bluuebunny/crossref_metadata_2025_split huggingface dataset:
Runx-dependent expression of PKC is critical for cell survival in the sea urchin embryo
Authors: Dickey-Sims Carrie , Robertson Anthony J , Rupp Dawn E , McCarthy John J , Coffman James A 
Published: August 2005

Abstract

Background

Runx transcription factors play critical roles in the developmental control of cell fate and contribute variously as oncoproteins and tumor suppressors to leukemia and other cancers. To discover fundamental Runx functions in the cell biology of animal development, we have employed morpholino antisense-mediated knockdown of the sea urchin Runx protein SpRunt-1. Previously we showed that embryos depleted of SpRunt-1 arrest development at early gastrula stage and underexpress the conventional protein kinase C SpPKC1.

Results

We report here that SpRunt-1 deficiency leads to ectopic cell proliferation and extensive apoptosis. Suppression of the apoptosis by pharmacological inhibition of caspase-3 prevents the ectopic proliferation and rescues gastrulation, indicating that many of the overt defects obtained by knockdown of SpRunt-1 are secondary to the apoptosis. Inhibition or knockdown of SpPKC1 also causes apoptosis, while cell survival is rescued in SpRunt-1 morphant embryos coinjected with SpPKC1 mRNA, suggesting that the apoptosis associated with SpRunt-1 deficiency is caused by the deficit in SpPKC1 expression. Chromatin immunoprecipitation indicates that SpRunt-1 interacts physically with SpPKC1 in vivo, and cis-regulatory analysis shows that this interaction activates SpPKC1 transcription.

Conclusions

Our results show that Runx-dependent activation of SpPKC1 is essential for maintaining protein kinase C activity at levels conducive to cell survival during embryogenesis.
Effect of gait speed on gait rhythmicity in Parkinson's disease: variability of stride time and swing time respond differently
Authors: Frenkel-Toledo Silvi , Giladi Nir , Peretz Chava , Herman Talia , Gruendlinger Leor , Hausdorff Jeffrey M 
Published: August 2005

Abstract

Background
The ability to maintain a steady gait rhythm is impaired in patients with Parkinson's disease (PD). This aspect of locomotor dyscontrol, which likely reflects impaired automaticity in PD, can be quantified by measuring the stride-to-stride variability of gait timing. Previous work has shown an increase in both the variability of the stride time and swing time in PD, but the origins of these changes are not fully understood. Patients with PD also generally walk with a reduced gait speed, a potential confounder of the observed changes in variability. The purpose of the present study was to examine the relationship between walking speed and gait variability.

Methods
Stride time variability and swing time variability were measured in 36 patients with PD (Hoehn and Yahr stage 2–2.5) and 30 healthy controls who walked on a treadmill at four different speeds: 1) Comfortable walking speed (CWS), 2) 80% of CWS 3) 90% of CWS, and 4) 110% of CWS. In addition, we studied the effects of walking slowly on level ground, both with and without a walker.

Results
Consistent with previous findings, increased variability of stride time and swing time was observed in the patients with PD in CWS, compared to controls. In both groups, there was a small but significant association between treadmill gait speed and stride time variability such that higher speeds were associated with lower (better) values of stride time variability (p = 0.0002). In contrast, swing time variability did not change in response to changes in gait speed. Similar results were observed with walking on level ground.

Conclusion
The present results demonstrate that swing time variability is independent of gait speed, at least over the range studied, and therefore, that it may be used as a speed-independent marker of rhythmicity and gait steadiness. Since walking speed did not affect stride time variability and swing time variability in the same way, it appears that these two aspects of gait rhythmicity are not entirely controlled by the same mechanisms. The present findings also suggest that the increased gait variability in PD is disease-related, and not simply a consequence of bradykinesia.
Evidence for a second class of S-adenosylmethionine riboswitches and other regulatory RNA motifs in alpha-proteobacteria
Authors: Corbino Keith A , Barrick Jeffrey E , Lim Jinsoo , Welz Rüdiger , Tucker Brian J , Puskarz Izabela , Mandal Maumita , Rudnick Noam D , Breaker Ronald R 
Published: August 2005

Abstract
Background
Riboswitches are RNA elements in the 5' untranslated leaders of bacterial mRNAs that directly sense the levels of specific metabolites with a structurally conserved aptamer domain to regulate expression of downstream genes. Riboswitches are most common in the genomes of low GC Gram-positive bacteria (for example, Bacillus subtilis contains examples of all known riboswitches), and some riboswitch classes seem to be restricted to this group.

