bluuebunny/crossref_metadata_2025 huggingface dataset:
A novel microsurgery method for intact plant tissue at the single cell level using ArF excimer laser microprojection
Authors: Kajiyama Shin'ichiro , Shoji Takeshi , Okuda Shinya , Izumi Yoshihiro , Fukusaki Ei‐ichiro , Kobayashi Akio
Published: September 2005

A novel microsurgery technique for the partial removal of rigid cell‐walls in intact plant tissue is established. Using a size‐variable slit, an ArF excimer laser was microprojected on the surface of the targeted cell, and this method enabled the area‐ and depth‐controllable processing of the cortical structure of plant cells including the cuticle and cell wall layer. In epidermal cells of all tested plants, viabilities of more than 90% were retained 24 h after irradiation. Scanning electron microscope (SEM) observation revealed that the cuticle layer of the irradiated region was completely ablated, and the cellulose microfibrils of the secondary cell wall were partially removed; furthermore, 4 days after laser treatment, the regeneration of cell wall fibrils was observed. As a model experiment, the transient expression of synthetic green fluorescent protein (sGFP) was performed by the microinjection of cauliflower mosaic virus (CMV) 35S promoter‐derived sGFP gene through an “aperture” in the treated cell surface. Moreover, micron‐sized fluorescent beads were successfully introduced by the same method into the onion cells indicating that this method can be used to introduce foreign materials as large as organelles. © 2005 Wiley Periodicals, Inc.
Characteristics of protein partitioning in an aqueous micellar‐gel system
Authors: van den Broeke L.J.P. , van Roosmalen D. , Dohmen‐Speelmans M.P.J. , Dietz C.H.J.T. , van der Wielen L.A.M. , Keurentjes J.T.F.
Published: September 2005

Partitioning of proteins has been studied experimentally in a system combining a gel‐bead phase and a nonionic micellar phase. The micellar phase consists of cylindrically shaped micelles, which are completely excluded from the gel‐bead phase. Partitioning of single‐component protein solutions (myoglobin, ovalbumin, and BSA) is determined by excluded‐volume interactions in the micellar phase, and as a result the proteins prefer the gel‐bead phase to the micellar phase. The protein concentration inside the gel beads increases with an increase in volume fraction of the micelles and increases with an increase in the size of the proteins. The protein partition coefficients obtained for a binary mixture of myoglobin and bovine serum albumin (BSA) show the same protein concentration dependence as the single‐component protein partition coefficients. © 2005 Wiley Periodicals, Inc.
Phytol‐modified heme in mesoporous silica: Conjugates as models of hemoproteins
Authors: Itoh Tetsuji , Yano Kazuhisa , Kajino Tsutomu , Inada Yuji , Fukushima Yoshiaki
Published: September 2005

A ferriprotoporphyrin, hemin (Fe3+), modified with 3,7,11,15‐tetramethyl‐2‐hexadecen‐1‐ol, phytol, was adsorbed in nano‐spaces of about 4 nm in diameter in mesoporous silica (FSM; folded‐sheet mesoporous material) forming a phytol‐modified hemin (Fe3+)–FSM nano‐conjugate. The properties and the structure of the conjugate were studied by UV‐visible light absorption, IR absorption spectroscopy, and a nitrogen adsorption isotherm. Although the hemin without phytol could not be adsorbed to the mesoporous silica, modification with phytol imparted preferential adsorption properties. The conjugate was not only stable but also had a peroxidase‐like activity in a 0.1% hydrogen peroxide solution, while free hemin in the solution was easily destroyed. The hemin (Fe3+) in the FSM was reduced to heme (Fe2+) by hydrazine. The phytol‐modified heme (Fe2+)–FSM conjugate formed an O2–heme complex with a superoxide type structure, resembling oxyhemoglobin or oxymyoglobin, which has not been previously observed for free heme in solution. The addition of carbon monoxide or nitrogen monoxide to the phytol‐modified heme (Fe2+)–FSM conjugate caused the formation of CO– or NO–heme complex in the nano‐spaces of the FSM. These properties are attributed not only to the Fe‐complex but also to the cooperative functions of the heme with mesoporous silica, resembling properties of a natural heme–protein conjugate; hemoglobin or peroxidase. These results are an elegant example of biomimetic nano‐technology. © 2005 Wiley Periodicals, Inc.
Regions of Tau Implicated in the Paired Helical Fragment Core as Defined by NMR
Authors: Sillen Alain , Leroy Arnaud , Wieruszeski Jean‐Michel , Loyens Anne , Beauvillain Jean‐Claude , Buée Luc , Landrieu Isabelle , Lippens Guy
Published: September 2005

We have studied the mature Alzheimer‐like fibers of tau by fluorescence and NMR spectroscopy. Assembly of the protein into paired helical filaments after incubation with heparin at 37 °C was verified by electron microscopy and size‐exclusion chromatography. NMR spectroscopy on these mature fibers revealed different regions of residual mobility for tau: the N‐terminal domain was found to maintain solution‐like dynamics and was followed by a large domain of decreasing mobility; finally the core region was distinguished by a solid‐like character. Heteronuclear‐NOE data indicate that the decreasing mobility is due to both a slowing down of the rapid nanosecond movements and the introduction of slower movements that lead to exchange broadening. Fluorescence spectroscopy confirmed the presence of this rigid core, and some degree of protection from hydrogen exchange for those residues was observed. Hence, our data give a more precise picture of the dynamics of tau when it is integrated into mature filaments and should provide further understanding of the molecular processes that govern aggregation.
Site‐Selective DNA Hydrolysis by CeIV–EDTA with the Use of One Oligonucleotide Additive Bearing Two Monophosphates
Authors: Chen Wen , Komiyama Makoto
Published: September 2005

