bluuebunny/crossref_metadata_2025 huggingface dataset:
Electronic and magnetic properties of MnSnAs2
Authors: Cho Sunglae , Choi Sungyoul , Cha Gi‐Beom , Hong Soon Cheol , Park Yongsup , Park Hyun‐Min , Kim Yunki , Ketterson John B.
Published: May 2004

We have synthesized MnSnAs2 single crystals using the vertical temperature gradient solidification method. The crystal structure of MnSnAs2 is chalcopyrites, which are “genealogically” related to the more familiar tetrahedrally‐coordinated zinc‐blende materials, with lattice constants of a = 5.794 Å, c = 11.365 Å. Using the experimentally determined lattice constants and crystal structure, we carried out first principles electronic structure calculations, using the full‐potential linearized augmented plane wave (FLAPW) method in the local density approximation (LDA). The lowest total energies were observed for the AFM state, indicating that AFM ordering in the system is energetically favored at 0 K. We find that MnSnAs2 is metallic in the electronic calculation. Interestingly, MnSnAs2 exhibited ferromagnetism with TC = 328 K. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Resistivities and magnetoresistances of pure, Co‐ and V‐doped Ge single crystals
Authors: Choi Jiyoun , Choi Sungyoul , Hong Soon Cheol , Park Yongsup , Park Hyun‐Min , Kim Y. C. , Cho Sunglae
Published: May 2004

We have grown pure, Co‐ and V‐doped Ge bulk single crystals using the vertical gradient solidification method. We measured electrical resistivities, magnetoresistances (MRs) and Hall coefficients of V0.015Ge0.985 and Co0.02Ge0.98 single crystals. The resistivities rapidly increased at low temperature, which might be used for cryogenic thermometer. The MR ratios of V0.015Ge0.985 and Co0.02Ge0.98 are 130 and 90% at 77 K in the field of 5 T, respectively. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Quantitative study of magnetoresistance in patterned Ni80Fe20 wires
Authors: Tsai J. L. , Hsieh J. H. , Chen T. Y. , Liou S. H. , Lee S. F. , Yao Y. D.
Published: May 2004

The domain wall resistivity of the patterned Ni80Fe20 zigzag wires has been studied as functions of the number of corners and temperature in zigzag wires. The quantitative ratio of domain wall magnetoresistance (MR) is estimated by two methods. One is the discontinuous jump that represent the domain state sweep between two states in MR curve. The other is the angular dependence on the resistance at remanent state. The ratio of domain wall MR increased when domain wall number density over total wire length (DWs/L) changed from 12/73 to 34/73 with film thickness 40 nm at 10–300 K. Especially, the ratio of domain wall MR decreased slightly as the temperature ranged from 10 to 300 K. The anisotropic magnetoresistance (AMR) has been subtracted in the calculation. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Effects of surfactant on properties of magnetic fluids for biomedical application
Authors: Park S. I. , Lim J. H. , Kim J. H. , Yun H. I. , Roh J. S. , Kim C. G. , Kim C. O.
Published: May 2004

Biocompatible magnetic fluids are applied for medical diagnosis and therapy. In this work, magnetic particles were prepared and then were coated with various 2nd surfactants for obtaining the water‐based magnetic fluids by chemical coprecipitation. Toxicity of each fluid sample was estimated using Sprague–Dawley rats. Finally, the used samples resulted in severe toxic reactions through in vitro, indicating that all samples can not be seen as biocompatible agents or suggesting the possibilities of another effects. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Transport properties of metal/insulator/semiconductor tunnel junctions
Authors: Lee J. H. , Park S. Y. , Jun Kyung‐In , Shin K.‐H. , Hong Jinki , Rhie K. , Lee B. C.
Published: May 2004

The transport properties of ferromagnet/Al2O3/semiconductor tunnel junctions were investigated. Si and GaAs substrates were used, and CoFe and NiFe were taken for ferromagnets. Diode characteristics were observed in current‐voltage curves. The dependences on the Al2O3 thickness and temperature were also studied. It is found that the Al2O3 layer plays a crucial role in preventing inter‐diffusion at the interface. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Effect of Solenostemma argel on oviposition, egg hatchability and viability of Culex pipiens L. larvae
Authors: Al‐Doghairi Mohammed , El‐Nadi Abdelrahman , Elhag Eltayeb , Al‐Ayedh Hassan
Published: May 2004

Methanolic extracts of aerial parts of the medicinal plant Argel (Solenostemma argel (Del.) Hayne), incorporated into rearing media of Culex pipiens L. showed effect on oviposition, egg hatchability and larval viability. Acute toxicity of S. argel extract was found to possess LC50 of 0.037, 0.031, 0.009 and 0.007 ppm and the LC95 was found 0.394, 0.293, 0.065 and 0.030 ppm, after 1, 2, 4 and 7 days against the larva of C. pipiens under laboratory conditions.

The ovicidal effect of S. argel was relatively less pronounced, however, the 0.1% concentration reduced egg hatch by 33.7%. The mortality of the newly hatched larvae, reared from eggs in this media, reached 100% at concentrations as low as 0.025%, 2 days post hatching. Complete suppression of oviposition within the ﬁrst 2 days was observed, however its action was gradually lost thereafter.

