bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modelling the network of cell cycle transcription factors in the yeast Saccharomyces cerevisiae
Authors: Cokus Shawn , Rose Sherri , Haynor David , Grønbech-Jensen Niels , Pellegrini Matteo 
Published: August 2006

Abstract

Background
Reverse-engineering regulatory networks is one of the central challenges for computational biology. Many techniques have been developed to accomplish this by utilizing transcription factor binding data in conjunction with expression data. Of these approaches, several have focused on the reconstruction of the cell cycle regulatory network of Saccharomyces cerevisiae. The emphasis of these studies has been to model the relationships between transcription factors and their target genes. In contrast, here we focus on reverse-engineering the network of relationships among transcription factors that regulate the cell cycle in S. cerevisiae.

Results
We have developed a technique to reverse-engineer networks of the time-dependent activities of transcription factors that regulate the cell cycle in S. cerevisiae. The model utilizes linear regression to first estimate the activities of transcription factors from expression time series and genome-wide transcription factor binding data. We then use least squares to construct a model of the time evolution of the activities. We validate our approach in two ways: by demonstrating that it accurately models expression data and by demonstrating that our reconstructed model is similar to previously-published models of transcriptional regulation of the cell cycle.

Conclusion
Our regression-based approach allows us to build a general model of transcriptional regulation of the yeast cell cycle that includes additional factors and couplings not reported in previously-published models. Our model could serve as a starting point for targeted experiments that test the predicted interactions. In the future, we plan to apply our technique to reverse-engineer other systems where both genome-wide time series expression data and transcription factor binding data are available.
β-lactam antibiotic-induced release of lipoteichoic acid from Staphylococcus aureus leads to activation of neutrophil granulocytes
Authors: Lotz Sonja , Starke Andrea , Ziemann Christian , Morath Siegfried , Hartung Thomas , Solbach Werner , Laskay Tamás 
Published: August 2006

Abstract

Background
Polymorphonuclear neutrophil granulocytes (PMN) are phagocytes of the first line of antimicrobial defense. Previously we demonstrated that lipoteichoic acid (LTA) from Staphylococcus aureus (S. aureus) directly activates neutrophil granulocytes. Others have reported that exposure of S. aureus to β-lactam antibiotics leads to LTA release. In the present study we addressed the question whether exposure of S. aureus to β-lactam antibiotics or antibiotics of other groups results in the generation of PMN-stimulating activity and whether this activity can be attributed to LTA.

Methods

S. aureus were exposed to flucloxacillin, a β-lactam antibiotic or to the protein synthesis-inhibitors erythromycin and gentamicin, or to ciprofloxacin, a gyrase inhibitor. Supernatants of the antibiotic-treated bacteria were assayed for their LTA content and for their effect on PMN functions.

Results
We observed that exposure of S. aureus to flucloxacillin and, to a lesser degree to ciprofloxacin, but not to erythromycin or gentamicin led to LTA release. Co-incubation of neutrophil granulocytes with LTA-containing supernatants led to PMN activation as assed by morphological changes, release of IL-8, delay of spontaneous apoptosis and enhanced phagocytic activity. Depletion of LTA from the supernatants markedly reduced their PMN-activating capacity.

Conclusion
The findings suggest that, via the activation of PMN, antibiotic-induced LTA release from S. aureus leads to enhanced antimicrobial activity of the innate immune defense mechanisms.
Economic evaluation of a clinical protocol for diagnosing emergency patients with suspected pulmonary embolism
Authors: Gospodarevskaya Elena V , Goergen Stacy K , Harris Anthony H , Chan Thomas , de Campo John F , Wolfe Rory , Gan Eng T , Wheeler Michael B , McKay John 
Published: August 2006

Abstract

Background
The objective of this paper is to estimate the amount of cost-savings to the Australian health care system from implementing an evidence-based clinical protocol for diagnosing emergency patients with suspected pulmonary embolism (PE) at the Emergency department of a Victorian public hospital with 50,000 presentations in 2001–2002.

Methods
A cost-minimisation study used the data collected in a controlled clinical trial of a clinical protocol for diagnosing patients with suspected PE. Thenumber and type of diagnostic tests in a historic cohort of 185 randomly selected patients, who presented to the emergency department with suspectedPE during an eight month period prior to the clinical trial (January 2002 -August 2002) were compared with the number and type of diagnostic tests in745 patients, who presented to the emergency department with suspected PE from November 2002 to August 2003. Current Medicare fees per test were usedas unit costs to calculate the mean aggregated cost of diagnostic investigation per patient in both study groups. A t-test was used to estimate the statistical significance of the difference in the cost of resources used for diagnosing PE in the control and in the intervention group.