Two deoxyuridine derivatives each bearing a monophosphate group at the 5‐position with a C3 linker, were incorporated into an oligonucleotide. By using this modified oligonucleotide, a bulge was formed at a predetermined position in a DNA substrate, and two monophosphate groups were placed at both junctions of the bulge. Upon treatment of the mixture with CeIV–EDTA at pH 7.0, the phosphodiester linkages at the bulge site were selectively and efficiently hydrolyzed. The monophosphate groups introduced into the bulge site greatly accelerated site‐selective DNA scission. Compared with the previously reported two‐additive system, which combines two oligonucleotide additives each with a monophosphate at their termini, the present one‐additive system is simpler and more convenient. Furthermore, site‐selective DNA hydrolysis by using this one‐additive system is successful even at high reaction temperatures (e.g., 55 °C). This reflects the thermodynamic stability of the duplexes formed between the substrate and the additive DNA.
Dichroic, Dinuclear μ2‐(η2‐NO)‐Nitrosoaniline‐Bridged Complexes of Rhenium of the Type [{(CO)3Re(μ‐X)}2ONC6H4NR2] (X = Cl, Br, I; R = Me, Et)
Authors: Krinninger Christoph , Högg Christof , Nöth Heinrich , Gálvez Ruiz Juan Carlos , Mayer Peter , Burkacky Ondrej , Zumbusch Andreas , Lorenz Ingo‐Peter
Published: September 2005

A series of unusual dinuclear μ2‐(η2‐NO)‐nitrosoaniline‐bridged complexes [{(CO)3Re(μ‐X)}2ONC6H4NR2] (X = Cl, Br, I; R = Me, Et) with dichroic properties have been synthesised by reaction of pentacarbonylhalogenorhenium(I) [(CO)5ReX] (X = Cl, Br, I) with the corresponding nitrosoaniline derivatives R2NC6H4NO (R = Me, Et). The deeply coloured solutions in CH2Cl2 show broad UV/Vis absorptions from 595 to 620 nm depending on the halogen bridges and N substituents. Single crystals of all six compounds exhibit a pronounced linear dichroism. The molecular structures have been determined by single‐crystal X‐ray analyses. All the compounds contain two face‐shared octahedra, with two halogens and one NO ligand as bridges. The NO ligand coordinates in a nonsymmetrical η2‐like fashion with N or O coordination to each Re centre. Therefore, the C‐nitroso group and the planar NC2 moiety of NR2 both lie almost exactly within the symmetry plane of the dinuclear complexes. These complexes belong to the novel and simple class of neutral dinuclear C‐nitroso complexes that include the rare, non‐assisted μ2‐(η2‐NO) ligand function and have only single halogen atoms in bridging positions.
Solid‐Phase Synthesis of Lipidated Peptides
Authors: Lumbierres Maria , Palomo Jose M. , Kragol Goran , Roehrs Sonja , Müller Oliver , Waldmann Herbert
Published: September 2005

A new flexible and efficient methodology for the solid‐phase synthesis of lipidated peptides has been developed. The approach is based on the use of previously synthesized building blocks and overcomes the limitations of previously reported methods, since long doubly lipidated peptides can be synthesized by using this route. Furthermore, it was thus possible to prepare a large number of N‐ and H‐Ras peptides bearing a wide range of reporter and/or linking groups—efficient tools for the investigation of biological processes. In terms of efficiency and flexibility this solid‐phase method is superior to the solution‐phase synthesis. It gives pure peptides in multimilligram amounts within a much shorter time and with superior overall yield.
Synthesis and Luminescence Properties of Ag2S and PbS Clusters in Zeolite A
Authors: Leiggener Claudia , Calzaferri Gion
Published: September 2005

Zeolite A provides a suitable environment to host Ag2S and PbS clusters, so that spectroscopic investigations on very small particles are possible. The Ag2S monomer is colorless and shows photoluminescence at 490 nm with a lifetime of 300 μs, while the absorption and luminescence of Ag4S2 and larger clusters are red‐shifted. The properties of these Ag2S/zeolite A materials depend on the co‐cations. Results for Li+, Na+, K+, Rb+, Cs+, Mg2+, Ca2+, and Sr2+ are reported. Excitation energy transfer between Ag2S and Ag4S2 has been studied in materials containing Ca2+ co‐cations. PbS particles can be prepared by the same method as Ag2S in the cavities of zeolite A. The PbS monomers obtained are yellow and show photoluminescence at 570 nm, with a lifetime of 700 ns.
Molecular Junctions Composed of Oligothiophene Dithiol‐Bridged Gold Nanoparticles Exhibiting Photoresponsive Properties
Authors: Huang Wei , Masuda Gou , Maeda Seisuke , Tanaka Hirofumi , Ogawa Takuji
Published: September 2005