Bioactive effects were mainly attributed to the presence of a variety of bioactive organic substances mainly terpenes, pergenine glucosides, alkaloids and sterols. Copyright © 2004 John Wiley & Sons, Ltd.
Tetrandrine induces apoptosis in hepatic stellate cells
Authors: Zhao Yu‐Zhe , Kim Ji‐Young , Park Eun‐Jeon , Lee Sung Hee , Woo Sun‐Wook , Ko Geonil , Sohn Dong Hwan
Published: May 2004

We have previously reported that tetrandrine reduced hepatic stellate cell activation and collagen accumulation in liver ﬁbrosis induced by biliary obstruction. In the present study, we examined the apoptosis‐inducing effect of tetrandrine on activated hepatic stellate cells, as the therapeutic goal in hepatic ﬁbrosis is to eliminate the activated hepatic stellate cells by apoptosis. We used rat hepatic stellate cells transformed by Simian virus 40 (T‐HSC/Cl‐6) to overcome the limitations inherent in studying primary cultures of hepatic stellate cells. Tetrandrine treatment at doses of 25 and 50 µg/ml for 12 h induced apoptosis as conﬁrmed by DNA fragmentation and increased sub‐G1 DNA content as detected by ﬂow cytometric analysis. Tetrandrine also induced the activation of caspase‐3 protease and subsequent proteolytic cleavage of poly(ADP‐ribose) polymerase. In conclusion, our results demonstrate that tetrandrine induces apoptosis of T‐HSC/Cl‐6 cells, and these results should contribute to the development of new agents for the treatment of hepatic ﬁbrosis. Copyright © 2004 John Wiley & Sons, Ltd.
Advances in chemistry and bioactivity of the genus Uncaria
Authors: Laus Gerhard
Published: May 2004

The alkaloids of the pantropical genus Uncaria (Rubiaceae) were reviewed extensively by Phillipson et al. in (1978) Since then a host of papers with new results has been published. The compounds discovered are from three major groups: (1) alkaloids; (2) terpenoids; and (3) ﬂavonoids. Some highly unusual structures have been reported. Although there are at least 35 species of Uncaria known, recent research focussed on a relatively small number of species. During recent years bioactivity of extracts and pure compounds isolated from Uncaria species have been increasingly investigated. These include anticonvulsive, antiinﬂammatory, antimutagenic, antioxidant, cytoprotective, hypotensive, and immunoregulatory effects. The literature since 1978 is reviewed and 133 references are given. Copyright © 2004 John Wiley & Sons, Ltd.
Structure of stable double‐ionic model water clusters of quaternary alkylammonium surfactants with some monovalent counterions as derived by the DFT method
Authors: Zieliński Ryszard , Szymusiak Henryk
Published: May 2004

We have performed DFT calculations on stability of model water clusters of alkylammonium surfactants with different monovalent counterions, such as fluoride, chloride, bromide, hydroxide, nitrate, perchlorate, and tetrafluoroborate. We have found that stable water clusters are formed if they contain at least three molecules of water. We can distinguish two types of stable water clusters of ammonium salts: stable neutral water clusters and double‐ionic water clusters. According to the results of our DFT calculations, the first type of cluster is more stable by ca. 3–7 kcal/mol. We have found several types of stable double‐ionic water clusters of alkylammonium salts with different counterions. In each case, the stable structures have some element of symmetry and they are stabilized by hydrogen bonding. The computed energy of double‐ionic cluster formation of hydrated alkylammonium salts with different counterions correlates quite well with experimental data of the critical micelle concentration (CMC), indicating a role of hydration phenomena in the process of micelle formation. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004
Density functional theory for superconductors
Authors: Lathiotakis N. N. , Marques M. A. L. , Lüders M. , Fast L. , Gross E. K. U.
Published: May 2004

Two recently proposed exchange‐correlation functionals describing the superconducting phase of matter are reviewed and further explored: Whereas the first is a generalization of the local density approximation dealing with purely electronic correlations, the second is a functional derived from Kohn–Sham perturbation theory that includes electronic and phononic correlations on the same footing. Superconducting properties of simple metals obtained with the latter functional agree rather well with experimental results. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004
The (100), (110), and (111) Cu surfaces revisited by the semiempirical LCAO method
Authors: Cortona Pietro , Sapet Christophe
Published: May 2004

The electronic properties of surfaces covered by adsorbates are often investigated by means of the semiempirical LCAO method. This implicitly requires the existence of parameters that correctly account for the bulk as well as for the surface electronic structure of the substrate. We will show that, in general, such parameters cannot be found by fitting just the available experimental data for the bulk band structure: some results for the surface states must also be taken into account. We have found that very few data, for just one surface, are sufficient to select a set of parameters that give electronic bands in good agreement with experiment for the bulk as well as for the three low‐order surfaces that we have investigated. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004
A comparison of goodness of fit tests for age‐related reference ranges
Authors: Pan H. , Cole T. J.
Published: May 2004

Age‐related reference ranges based on cubic spline or kernel‐based smoothing methods lack a parametric framework with which to assess goodness of fit, as the distribution of the log‐likelihood ratio comparing models with different degrees of smoothing is not known in general. Several methods have been proposed to assess goodness of fit in this case: Healy's grid test, Royston's Q tests and van Buuren's worm plot. Here we compare the performance of the various methods, including an extension of the Q tests, and show how they can be used, with other information including the appearance of the fitted curves, to inform the choice of model for age‐related reference ranges of height and weight in a large Dutch data set. Copyright © 2004 John Wiley & Sons, Ltd.
Simultaneous inference for longitudinal data with detection limits and covariates measured with errors, with application to AIDS studies
Authors: Wu Lang
Published: May 2004

