bluuebunny/crossref_metadata_2025_split huggingface dataset:
A direct comparison of protein interaction confidence assignment schemes
Authors: Suthram Silpa , Shlomi Tomer , Ruppin Eytan , Sharan Roded , Ideker Trey 
Published: July 2006

Abstract

Background
Recent technological advances have enabled high-throughput measurements of protein-protein interactions in the cell, producing large protein interaction networks for various species at an ever-growing pace. However, common technologies like yeast two-hybrid may experience high rates of false positive detection. To combat false positive discoveries, a number of different methods have been recently developed that associate confidence scores with protein interactions. Here, we perform a rigorous comparative analysis and performance assessment among these different methods.

Results
We measure the extent to which each set of confidence scores correlates with similarity of the interacting proteins in terms of function, expression, pattern of sequence conservation, and homology to interacting proteins in other species. We also employ a new metric, the Signal-to-Noise Ratio of protein complexes embedded in each network, to assess the power of the different methods. Seven confidence assignment schemes, including those of Bader et al., Deane et al., Deng et al., Sharan et al., and Qi et al., are compared in this work.

Conclusion
Although the performance of each assignment scheme varies depending on the particular metric used for assessment, we observe that Deng et al. yields the best performance overall (in three out of four viable measures). Importantly, we also find that utilizing any of the probability assignment schemes is always more beneficial than assuming all observed interactions to be true or equally likely.
Effect of Raloxifene on Bone Mineral Density in Premenopausal Women at Increased Risk of Breast Cancer
Authors: Eng-Wong J. , Reynolds J. C. , Venzon D. , Liewehr D. , Gantz S. , Danforth D. , Liu E. T. , Chow C. , Zujewski J. 
Published: July 2006

Abstract
Context: Raloxifene is a promising breast cancer prevention agent in postmenopausal women at increased risk for breast cancer. The effects of raloxifene in premenopausal women are unknown.
Objective: We evaluated the effect of raloxifene in premenopausal women at increased risk for breast cancer on bone mineral density (BMD).
Design: This was a phase II clinical trial.
Setting: This study was conducted at an academic medical center.
Participants: Thirty-seven premenopausal women at increased risk for breast cancer enrolled in the trial. Thirty subjects began treatment and 27 were evaluable.
Intervention: Raloxifene (60 mg daily) and elemental calcium (500 mg daily) were given for 2 yr. Subjects were followed up off medications for 1 yr.
Main Outcome Measure: The primary end point was the intrasubject percent change in BMD at 1 yr measured by dual-energy x-ray absorptiometry.
Results: The mean baseline lumbar spine density was 1.027 g/cm2. Lumbar spine density decreased 2.3% at 1 yr (P &lt; 0.00001) and 3.5% at 2 yr (P &lt; .00001). Percent change from yr 2 to 3 was +1.4%. The mean baseline total hip bone density was 0.905 g/cm2. Total hip density decreased 0.3% at 1 yr and 1.0% at 2 yr (P = 0.033). Percent change from yr 2 to 3 was +1.7%.
Conclusions: Raloxifene use is associated with a decrease in BMD in premenopausal women at increased risk for breast cancer. The clinical significance of this decrease is unknown and is attenuated with stopping raloxifene.
Serum Thyrotropin Concentration as a Novel Predictor of Malignancy in Thyroid Nodules Investigated by Fine-Needle Aspiration
Authors: Boelaert K. , Horacek J. , Holder R. L. , Watkinson J. C. , Sheppard M. C. , Franklyn J. A. 
Published: July 2006