Results
The trial demonstrated that diagnosing PE using an evidence-based clinical protocol was as effective as the existing clinical practice. The clinical protocol offers the advantage of reducing the use of diagnostic imaging, resulting in an average cost savings of at least $59.30 per patient.

Conclusion
Extrapolating the observed cost-savings of $59.30 per patient to the wholeof Australia could potentially result in annual savings between $3.1 million to $3.7 million.
Preparing clinical-grade myeloid dendritic cells by electroporation-mediated transfection of in vitro amplified tumor-derived mRNA and safety testing in stage IV malignant melanoma
Authors: Markovic Svetomir N , Dietz Allan B , Greiner Carl W , Maas Mary L , Butler Greg W , Padley Douglas J , Bulur Peggy A , Allred Jacob B , Creagan Edward T , Ingle James N , Gastineau Dennis A , Vuk-Pavlovic Stanimir 
Published: August 2006

Abstract

Background
Dendritic cells (DCs) have been used as vaccines in clinical trials of immunotherapy of cancer and other diseases. Nonetheless, progress towards the use of DCs in the clinic has been slow due in part to the absence of standard methods for DC preparation and exposure to disease-associated antigens. Because different ex vivo exposure methods can affect DC phenotype and function differently, we studied whether electroporation-mediated transfection (electrotransfection) of myeloid DCs with in vitro expanded RNA isolated from tumor tissue might be feasible as a standard physical method in the preparation of clinical-grade DC vaccines.

Methods
We prepared immature DCs (IDCs) from CD14+ cells isolated from leukapheresis products and extracted total RNA from freshly resected melanoma tissue. We reversely transcribed the RNA while attaching a T7 promoter to the products that we subsequently amplified by PCR. We transcribed the amplified cDNA in vitro and introduced the expanded RNA into IDCs by electroporation followed by DC maturation and cryopreservation. Isolated and expanded mRNA was analyzed for the presence of melanoma-associated tumor antigens gp100, tyrosinase or MART1. To test product safety, we injected five million DCs subcutaneously at three-week intervals for up to four injections into six patients suffering from stage IV malignant melanoma.

Results
Three preparations contained all three transcripts, one isolate contained tyrosinase and gp100 and one contained none. Electrotransfection of DCs did not affect viability and phenotype of fresh mature DCs. However, post-thaw viability was lower (69 ± 12 percent) in comparison to non-electroporated cells (82 ± 12 percent; p = 0.001). No patient exhibited grade 3 or 4 toxicity upon DC injections.

Conclusion
Standardized preparation of viable clinical-grade DCs transfected with tumor-derived and in vitro amplified mRNA is feasible and their administration is safe.
Alexithymia and anxiety in female chronic pain patients
Authors: Celikel Feryal Cam , Saatcioglu Omer 
Published: August 2006

Abstract

Objectives
Alexithymia is highly prevalent among chronic pain patients. Pain is a remarkable cause for high levels of chronic anxiety. The purpose of this study was to investigate the prevalence of alexithymia and to determine anxiety levels among DSM-IV somatoform pain disorder (chronic pain) female patients and to examine the relationship between alexithymia and the self-reporting of pain.

Methods
Thirty adult females (mean age: 34,63 ± 10,62 years), who applied to the outpatient psychiatry clinic at a public hospital with the diagnosis of chronic pain disorder (DSM-IV), were included in the study. Thirty seven healthy females (mean age: 34,46 ± 7,43 years), who matched for sociodemographic features with the patient group, consisted the control group. A sociodemographic data form, 26-item Toronto Alexithymia Scale (TAS-26), Spielberger Trait Anxiety Inventory (STAI) were administered to each subject and information was obtained on several aspects of the patients' pain, including intensity (measured by VAS), and duration.

Results
Chronic pain patients were found significantly more alexithymic than controls. There was a positive correlation between TAS-26 scores and the duration of pain. The alexithymic and nonalexithymic group did not differ in their perception of pain. Neither positive correlation nor significant difference was found between alexithymia and trait anxiety in pain patients.