In AIDS studies such as HIV viral dynamics, statistical inference is often complicated because the viral load measurements may be subject to left censoring due to a detection limit and time‐varying covariates such as CD4 counts may be measured with substantial errors. Mixed‐effects models are often used to model the response and the covariate processes in these studies. We propose a unified approach which addresses the censoring and measurement errors simultaneously. We estimate the model parameters by a Monte‐Carlo EM algorithm via the Gibbs sampler. A simulation study is conducted to compare the proposed method with the usual two‐step method and a naive method. We find that the proposed method produces approximately unbiased estimates with more reliable standard errors. A real data set from an AIDS study is analysed using the proposed method. Copyright © 2004 John Wiley & Sons, Ltd.
Minimization of sample size when comparing two small probabilities in a non‐inferiority safety trial
Authors: de Boo Theo M. , Zielhuis Gerhard A.
Published: May 2004

In clinical trials success rates of two treatments to be compared often range from 10 to 90 per cent. When the comparison probabilities are (much) smaller than 10 per cent, standard methods for sample size and power calculations may provide invalid results. This situation may occur when there is interest in safety rather than in efficacy. In such trials, no more patients should be included than strictly necessary. We compared the results of maximum likelihood methods for the computation of sample sizes in a non‐inferiority trial, including exact procedures and considered unequal sample sizes for experimental and reference treatment. An exact, unequal sample size maximum likelihood procedure is advocated when the specified non‐zero risk difference under the null hypothesis is not too large. Such a procedure is also indicated when the parameter of interest is the relative risk, rather than the risk difference. Copyright © 2004 John Wiley & Sons, Ltd.
Gene expression profiling for prognosis using Cox regression
Authors: Pawitan Y. , Bjöhle J. , Wedren S. , Humphreys K. , Skoog L. , Huang F. , Amler L. , Shaw P. , Hall P. , Bergh J.
Published: May 2004

Given the promise of rich biological information in microarray data we will expect an increasing demand for a robust, practical and well‐tested methodology to provide patient prognosis based on gene expression data. In standard settings, with few clinical predictors, such a methodology has been provided by the Cox proportional hazard model, but no corresponding methodology is available to deal with the full set of genes in microarray data. Furthermore, we want the procedure to be able to deal with the general survival data that include censored information. Conceptually such a procedure can be constructed quite easily, but its implementation will never be straightforward due to computational problems. We have developed an approach that relies on an extension of the Cox proportional likelihood that allows random effects parameters. In this approach, we use the full set of genes in the analysis and deal with survival data in the most general way. We describe the development of the model and the steps in the implementation, including a fast computational formula based on a subsampling of the risk set and the singular value decomposition. Finally, we illustrate the methodology using a data set obtained from a cohort of breast cancer patients. Copyright © 2004 John Wiley & Sons, Ltd.
Sample size determination for comparing several survival curves with unequal allocations
Authors: Halabi Susan , Singh Bahadur
Published: May 2004

Ahnn and Anderson derived sample size formulae for unstratified and stratified designs assuming equal allocation of subjects to three or more treatment groups. We generalize the sample size formulae to allow for unequal allocation. In addition, we define the overall probability of death to be equal to one minus the censored proportion for the stratified design. This definition also leads to a slightly different definition of the non‐centrality parameter than that of Ahnn and Anderson for the stratified case. Assuming proportional hazards, sample sizes are determined for a prespecified power, significance level, hazard ratios, allocation of subjects to several treatment groups, and known censored proportion. In the proportional hazards setting, three cases are considered: (1) exponential failures–exponential censoring, (2) exponential failures–uniform censoring, and (3) Weibull failures (assuming same shape parameter for all groups)–uniform censoring. In all three cases of the unstratified case, it is assumed that the censoring distribution is the same for all of the treatment groups. For the stratified log‐rank test, it is assumed the same censoring distribution across the treatment groups and the strata. Further, formulae have been developed to provide approximate powers for the test, based upon the first two or first four‐moments of the asymptotic distribution.

We observe the following two major findings based on the simulations. First, the simulated power of the log‐rank test does not depend on the censoring mechanism. Second, for a significance level of 0.05 and power of 0.80, the required sample size n is independent of the censoring pattern. Moreover, there is very close agreement between the exact (asymptotic) and simulated powers when a sequence of alternatives is close to the null hypothesis. Two‐moment and four‐moment power series approximations also yield powers in close agreement with the exact (asymptotic) power. With unequal allocations, our simulations show that the empirical powers are consistently above the target value of prespecified power of 0.80 when 50 per cent of the patients are allocated to the treatment group with the smallest hazard. Copyright © 2004 John Wiley & Sons, Ltd.
Cure fraction estimation from the mixture cure models for grouped survival data
Authors: Yu Binbing , Tiwari Ram C. , Cronin Kathleen A. , Feuer Eric J.
Published: May 2004