Three oligothiophene dithiols with different numbers of thiophene rings (3, 6 or 9) have been synthesized and characterized. The X‐ray single crystal structures of terthiophene 2 and sexithiophene 5 are reported herein to show the exact molecular lengths, and to explain the difference between their UV‐visible spectra arising from the different packing modes. These dithiols with different chain lengths were then treated with 2‐dodecanethiol‐protected active gold nanoparticles (Au‐NPs) by means of in situ thiol‐to‐thiol ligand exchange in the presence of 1 μm gap Au electrodes. Thus the molecular junctions composed of self‐assembled films were prepared, in which oligothiophene dithiol‐bridged Au‐NPs were attached to two electrodes by means of AuS bonded contacts. The morphologies and current–voltage (I–V) characteristics of these films were studied by SEM and AFM approaches, which suggested that the thickness of the films (3–4 layers) varied within the size of one isolated Au‐NP and typical distance‐dependent semiconductor properties could be observed. Temperature dependent I–V measurements for these molecular junctions were performed in which the films served as active elements in the temperature range 6–300 K; classical Arrhenius plots and subsequent linear fits were carried out to give the activation energies (ΔE) of devices. Furthermore, preliminary studies on the photoresponsive properties of these devices were explored at 80, 160, and 300 K, respectively. Physical and photochemical mechanisms were used to explain the possible photocurrent generation processes. To the best of our knowledge, this is the first report in which oligothiophene dithiols act as bridging units to link Au‐NPs, and also the first report about functionalized Au‐NPs exhibiting photoresponse properties in the solid state.
Asymmetric Conjugate Reduction of α,β‐Unsaturated Ketones and Esters with Chiral Rhodium(2,6‐bisoxazolinylphenyl) Catalysts
Authors: Kanazawa Yoshinori , Tsuchiya Yasunori , Kobayashi Kazuki , Shiomi Takushi , Itoh Jun‐ichi , Kikuchi Makoto , Yamamoto Yoshihiko , Nishiyama Hisao
Published: September 2005

New asymmetric conjugate reduction of β,β‐disubstituted α,β‐unsaturated ketones and esters was accomplished with alkoxylhydrosilanes in the presence of chiral rhodium(2,6‐bisoxazolinylphenyl) complexes in high yields and high enantioselectivity. (E)‐4‐Phenyl‐3‐penten‐2‐one and (E)‐4‐phenyl‐4‐isopropyl‐3‐penten‐2‐one were readily reduced at 60 °C in 95 % ee and 98 % ee, respectively, by 1 mol % of catalyst loading. (EtO)2MeSiH proved to be the best hydrogen donor of choice. tert‐Butyl (E)‐β‐methylcinnamate and β‐isopropylcinnamate could also be reduced to the corresponding dihydrocinnamate derivatives up to 98 % ee.
Atropisomeric property of 1‐(2,6‐difluorobenzyl)‐3‐[(2R)‐amino‐2‐phenethyl]‐5‐(2‐fluoro‐3‐methoxyphenyl)‐6‐methyluracil
Authors: Tucci Fabio C. , Hu Tao , Mesleh Michael F. , Bokser Allan , Allsopp Eric , Gross Timothy D. , Guo Zhiqiang , Zhu Yun‐Fei , Struthers R. Scott , Ling Nicholas , Chen Chen
Published: September 2005

1‐(2,6‐Difluorobenzyl)‐3‐[(2R)‐amino‐2‐phenethyl]‐5‐(2‐fluoro‐3‐methoxyphenyl)‐6‐methyluracil (6), a potent and orally active antagonist of the human gonadotropin‐releasing hormone receptor, exists as a pair of atropisomers in solution, which was detected by NMR spectroscopy, and separable by HPLC. In addition to a (R)‐configured benzylamine, there is a second stereogenic element due to the presence of a chiral axis between the substituted 5‐phenyl group and the uracil core. The rate constant of the interconversion (k = 5.07 × 10−5 s−1) of these two atropisomers was determined by proton NMR analysis of a diastereoisomer‐enriched sample in aqueous solution at 25°C, and the corresponding Gibbs free energy ΔG# of rotation barrier (97.4 kJ mol−1) was calculated using the Eyring equation. The diastereoisomer half‐life at physiological temperature (37°C) in aqueous media was estimated to be about 46 min. © 2005 Wiley‐Liss, Inc. Chirality 17:559–564, 2005.
Optical resolution by crystallization from melt using enantiomer derivatives as resolving agents: Nonlinear behavior of resolving agent mixtures
Authors: Schindler József , Egressy Márton , Bálint József , Hell Zoltán , Fogassy Elemér
Published: September 2005

Substituted racemic 1‐phenylethylamine derivatives were reacted in molten phase with chiral N‐substituted 1‐phenylethylamine dicarboxylic acid derivatives (4–9), and their mixtures (e.g., 4+6, 7+8, etc.) in different ratios, and the crystalline quasi‐racemic diastereomers so formed were separated. Nonlinear behavior of the mixtures of resolving agents having related structure and considerable positive and negative chiral–chiral interactions were observed. © 2005 Wiley‐Liss, Inc. Chirality 17:565–569, 2005.
Evaluation of chiral discrimination of highly negatively charged enantiomers by quaternary ammonium β‐cyclodextrin using 1H NMR
Authors: Liu Qinfeng , Viranga Tillekeratne L.M. , Kim Yong‐Wah , Kirchhoff Jon R. , Hudson Richard A.
Published: September 2005

The positively charged quaternary ammonium cyclodextrin, QA‐β‐CD, was previously used as a chiral selector to achieve baseline resolution of two of the dianionic enantiomers of disodium 3‐(p‐isothiocyanatophenoxy)‐3‐(p‐isothiocyanatophenyl)propane‐1,2‐disulfate by capillary electrophoresis. The basis of the chiral discrimination between QA‐β‐CD and the enantiomers was investigated by 1H NMR spectroscopy. COSY and NOESY spectra were used to infer the role that molecular interactions and the stereocenters have upon association of QA‐β‐CD with the enantiomers. A parallel two‐step complexation model is used to rationalize the NMR and the chiral discrimination observed during separation of the enantiomers. © 2005 Wiley‐Liss, Inc. Chirality 17:570–576, 2005.
Computational study of conformational and chiroptical properties of (2R,3S,4R)‐(+)‐3,3′,4,4′,7‐flavanpentol
Authors: Cappelli Chiara , Bronco Simona , Monti Susanna
Published: September 2005

