Positional dependence at several positions of C terminus
Authors: Petukhov Michael , Uegaki Koichi , Yumoto Noboru , Serrano Luis
Published: July 2002

In this study, we have analyzed experimentally the helical intrinsic propensities of noncharged and nonaromatic residues at different C‐terminal positions (C1, C2, C3) of an Ala‐based peptide. The effect was found to be complex, resulting in extra stabilization or destabilization, depending on guest amino acid and position under consideration. Polar (Ser, Thr, Cys, Asn, and Gln) amino acids and Gly were found to have significantly larger helical propensities at several C‐terminal positions compared with the α‐helix center (−1.0 kcal/mole in some cases). Some of the nonpolar residues, especially β‐branched ones (Val and Ile) are significantly more favorable at position C3 (−0.3 to −0.4 kcal/mole), although having minor differences at other C‐terminal positions compared with the α‐helix center. Leu has moderate (−0.1 to −0.2 kcal/mole) stabilization effects at position C2 and C3, whereas being relatively neutral at C1. Finally, Met was found to be unfavorable at C1 and C2 ( +0.2 kcal/mole) and favorable at C3 (−0.2 kcal/mole). Thus, significant differences found between the intrinsic helical propensities at the C‐terminal positions and those in the α‐helix center must be accounted for in helix/coil transition theories and in protein design.
Synchronization of driven nonlinear oscillators
Authors: Jensen R. V.
Published: July 2002

Mathematical models of nonlinear oscillators are used to describe a wide variety of physical and biological phenomena that exhibit self-sustained oscillatory behavior. When these oscillators are strongly driven by forces that are periodic in time, they often exhibit a remarkable “mode-locking” that synchronizes the nonlinear oscillations to the driving force. The purpose of this paper is to demonstrate that a similar phenomenon occurs when nonlinear oscillators are strongly driven by a force that is varying randomly in time. In this case the synchronization is less obvious for a single oscillator, but when several oscillators with different initial conditions or phases are driven with the same aperiodic force, their fluctuating behavior may reliably converge to an identical response. Analytical estimates are derived for the conditions, rates, and structural stability for the synchronization of a broad class of aperiodically driven nonlinear oscillators.
The geometry of elastic collisions and Heron’s law
Authors: Kocik Jerzy
Published: July 2002

Elastic collision of two balls on a line is discussed in terms of their configuration space. The optical-mechanical analogy is analyzed in this context. In particular, the law of collision is reinterpreted as Heron’s law of light reflection.
Lip–jaw and tongue–jaw coordination during rate-controlled syllable repetitions
Authors: Hertrich Ingo , Ackermann Hermann
Published: July 2002

The present study investigated the relationship between functionally relevant compound gestures and single-articulator component movements of the jaw and the constrictors lower lip and tongue tip during rate-controlled syllable repetitions. In nine healthy speakers, the effects of speaking rate (3 vs 5 Hz), place of articulation, and vowel type during stop consonant–vowel repetitions (/pa/, /pi/, /ta/, /ti/) on the amplitude and peak velocity of differential jaw and constrictor opening–closing movements were measured by means of electromagnetic articulography. Rather than homogeneously scaled compound gestures, the results suggest distinct control mechanisms for the jaw and the constrictors. In particular, jaw amplitude was closely linked to vowel height during bilabial articulation, whereas the lower lip component amplitude turned out to be predominantly rate sensitive. However, the observed variability across subjects and conditions does not support the assumption that single-articulator gestures directly correspond to basic phonological units. The nonhomogeneous effects of speech rate on articulatory subsystem parameters indicate that single structures are differentially rate sensitive. On average, an increase in speech rate resulted in a more or less proportional increase of the steepness of peak velocity/amplitude scaling for jaw movements, whereas the constrictors were less rate sensitive in this respect. Negative covariation across repetitions between jaw and constrictor amplitudes has been considered an indicator of motor equivalence. Although significant in some cases, such a relationship was not consistently observed across subjects. Considering systematic sources of variability such as vowel height, speech rate, and subjects, jaw–constrictor amplitude correlations showed a nonhomogeneous pattern strongly depending on place of articulation.
Dissipation in solids: Thermal oscillations of atoms
Authors: Çelik Cem E. , Akay Adnan
Published: July 2002

Dissipation in solids describes conversion of kinetic energy to thermal energy. Heat capacity of a solid relates to the kinetic energy of the oscillations of its atoms with the assumption that they are in thermal equilibrium. Previous studies investigated criteria related to thermal relaxation, the process by which thermal equilibrium is established. They examined conditions for irreversible distribution of energy among the modes of a nonlinear periodic structure that represents atoms in a solid. These studies all point to the chaotic behavior of a freely vibrating nonlinear lattice as the kernel of the problem in addressing thermal relaxation. This paper extends the results of previous studies on thermalization to modeling of dissipation as energy absorption that takes place during forced vibration of particles in a nonlinear lattice. Results show that dissipation and chaotic behavior of the particles develop simultaneously. Such behavior develops when the forcing frequency falls within a resonance band. The results also support the argument that for a real solid, both in terms of size and complexity, resonance bands overlap significantly broadening the frequency range within which dissipation takes place.
A Capillary Model for Non-Darcy Flow through Porous Media
Authors: Klausner Y. , Kraft R.
Published: July 2002