Results
We used comparative sequence analysis and structural probing to identify five RNA elements (serC, speF, suhB, ybhL, and metA) that reside in the intergenic regions of Agrobacterium tumefaciens and many other α-proteobacteria. One of these, the metA motif, is found upstream of methionine biosynthesis genes and binds S-adenosylmethionine (SAM). This natural aptamer most likely functions as a SAM riboswitch (SAM-II) with a consensus sequence and structure that is distinct from the class of SAM riboswitches (SAM-I) predominantly found in Gram-positive bacteria. The minimal functional SAM-II aptamer consists of fewer than 70 nucleotides, which form a single stem and a pseudoknot. Despite its simple architecture and lower affinity for SAM, the SAM-II aptamer strongly discriminates against related compounds.

Conclusion
SAM-II is the only metabolite-binding riboswitch class identified so far that is not found in Gram-positive bacteria, and its existence demonstrates that biological systems can use multiple RNA structures to sense a single chemical compound. The two SAM riboswitches might be 'RNA World' relics that were selectively retained in certain bacterial lineages or new motifs that have emerged since the divergence of the major bacterial groups.
Genome-wide promoter extraction and analysis in human, mouse, and rat
Authors: Xuan Zhenyu , Zhao Fang , Wang Jinhua , Chen Gengxin , Zhang Michael Q 
Published: August 2005

AbstractLarge-scale and high-throughput genomics research needs reliable and comprehensive genome-wide promoter annotation resources. We have conducted a systematic investigation on how to improve mammalian promoter prediction by incorporating both transcript and conservation information. This enabled us to build a better multispecies promoter annotation pipeline and hence to create CSHLmpd (Cold Spring Harbor Laboratory Mammalian Promoter Database) for the biomedical research community, which can act as a starting reference system for more refined functional annotations.
Matrix-Isolation Spectroscopy Using Solid Parahydrogen as the Matrix: Application to High-Resolution Spectroscopy, Photochemistry, and Cryochemistry
Authors: Momose Takamasa , Shida Tadamasa 
Published: August 2005

Abstract
Solid parahydrogen is an excellent matrix for matrix-isolation spectroscopy. First, spectroscopic resolution exceeds the resolution attainable in conventional matrices so that detailed analysis of rotational structure of molecules in the solid phase may be performed in favorable cases. Secondly, in situ photolysis is feasible on account of the subduction of the cage effect in solid parahydrogen, which is in sharp contrast to the system in rare gas matrices. In this Account we describe 1) relevant properties of solid parahydrogen in connection with its use as the matrix, 2) outlines of experimental procedures using solid parahydrogen as the matrix, 3) examples of high-resolution spectroscopic studies, and 4) examples of studies on photochemistry and cryochemistry.
Structure and Magnetic Properties of a Chain Complex with Alternating Ru(II,III) Dimer and Nitroxide Radical Arrangement [Ru2(O2CCMe3)4(nitph)]n(BF4)n, nitph = 2-Phenyl-4,4,5,5-tetramethyl-4,5-dihydro-1H-imidazol-1-oxyl 3-N-Oxide
Authors: Handa Makoto , Sayama Yasuyoshi , Mikuriya Masahiro , Nukada Ryoji , Hiromitsu Ichiro , Kasuga Kuninobu 
Published: August 2005

Abstract
A chain complex of diruthenium(II,III) cation dimer linked by a nitroxide radical, [Ru2(O2CCMe3)4(nitph)]n(BF4)n (nitph = 2-phenyl-4,4,5,5-tetramethyl-4,5-dihydro-1H-imidazol-1-oxyl 3-N-oxide), has been prepared and characterized. The structure with an alternating alignment of Ru(II,III) core and nitph has been confirmed by the X-ray crystal analysis. The magnetic moment decreased steadily with decrease of temperature, against the expectation of ferrimagnetic behavior based on the alternated alignment of S1 = 3/2 (for Ru(II,III) core) and S2 = 1/2 (for nitph). It has been found that the zero-field splitting plays an important role in the magnetic behavior in addition to the interaction between the Ru(II,III) core and nitph.
Spectral Properties of Cytochrome c553 and a Membrane-Bound Cytochrome b from Alcaligenes xylosoxidans GIFU 1051
Authors: Sakurai Nobuhiko , Kumita Hideyuki , Sakurai Takeshi , Masuda Hideki 
Published: August 2005