Mixture cure models are usually used to model failure time data with long‐term survivors. These models have been applied to grouped survival data. The models provide simultaneous estimates of the proportion of the patients cured from disease and the distribution of the survival times for uncured patients (latency distribution). However, a crucial issue with mixture cure models is the identifiability of the cure fraction and parameters of kernel distribution. Cure fraction estimates can be quite sensitive to the choice of latency distributions and length of follow‐up time. In this paper, sensitivity of parameter estimates under semi‐parametric model and several most commonly used parametric models, namely lognormal, loglogistic, Weibull and generalized Gamma distributions, is explored. The cure fraction estimates from the model with generalized Gamma distribution is found to be quite robust. A simulation study was carried out to examine the effect of follow‐up time and latency distribution specification on cure fraction estimation. The cure models with generalized Gamma latency distribution are applied to the population‐based survival data for several cancer sites from the Surveillance, Epidemiology and End Results (SEER) Program. Several cautions on the general use of cure model are advised. Copyright © 2004 John Wiley & Sons, Ltd.
The SAFOD Pilot Hole seismic array: Wave propagation effects as a function of sensor depth and source location
Authors: Chavarria J. Andres , Malin Peter E. , Shalev Eylon
Published: May 2004

In July 2002 we installed a vertical array of seismometers in the San Andreas Fault Observatory at Depth (SAFOD) Pilot Hole (PH). The bottom of this 32 level, 1240 m long array of 3‐ components is located at a depth of ∼2100 m below ground. Surface‐explosion and microearthquake seismograms recorded by the array give valuable insights into the structure of the SAFOD site. The ratios of P‐ and S‐wave velocities (Vp/Vs) along the array suggest the presence of two faults intersecting the PH. The Vp/Vs ratios also depend on source location, with high values to the NW, and lower ones to the SE, correlating with high and low creep rates along the SAF, respectively. Since higher ratios can be produced by increasing fluid saturation, we suggest that this effect might account for both our observations and their correlation with the creep distribution.
Determining SAFOD area microearthquake locations solely with the Pilot Hole seismic array data
Authors: Oye Volker , Chavarria J. Andres , Malin Peter E.
Published: May 2004

In August 2002, an array of 32 three‐component geophones was installed in the San Andreas Fault Observatory at Depth (SAFOD) Pilot Hole (PH) at Parkfield, CA. As an independent test of surface‐observation‐based microearthquake locations, we have located such events using only data recorded on the PH array. We then compared these locations with locations from a combined set of PH and Parkfield High Resolution Seismic Network (HRSN) observations. We determined the uncertainties in the locations as they relate to errors in the travel time picks and the velocity model by the bootstrap method. Based on the PH and combined locations, we find that the “C2” cluster to the northeast of the PH has the smallest location uncertainties. Events in this cluster also have the most similar waveforms and largest magnitudes. This confirms earlier suggestions that the C2 cluster is a promising target for the SAFOD Main Hole.
Monthly averaged ozone and nitrous oxide from the Improved Limb Atmospheric Spectrometer (ILAS) in the Northern and Southern Hemisphere polar regions
Authors: Khosrawi Farahnaz , Müller Rolf , Proffitt Michael H. , Nakajima Hideaki
Published: May 2004

Northern and southern hemispheric averaged ozone (O3) and nitrous oxide (N2O) measured by the Improved Limb Atmospheric Spectrometer (ILAS) were used to examine photochemical and dynamical changes in high‐latitude O3 distributions. Using correlations of O3 versus N2O, the ILAS data are organized monthly in both hemispheres by partitioning these data into equal bins of altitude or potential temperature. The resulting families of curves help to differentiate O3 changes due to photochemistry from those due to transport. Our study extends the work of Proffitt et al. [2003] for the Northern Hemisphere to the Southern Hemisphere. Further, our study confirms and extends their results for the Northern Hemisphere by applying their analysis to a significantly greater altitude range. As in the Northern Hemisphere, the families of curves for the altitude, and potential temperature bins in the Southern Hemisphere are separated and generally do not cross. In both hemispheres a better separation is found for the potential temperature binning. In the Southern Hemisphere November and December data, preserved photochemical O3 loss is evident in the lower stratosphere. Further, summer ozone loss is evident in the Southern Hemisphere from January to March. In the Arctic, ongoing photochemical O3 loss is evident in the Northern Hemisphere spring data. While at higher altitudes the correlation between N2O and O3 is generally positive (increasing N2O with increasing O3), at lower levels the correlation is negative. This change of correlation from positive to negative can be interpreted in terms of photochemical and dynamical processes. Strong descent causes a steepening of the positively correlated curves, while the curves change their slope from positive to negative if photochemical destruction of O3 is present and descent is weak. The level of slope change is also photochemically influenced and therefore changes with season. Data sets such as the one derived here may be useful for testing atmospheric models and for identifying future changes in stratospheric ozone.
Gossip in Evolutionary Perspective
Authors: Dunbar R. I. M.
Published: May 2004

Conversation is a uniquely human phenomenon. Analyses of freely forming conversations indicate that approximately two thirds of conversation time is devoted to social topics, most of which can be given the generic label gossip. This article first explores the origins of gossip as a mechanism for bonding social groups, tracing these origins back to social grooming among primates. It then asks why social gossip in this sense should form so important a component of human interaction and presents evidence to suggest that, aside from servicing social networks, a key function may be related explicitly to controlling free riders. Finally, the author reviews briefly the role of social cognition in facilitating conversations of this kind.
phyllopod
is a target gene of proneural proteins in
Drosophila
external sensory organ development
Authors: Pi Haiwei , Huang Shao-Kuei , Tang Chiou-Yang , Sun Y. Henry , Chien Cheng-Ting
Published: May 2004