Abstract
Context: Thyroid nodules and goiter are common, and fine-needle aspiration biopsy (FNAB) is the first investigation of choice in distinguishing benign from malignant disease.
Objective: The objective of the study was to assess whether simple clinical and biochemical parameters can predict the likelihood of thyroid malignancy in subjects undergoing FNAB.
Design: The design was a prospective cohort.
Setting: The study was conducted at a single secondary/tertiary care clinic.
Participants: One thousand five hundred consecutive patients without overt thyroid dysfunction (1304 females and 196 males, mean age 47.8 yr) presenting with palpable thyroid enlargement between 1984 and 2002 were evaluated by FNAB of the thyroid.
Intervention(s): There were no interventions.
Main Outcome Measures: Goiter type was assessed clinically and classified as diffuse in 183, multinodular in 456, or solitary nodule in 861 cases. Serum TSH concentration at presentation was measured in a sensitive assay in patients presenting after 1988 (n = 1183). The final cytological or histological diagnosis was determined after surgery (n = 553) or a minimum 2-yr clinical follow-up period (mean 9.5 yr, range 2–18 yr).
Results: The overall sensitivity and specificity of FNAB in predicting malignancy were 88 and 84%, respectively. The risk of diagnosis of malignancy rose in parallel with the serum TSH at presentation, with significant increases evident in patients with serum TSH greater than 0.9 mU/liter, compared with those with lower TSH. Binary logistic regression analysis revealed significantly increased adjusted odds ratios (AORs) for the diagnosis of malignancy in subjects with serum TSH 1.0–1.7 mU/liter, compared with TSH less than 0.4 mU/liter [AOR 2.72, 95% confidence interval (CI) 1.02–7.27, P = 0.046], with further increases evident in those with TSH 1.8–5.5mU/liter (AOR 3.88, 95% CI 1.48–10.19, P = 0.006, compared with TSH &lt; 0.4 mU/liter) and greater than 5.5 mU/liter (AOR 11.18, 95% CI 3.23–8.63, P &lt; 0.001, compared with TSH &lt; 0.4 mU/liter). Males (AOR 1.8, 95% CI 1.04–3.1, P = 0.04), younger patients (AOR 1.1, 95% CI 1.01–1.15, P = 0.025), and those with clinically solitary nodules (AOR 2.53, 95% CI 1.5–4.28, P = 0.001) were also at increased risk. Based on these findings, a formula to predict the risk of the diagnosis of thyroid malignancy in individual patients, taking into account their gender, age, goiter type determined clinically, and serum TSH, was calculated.
Conclusions: The risk of malignancy in a thyroid nodule increases with serum TSH concentrations within the normal range. In addition to patient’s gender, age, and goiter type, the serum TSH concentration at presentation is an independent predictor of the presence of thyroid malignancy. We propose that these simple clinical and biochemical factors can serve as an adjunct to FNAB in predicting risk of malignancy.
Cushing’s Syndrome: Important Issues in Diagnosis and Management
Authors: Findling James W. , Raff Hershel 
Published: July 2006

AbstractContext: The diagnosis, differential diagnosis, and treatment of Cushing’s syndrome are challenging problems in clinical endocrinology. We focus on critical questions addressing screening for Cushing’s syndrome, differentiation of Cushing’s subtypes, and treatment options.Evidence Acquisition: Ovid’s MEDLINE (1996 through April 2006) was used to search the general literature. We also relied on previously published reviews and a recent monograph and cite a mix of primary articles and recent reviews.Evidence Synthesis: Although this article represents our opinion, it draws heavily on a recent consensus statement from experts in the field and a recent monograph on Cushing’s syndrome.Conclusions: We concluded that: 1) measurement of late-night or bedtime salivary cortisol is a useful approach to screen for Cushing’s syndrome; 2) measurement of suppressed plasma ACTH by immunometric assay is useful to differentiate ACTH-dependent and -independent Cushing’s syndrome; 3) inferior petrosal sinus sampling for ACTH should be performed in patients with ACTH-dependent hypercortisolism in whom a pituitary magnetic resonance imaging is normal or equivocal (in the absence of a pituitary ACTH gradient, prolactin levels should be measured to confirm the integrity of venous sampling); 4) computed tomography of the chest and abdomen and somatostatin receptor scintigraphy should be performed in patients with the occult ectopic ACTH syndrome; and 5) patients with Cushing’s disease should be referred to a neurosurgeon with extensive experience operating on corticotroph microadenomas. Bilateral laparoscopic adrenalectomy should be considered in patients with Cushing’s disease who fail therapies directed at the pituitary.
Hydrodimerization of Methyl Acrylate Catalyzed by Halogenotris(triphenylphosphine)cobalt
Authors: Kanai Hiroyoshi , Ishii Keiji 
Published: July 2006

Abstract
Methyl acrylate was hydrodimerized in a methanolic solution by CoX(PPh3)3 (X=halogen) into dimethyl adipate. The in situ prepared cobalt complexes from cobalt halides, triphenylphosphine, and zinc gave higher yields of the hydrodimer in the presence of alkali halides. A mechanism is proposed which involves the protonation of Co(I)–methyl acrylate π-complex to give (2-methoxycarbonylethyl)cobalt complex, followed by a further addition of methyl acrylate.
Deactivation of Excited 2-Naphthylamine Due to Hydrogen Bonding Interaction with Pyridines. Fluorescence and Picosecond Laser Photolysis Studies
Authors: Ikeda Noriaki , Okada Tadashi , Mataga Noboru 
Published: July 2006