Abstract
Cytochrome c553 and cytochrome b were isolated from soluble and membrane fractions of Alcaligenes xylosoxidans GIFU 1051, respectively, and their spectroscopic characterizations have been performed. Cytochrome c553 has been shown to be in the low spin state both in the oxidized and reduced forms at room temperature by the absorption and magnetic circular dichroism (MCD) spectra, while the high spin heme has been also observed in the cryogenic electron paramagnetic resonance (EPR) spectra. Exogenous small ligands such as NO and CO bind to cytochrome c553 by expelling the axial His ligand. The membrane-bound cytochrome b has two heme b centers in a protein molecule which are the active centers of NO reductase, the cytochrome bc complex, although the enzyme activity was rather low. The absorption, MCD, and EPR spectra of the membrane-bound cytochrome b showed that two heme b centers are in the different electronic states, the high and low spin states. Cytochrome c553 is the natural electron donor to the membrane-bound NO reductase, although the interprotein electron-transfer could not been studied because of the low enzyme activity of the cytochrome b subunit.
Intercalation of Dendritic Polyamines by α- and γ-Zirconium Phosphates
Authors: Kijima Tsuyoshi , Ohe Kaoru , Sasaki Fumie , Yada Mitsunori , Machida Masato 
Published: August 2005

Abstract
Tridentate polyamines, N(CH2CH2NH2)3 and N(RNH2)3 (R = CH2CH2CONHCH2CH2), react with both α- and γ-zirconium phosphates to give an intercalated phase in which the amine molecules are fully loaded as an interdigitating monolayer with their flatted molecular planes highly titles relative to the inorganic layers. On the other hand, although hexadentate polyamine, N(RN(RNH2)2)3, forms a more expanded intercalate from its dilute solution, the longer chain amine can not be intercalated from its concentrated solution, due to the entanglement of dissolved molecules.
Oxidation Chemistry of 1,3-Dimethylxanthine at Stationary Pyrolytic Graphite Electrode
Authors: Goyal Rajendra N , Singhal Naveen K 
Published: August 2005

Abstract
The electrochemical oxidation of 1,3-dimethylxanthine has been studied in the pH range 2.3—10.3 at a pyrolytic graphite electrode. The conjugate base has been found as the electroactive species oxidized over the entire pH range. The 4e, 4H+ charge transfer step is followed by competitive irreversible chemical reactions. The decomposition of UV-absorbing intermediate generated during the electrooxidation has been found to follow first-order kinetics. The products of the EC reaction have been separated by HPLC and gel-permeation chromatography and characterized by mp, 1H NMR, and mass spectra. The presence of methyl groups at positions 1 and 3 has been found to affect the course of mechanism, because the positive charge developed on nitrogen does not permit ring contraction. A tentative mechanism has also been suggested.
Mass-Spectrometric Study on Ion-Molecule Reactions of CH5+, C2H5+, and C3H5+ with Monosubstituted Benzenes Carrying a Carbonyl Group
Authors: Tsuji Masaharu , Nishimura Yukio 
Published: August 2005

Abstract
The gas-phase ion-molecule reactions of CH5+, C2H5+, and C3H5+ with five monosubstituted benzenes carrying a carbonyl group (PhCOX: X = H, CH3, C2H5, Ph, COPh) have been studied using an ion-trap type of GC/MS at a low CH4 pressure. The major product channels are proton transfer to the O-atom in a substituent, with or without further decomposition due to the elimination of CO, PhH, or (PhH + CO). Small amounts of initial adduct ions and their decomposition products are found in some reactions with C3H5+. The reaction mechanism is discussed, based on product ion distributions and semi-empirical calculations of the energies of intermediates and products.
Formation of Sodalite-Like Zincophosphate Framework from Zn/Al-Layered Double Hydroxide as a Starting Material
Authors: Fuda Kiyoshi , Shindo Osamu , Murakami Kenji , Matsunaga Toshiaki 
Published: August 2005