A parallel capillary porous flow model is constructed from capillaries with “wall forces.” The model exhibits critical pressure gradients and nonlinear discharge velocity at low pressure gradients, while for high gradients the discharge velocity is linear.
Dynamic Compression of Clay under an Explosive Pulse
Authors: Kondner Robert L. , Forrest James B.
Published: July 2002

The dynamic stress-strain-time response of a clay in compression is studied using a high-speed explosive pulse type of apparatus. The rise times of the applied stress pulses are the order of magnitude of 0.2 msec and the entire test durations are approximately 3.0 msec. Compressive loading is obtained with a piston using the high pressure developed by firing a Springfield 30–06 cartridge into a combustion chamber. Measurements include forces at the top and bottom of the test specimen, deformation of the specimen, and acceleration as well as velocity of the upper platen. Dynamic stress-strain response exhibits an under-linear type of nonlinearity for a wide range of consistencies (moisture contents) generally encountered in field applications. Effects of moisture content are conveniently handled in terms of a nondimensional dynamic stress-strength parameter using the static ultimate unconfined compressive strength as a consistency index. The nonlinear effects are represented in terms of a two-constant hyperbolic stress-strain relation. The two hyperbolic constants are measures of the initial tangent modulus and the ultimate strength of the clay. These constants are easily obtained as the intercept and slope of the straight line approximation of the experimental data when presented in transformed hyperbolic coordinates. Because of the multiphase nature of clay, the results may be of value in studying the response characteristics of other composite materials.
An Incremental Method for the Solution of Static Boundary Value Problems in Finite Elasticity
Authors: Valanis K. C. , Blatz Paul J.
Published: July 2002

A method is proposed for the solution of boundary value problems in finite elasticity. In this method successive small increments of the prescribed surface displacements and/or stresses and/or body forces are applied until the final prescribed values of these quantities are reached. The method lends itself to straightforward numerical analysis because the differential equations and boundary conditions that must be satisfied, at each increment, are linear in the incremental displacements. The problem is formulated in cartesian as well as curvilinear coordinates and in the material as well as in the spatial coordinate system. No restrictions are placed on the form of the strain energy function, but specific forms of the equations are given for a Neo-Hookean material.
Rheologic Behavior of Clay Soils Subjected to Dynamic Loads
Authors: Krizek Raymond J.
Published: July 2002

The emphasis of this presentation is directed toward (1) indicating typically the current state-of-the-art with regard to experimentally observed rheologic response characteristics of clay soils subjected to dynamic loadings, both with and without inertial effects, and (2) evaluating the applicability of linear viscoelastic theory to characterize this response. Primary concern is given to steady-state vibratory and single pulse loadings, and the particular soil properties considered include dynamic modulus and compliance, strength, energy dissipation, viscosity, relaxation time, compaction, and wave propagation velocity and attenuation. In addition, a qualitative thermodynamic interpretation of the observed constitutive response is advanced. A special effort is made to illustrate the influence on soil behavior of several often overlooked factors, such as certain material characteristics of the soil (nature of pore fluid, particle orientation and arrangement, method of preparing specimens, etc.) and type of testing conditions (specimen size and geometry, boundary conditions, etc.).
Rheologic Behavior of Cohesionless Soils Subjected to Dynamic Loads
Authors: Krizek Raymond J.
Published: July 2002

An effort is made in this state-of-the-art paper to present a representative sample of the experimentally observed rheologic response characteristics of cohesionless soils subjected to dynamic loadings, both with and without inertial effects, and to evaluate the usefulness of various idealized continuum and particulate theories for describing this response. Following brief discussion of some fundamental stress-strain-strength characteristics of cohesionless soils, their general behavior under dynamic loads is discussed. Then, their dynamic response is conveniently divided into two categories: reduction in volume and constitutive properties, and each is examined in some detail. The former includes conditions, such as compaction and liquefaction, which are associated with gross alterations in the soil structure; the latter is concerned with the stress-strain relation, hysteretic response, and wave propagation characteristics of the soil throughout the range of deformation encountered. Particular emphasis is given to distinguishing between small-strain and large-strain response and the approximations which are acceptable for each case.
Normal Stresses and Weissenberg Effect
Authors: Kundu Pijush K.
Published: July 2002

