bluuebunny/crossref_metadata_2025_split huggingface dataset:
p53 Transgenic Mice Are Highly Susceptible to 4-Nitroquinoline-1-Oxide-Induced Oral Cancer
Authors: Zhang Zhongqiu , Wang Yian , Yao Ruisheng , Lubet Ronald A. , You Ming 
Published: June 2006

AbstractIn this study, we did a bioassay employing mice with a dominant-negative p53 mutation (p53Val135/WT) to assess whether a germ-line p53 mutation predisposed mice toward the development of squamous cell carcinomas (SCC) in the oral cavity. Treatment of the mouse oral cavity with 4-nitroquinoline-1-oxide produced a 66%, 91%, and 20% tumor incidence in the oral cavity, esophagus, and forestomach/stomach, respectively, in p53Val135/WT mice. In contrast, only a 25%, 58%, and 4% tumor incidence was observed in oral cavity, esophagus, and forestomach/stomach, respectively, in wild-type littermates (p53WT/WT). The most striking difference between p53Val135/WT and p53WT/WT mice following the carcinogen treatment was the higher prevalence and more rapid development of SSC in p53Val135/WT mice than in wild-type mice. To identify the precise genes or pathways involved in these differences during tumor development, we examined gene expression profiles of 4-nitroquinoline-1-oxide-treated normal tongues as well as tongue SCC in p53Val135/WT and p53WT/WT mice. Microarray and GenMAPP analysis revealed that dominant-negative p53 (135Valp53) affects several cellular processes involved in SCC development. Affected processes included apoptosis and cell cycle arrest pathways, which were modulated in both tumor and normal epithelium. These results showed that reduction of p53-dependent apoptosis and increases in cell proliferation might contribute to the observed increase in oral cavity and gastroesophageal malignancies in p53Val135/WT mice as well as to the more rapid growth and progression of tumors. (Mol Cancer Res 2006;4(6):401–10)
Association algorithm to mine the rules that govern enzyme definition and to classify protein sequences
Authors: Chiu Shih-Hau , Chen Chien-Chi , Yuan Gwo-Fang , Lin Thy-Hou 
Published: June 2006

Abstract

Background
The number of sequences compiled in many genome projects is growing exponentially, but most of them have not been characterized experimentally. An automatic annotation scheme must be in an urgent need to reduce the gap between the amount of new sequences produced and reliable functional annotation. This work proposes rules for automatically classifying the fungus genes. The approach involves elucidating the enzyme classifying rule that is hidden in UniProt protein knowledgebase and then applying it for classification. The association algorithm, Apriori, is utilized to mine the relationship between the enzyme class and significant InterPro entries. The candidate rules are evaluated for their classificatory capacity.

Results
There were five datasets collected from the Swiss-Prot for establishing the annotation rules. These were treated as the training sets. The TrEMBL entries were treated as the testing set. A correct enzyme classification rate of 70% was obtained for the prokaryote datasets and a similar rate of about 80% was obtained for the eukaryote datasets. The fungus training dataset which lacks an enzyme class description was also used to evaluate the fungus candidate rules. A total of 88 out of 5085 test entries were matched with the fungus rule set. These were otherwise poorly annotated using their functional descriptions.

Conclusion
The feasibility of using the method presented here to classify enzyme classes based on the enzyme domain rules is evident. The rules may be also employed by the protein annotators in manual annotation or implemented in an automatic annotation flowchart.
Identical probes on different high-density oligonucleotide microarrays can produce different measurements of gene expression
Authors: Zhang LanMin , Yoder Sean J , Enkemann Steven A 
Published: June 2006

AbstractBackgroundThere are many potential sources of variability in a microarray experiment. Variation can arise from many aspects of the collection and processing of samples for gene expression analysis. Oligonucleotide-based arrays are thought to minimize one source of variability as identical oligonucleotides are expected to recognize the same transcripts during hybridization.ResultsWe demonstrate that although the probes on the U133A GeneChip arrays are identical in sequence to probes designed for the U133 Plus 2.0 arrays the values obtained from an experimental hybridization can be quite different. Nearly half of the probesets in common between the two array types can produce slightly different values from the same sample. Nearly 70% of the individual probes in these probesets produced array specific differences.ConclusionThe context of the probe may also contribute some bias to the final measured value of gene expression. At a minimum, this should add an extra level of caution when considering the direct comparison of experiments performed in two microarray formats. More importantly, this suggests that it may not be possible to know which value is the most accurate representation of a biological sample when comparing two formats.
Can antibiotic prescriptions in respiratory tract infections be improved? A cluster-randomized educational intervention in general practice – The Prescription Peer Academic Detailing (Rx-PAD) Study [NCT00272155]
Authors: Gjelstad Svein , Fetveit Arne , Straand Jørund , Dalen Ingvild , Rognstad Sture , Lindbaek Morten 
Published: June 2006