Abstract
The reaction between Zn/Al-layered double hydroxide (LDH) carbonate and Na2HPO4 in a suspension system was investigated under mild hydrothermal conditions. A sodalite-type sodium zincophosphate which incorporated a small amount of Al atoms was obtained at pH = 10.0, T = 358 K, under atmospheric pressure. The reaction was found to be sensitive to the reaction conditions. The obtained sodalite-like compound was characterized with FT-IR, powder XRD with Rietveld Refinement and thermal analyses. The product has a quite similar structure to that of the pure sodalite-like sodium zincophosphate, but showed an improved thermal stability compared to that of the pure one without Al.
Copper(II)–Lanthanide(III) Complexes of Symmetric Dinucleating Macrocycle with Two Phenolate Bridges
Authors: Manseki Kazuhiro , Kumagai Motoko , Sakamoto Masatomi , Sakiyama Hiroshi , Nishida Yuzo , Matsumoto Akira , Sadaoka Yoshihiko , Ohba Masaaki , Okawa Hisashi 
Published: August 2005

Abstract
The first heteronuclear copper(II)–lanthanide(III) complexes, CuLn(fsal-2,2)(NO3)3(H2O)n (n = 2 for Ln = Nd and n = 1 for Ln = Eu and Gd), of a symmetric macrocyclic dinucleating Schiff base ligand, H2fsal-2,2, which is a condensation product of two molecules of 2,6-diformyl-4-methylphenol and two molecules of ethylenediamine, were synthesized by the reaction of [N,N′-bis(3-formyl-5-methylsalicylidene)ethylenediaminato]copper(II) and ethylenediamine in the presence of lanthanide(III) ion as a template, where fsal-2,2 denotes the dianion formed by the deprotonation of two phenolic hydroxyl groups in H2fsal-2,2. The absorption spectra suggested that substrates possessing N- and O-donor groups, such as amino alcohols, are specifically bound at the Cu–Ln center through nitrogen-coordination to the copper site and through oxygen-coordination to the lanthanide site. The fluorescence intensity of Eu(III) decreased drastically upon forming the Cu–Eu complex. A cryomagnetic susceptibility measurement indicated a ferromagnetic spin-spin interaction between Cu(II) and Gd(III) ions.
Ultrasonic Effects on Electroorganic Processes. Part 9. Current Efficiency and Product Selectivity in the Electroreduction of Alkyl Halides to Alkyl Stannanes at a Reactive Tin Cathode
Authors: Atobe Mahito , Nonaka Tsutomu 
Published: August 2005

Abstract
The ultrasonic effects on the electroreduction of methyl and allyl halides (RX) to the corresponding stannanes (R3SnSnR3 and R4Sn) at a reactive (consumable) tin cathode were examined. The current efficiency and product selectivity for the reduction were found to be greatly affected by ultrasonic irradiation. For instance, the selectivity for (CH3)3SnSn(CH3)3 to (CH3)4Sn from CH3I was significantly increased under irradiation. This fact is rationalized as being due to because the intermediate species [(CH3)3Sn·] formed by the primary one-electron reduction of CH3I are activated for their coupling by mobilization on/from the cathode surface under irradiation. On the other hand, the ultrasonic effects on the reduction of CH3Br and C3H5Br seemed to be slightly different from those in the reduction of CH3I.
The One-Electron Transfer Induced Photocycloreversion of Stilbazolium Cyclodimers
Authors: Nakamura Tomotaka , Takagi Katsuhiko , Sawaki Yasuhiko 
Published: August 2005