Conformational analysis of (2R,3S,4R)‐(+)‐3,3′,4,4′,7‐flavanpentol, a flavonoid compound displaying both antioxidant and pro‐oxidant properties, is performed by molecular mechanics and density functional theory calculations both in the gas phase and in methanol solution by using the Polarizable Continuum Model. Nine different conformations are identified. Absorption (UV) and circular dichroism (CD) spectra and optical rotations are calculated by means of time dependent density functional theory (TDDFT) and compared with experiments. The effects of a complex environment formed by water and proline‐rich peptide molecules on the conformational characteristics of (2R,3S,4R)‐(+)‐3,3′,4,4′,7‐flavanpentol and therefore on its UV and CD spectra are investigated by atomistic molecular dynamics simulations. © 2005 Wiley‐Liss, Inc. Chirality 17:577–589, 2005.
Role of cyclic AMP response element binding protein in human leukemias
Authors: Shankar Deepa B. , Cheng Jerry C. , Sakamoto Kathleen M.
Published: September 2005

Acute myeloid leukemia (AML) in adults has a 20% 5‐year disease‐free survival despite treatment with aggressive cytotoxic chemotherapy. Previous work from our laboratory demonstrated that the majority of patients with acute lymphoid and myeloid leukemia overexpress CREB in the bone marrow. CREB overexpression is associated with poor initial outcome of clinical disease in AML patients. CREB is a transcription factor that functions in glucose homeostasis, growth‐factor‐dependent cell survival, and memory. Signaling by hematopoietic growth factors, such as GM‐CSF, results in activation of CREB and up‐regulation of CREB target genes. To study its role in hematopoiesis, we overexpressed CREB in leukemia cell lines and in mice. CREB overexpression resulted in increased survival and proliferation of myeloid cells and blast‐transformation of bone marrow progenitor cells from transgenic mice expressing CREB in the myeloid lineage. CREB transgenic mice also develop myeloproliferative disease after 1 year. Thus, CREB acts as a protooncogene to regulate hematopoiesis and contributes to the leukemia phenotype. Our results suggest that CREB‐dependent pathways may serve as targets for directed therapies in leukemia in the future. Cancer 2005. © 2005 American Cancer Society.
Anaplastic large cell lymphoma treated with a leukemia‐like therapy
Authors: Rosolen Angelo , Pillon Marta , Garaventa Alberto , Burnelli Roberta , d'Amore Emanuele S. , Giuliano Maria , Comis Margherita , Cesaro Simone , Tettoni Katia , Luisa Moleti Maria , Tamaro Paolo , Visintin Gianluca , Zanesco Luigi
Published: October 2005

BACKGROUND

Childhood anaplastic large cell lymphoma (ALCL) is a well defined entity with a rather poor prognosis. Different approaches have been adopted in the treatment of ALCL in various cooperative trials, including short high‐dose intensive therapy and leukemia‐like protocols. In the early 1990s, the Italian Association of Pediatric Hematology and Oncology (AIEOP) initiated a multicenter trial for the treatment of ALCL based on a modified LSA2‐L2 protocol.

METHODS

Thirty‐four consecutive eligible children with newly diagnosed ALCL were enrolled in the AIEOP LNH‐92 protocol. Treatment was comprised of an induction of remission phase, followed by consolidation and maintenance for a total duration of 24 months, independently of disease stage.

RESULTS

Thirty of 34 patients (88%) achieved complete disease remission and 8 patients experienced disease recurrence. With a median follow‐up of 8.4 years, the probabilities of survival and event‐free survival were 85% (range, 79–91%) and 65% (range, 57–73%), respectively. Therapy was well tolerated and hematologic toxicity was the most frequent toxicity.

CONCLUSIONS

The leukemia‐like protocol AIEOP LNH‐92 was found to be an effective treatment for childhood ALCL. Its long duration may be beneficial to specific patient subgroups, but optimal treatment duration in ALCL remains to be elucidated. Cancer 2005. © 2005 American Cancer Society.
Projection patterns of gustatory neurons in the suboesophageal ganglion and tritocerebrum of mosquitoes
Authors: Ignell Rickard , Hansson Bill S.
Published: September 2005

Mosquitoes are heavily dependent on gustatory information when feeding. Following the recent elucidation of the molecular basis of gustation in the malaria mosquito, we present a detailed study of primary central projections of gustatory receptor neurons into the brain in the malaria (Anopheles gambiae) and yellow fever (Aedes aegypti) mosquito. In the brain we provide a detailed map of the areas targeted and describe a number of intrinsic neural elements connecting primary taste areas to higher brain levels. The morphological features described are discussed and compared to earlier reports in other insects as, e.g., the fruitfly, Drosophila. J. Comp. Neurol. 492:214–233, 2005. © 2005 Wiley‐Liss, Inc.
Prefrontal cortex in the rat: Projections to subcortical autonomic, motor, and limbic centers
Authors: Gabbott Paul L.A. , Warner Tracy A. , Jays Paul R.L. , Salway Phillip , Busby Sarah J.
Published: September 2005