Proneural basic helix-loop-helix (bHLH) proteins initiate neurogenesis in both vertebrates and invertebrates. The
Drosophila
Achaete (Ac) and Scute (Sc) proteins are among the first identified members of the large bHLH proneural protein family.
phyllopod
(
phyl
), encoding an ubiquitin ligase adaptor, is required for
ac
- and
sc
-dependent external sensory (ES) organ development. Expression of
phyl
is directly activated by Ac and Sc. Forced expression of
phyl
rescues ES organ formation in
ac
and
sc
double mutants.
phyl
and
senseless
, encoding a Zn-finger transcriptional factor, depend on each other in ES organ development. Our results provide the first example that bHLH proneural proteins promote neurogenesis through regulation of protein degradation.
Dehydroepiandrosterone and allopregnanolone protect sympathoadrenal medulla cells against apoptosis via antiapoptotic Bcl-2 proteins
Authors: Charalampopoulos Ioannis , Tsatsanis Christos , Dermitzaki Erene , Alexaki Vasilia-Ismini , Castanas Elias , Margioris Andrew N. , Gravanis Achille
Published: May 2004

The neuroactive steroids dehydroepiandrosterone (DHEA), its sulfate ester DHEA sulfate (DHEAS), and allopregnanolone (Allo), produced by the CNS and the adrenals, appear to exert a protective effect in hippocampal and cortical neuron ischemia- and excitotoxicity-induced injury. We hypothesized that they may also play a protective role on the adrenal medulla, an important part of the sympathetic nervous system, and the tissue adjacent to their primary site of production. DHEA, DHEAS, and Allo protected rat chromaffin cells and the rat pheochromocytoma PC12 cell line, an established model for the study of adrenomedullary cell apoptosis and survival, against serum deprivation-induced apoptosis. Their effects were time- and dose-dependent, with EC
50
1.8, 1.1, and 1.5 nM, respectively. The antiapoptotic effect of DHEA DHEAS and Allo was compared to that of a long list of structurally related compounds and was found to be structure-specific, confined mainly to conformation 3β-OH-Δ
5
for androstenes and 3α-OH for pregnanes. Indeed, 3-keto, Δ
4
, or C7 hydroxylated androstenes and 3β pregnanes were ineffective. The prosurvival effect of DHEA(S) and Allo was
N
-methyl-D-aspartate-, GABA
A
-, sigma1-, or estrogen receptor-independent. It involved the antiapoptotic Bcl-2 proteins, their role being
sine qua non
for their action because Bcl-2 antisense oligonucleotides reversed their effects. Finally, DHEA(S) and Allo activated cAMP response element-binding protein and NF-κB, upstream effectors of antiapoptotic Bcl-2 protein expression. They also activated the antiapoptotic kinase PKCα/β, a posttranslational activator of Bcl-2 protein. Our findings suggest that decline of DHEA(S) and Allo during aging or stress may leave the adrenal medulla unprotected against proapoptotic challenges.
Resonant optical rectification in bacteriorhodopsin
Authors: Groma Géza I. , Colonna Anne , Lambry Jean-Christophe , Petrich Jacob W. , Váró György , Joffre Manuel , Vos Marten H. , Martin Jean-Louis
Published: May 2004

The relative role of retinal isomerization and microscopic polarization in the phototransduction process of bacteriorhodopsin is still an open question. It is known that both processes occur on an ultrafast time scale. The retinal trans→cis photoisomerization takes place on the time scale of a few hundred femtoseconds. On the other hand, it has been proposed that the primary light-induced event is a sudden polarization of the retinal environment, although there is no direct experimental evidence for femtosecond charge displacements, because photovoltaic techniques cannot be used to detect charge movements faster than picoseconds. Making use of the known high second-order susceptibility χ
(2)
of retinal in proteins, we have used a nonlinear technique, interferometric detection of coherent infrared emission, to study macroscopically oriented bacteriorhodopsin-containing purple membranes. We report and characterize impulsive macroscopic polarization of these films by optical rectification of an 11-fs visible light pulse in resonance with the optical transition. This finding provides direct evidence for charge separation as a precursor event for subsequent functional processes. A simple two-level model incorporating the resonant second-order optical properties of retinal, which are known to be a requirement for functioning of bacteriorhodopsin, is used to describe the observations. In addition to the electronic response, long-lived infrared emission at specific frequencies was observed, reflecting charge movements associated with vibrational motions. The simultaneous and phase-sensitive observation of both the electronic and vibrational signals opens the way to study the transduction of the initial polarization into structural dynamics.
Cti1/C1D interacts with condensin SMC hinge and supports the DNA repair function of condensin
Authors: Chen Ee Sin , Sutani Takashi , Yanagida Mitsuhiro
Published: May 2004

Condensin is a conserved five-subunit complex containing two SMC (structural maintenance of chromosomes) and three non-SMC subunits and plays a major role in mitotic chromosome condensation. Condensin also acts in interphase and is required for DNA repair and replication checkpoint control. We attempted to study the function of the condensin in greater detail by means of the isolation of interacting proteins with the two-hybrid system. Using the hinge domain of Cut3/SMC4 as bait, we found one Cut three-interacting (Cti) 14-kDa nuclear protein, Cti1. GST pull-down assay and immunoprecipitation supported physical interaction between Cti1 and condensin. Cti1 is similar to human C1D, which associates tightly with genomic DNA and functions to activate DNA protein kinase. SpC1D is essential for viability. The null mutant could germinate but arrest after replication, indicating that it is required for interphase growth. Importantly, an elevated dosage of spC1D suppressed the temperature, UV irradiation, and hydroxyurea sensitivity of the mutant of Cnd2, a non-SMC subunit of condensin. Upon exposure to hydroxyurea, spC1D accumulated on the nuclear chromatin, and the fraction of spC1D that was chromatin-bound increased. Cti1 is the first example of the protein that interacts with the hinge domain of SMC. Cti1 may have a supporting role for the DNA repair function of condensin.
XLαs, the extra-long form of the α-subunit of the Gs G protein, is significantly longer than suspected, and so is its companion Alex
Authors: Abramowitz Joel , Grenet Dagoberto , Birnbaumer Mariel , Torres Hector N. , Birnbaumer Lutz
Published: May 2004