AbstractBackgroundMore than half of all antibiotic prescriptions in general practice are issued for respiratory tract infections (RTIs), despite convincing evidence that many of these infections are caused by viruses. Frequent misuse of antimicrobial agents is of great global health concern, as we face an emerging worldwide threat of bacterial antibiotic resistance. There is an increasing need to identify determinants and patterns of antibiotic prescribing, in order to identify where clinical practice can be improved.Methods/DesignApproximately 80 peer continuing medical education (CME) groups in southern Norway will be recruited to a cluster randomized trial. Participating groups will be randomized either to an intervention- or a control group. A multifaceted intervention has been tailored, where key components are educational outreach visits to the CME-groups, work-shops, audit and feedback. Prescription Peer Academic Detailers (Rx-PADs), who are trained GPs, will conduct the educational outreach visits. During these visits, evidence-based recommendations of antibiotic prescriptions for RTIs will be presented and software will be handed out for installation in participants PCs, enabling collection of prescription data. These data will subsequently be linked to corresponding data from the Norwegian Prescription Database (NorPD). Individual feedback reports will be sent all participating GPs during and one year after the intervention. Main outcomes are baseline proportion of inappropriate antibiotic prescriptions for RTIs and change in prescription patterns compared to baseline one year after the initiation of the tailored pedagogic intervention.DiscussionImprovement of prescription patterns in medical practice is a challenging task. A thorough evaluation of guidelines for antibiotic treatment in RTIs may impose important benefits, whereas inappropriate prescribing entails substantial costs, as well as undesirable consequences like development of antibiotic resistance. Our hypothesis is that an educational intervention program will be effective in improving prescription patterns by reducing the total number of antibiotic prescriptions, as well as reducing the amount of broad-spectrum antibiotics, with special emphasis on macrolides.
The influence of MMP-14, TIMP-2 and MMP-2 expression on breast cancer prognosis
Authors: Têtu Bernard , Brisson Jacques , Wang Chang Shu , Lapointe Hélène , Beaudry Geneviève , Blanchette Caty , Trudel Dominique 
Published: June 2006

Abstract
Introduction
Matrix metalloproteinase (MMP)-2 is very active at degrading extracellular matrix. It is under the influence of an activator, membrane type 1 MMP (MMP-14), and the tissue inhibitor of metalloproteases (TIMP)-2. We hypothesized that the individual expression of these three markers or their balance may help to predict breast cancer prognosis.

Methods
MMP-2, MMP-14 and TIMP-2 expression has been evaluated by 35S mRNA in situ hybridization on paraffin material of 539 breast cancers without distant metastasis at diagnosis and with a median follow-up of 9.2 years.

Results
MMP-2 and MMP-14 mRNA was detected primarily in reactive stromal cells whereas TIMP-2 mRNA was expressed by both stromal and cancer cells. Of the three molecules, an adjusted Cox model revealed that high MMP-14 mRNA (≥ 10% cells) alone predicted a significantly shorter overall survival (p = 0.031) when adjusted for clinical factors (tumor size and number of involved lymph nodes). Prognostic significance was lost when further adjusted for Her-2/neu and urokinase-type plasminogen activator (p = 0.284). Furthermore, when all three components were analyzed together, the survival was worst for patients with high MMP-2/high MMP-14/low TIMP-2 (5 year survival = 60%) and best with low MMP-2/low MMP-14/high TIMP-2 (5 year survival = 74%), but the difference did not reach statistical significance (p = 0.3285).