Abstract
The irradiation of iodide salts of stereo isomeric stilbazolium cyclodimers in their CT bands (ca. 355 nm) resulted in a one-electron transfer induced photocycloreversion, which led to the formation of stilbazolium ions; the quantum yields (Φ) being highly sensitive to their structures, i.e., the Φ for syn-Head-to-Head (syn-HH) was found to be 0.35, for syn-Head-to-Tail (syn-HT) 0.0026, and for anti-Head-to-Head (anti-HH) 0.00095, respectively. This reaction shows a distinct contrast to photocycloreversion by irradiation at 255 nm, which resulted in a highly efficient, but nonselective, splitting, the Φ’s being in the range of 0.3—0.8. In the photosensitized cycloreversion of methyl sulfate salts of dimers using 9,10-dimethoxyanthracene (DMA) as a sensitizer, the quantum efficiencies show a structural dependence similar to the above case of irradiation at their CT bands. Cosensitization with DMA and 1-cyanonaphthalene as an electron mediator resulted in relative quantum yields showing a close coincidence to the yields in the irradiation of the CT band, i.e., 254 : 2.6 : 1 for syn-HH, syn-HT, and anti-HH, respectively. This implies that the one-electron transfer mechanism can be initiated both by CT band irradiation as well as DMA sensitization. It can be concluded that the structural dependence of the quantum efficiencies is attributed to the through-bond interaction of two pyridinium rings, which facilitates the splitting of the C–C bond in the cyclobutane ring.
Mechanistic Studies on Cyclopalladation of the Solvated Palladium(II) Complexes with N-Benzyl Triamine Ligands in Various Solvents. Crystal Structures of [Pd(Sol)(Bn2Medptn)](BF4)2 (Sol = Acetonitrile and N,N-Dimethylformamide; Bn2Medptn = N,N′-Dibenzyl-4-methyl-4-azaheptane-1,7-diamine) and [Pd(H−1Bn2Medptn-C,N,N′,N″)]CF3SO3
Authors: Yagyu Takeyoshi , Aizawa Sen-ichi , Funahashi Shigenobu 
Published: August 2005

Abstract
Several solvated palladium(II) complexes with the potentially cyclopalladating dibenzyl ligand have been synthesized. These include [Pd(CH3CN)(Bn2Medptn)](BF4)2 (1) (Bn2Medptn = N, N′-dibenzyl-4-methyl-4-azaheptane-1,7-diamine), [Pd(dmf)(Bn2Medptn)](BF4)2 (2) (dmf = N,N-dimethylformamide), and [Pd(dmso)(Bn2Medptn)](BF4)2 (3) (dmso = dimethyl sulfoxide), their cyclopalladated complex, [Pd(H−1Bn2Medptn-C,N,N′,N″)]CF3SO3 (4), the solvated monobenzyl complex, [Pd(CH3CN)(BnMedptn)](BF4)2 (5) (BnMedptn = N-(3-aminopropyl)-N′-benzyl-N-methyl-1,3-propanediamine), and its deuterated complex, [Pd(CH3CN)(BnMedptn-d7)](BF4)2 (6) (BnMedptn-d7 = N-(3-aminopropyl)-N′-heptadeuteriobenzyl-N-methyl-1,3-propanediamine). The crystal structures of 1·CH3CN·CH2Cl2, 2, and 4 have been determined by X-ray structure analysis to characterize the reactant and the product for the cyclopalladation of the solvated complexes, where one of the ortho carbons of 1 is directed toward the palladium(II) center (Pd···C(1) = 3.513(9) Å). The rate constants for the cyclopalladation of 1 at 25 °C in various solvents increase in the order DMF &lt; DMSO &lt;&lt; pyridine, but the reaction does not proceed in acetonitrile or nitromethane. The activation parameters for the cyclopalladation in neat solvent have been obtained as follows: k298 = 5.74 × 10−6 s−1, ΔH‡ = 104.0 ± 1.2 kJ mol−1 and ΔS‡ = 3.5 ± 3.9 J K−1 mol−1 for 1 in DMF, k298 = 3.13 × 10−4 s−1, ΔH‡ = 83.8 ± 2.6 kJ mol−1 and ΔS‡ = −31.0 ± 8.8 J K−1 mol−1 for 1 in DMSO, k298 = 1.30 × 10−4 s−1, ΔH‡ = 81.2 ± 0.5 kJ mol−1 and ΔS‡ = −47.0 ± 1.8 J K−1 mol−1 for 5 in DMF, k298 = 1.76 × 10−3 s−1 for 5 in DMSO, k298 = 1.26 × 10−5s−1, ΔH‡ = 92.8 ± 1.4 kJ mol−1 and ΔS‡ = −27.5 ± 4.4 J K−1 mol−1 for 6 in DMF and k298 = 2.69 × 10−4 s−1 for 6 in DMSO. The activation enthalpy is reduced as the solvent basicity increases. The kinetic isotope effects (kH/kD) for the cyclopalladation of the monobenzyl complex at 25 °C are calculated to be 10.3 in DMF and 6.5 in DMSO using the rate constants for 5 and 6. It is confirmed from the kinetic results obtained that the nucleophilic attack of the basic solvent on the ortho proton is essential for the C–H bond cleavage observed in the activation process. In addition, the fact that the rate constant for the cyclopalladation is proportionally dependent on the concentration of DMSO in nitromethane strongly suggests that the solvent-dissociation pre-equilibrium is negligible in neat basic solvent.
Solvatochromic Linear Solvation Energy Relationships for Solubility of O2 in Various Solvents
Authors: Che Yong , Tokuda Koichi , Ohsaka Takeo 
Published: August 2005