This paper describes the quantitative areal and laminar distribution of identified neuron populations projecting from areas of prefrontal cortex (PFC) to subcortical autonomic, motor, and limbic sites in the rat. Injections of the retrograde pathway tracer wheat germ agglutinin conjugated with horseradish peroxidase (WGA‐HRP) were made into dorsal/ventral striatum (DS/VS), basolateral amygdala (BLA), mediodorsal thalamus (MD), lateral hypothalamus (LH), mediolateral septum, dorsolateral periaqueductal gray, dorsal raphe, ventral tegmental area, parabrachial nucleus, nucleus tractus solitarius, rostral/caudal ventrolateral medulla, or thoracic spinal cord (SC). High‐resolution flat‐map density distributions of retrogradely labelled neurons indicated that specific PFC regions were differentially involved in the projections studied, with medial (m)PFC divided into dorsal and ventral sectors. The percentages that WGA‐HRP retrogradely labelled neurons composed of the projection neurons in individual layers of infralimbic (IL; area 25) prelimbic (PL; area 32), and dorsal anterior cingulate (ACd; area 24b) cortices were calculated. Among layer 5 pyramidal cells, approximately 27.4% in IL/PL/ACd cortices projected to LH, 22.9% in IL/ventral PL to VS, 18.3% in ACd/dorsal PL to DS, and 8.1% in areas IL/PL to BLA; and 37% of layer 6 pyramidal cells in IL/PL/ACd projected to MD. Data for other projection pathways are given. Multiple dual retrograde fluorescent tracing studies indicated that moderate populations (<9%) of layer 5 mPFC neurons projected to LH/VS, LH/SC, or VS/BLA. The data provide new quantitative information concerning the density and distribution of neurons involved in identified projection pathways from defined areas of the rat PFC to specific subcortical targets involved in dynamic goal‐directed behavior. J. Comp. Neurol. 492:145–177, 2005. © 2005 Wiley‐Liss, Inc.
Direct time integration of rigid body motion with discrete‐impulse midpoint approximation: explicit Newmark algorithms
Authors: Krysl P.
Published: October 2005

We address time integration of computational mechanical models where the evaluation of the forcing is expensive (molecular dynamics, for example), and hence we investigate integrators that are explicit in the forcing evaluations. The point of departure is the midpoint rule, either in the classical form for the vector space setting, or the Lie form for the rotation group. By introducing discrete, concentrated impulses we approximate the forcing imparted to the system over the time step, and thus we formulate two adjoint explicit first‐order integrators. These may be composed to yield a second‐order integrator which inherits the good properties of the first‐order integrators, in our case symplecticity and momentum conservation. Thus, we get the classical Newmark algorithm for translational motion (vector space dynamics), or the rotation‐group counterpart of the vector space integrator, which we call the explicit midpoint Lie Newmark algorithm. Enunciation of the parallels between these two algorithms is the main accomplishment of this contribution. Copyright © 2005 John Wiley & Sons, Ltd.
New tools for visualization and analysis of morphogenesis in spherical embryos
Authors: Tyszka J. Michael , Ewald Andrew J. , Wallingford John B. , Fraser Scott E.
Published: September 2005

Many classical models of development, including amphibians, fish, and echinoderms, have embryos that are approximately spherical and contain concentric cell layers during early development. Neighbor relationships in such curved cell layers are not conveniently assayed or measured by conventional physical or optical sectioning techniques. To answer these challenges, we have constructed computational methods that correct for spherical distortion in 2D images and that allow extraction of concentric cell layers from 3D digital images. These methods for quantitative analysis and visualization of early development in spherical embryos are introduced by using them for the quantitative analysis of 2D and 3D images of gastrula stage Xenopus laevis. Developmental Dynamics 234:974–983, 2005. © 2005 Wiley‐Liss, Inc.
Transient natural convection of low‐Prandtl‐number fluids in a differentially heated cavity
Authors: Mohamad A. A. , Viskanta R.
Published: October 2005

The transient convective motion in a two‐dimensional square cavity driven by a temperature gradient is analysed. The cavity is filled with a low‐Prandtl‐number fluid and the vertical walls are maintained at constant but different temperatures, while the horizontal boundaries are adiabatic. A control volume approach with a staggered grid is employed to formulate the finite difference equations. Numerically accurate solutions are obtained for Prandtl numbers of 0·001, 0·005 and 0·01 and for Grashof numbers up to 1 × 107. It was found that the flow field exhibits periodic oscillation at the critical Grashof numbers, which are dependent on the Prandtl number. As the Prandtl number is decreased, the critical Grashof number and the frequency of oscillation decrease. Prior to the oscillatory flow, steady state solutions with an oscillatory transient period were predicted. In addition to the main circulation, four weak circulations were predicted at the corners of the cavity.
A new approach to potential flow around axisymmetric bodies
Authors: Yücel Nuri̇ , Altaç Zekeri̇ya
Published: October 2005

A new method is introduced to solve potential flow problems around axisymmetric bodies. The approach relies on expressing the infinite series expansion of the Laplace equation solution in terms of a finite sum which preserves the Laplace solution for the potential function under a Neumann‐type boundary condition. Then the coefficients of the finite sum are calculated in a least squares approximation sense using the Gram‐Schmidt orthonormalization method. Sample benchmark problems are presented and discussed in some detail. The solutions are accurate and converged faster when a rather small number of terms were used. The method is simple and can be easily programmed.
Numerical methods for water‐wave radiation problems
Authors: Liapis Stergios
Published: October 2005