Conclusion
Of the MMP-14/TIMP-2/MMP-2 complex, MMP-14 was the factor most significantly associated with the outcome of breast cancer and was an independent factor of poor overall survival when adjusted for clinical prognostic factors, but not for certain ancillary markers.
Theoretical Explanation of the Hydrogen Wave on a Platinum Single Crystal Electrode
Authors: Narumi Hideyuki 
Published: June 2006

Abstract
Voltammograms observed on basal planes of a Pt single crystal electrode in 0.1 M HClO4 were analyzed theoretically. Adsorbed hydrogen atoms were assumed to form 2-dimensional (111), (100), and (110) lattices. These lattices were treated by applying the Hückel method to an elementary domain consisting of 400 × 200 lattice points with periodic boundary conditions. Results explained the essential aspects of the butterfly at Pt(111) and the hydrogen waves at Pt(100) and Pt(110). The lateral interactions of the adsorbed hydrogen atoms were attractive in all cases and their values were estimated. The value at Pt(110) reproduced the previous one derived from the adsorption isotherm analysis. The square-shaped wave observed at Pt(111) in a potential range of 0.05—0.35 V was explained by an entirely different model for a freely moving particle. The analysis suggested that the square wave is due to electrons which move freely in the adsorption layer. The Hückel method was further applied to 3-dimensional lattices having 2 to 3 layers. Results suggested a striking effect of the absorbed hydrogen beneath the surface on the hydrogen wave.
Equation of State of Acetic Acid Derived by Molecular-Dynamics Simulations on a Rigid-Molecule Model
Authors: Kataoka Yosuke , Matsumoto Mitsuhiro 
Published: June 2006

Abstract
The equation of state of an acetic acid fluid was derived by molecular-dynamics simulations on a rigid-molecule model. The optimized potential for liquid simulations (OPLS) given by Briggs, Nguyen, and Jorgensen was assumed. Only the Z form was adopted in the two conformers in order to save central processing unit (CPU) time to perform the molecular-dynamics simulation at many state points. Microcanonical simulations were performed for 729 states. The system had 256 molecules in the cubic basic cell. The equation of state was obtained by a least-squares fitting. The critical point and liquid-vapor phase boundary were compared with the observed values. Dimerization was also observed by 27 long runs in the gaseous phase around the liquid–vapor phase boundary. The main structure is hydrogen-bonded chains in the liquid phase. The excess entropy after subtracting the ideal gas term is −10R at low temperatures. This is compared with −8R in liquid water. These comparisons show that the present model can be used to simulate the hydrogen-bonded fluid of acetic acid.
Relationship between the π-Electron Distribution and the Symmetry of Cyclic C6H6 Systems
Authors: Ichikawa Hiroshi , Kagawa Hirotaka 
Published: June 2006

Abstract
In an attempt to comfirm the role of π electrons in benzene, the relationship between the π-electron distribution and the preferred symmetry in C6H6 systems was examined. It was shown that under the restriction of being planar, the C6H66+ system has a D6h geometry, which is fragile towards shrinking as well as a distortion, and is also fragile at saddle points towards bending. When π electrons are added to such a system, the π electrons distribute in the way of either D6h or D2h symmetry according to the number of electrons. When the π-electron distribution is D6h-symmetric, non-distortive (i.e., those along the A1g coordinate) forces are produced; when it is D2h-symmetric, distortive forces, i.e., those that break the D6h symmetry, appear. Optimization leads to a symmetry which is pre-determined by the π-electron distribution. In this way, it was elucidated that π electrons in benzene have a tendency to form a uniform distribution.
Organic Metal with a High Oxidation State (+5/3), (TTM–TTP)(I3)5/3
Authors: Mori Takehiko , Misaki Yohji , Yamabe Tokio 
Published: June 2006

Abstract
The crystal structure of the title compound, where TTM–TTP is 2,5-bis [4,5-bis(methylthio)-1,3-dithiol-2-ylidene]-1,3,4,6-tetrathiapentalene, has been determined by X-ray analysis. The donors form a uniform stack, which is responsible for metallic conduction down to TMI = 20 K. The anions are composed of discrete I3− and an infinite chain of I3−. Each donor has anomalously large positive charge of +5/3.
Theoretical Study of Water-Exchange Reactions of Hexahydrated Divalent Cations in the First Transition Series: Relationship between Reaction Mechanism and Stability of Heptacoordinated Species
Authors: Tsutsui Yuko , Wasada Hiroaki , Funahashi Shigenobu 
Published: June 2006