Discussion
Alexithymia may be important in addressing the diversity of subjective factors involved in pain. The conceptualization of alexithymia as a personality trait as well as a secondary state reaction is underlined by our data.
Nutrient Intake, Weight, and Leu7Pro Polymorphism in Prepro-Neuropeptide Y in Children
Authors: Karvonen Matti K. , Ruottinen Soile , Koulu Markku , Pesonen Ullamari , Niinikoski Harri , Rask-Nissilä Leena , Simell Olli , Rönnemaa Tapani 
Published: August 2006

Abstract
Context: The important role of neuropeptide Y (NPY) in the regulation of food intake and energy balance has been firmly documented in rodents, but human data are sparse. The recently identified functional Leu7Pro polymorphism in the signal peptide region of the prepro-NPY is a useful tool for the investigation of the role of NPY in men. Pro7 substitution has been associated with the following: plasma NPY concentration, the risk factors of cardiovascular disease, birth weight of children, serum triglyceride concentration, and the function of vascular endothelium.
Objective: The objective of this study was to analyze the connection between Leu7Pro polymorphism and relative weight, nutrient intakes, and serum lipids in early childhood. We closely followed 647 healthy Finnish children participating in the Special Turku Risk Factor Intervention Project through their first 9 yr of life.
Results: Leu7Pro polymorphism showed no relation to intakes of energy, macronutrients, or the relative weight in either gender. However, Pro7 substitution was associated with serum triglyceride concentration in boys at the ages of 5, 7, and 9 yr.
Conclusion: The functional Leu7Pro polymorphism is not likely to be involved in the regulation of adiposity or major nutrient preferences in childhood. In boys, the Pro7 variant may have impact on serum triglyceride concentration.
Midlife Plasma Insulin-Like Growth Factor I and Cognitive Function in Older Men
Authors: Okereke Olivia I. , Kang Jae H. , Ma Jing , Gaziano J. Michael , Grodstein Francine 
Published: August 2006

AbstractContext: Emerging biological and epidemiological evidence suggests possible benefits of higher IGF-I levels in cognitive aging.Objective: The objective of the study was to examine the relation of midlife plasma IGF-I levels to late-life cognition.Design, Setting, and Participants: We conducted a secondary analysis from the Physicians’ Health Study II, a prospective cohort of U.S. male physicians. Participants provided blood samples from 1982 to 1984 (mean age 57 yr). Using stored samples, we measured free IGF-I in 376 men and total IGF-I and IGF binding protein-3 in 460 men. Starting in 2001, we administered telephone-based tests of general cognition [the Telephone Interview of Cognitive Status (TICS)], verbal memory, and category fluency. We estimated multivariable-adjusted mean differences in cognitive performance across levels of free IGF-I and IGF-I to IGF binding protein-3 molar ratio.Main Outcome Measures: Global score (averaging performance across all individual cognitive tests), the TICS, and a verbal memory score were measured.Results: Each sd increment in free IGF-I was associated with a multivariable-adjusted increase of 0.08 U (P = 0.02) on the global score. This mean difference was equivalent to that observed between men 2 yr apart in age: i.e. each sd increase in free IGF-I appeared cognitively equivalent to staying 2 yr younger. No significant mean differences in TICS scores were observed across free IGF-I levels. For verbal memory, each sd increment in free IGF-I was associated with an adjusted mean difference of 0.08 U (P = 0.03). Results appeared consistent for the molar ratio but were not statistically significant.Conclusion: Higher midlife free IGF-I may be associated with better late-life cognition.
Complexation of Inorganic Anions with Heptakis(6-butylamino-6-deoxy)-β-cyclodextrin and Its Analogs in Acidic Media
Authors: Matsui Yoshihisa , Tanemura Eiji , Nonomura Tohoru 
Published: August 2006

Abstract
Heptakis(6-butylamino-6-deoxy)-β-cyclodextrin (2) forms 1 : 1 complexes with several inorganic anions in 0.10 mol dm−3 HCl or DCl at 25 °C. The binding constant for a complex of 2 with the SO42− ion was remarkably larger than those for complexes of 2 with univalent anions and those for complexes of the α- (1) and γ-cyclodextrin (3) analogs with the SO42− ion. The circular arrangement of the protonated amino groups in 2 may be advantageous for electrostatic interactions with the bivalent anion.
Cadmium (53P1)-Photosensitized Luminescence of Some Compounds Containing Two Functional Groups
Authors: Ahmed Omar , Yamamoto Shunzo , Sueishi Yoshimi , Nishimura Norio 
Published: August 2006