Because of the use of alternate exons 1, mammals express two distinct forms of Gsα-subunits: the canonical 394-aa Gsα present in all tissues and a 700+-aa extra-long αs (XLαs) expressed in a more restricted manner. Both subunits transduce receptor signals into stimulation of adenylyl cyclase. The XL exon encodes the XL domain of XLαs and, in a parallel ORF, a protein called Alex. Alex interacts with the XL domain of XLαs and inhibits its adenylyl cyclase-stimulating function. In mice, rats, and humans, the XL exon is thought to contribute 422.3, 367.3, and 551.3 codons and to encode Alex proteins of 390, 357, and 561 aa, respectively. We report here that the XL exon is longer than presumed and contributes in mice, rats, and humans, respectively, an additional 364, 430, and 139 codons to XLαs. We called the N-terminally extended XLαs extra-extra-long Gsα, or XXLαs. Alex is likewise longer. Its ORF also remains open in the 5′ direction for ≈2,000 nt, giving rise to Alex-extended, or AlexX. RT-PCR of murine total brain RNA shows that the entire XXL domain is encoded in a single exon. Furthermore, we discovered two truncated forms of XXLαs, XXLb1 and XXLb2, in which, because of alternative splicing, the Gsα domain is replaced by different sequences. XXLb proteins are likely to be found as stable dimers with AlexX. The N-terminally longer proteins may play regulatory roles.
Dramatic acceleration of protein folding by stabilization of a nonnative backbone conformation
Authors: Di Nardo Ariel A. , Korzhnev Dmitry M. , Stogios Peter J. , Zarrine-Afsar Arash , Kay Lewis E. , Davidson Alan R.
Published: May 2004

Through a mutagenic investigation of Gly-48, a highly conserved position in the Src homology 3 domain, we have discovered a series of amino acid substitutions that are highly destabilizing, yet dramatically accelerate protein folding, some up to 10-fold compared with the wild-type rate. The unique folding properties of these mutants allowed for accurate measurement of their folding and unfolding rates in water with no denaturant by using an NMR spin relaxation dispersion technique. A strong correlation was found between β-sheet propensity and the folding rates of the Gly-48 mutants, even though Gly-48 lies in an unusual non-β-strand backbone conformation in the native state. This finding indicates that the accelerated folding rates of the Gly-48 mutants are the result of stabilization of a nonnative β-strand conformation in the transition-state structure at this position, thus providing the first, to our knowledge, experimentally elucidated example of a mechanism by which folding can occur fastest through a nonnative conformation. We also demonstrate that residues that are most stabilizing in the transition-state structure are most destabilizing in the native state, and also cause the greatest reductions in
in vitro
functional activity. These data indicate that the unusual native conformation of the Gly-48 position is important for function, and that evolutionary selection for function can result in a domain that folds at a rate far below the maximum possible.
Shape insensitive optimal adhesion of nanoscale fibrillar structures
Authors: Gao Huajian , Yao Haimin
Published: May 2004

Gecko and many insects have adopted nanoscale fibrillar structures on their feet as adhesion devices. Here, we consider adhesion between a single fiber and a substrate by van der Waals or electrostatic interactions. For a given contact area
A
, the theoretical pull-off force of the fiber is σ

th
A

where σ

th

is the theoretical strength of adhesion. We show that it is possible to design an optimal shape of the tip of the fiber to achieve the theoretical pull-off force. However, such design tends to be unreliable at the macroscopic scale because the pull-off force is sensitive to small variations in the tip shape. We find that a robust design of shape-insensitive optimal adhesion becomes possible only when the diameter of the fiber is reduced to length scales on the order of 100 nm. In general, optimal adhesion could be achieved by a combination of size reduction and shape optimization. The smaller the size, the less important the shape. At large contact sizes, optimal adhesion could still be achieved if the shape can be manufactured to a sufficiently high precision. The robust design of optimal adhesion at nanoscale provides a plausible explanation for the convergent evolution of hairy attachment systems in biology.
Norepinephrine-deficient mice lack responses to antidepressant drugs, including selective serotonin reuptake inhibitors
Authors: Cryan John F. , O'Leary Olivia F. , Jin Sung-Ha , Friedland Julie C. , Ouyang Ming , Hirsch Bradford R. , Page Michelle E. , Dalvi Ashutosh , Thomas Steven A. , Lucki Irwin
Published: May 2004