Abstract
We studied the characteristics of model intermediary species on reaction pathways using the ab initio molecular orbital method in order to explain a change in the mechanistic behavior of the water-exchange reaction of hexahydrated divalent cations when the central elements were changed in the first transition series. Calculations show that the hexacoordinated species binding to the entering water in the second shell, the dissociative pentacoordinated species of scandium(II) and copper(II) ions, and the associative heptacoordinated species of scandium(II) ion are at local minima, whereas the heptacoordinated species of copper(II) ion is at a second-order saddle point. We also considered calcium(II) and zinc(II) ions in order to examine the correlation between the intermediary species and the reaction mechanisms. All of the intermediary species for calcium(II) and zinc(II) ions resemble those of scandium(II) and copper(II) ions, respectively. The dissociative mechanism can operate for both the calcium(II) and zinc(II) ions. The associative mechanism, however, can operate only for the calcium(II) ion, and the zinc(II) ion has no meaningful stationary point on the reaction path. We also considered the effect of the electronic structures on the reaction mechanisms. We conclude as the following: The dissociative mechanism is operative for a water exchange of all members of the first transition series. An associative mechanism is expected for the water-exchange reaction of the earlier members, which have stable heptacoordinated species. The possibility of the operation of the associative mechanism depends on the existence of appropriate associative heptacoordinated species.
Electron Transfer from Tetrathiafulvalenes to Photoexcited C70 Studied by Observing Transient Absorption in the Near-IR Region
Authors: Alam Maksudul M , Watanabe Akira , Ito Osamu 
Published: June 2006

Abstract
The photoinduced electron transfer between C70 and tetrathiafulvalene or bis(ethylenedithio)tetrathiafulvalene in polar and nonpolar solvents and their mixture has been investigated by nanosecond laser photolysis/transient absorption spectroscopy in the visible and near-IR regions. The transient absorption bands of the triplet state of C70 observed in polar solvents decayed upon addition of tetrathiafulvalenes accompanied by the appearance of the transient absorption bands of the radical anion of C70. In benzene, the quenching of the triplet state of C70 was observed without the appearance of the radical anion of C70 within a nanosecond laser pulse, suggesting a collisional quenching of the triplet state of C70 with tetrathiafulvalenes. The quantum yield for the formation of the radical anion via the triplet state of C70 was about 1 for tetrathiafulvalene in benzonitrile. The quantum yield decreased in less polar solvents. The back electron transfer rates were also evaluated in polar solvents.
A Resonance Light-Scattering Analysis of the Suprahelical Helixes of Nucleic Acids Induced by 5,10,15,20-Tetrakis[4-(trimethyammonio)phenyl]porphine
Authors: Huang Cheng Zhi , Li Ke An , Tong Shen Yang 
Published: June 2006

Abstract
This paper discusses the usefulness of resonance light-scattering spectroscopy (RLSS), which can be obtained by using an ordinary spectrofluorimeter, for the analysis of the suprahelical helixes of nucleic acids induced by 5,10,15,20-tetrakis[4-(trimethyammonio)phenyl]porphine (H2tapp). Depending on the acidity of the aqueous solution, the titled porphyrin has two species, [H2tapp]4+ and [H4tapp]6+. Both species can stack on appropriate conditions along the surface of nucleic acids in the mode of long-range assembly; and this leads to the formation of suprahelical helixes of nucleic acids. Enhanced resonance light-scattering signals can be observed for the porphyrin-induced suprahelical helixes of nucleic acids with the maximal resonance light scattering near to 432 nm for [H2tapp]4+ and near to 452 nm for [H4tapp]6+. The exciton splitting signals, which are generally associated with the aggregation of porphyrins, as described by molecular-exciton theory, are observed at 428 nm in the RLS spectra, analogous to the circular dichroism spectra when the molar ratio of [H2tapp]4+ to nucleic acids (R) is greater than 0.89. These results indicate that porphyrin–porphyrin interactions occur in the suprahelical helixes of nucleic acids.
Solvent Extraction of Anionic Silver(I) Thiocyanate Complex as Ion-Pairs with Tetrabutylammonium Ions into Chloroform and 4-Methyl-2-pentanone
Authors: Ohmiya Yasunobu , Dung Nguyen Thi Kim , Sekine Tatsuya 
Published: June 2006