A boundary integral equation method is used to compute the forces acting on bodies oscillating at or near the free surface of a fluid. This method relies on the use of a Green function representing the potential of a unit pulsating source beneath the free surface. A peculiarity of the boundary integral equation method in the presence of a free surface is that it breaks down at certain characteristic frequencies also known as ‘irregular frequencies’. The objectives of the present study are to develop simple and efficient algorithms for the numerical evaluation of the Green function as well as a method for removing the irregular frequencies. In particular, systematic expansions for the Green function have been developed. These algorithms are very efficient and remarkably simple to implement numerically. In order to remove the irregular frequencies, the boundary integral equation is supplemented by the first N null‐field equations. As a result the first N irregular frequencies are eliminated. This method introduces a very small additional computational cost and is general enough so that it can be applied to any free surface problem.
Unsteady supersonic flow over an oscillatory aerofoil using a second‐order TVD scheme
Authors: Kim Jae‐Soo
Published: October 2005

The unsteady flow over an oscillatory NACA0012 aerofoil has been simulated by the calculation with Euler equations. The equations are discretized by an implicit Euler in time, and a second‐order space‐accurate TVD scheme based on flux vector splitting with van Leer's limiter. Modified eigenvalues are proposed to overcome the slope discontinuities of split eigenvalues at Mach = 0·0 and ± 1·0, and to generate a bow shock in front of the aerofoil. A moving grid system around the aerofoil is generated by Sorenson's boundary fitted co‐ordinates for each time step. The calculations have been done for two angles of attack θ = 5·0° sin (ωt) and θ = 3·0° + 3·0° sin (ωt) for the free‐stream Mach numbers 2·0 and 3·0. The results show that pressure and Mach cells flow along characteristic lines. To examine unsteady effects, the responses of wall pressure and normal force coefficients are analysed by a Fourier series expansion.
An integrated modelling system for coastal area dynamics
Authors: Klevanny K. A. , Matveyev G. V. , Voltzinger N. E.
Published: October 2005

Two‐dimensional initial‐boundary value problems are considered for the shallow water equations and the equation of advection and dispersion of pollutants. The problems are solved in curvilinear boundary fitted co‐ordinates. The transformed equations are integrated on a regular grid by the semi‐implicit and implicit finite difference methods. Based on the numerical method, the integrated modelling system Cardinal for coastal area dynamics and pollution processes is developed for application on personal computers. Examples of computations are given.
Effective downstream boundary conditions for incompressible Navier–Stokes equations
Authors: Bruneau Ch.‐H. , Fabrie P.
Published: October 2005

The aim of this paper is to give open boundary conditions for the incompressible Navier–Stokes equations. From a weak formulation in velocity–pressure variables, some natural boundary conditions involving the traction or pseudotraction and inertial terms are established. Numerical experiments on the flow behind a cylinder show the efficiency of these conditions, which convey properly the vortices downstream. Comparisons with other boundary conditions for the velocity and pressure are also performed.
Injectable bone cements for use in vertebroplasty and kyphoplasty: State‐of‐the‐art review
Authors: Lewis Gladius
Published: September 2005

Vertebroplasty (VP) and kyphoplasty (KP) are minimally invasive surgical procedures that have recently been introduced for the medical management of osteoporosis‐induced vertebral compression fractures. The aim of VP is to stabilize the fractured vertebral body, while the goals of KP are to stabilize the fractured vertebral body and to restore its height to as near its prefracture level as possible. Both procedures involve injection of the setting dough of an injectable bone cement (IBC) into the fractured vertebral body, thereby highlighting the indispensable role that the IBC plays. Although there is a very large literature on IBCs, no detailed critical review of it has been published. Such a review is the subject of the present work, which is in seven parts. The review opens with a succinct introduction to VP and KP. The topics covered in the parts that follow are: (1) a listing of the 18 most desirable properties of an IBC (e.g., easy injectability, high radiopacity, and a resorption rate that is neither too high nor too low); (2) descriptions of the four classes of IBCs (calcium phosphates, acrylic bone cements, calcium sulfates, and composites); (3) concerns that have been raised with regard to the use of IBCs (such as the potential for thermal necrosis of tissue at the peri‐augmentation site, when an acrylic bone cement is used); (4) explicative summaries of the main findings of literature studies on the influence of nine factors (such as powder particle size, powder‐to‐liquid ratio, and the method used to mix the powder and the liquid) on the values of various properties of IBCs; (5) explicative summaries of the main findings of literature studies on five fundamental matters, such as the aging mechanism of the powder, the thermokinetics of a setting dough, and the influence of the type of IBC used on various ex vivo biomechanical performance measures of VP‐ and KP‐augmented vertebral bodies; and (6) descriptions of topics in six areas for future research, such as the determination of an overall index of the fatigue performance of an IBC and the development of internationally recognized standardized testing protocols to employ when a synthetic cancellous bone void model is used in the rapid in vitro screening of IBCs. The review ends with a summary of the most salient points and observations made. © 2005 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 2006
Meniscal replacement in dogs. Tissue regeneration in two different materials with similar properties
Authors: Tienen T. G. , Heijkants R. G. J. C. , de Groot J. H. , Schouten A. J. , Pennings A. J. , Veth R. P. H. , Buma P.
Published: October 2005