Abstract
The cadmium (53P1)-sensitized luminescence of some aliphatic compounds which have two functional groups have been studied under the conditions of steady-state illumination at temperatures between 473 and 573 K. It was found that 1,2-dimethoxyethane (DMOE), 2-methoxyethylamine (2-MOEA), and 3-methoxypropylamine (3-MOPA) have two emission bands (wavelengths at the peaks of these bands are about 400 and 455 nm for DMOE and about 460 and 500 nm for 2-MOEA and 3-MOPA), while 2-aminoethanol (2-AEA) and 3-amino-1-propanol (3-APA) do not have any emission band. These two bands were assigned to two kinds of 1 : 1 exciplex (cyclic and acyclic ones) between an excited cadmium atom and a substrate molecule. From the temperature dependence of the emission intensity ratios of these bands, the enthalpy changes (ΔH°) of the equilibrium between two exciplexes were evaluated. The values of ΔH° are correlated to the energy differences between the wavelengths of two emission bands.
Ion-Molecule Reactions of CO2+ with Butane and Isobutane at Thermal Energy
Authors: Tsuji Masaharu , Matsumura Ken-ichi , Funatsu Tsuyoshi , Nishimura Yukio , Obase Hiroshi , Kagawa Shinji , Kanetaka Yasuhito 
Published: August 2006

Abstract
Rate constants and product ion distributions have been determined for thermal energy reactions of CO2+ with n-C4H10 and i-C4H10 by using an ion-beam apparatus. The total rate constants are (9.8 ± 2.0) × 10−10 and (1.0 ± 0.2) × 10−9 cm3 s−1 for n-C4H10 and i-C4H10, respectively. These values amount to about 75% of the collision rate constants estimated from the Langevin theory. C4H9+, C3Hn+ (n = 5—7), and C2Hn+ (n = 3—5) are produced from n-C4H10 with branching ratios of 6, 56, and 38%, while C4H9+ and C3Hn+ (n = 5—7) are formed from i-C4H10 with branching ratios of 7 and 93%, respectively. The lack of C2Hn+ fragments from i-C4H10 is attributed to a low probability of significant rearrangement of chemical bonds for the formation of the C2Hn+ fragments. The product ion distribution in the CO2+/n-C4H10 reaction is in good agreement with that predicted from the fragmentation pattern of n-C4H10+ at 13.78 eV, indicating that the CO2+/n-C4H10 reaction proceeds through a near-resonant charge transfer without momentum transfer.
Different Routes in the Forward and Backward Occurrences of the Hydrogen Electrode Reaction on Pt Single Crystal Electrodes in Acid Solution
Authors: Kita Hideaki , Gao Yunzhi , Ye Shen , Shimazu Katsuaki 
Published: August 2006

Abstract
The hydrogen evolution and ionization reactions were studied on Pt single crystal electrodes in N2 or H2 saturated, acidic solutions. The hydrogen evolution reaction was structure insensitive and the ionization reaction was structure dependent. The Tafel constants of the respective reactions, and , and the reaction orders, and , with respect to proton, did not satisfy the relationships, + = 2 and − = −2, deduced by the rate-determining step which is the same for the hydrogen evolution and ionization reactions; The results were, + ≈ 4 and − ≈ −4. These suggest that the rate-determining steps is different for the evolution and ionization reactions in acidic solutions. A tentative model for the reaction routes was proposed.
Kinetic Studies of the Reaction of Nitrous Acid with Iodide Ion in the Presence of Molecular Oxygen in an Acid Solution
Authors: Kimura Masaru , Sato Miyuki , Murase Tomoko , Tsukahara Keiichi 
Published: August 2006

Abstract
The kinetics of the reaction between nitrous acid and iodide ion were studied in the presence of molecular oxygen (O2) in an acid solution (pH 1.9—3.1); much larger amounts of the triiodide ion than expected from the amounts of nitrous acid were formed under conditions of the iodide ion in excess over nitrous acid. The initial rates for the formation of I2 and I3− increased proportionally with increasing both the O2 and nitrous acid contents, and increased greatly with decreasing the pH in the solution. The reaction rate was also decreased by bubbling either air or O2 through the reacting solution, depending on the bubbling velocity. A chain mechanism is proposed to account for the results obtained in the dark: 2HNO2 + 2I− + 2H+ → 2NO + I2 + 2H2O; 2NO + O2 → 2NO2; 2NO2 N2O4; N2O4 + 2I− + 2H+ → 2HNO2 + I2; I2 + I− I3−. The rate-determining step was the reaction of NO with O2. The addition of trace amounts of copper(II) or iron(II) ion enhanced the formation of I2 and I3− due to the occurrence of reactions of I− with the metal ions. Such an acceleration effect by the metal ions, however, could be diminished by the addition of ethylenediaminetetraacetic acid. Although the rate of the reaction of HNO2 with I− was not greatly changed by the irradiation of visible light during the initial period of reaction, it was greatly accelerated after some formation of I2 and I3−, being dependent on not only the light intensity, but also on the concentrations of H+ and I− ions. The effects of the metal ions as well as visible light are also accounted for by the above-mentioned mechanism.
Studies on Fused Azoles: Synthesis of Several New Polyfunctionally Substituted Fused Pyrazoles
Authors: Sadek Kamal Usef , Selim Maghraby Ali , Elnagdi Mohamed Hilmy , Otto Hans Hartwig 
Published: August 2006