Abstract
Solvent extraction of silver(I) from aqueous 1 mol dm−3 Na(SCN, NO3) solutions, where the thiocyanate ion concentration was higher than 1 × 10−3 mol dm−3 and pH was 3, into chloroform and into 4-methyl-2-pentanone (MIBK) was studied in the presence of tetrabutylammonium ions (tba+) at 298 K. The extraction equilibria of the ion-pairs, tba+SCN− and tba+NO3− into these solvents were also determined. The experimental data were well explained by extraction of tba+Ag(SCN)2− into chloroform and both tba+Ag(SCN)2− and Na+Ag(SCN)2− into MIBK and by formation of Ag(SCN)n1−n, where n was 2 to 4 in the aqueous phase. More than half of the initial amount of tba+ in the aqueous phase was extracted as tba+SCN− and tba+NO3−. The analysis of the extraction data of silver(I) should be made by taking the decrease in the tba+ concentration due to these extractions into account. No dissociation of the ion-pairs was found in chloroform but the extracted ion-pairs were partially dissociated in MIBK. In the presence of 1 × 10−3 mol dm−3 tba+ in the initial aqueous phase, the extraction of silver(I) was much better into MIBK than into chloroform under otherwise identical conditions. The extraction and dissociation constants of the above species and the stability constants of the anionic thiocyanate complexes of silver(I) in the aqueous phase were calculated.
The Photolyses of 2,6- and 2,4-Difluorohalobenzenes
Authors: Song Yong-Qi , Yuzuri Tomoaki , Suezawa Hiroko , Sakakibara Kazuhisa , Hirota Minoru , Nakada Masahiro 
Published: June 2006

Abstract
Photolyses of 2,6- and 2,4-difluorobromobenzenes in acetonitrile gave isomerized and brominated products in addition to 1,3-difluorobenzene produced by the dehalogenation. The reactions were compared with similar reactions of the corresponding chloro- and iodoarenes. In general, photolytic cleavage of the C–X bond of 2,6-difluorohalo(X)benzene was shown to proceed more easily than the corresponding 2,4-difluorohalo compound.
Aldol Reaction and Robinson-Type Annelation Catalyzed by Lanthanoid Triisopropoxides
Authors: Okano Tamon , Satou Yoshikazu , Tamura Motoshi , Kiji Jitsuo 
Published: June 2006

Abstract
Lanthanoid triisopropoxides are active catalysts for aldol reactions. Aldehydes give the corresponding β-hydroxyaldehydes at low temperatures in good yields, whereas ketones are less reactive, but form condensation products at high temperatures. Exceptionally, γ- or δ-diketones easily undergo condensation to give five- and six-membered unsaturated ketones in high yields. The lanthanoid propoxides, catalyzing the Michael addition of ketones to α,β-unsaturated ketones, which give δ-diketones, are also good catalysts for the Robinson-type annelation. In these reactions, the catalytic activity of the lanthanum propoxide is higher than those of the heavy lanthanoid propoxides, and is almost comparable to that of sodium isopropoxide. Since aluminum triisopropoxide shows poor activity, the lanthanoid propoxides are considerably basic for trivalent metal alkoxides.
Conformational Behavior of Methyl (3R)-3-{[(3′R)-3′ -Hydroxybutanoyl]oxy}butanoate in Solutions: Effect of Intramolecular Hydrogen Bond
Authors: Li Jun , Uzawa Jun , Doi Yoshiharu 
Published: June 2006

Abstract
Methyl (3R)-3-{[(3′R)-3′-hydroxybutanoyl]oxy}butanoate (MHBOB) has been prepared as a model compound of the hydroxy terminal part of poly[(R)-3-hydroxybutanoate] [P(3-HB)]; the NMR assignments and conformational analyses of the compound are reported. The NMR assignments of MHBOB were made by means of two-dimensional pulsed field gradient 1H–1H COSY and 1H–13C HMBC (heteronuclear multiple-bond correlation) spectroscopy. The conformational behavior of MHBOB generated by rotation about two CH2–CH bonds was investigated in chloroform and in aqueous solution at various temperatures by analysis of vicinal coupling in the 500-MHz 1H NMR spectra. In both chloroform and aqueous solution, the monomer unit adjacent to the methoxy group was found to adopt a similar conformational distribution to that of the P(3-HB) polymer backbone, in which the trans and gauche conformers were predominant, while the another gauche conformer was suppressed to almost zero. On the other hand, the monomer unit adjacent to the hydroxy group had a different conformational distribution relative to that of the other monomer unit, due to the formation of an intramolecular hydrogen bond between hydroxy and carbonyl groups. In chloroform, only the gauche conformer was predominant at temperatures between −60 and 57 °C, and even the fraction of another gauche conformer was higher than that of trans conformer at low temperatures below 0 °C. In aqueous solution, the fraction of gauche conformer was also higher than that of trans conformer, suggesting the formation of the intramolecular hydrogen bond. However, the formation of the intramolecular hydrogen bond in aqueous solution was not so strong as that in chloroform.