In earlier studies, meniscal replacement with a porous polymer implant led to regeneration of neo‐meniscal tissue. To evaluate the influence of the chemical properties on the tissue regeneration in the implant, in the present study, the meniscus in the dog's knee was replaced with either an aromatic 4,4‐diphenylmethanediisocyanate based polyesterurethane implant (Estane) (n = 6) or with an aliphatic 1,4‐butanediisocyanate based polyesterurethane implant (PCLPU) (n = 6). After 6 months, the knee joints were resected and the tissue behavior in the two different prostheses was evaluated microscopically. In both prostheses, a meniscus‐like distribution of the tissue phenotype was found with collagen type I in the peripheral fibrous zones and collagen type II in the central, more cartilaginous zones. The compression‐stress behavior of the implant‐tissue construct remained in between the stiffness of the polymer material and that of the native meniscus. The PCLPU implant seemed to provoke less synovial tissue reaction. After meniscectomy solely, in 5 out of 6 cases, a meniscus‐like regenerate was formed. Furthermore, the articular cartilage degeneration after placing a PCLPU implant did also not exceed the degeneration after the Estane implant or after meniscectomy. The differences between these two implants did not seem to influence the tissue regeneration in the implant. However, PCLPU seemed to evoke less tissue reaction and, therefore, is thought to be less or even nontoxic as compared with the Estane implant. Therefore, for studies in the future, the authors prefer the PCLPU prostheses for replacement of the meniscus. © 2005 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 2006
Injectable biomaterials for incontinence and vesico‐ureteral reflux: Current status and future promise
Authors: Tsai Chi‐Chun , Lin Victor , Tang Liping
Published: October 2005

Many injectable biomaterials have been produced as bulking agents for compression of urethral sphincter or ureteral orifice for treating adult stress incontinence or vesico‐ureteral reflux in pediatrics. The agents being developed include glutaraldehyde crosslinked collagen, dextranomer/hyaluronic acid copolymer, pyrolytic carbon‐coated zirconium oxide beads, polydimethyl‐siloxane microparticles, polytetrafluoroethylene paste, autologous fats, autologous chondrocytes, and others. Though less invasive nature of these agents has gained their popularity as a quick solution of the disease symptoms, most of such treatments fail to produce good long‐term efficacy. The failure is likely caused by the rapid degradation of material implants and the lack of tissue regeneration/integration properties. We thus believe that a good injectable biomaterial for incontinence should possess the following two properties: (1) to resist degradation and to reside in the implantation sites for a long period of time or (2) to enhance tissue regeneration and to establish permanent periurethral or subureteric tissue. Here we report some recent results for supporting this hypothesis. © 2005 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 2006
Study of hepatocyte differentiation using embryonic stem cells
Authors: Lavon Neta , Benvenisty Nissim
Published: October 2005

The liver has many crucial functions including metabolizing dietary molecules, detoxifying compounds, and storing glycogen. The hepatocytes, comprising most of the liver organ, progressively modify their gene expression profile during the fetal development according to their roles in the different phases of development. Embryonic stem (ES) cells serve as a major tool in understanding liver development. These cells may also serve as a source of hepatic cells for cellular therapy. In this review, we aim to summarize the research that has been performed in the field of hepatocyte differentiation from mouse and human ES cells. We discuss the various methodologies for the differentiation of ES cells towards hepatic cells using either spontaneous or directed differentiation protocols. Although many protocols for differentiating ES cells to hepatic cells have been developed, the analysis of their status is not trivial and can lead to various conclusions. Hence, we discuss the issues of analyzing hepatocytes by means of the specificity of the markers for hepatocytes and the status of the cells as fetal or adult hepatocytes. © 2005 Wiley‐Liss, Inc.
Inner nuclear membrane and signal transduction
Authors: Worman Howard J.
Published: October 2005

Recent research has shown that the inner nuclear membrane is a site for regulation of signal transduction from the plasma membrane to the nucleus. This has coincided with discoveries showing that mutations in extrinsic and intrinsic inner nuclear membrane proteins cause a variety of inherited diseases. In most instances, the mechanisms by which mutations in inner nuclear membrane proteins cause disease are not understood. In at least one case, however, an alteration in signal transduction appears to underlie disease pathogenesis. J. Cell. Biochem. © 2005 Wiley‐Liss, Inc.
Absence of SPARC in lens epithelial cells results in altered adhesion and extracellular matrix production in vitro
Authors: Weaver Matt S. , Sage E. Helene , Yan Qi
Published: October 2005

The matricellular protein SPARC (also known as osteonectin and BM‐40) is expressed abundantly in lens epithelium. That SPARC‐null mice exhibit early cataractogenesis, indicates a role for SPARC in the maintenance of lens transparency. Comparison of cultured wild‐type and SPARC‐null lens epithelial cells revealed significant changes in adhesion to different substrates. SPARC‐null lens cells displayed enhanced attachment and spreading, focal adhesion formation, and resistance to trypsin detachment in comparison to wild‐type cells. In the absence of SPARC, there was increased deposition of the ECM protein laminin‐1 (LN‐1). Proteins associated with focal adhesions were increased in SPARC‐null versus wild‐type lens cells: levels of α6‐integrin heterodimers, talin, and paxillin phosphorylated on tyrosine were enhanced significantly, as was the association of β1‐integrin with talin and paxillin. Restoration of the wild‐type phenotype in SPARC‐null cultures was accomplished through genetic rescue by stable transfection of SPARC cDNA. Our findings indicate that SPARC is counter‐adhesive for murine lens epithelial cells and demonstrate that multiple factors contribute to this activity. We also identify SPARC as a modulator of LN‐1 secretion and deposition by these cells, an activity important in epithelial cell‐ECM interactions in the ocular lens. J. Cell. Biochem. © 2005 Wiley‐Liss, Inc.
The GROMOS software for biomolecular simulation: GROMOS05
Authors: Christen Markus , Hünenberger Philippe H. , Bakowies Dirk , Baron Riccardo , Bürgi Roland , Geerke Daan P. , Heinz Tim N. , Kastenholz Mika A. , Kräutler Vincent , Oostenbrink Chris , Peter Christine , Trzesniak Daniel , van Gunsteren Wilfred F.
Published: October 2005