Abstract
Linear solvation energy relationships for solution of O2 in 27 solvents have been examined. Multiple linear regression equations for mole fraction solubility of O2 are developed based on Hildebrand’s solubility parameter as well as the π*, α, and β solvatochromic parameters describing the solvent polarizability/dipolarity, hydrogen bond acidity and hydrogen bond basicity, respectively. Use of the combination of these parameters enables the medium effect on solution of O2 to be correlated and interpreted in a conceptually simple manner.
Preparation, Stereochemistry, and Reactivity of Linear-Type S-Bridged MCrIIIM (M = RhIII, IrIII) Trinuclear Complexes with 2-Aminoethanethiolate (aet). Crystal Structures of ΔΛ-[Cr{M(aet)3}2]3+
Authors: Miyashita Yoshitaro , Sakagami Narumi , Yamada Yasunori , Konno Takumi , Hidaka Jinsai , Okamoto Ken-ichi 
Published: August 2005

Abstract
S-Bridged trinuclear complexes, [CrIII{M(aet)3}2]3+, (M = RhIII (1), IrIII (2); aet = NH2CH2CH2S−) were newly prepared by the reaction of fac(S)-[M(aet)3] with chromium(III) nitrate. They were separated and optically resolved into the ΔΔ, ΛΛ, and ΔΛ isomers. Of these isomers for 1 and 2, the crystal structures of the ΔΛ isomers (1a and 2a) were determined by an X-ray diffraction method. Each of 1a and 2a consists of two fac(S)-[M(aet)3] subunits, a central Cr atom, three nitrates, and three water molecules, [Cr{M(aet)3}2](NO3)3·3H2O, in which three metals are aligned so as to be exactly linear. The central Cr atom is situated in an octahedral environment with the CrIIIS6 chromophore, which is formed by the coordination of two terminal fac(S)-[M(aet)3] units. The other isomers for 1 and 2 were characterized by the absorption and CD spectra, the molar conductivity, and the magnetic susceptibility. Each cyclic voltammogram of ΔΛ-[Cr{M(aet)3}2]3+ in water showed a reversible redox couple (M(IV)/M(III)) and an irreversible reduction wave (Cr(III)/Cr(II)). The stabilities of the S-bridged MCrIIIM complexes are also discussed in relation to the Cr–S bond strengths.
Photodimerizations of 1,5- and 1,7-Azulenequinones: Solvent, Substituent, and Concentration Effects on the Product Distribution
Authors: Kawakami Hiroko , Yan Yong Zhe , Kato Nobuo , Mori Akira , Takeshita Hitoshi , Nozoe the late Tetsuo 
Published: August 2005

Abstract
Azulenequinones gave dimers when they were irradiated with a high-pressure mercury lamp. In polar solvents, head-to-head dimers were predominant, whereas head-to-tail dimers increased in less polar solvents. From 3-methoxy-1,5-azulenequinone, four products were obtained, while bromoazulenequinones and 1,5-azulenequinone gave a single dimer. The product distribution was dependent on the polarity of solvents, substituents, and concentrations.