It has been shown that the sign and magnitude, of the Weissenberg effect in a viscoelastic liquid depends on the method of observation, namely, through the shape of the free surface or through the height difference of radial tappings. The Oldroyd A and the Walters A′ fluids display the negative Weissenberg effect as far as the free surface is concerned, but they display the positive effect in radial tappings. The Oldroyd B as well as the Walters B′ fluid display identical positive effect in both types of observations. The second order fluid displays the positive effect in radial tappings, but may display either effect when the free surface is observed.
Static Solutions with Phase Change for a Nematic Liquid Crystal in a Pipe
Authors: Currie P. K.
Published: July 2002

An examination is made of the static orientation solutions for a nematic liquid crystal in a pipe, including those involving phase changes near the center of the pipe. It is found that solutions both with and without phase change are possible if the pipe radius is sufficiently large, but that below a critical value of the pipe radius all solutions involve phase change.
Non-Uniqueness of Determination of Molecular Weight Distribution Dependence of Properties by Blending Experiments
Authors: Wissbrun Kurt F.
Published: July 2002

It is shown that in general blending experiments alone do not determine unique relations for the dependence of polymer properties upon molecular weight distribution. In particular, two theoretical expressions for the steady shear elastic compliance of molten polymer lead to identical property blending rules.
Unfairness to Patients With Alzheimer Disease in Medicare’s Coverage of Antiamyloid Immunotherapy
Authors: Stern Andrew M. , Selkoe Dennis J.
Published: August 2022

This Viewpoint discusses the US Center for Medicare and Medicaid Services’ decision on aducanumab, a drug that can treat Alzheimer disease.
Prevalence of Disordered Eating and Associations With Sex, Pubertal Maturation, and Weight in Children in the US
Authors: Murray Stuart B. , Blashill Aaron J. , Calzo Jerel P.
Published: August 2022

This cross-sectional study assesses the prevalence of disordered eating in children and its associations with sex, pubertal maturation, and weight.
Questioning the Value of Compliance-Oriented Programs With Traumatized Children and Youth
Authors: Collin-Vézina Delphine , Carnevale Franco A.
Published: August 2022

This Viewpoint aims to question the value of compliance-oriented programs’ principles as they apply to traumatized children and youth.
Ultrahigh‐Content CoP Cluster as a Dual‐Atom‐Site Electrocatalyst for Accelerating Polysulfides Conversion in Li–S Batteries
Authors: Feng Yutong , Zu Lianhai , Yang Shanshan , Chen Lu , Liao Kexuan , Meng Shuo , Zhang Chi , Yang Jinhu
Published: August 2022

Single‐atom catalysts (SACs) show high catalytic efficiency in accelerating conversion of lithium polysulfides (LiPS), and are thus promising for suppressing the shuttle effect observed in lithium−sulfur batteries (LSBs); however, single‐atom catalytic sites with low content of catalysts largely restrict their catalytic effect. Herein, a CoP cluster supported by a N‐doped carbon matrix (CoP cluster/NC) with atomic‐level dispersion and an ultrahigh content (25.5 wt.%) of Co atoms is fabricated via an in situ low‐temperature phosphorization strategy and employed as a dual‐atom‐site catalyst for catalyzing LiPS conversion. The CoP cluster/NC with abundant unsaturated CoP coordination provides dual‐atom sites of Co and P to dynamically adsorb/desorb sulfur species and Li+ ions, respectively, synergistically promoting the conversion of LiPS. The dual‐atom‐site catalytic mechanism is evidenced by substantial characterizations including X‐ray absorption fine structure measurements and density functional theory calculations. Consequently, the S@CoP cluster/NC cathode shows superior cycling and rate performance. Even at a high sulfur loading of 6.2 mg cm−2, a high areal capacity of 6.5 mAh cm−2 that surpasses most commercial lithium–ion batteries can be achieved. This study opens a new avenue in the development of advanced catalysts with new catalytic mechanisms for high‐performance LSBs.
Alloying at a Subnanoscale Maximizes the Synergistic Effect on the Electrocatalytic Hydrogen Evolution
Authors: Zou Quan , Akada Yuji , Kuzume Akiyoshi , Yoshida Masataka , Imaoka Takane , Yamamoto Kimihisa
Published: August 2022

Bonding dissimilar elements to provide synergistic effects is an effective way to improve the performance of metal catalysts. However, as the properties become more dissimilar, achieving synergistic effects effectively becomes more difficult due to phase separation. Here we describe a comprehensive study on how subnanoscale alloying is always effective for inter‐elemental synergy. Thirty‐six combinations of both bimetallic subnanoparticles (SNPs) and nanoparticles (NPs) were studied systematically using atomic‐resolution imaging and catalyst benchmarking based on the hydrogen evolution reaction (HER). Results revealed that SNPs always produce greater synergistic effects than NPs, the greatest synergistic effect was found for the combination of Pt and Zr. The atomic‐scale miscibility and the associated modulation of electronic states at the subnanoscale were much different from those at the nanoscale, which was observed by annular‐dark‐field scanning transmission electron microscopy (ADF‐STEM) and X‐ray photoelectron spectroscopy (XPS), respectively.