We present the latest version of the Groningen Molecular Simulation program package, GROMOS05. It has been developed for the dynamical modelling of (bio)molecules using the methods of molecular dynamics, stochastic dynamics, and energy minimization. An overview of GROMOS05 is given, highlighting features not present in the last major release, GROMOS96. The organization of the program package is outlined and the included analysis package GROMOS++ is described. Finally, some applications illustrating the various available functionalities are presented. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 1719–1751, 2005
An in silico method using an epitope motif database for predicting the location of antigenic determinants on proteins in a structural context
Authors: Batori Vincent , Friis Esben P. , Nielsen Henrik , Roggen Erwin L.
Published: September 2005

Presently X‐ray crystallography of protein–antibody complexes is still the most direct way of identifying B‐cell epitopes. The objective of this study was to assess the potential of a computer‐based epitope mapping tool (EMT) using antigenic amino acid motifs as a fast alternative in a number of applications not requiring detailed information, e.g. development of pharmaceutical proteins, vaccines and industrial enzymes. Using Gal d 4 as a model protein, the EMT was capable of identifying, in the context of the folded protein, amino acid positions known to be involved in antibody binding. The high sensitivity and positive predictive value of the EMT as well as the relevance of the structural associations suggested by the EMT indicated the existence of amino acid motifs that are likely to be involved in antigenic determinants. In addition, differential mapping revealed that sensitivity and positive predictive value were dependent on the minimum relative surface accessibility (RSA) of the amino acids included in the mapping, demonstrating that the EMTs accommodated for the fact that epitopes are three‐dimensional entities with various degrees of accessibility. The comparison with existing prediction scales demonstrated the superiority of the EMT with respect to physico‐chemical scales. The mapping tool also performed better than the available structural scales, but the significance of the differences remains to be established. Thus, the EMT has the potential of becoming a fast and simple alternative to X‐ray crystallography for predicting structural antigenic determinants, if detailed epitope information is not required. Copyright © 2005 John Wiley & Sons, Ltd.
Simplified heat exchange model for semiconductor laser diodes thermal parameters extraction
Authors: André P S , Antunes P , Teixeira A L J , Pinto J L
Published: September 2005

By investigating the heat flow mechanism in a semiconductor laser diode, we demonstrate a comprehensive technique for optical device thermal parameters extraction to be used in the prediction of the laser performance This accurate and precise heat exchange model takes into account the relevant heat exchange mechanism and mechanical considerations of the laser diode mounting. We measured the thermal response of a semiconductor laser diode attach to a substrate, deriving from those the device thermal parameters such as heat capacity and thermal conductance for the device and subtract. From the estimated values a prediction of the real laser temperature response is obtained directly from the measurements realized in the substrate.
Enhancement of transepidermal skin clearing agent delivery using a 980 nm diode laser
Authors: Stumpp O.F. , Welch A.J. , Milner T.E. , Neev J.
Published: September 2005

Background and Objectives

Patient compliant optical skin clearing requires non‐invasive topical delivery of clearing agents such as glycerol. This requires reducing the skin barrier function by disrupting stratum corneum integrity, which was achieved using a 980 nm diode laser with artificial absorption substrates on the skin surface. Reduction of light scattering has the potential to improve many current and novel diagnostic and therapeutic applications of lasers in medicine.

Study Design/Materials and Methods

In vivo hamster and rat skin was used to test optical skin clearing. Absorption substrates were applied to the skin after shaving. These included black ink, dark children's rub‐on tattoo, and carbon paper. 980 nm cw laser light was used to ablate these substrates and to heat the skin surface to enhance the diffusion of topically applied glycerol for optical skin clearing. Increased light penetration was determined from amplitude optical coherence tomography data.

Results

Results indicate an improvement of the ability to measure an OCT signal at a wavelength of 1,290 nm up to 42% deeper into in vivo rodent skin using a 980 nm laser with a fluence of less than 0.96 J/mm2 to alter the stratum corneum.

Conclusions

The use of an inexpensive diode laser can significantly enhance the delivery of topically applied glycerol for optical skin clearing. The laser use involves application of an absorption substrate onto the skin surface. Using carbon paper left no unwanted residue behind and is considered optimal for this purpose. Lasers Surg. Med. © 2005 Wiley‐Liss, Inc.
Flavins are source of visible‐light‐induced free radical formation in cells
Authors: Eichler Maor , Lavi Ronit , Shainberg Asher , Lubart Rachel
Published: September 2005

Background and Objectives

It has been hypothesized that reactive oxygen species (ROS) are created by an endogenous photosensitizer during low energy visible light illumination of tissue, and these ROS are responsible for reported biostimulative effects. This study aims to identify the endogenous photosensitizer responsible for ROS production by visible light.

Study Design/Materials and Methods

Electron paramagnetic resonance (EPR) spectroscopy was used to detect oxyradicals produced in cardiac and sperm cells during illumination by a halogen lamp. Oxyradical production was determined as a function of illumination wavelength, cell fraction, and molecular weight.

Results

Oxyradicals were created solely by the 400–500 nm range of visible light. The endogenous photosensitizer is found predominantly in the cytosol and is smaller than 12 kD. Flavin mononucleotide produces the same signal at concentrations consistent with reported intracellular free flavin concentrations.

Conclusions

A small, water soluble photosensitizer active only at wavelengths shorter than 500 nm is consistent with a flavin, which reproduces cellular signals at physiological concentrations. Thus, flavins are responsible for the photosensitization of the observed oxyradicals in cells. Lasers Surg. Med. © 2005 Wiley‐Liss, Inc.