Abstract
The synthesis of several new polyfunctionally substituted fused pyrazoles via reaction of 5-amino-3-methylthio-1H-pyrazole-4-carbonitrile (1) with different reagents is described.
One-Pot Synthesis of Tetraazabis(tropocoronand)s and Podands from Benzo[b]cyclohept[e][1,4]oxazine and α,ω-Polymethylenediamines
Authors: Shindo Kimio , Wakabayashi Hidetsugu , Ishikawa Sumio , Nozoe Tetsuo 
Published: August 2006

Abstract
The reactions of benzo[b]cyclohept[e][1,4]oxazine (9) with a 1.2 equivalent of α,ω-alkanediamines (2, n = 4—12) in ethanol at 80 °C afforded tropocoronands (5, n,n′ = 4,4—12,12) in a one-pot procedure and in high yields, while the reaction of 9 with an excess of 2 mainly gave tropopodands 12 (n,n′ = 4,4—6,6). The reactions of 9 with short-chain diamines 2 (n = 2,3) yielded bicyclic pyrazino or diazepino compounds as the main products. The reaction of 9 with ω-amino alcohol afforded the corresponding dihydroxy podands 23. The predicted pathways of the reaction of 9 with 2 were experimentally confirmed.
Oxidation of Lipids Induced by Dioctadecyl Hyponitrite and Di-t-butyl Hyponitrite in Organic Solution and in Aqueous Dispersions. Effects of Reaction Medium and Size of Radicals on Efficiency of Chain Initiation
Authors: Kigoshi Makoto , Sato Keizo , Niki Etsuo 
Published: August 2006

Abstract
The dynamics of the chain initiation of the oxidations of lipids by hyponitrites were studied in organic homogeneous solution and in aqueous dispersions of micelles and liposomal membranes. Di-t-butyl and distearyl hyponitrites were used in order to examine the effect of bulkiness of the alkoxyl radicals in different reaction media. Both hyponitrites induced the free radical-mediated chain oxidations of methyl linoleate in homogeneous solution and in aqueous emulsions and also of soybean phosphatidylcholine liposomal membranes. In aqueous dispersions, these lipophilic hyponitrites generated free radicals in the lipid compartment and aqueous radical-scavenging antioxidants could not suppress the oxidations induced by these hyponitrites. The efficiency of chain initiation decreased in the order of homogeneous solution &gt; micelles &gt; liposomal membranes in accordance with increasing viscosity of the medium. It was also dependent on the size of alkoxyl radical and distearyl hyponitrites was less efficient than di-t-butyl hyponitrite in initiating the chain oxidation in all of the above reaction media.
Mechanistic Study of the Photooxidation of Squalene Sensitized with 2,2′ : 5′,2″-Terthiophene and 2,2′-Bithiophene
Authors: Fujita Hitoshi , Tokiwa Kiminori , Sayama Katsuhide , Mori Hiroyuki , Sasaki Masako 
Published: August 2006

Abstract
To understand the photochemical basis of photodermatitis caused by 2,2′ : 5′,2″-terthiophene, photooxidation of squalene sensitized with 2,2′ : 5′,2″-terthiophene was studied with respect to mediation by singlet molecular oxygen, the activation energy, and the apparent quantum yield. Squalene was peroxidized in ethanol solution by irradiation with UV-A light in the presence of 2,2′ : 5′,2″-terthiophene and the related compound 2,2′-bithiophene. Involvement of singlet oxygen in the peroxidation was suggested on the basis of the suppressive effect of sodium azide and the enhancing effects of organic solvents which elongate the lifetime of singlet oxygen. The activation energy obtained, 11.2 kJ mol−1, was a reasonable value for oxidation of olefins by singlet oxygen. The quantum yields of peroxidation were estimated to 12.6 × 10−2 and 8.3 × 10−2 for photosensitization with 2,2′ : 5′,2″-terthiophene and 2,2′-bithiophene, respectively.