Mice unable to synthesize norepinephrine (NE) and epinephrine due to targeted disruption of the dopamine β-hydroxylase gene,
Dbh
, were used to critically test roles for NE in mediating acute behavioral changes elicited by different classes of antidepressants. To this end, we used the tail suspension test, one of the most widely used paradigms for assessing antidepressant activity and depression-related behaviors in normal and genetically modified mice.
Dbh
–/–
mice failed to respond to the behavioral effects of various antidepressants, including the NE reuptake inhibitors desipramine and reboxetine, the monoamine oxidase inhibitor pargyline, and the atypical antidepressant bupropion, even though they did not differ in baseline immobility from
Dbh
+/–
mice, which have normal levels of NE. Surprisingly, the effects of the selective serotonin reuptake inhibitors (SSRIs) fluoxetine, sertraline, and paroxetine were also absent or severely attenuated in the
Dbh
–/–
mice. In contrast, citalopram (the most selective SSRI) was equally effective at reducing immobility in mice with and without NE. Restoration of NE by using
l
-
threo
-3,4-dihydroxyphenylserine reinstated the behavioral effects of both desipramine and paroxetine in
Dbh
–/–
mice, thus demonstrating that the reduced sensitivity to antidepressants is related to NE function, as opposed to developmental abnormalities resulting from chronic NE deficiency. Microdialysis studies demonstrated that the ability of fluoxetine to increase hippocampal serotonin was blocked in
Dbh
–/–
mice, whereas citalopram's effect was only partially attenuated. These data show that NE plays an important role in mediating acute behavioral and neurochemical actions of many antidepressants, including most SSRIs.
The mechanism of transmembraneS-nitrosothiol transport
Authors: Zhang Yanhong , Hogg Neil
Published: May 2004

S-nitrosothiols have been suggested to play an important role in nitric oxide (NO)-mediated biological events. However, the mechanisms by which anS-nitrosothiol (or theS-nitroso functional group) is transferred across cell membrane are still poorly understood. We have demonstrated previously that the degradation ofS-nitrosoglutathione (GSNO) by cells absolutely required the presence of cystine in the extracellular medium and proposed a mechanism that involved the reduction of cystine to cysteine, followed by the reaction of cysteine with GSNO to formS-nitrosocysteine (CysNO), mixed disulfides, and nitrosyl anion. In the present study we have assessed the effect of cystine on the transfer of theS-nitroso functional group from the extracellular to the intracellular space. Using RAW 264.7 cells, we found that the presence ofl-cystine enhanced GSNO-dependentS-nitrosothiol uptake, increasing the intracellularS-nitrosothiol level from ≈60 pmol/mg of protein to ≈3 nmol/mg of protein. The uptake seems to depend on the reduction ofl-cystine tol-cysteine, which involves the\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} \begin{equation*}x_{c}^{-}\end{equation*}\end{document}amino acid transport system, the transnitrosation between GSNO andl-cysteine to forml-CysNO, and uptake ofl-CysNO via amino acid transport system L. Compared with GSNO, (Z)-1-[N-(3-ammoniopropyl)-N-[4-(3-aminopropylammonio)butyl]-amino]diazen-1-ium-1,2-diolate, an NO donor, is much less effective at intracellularS-nitrosothiol formation in the presence ofl-cystine orl-cysteine, suggesting that the biochemical changes that occur after exposure of cells toS-nitrosothiol, with respect to thiol chemistry, are distinctly different from those observed with NO.
Anteriorization of neural fate by inhibitor of β-catenin and T cell factor (ICAT), a negative regulator of Wnt signaling
Authors: Satoh Kiyotoshi , Kasai Mana , Ishidao Takefumi , Tago Kenichi , Ohwada Susumu , Hasegawa Yoshimi , Senda Takao , Takada Shinji , Nada Shigeyuki , Nakamura Tsutomu , Akiyama Tetsu
Published: May 2004

Inhibitor of β-catenin and T cell factor (ICAT) inhibits Wnt signaling by interfering with the interaction between β-catenin and T cell factor. Here we show that ICAT
–/–
embryos exhibit malformation of the forebrain and craniofacial bones and lack the kidney. Analysis of the neuronal differentiation of embryonic stem cells revealed that Wnt3a redirects the fate of neural progenitors to a posterior character, whereas ICAT induces forebrain cells by inhibiting Wnt signaling. Furthermore, ICAT
–/–
embryonic stem cells were found to differentiate into neuronal cells possessing a posterior character. These results suggest that ICAT plays an important role in the anteriorization of neural cells by inhibiting the posteriorizing activity of Wnt signaling.
Reversal of cystic fibrosis phenotype in a cultured Δ508 cystic fibrosis transmembrane conductance regulator cell line by oligonucleotide insertion
Authors: Zamecnik Paul C. , Raychowdhury Malay K. , Tabatadze David R. , Cantiello Horacio F.
Published: May 2004

Cystic fibrosis (CF) is a lethal genetic disorder that is due to mutations in the gene encoding the cAMP-activated anion CF transmembrane conductance regulator (CFTR) channel. A three-nucleotide base deletion (TTT), encoding phenylalanine in position 508 of the translatable CFTR sequence (accompanied by a C to T replacement immediately 5′ to the deletion), accounts for ≈75% of cases of the disease. In the present study, an oligonucleotide complex (CF4–CF6, 2′-0-methyl RNA–unmodified RNA oligonucleotide duplex, respectively) was used to restore CFTR function by insertion of missing bases in Δ508 CFTR mRNA from a cultured (Δ508) cell line. cAMP-activated whole-cell currents and Cl
–
transport were detected in CF4–CF6-treated, but not control Δ508, cells by patch-clamp and 6-methoxy-
N
-(3-sulfopropyl)quinolinium fluorescence (SPQ) quenching analyses, respectively. Further, the nucleotide addition in the deleted region of Δ508 CFTR was determined after amplification by RT-PCR. Insertion of UGU and replacement of U by C immediately 5′ to the deletion site in Δ508 mRNA appear to have taken place, with phenotypic but not genotypic reversion in tissue culture of treated cells. The mechanism of insertion of nucleotides has yet to be determined.
Design of temperature-sensitive mutants solely from amino acid sequence
Authors: Chakshusmathi Ghadiyaram , Mondal Kajari , Lakshmi G. Santosh , Singh Guramrit , Roy Ankita , Ch. Ravindra Babu , Madhusudhanan S. , Varadarajan Raghavan
Published: May 2004

Temperature-sensitive (Ts) mutants are a powerful tool with which to study gene function
in vivo
. Ts mutants are typically generated by random mutagenesis followed by laborious screening procedures. By using the
Escherichia coli
cytotoxin CcdB as a model system, simple procedures for generating Ts mutants at high frequency through site-directed mutagenesis were developed. Putative buried, hydrophobic residues are selected through analysis of the protein sequence. Residue burial is confirmed by ensuring that substitution of the residue by Asp leads to protein inactivation. At such sites, a Ts phenotype can typically be generated either by (
i
) substitution of two predicted, buried residues with the 18 remaining amino acids or (
ii
) introduction of Lys, Ser, Ala, and Trp at three to four predicted buried sites. By using these design strategies, 17 tight Ts mutants of CcdB were isolated at four predicted buried sites. The rules were further verified by making several Ts mutants of yeast Gal4 at residues 68, 69, and 70. No Ts mutants of either protein have been previously reported. Such Ts mutants of Gal4 can be used for conditional expression of a variety of genes by using the well characterized upstream-activating-sequence–Gal4 system.
Trigger factor binds to ribosome–signal-recognition particle (SRP) complexes and is excluded by binding of the SRP receptor
Authors: Buskiewicz Iwona , Deuerling Elke , Gu Shan-Qing , Jöckel Johannes , Rodnina Marina V. , Bukau Bernd , Wintermeyer Wolfgang
Published: May 2004

Trigger factor (TF) and signal recognition particle (SRP) bind to the bacterial ribosome and are both crosslinked to protein L23 at the peptide exit, where they interact with emerging nascent peptide chains. It is unclear whether TF and SRP exclude one another from their ribosomal binding site(s). Here we show that SRP and TF can bind simultaneously to ribosomes or ribosome nascent-chain complexes exposing a SRP-specific signal sequence. Based on changes of the crosslinking pattern and on results obtained by fluorescence measurements using fluorescence-labeled SRP, TF binding induces structural changes in the ribosome–SRP complex. Furthermore, we show that binding of the SRP receptor, FtsY, to ribosome-bound SRP excludes TF from the ribosome. These results suggest that TF and SRP sample nascent chains on the ribosome in a nonexclusive fashion. The decision for ribosome nascent-chain complexes exposing a signal sequence to enter SRP-dependent membrane targeting seems to be determined by the binding of SRP, which is stabilized by signal sequence recognition, and promoted by the exclusion of TF due to the binding of the SRP receptor to ribosome-bound SRP.
Activity-based probes for protein tyrosine phosphatases
Authors: Kumar Sanjai , Zhou Bo , Liang Fubo , Wang Wei-Qing , Huang Zhonghui , Zhang Zhong-Yin
Published: May 2004

Protein tyrosine phosphatases (PTPs) are involved in the regulation of many aspects of cellular activity including proliferation, differentiation, metabolism, migration, and survival. Given the large number and complexity of PTPs in cell signaling, new strategies are needed for the integrated analysis of PTPs in the whole proteome. Unfortunately, the activities of many PTPs are tightly regulated by posttranslational mechanisms, limiting the utility of standard genomics and proteomics methods for functional characterization of these enzymes. To facilitate the global analysis of PTPs, we designed and synthesized two activity-based probes that consist of α-bromobenzylphosphonate as a PTP-specific trapping device and a linker that connects the trapping device with a biotin tag for visualization and purification. We showed that these probes are active site-directed irreversible inactivators of PTPs and form a covalent adduct with PTPs involving the active site Cys residue. Additionally, we demonstrated that the probes are extremely specific toward PTPs while remaining inert to other proteins, including the whole proteome from
Escherichia coli
. Consequently, these activity-based PTP probes can be used to profile PTP activity in complex proteomes. The ability to interrogate the entire PTP family on the basis of changes in their activity should greatly accelerate both the assignment of PTP function and the identification of potential therapeutic targets.
Telomere length is reset during early mammalian embryogenesis
Authors: Schaetzlein Sonja , Lucas-Hahn Andrea , Lemme Erika , Kues Wilfried A. , Dorsch Martina , Manns Michael P. , Niemann Heiner , Rudolph K. Lenhard
Published: May 2004

The enzyme telomerase is active in germ cells and early embryonic development and is crucial for the maintenance of telomere length. Whereas the different length of telomeres in germ cells and somatic cells is well documented, information on telomere length regulation during embryogenesis is lacking. In this study, we demonstrate a telomere elongation program at the transition from morula to blastocyst in mice and cattle that establishes a specific telomere length set point during embryogenesis. We show that this process restores telomeres in cloned embryos derived from fibroblasts, regardless of the telomere length of donor nuclei, and that telomere elongation at this stage of embryogenesis is telomerase-dependent because it is abrogated in telomerase-deficient mice. These data demonstrate that early mammalian embryos have a telomerase-dependent genetic program that elongates telomeres to a defined length, possibly required to ensure sufficient telomere reserves for species integrity.