Abstract
The mechanism of the strong fluorescence quenching observed when two conjugated π-electron systems are directly connected by hydrogen bonding has been studied by means of transient absorption spectral measurements with ps as well as ns laser photolysis method and fluorescence measurement. The bimolecular rate constants of quenching of 2-naphthylamine fluorescence by pyridine and 4-cyanopyridine have been determined in various solvents. The bimolecular reaction rate of fluorescence quenching by pyridine is smaller than the diffusion controlled one in many cases and depends considerably upon the dipole moment and the ability of formation of hydrogen bonding chain of solvent. However, the quenching by 4-cyanopyridine is diffusion controlled in every solvent examined here. By means of ps laser photolysis method, the state formed by charge transfer from excited 2-naphthylamine to hydrogen bonded pyridine in the quenching process has been observed for the first time. The possibility of the hydrogen atom transfer due to the mechanism of charge transfer followed by proton transfer in hexane solution is also discussed.
Molecular Motion in Methylammonium Hexahalotellurates(IV) as Studied by Means of the Pulsed Nuclear Magnetic Resonance
Authors: Furukawa Yoshihiro , Kiriyama Hideko , Ikeda Ryuichi 
Published: July 2006

Abstract
Molecular motion in solid (CH3NH3)2TeX6 (X=Cl, Br, and I) was studied by measuring the spin-lattice relaxation time, T1, of 1H and 35Cl nuclei in several crystalline phases appearing below room temperature. A deep minimum of the proton T1 was observed in the low-temperature phase of all the compounds, indicating that the methylammonium ion performs a rapid reorientation as a whole about its three-fold axis. The activation energies, Ea, for the motion of cations are determined to be 7.0, 3.7, and 2.7 kJ/mol for X=Cl, Br, and I respectively. In (CH3NH3)2TeI6, which has the lowest Ea value, the relaxation process associated with the tunneling of the cation is apparent at low temperatures. For all the complexes studied, a shallow T1 minimum ascribable to the independent rotation of the CH3 and NH3 groups in the cation was observed on the high-temperature side of each deep T1 minimum. The 35Cl T1 of (CH3NH3)2TeCl6 exhibited a distinct minimum at the lower phase-transition point at 139 K and a discontinuity at the higher one near 230 K. The hindered rotation of the [TeCl6]2− octahedron occurs in the room-temperature phase, with an Ea value of 48 kJ/mol.
Reactions of trans- and cis-Dichlorobis(benzonitrile)platinum(II) with Acetylacetonate and Benzoylacetonate Carbanions. Formation of N-Acetyl β-Ketoamine Complexes by the Acetyl Group Migration
Authors: Uchiyama Toshihiko , Takagi Kazuhiko , Matsumoto Keiji , Ooi Shun’ichiro , Nakamura Yukio , Kawaguchi Shinichi 
Published: July 2006

Abstract
trans-Dichlorobis(benzonitrile) platinum(II) reacted with twice the molar amount of thallium(I) acetylacetonate and benzoylacetonate in dichloromethane at room temperature to afford mainly N-acetyl β-ketoamine chelates, trans-[Pt{N(COMe)=C(Ph)CH=COMe(and Ph)}2] (1a and 3a). This N,O-chelate structure of 1a was determined by X-ray analysis. Reactions of cis-[PtCl2(PhCN)2] gave C-acetyl and C-benzoyl β-ketoamine chelates, cis-[Pt{NH=C(Ph)C(COMe(and Ph))=COMe}2], together with other minor products. Formation of these β-ketoamine chelates is explained by the nucleophilic reactions of the β-diketonate carbanions at the coordinated cyanide carbon atom, followed by migration of the acetyl group or the methine proton of the nucleophiles onto the imino nitrogen atom formed during these reactions. In the presence of free β-diketones, migration of the acyl group was generally suppressed; this led to high yields of C-acyl complexes especially in reactions of cis-[PtCl2(PhCN)2]. In each case, the reaction proceeded with retention of the geometrical configuration around the central metal atom. The structures of other products, including a compound obtained by acid hydrolysis of 1a, were explored and discussed, based on IR and 2H NMR data.
Bis(β-diketonato)-palladram(II) and -platinum(II) Complexes
Authors: Okeya Seichi , Ooi Shun’ichiro , Matsumoto Keiji , Nakamura Yukio , Kawaguchi Shinichi 
Published: July 2006

Abstract
A number of palladium(II) and platinum(II) bis-chelates have been prepared which contain one kind of symmetric or unsymmetric β-diketonate anions, or involve two different β-diketonate anions. Existence of the cis and trans isomers in solution of the binary chelates of unsymmetric β-diketones was confirmed by 1H and 13C NMR spectroscopy. Geometrical isomerization of the palladium(II) complexes to attain equilibrium in solution is fast, while the platinum(II) complexes are quite inert. The mixed-ligand chelates are stable in solution, showing no sign of disproportionation. The isomeric pairs of bis(1-phenyl-1,3-butanedionato)palladium(II), bis(2,4-hexanedionato)palladium(II), and bis(1,1,1-trifluoro-2,4-pentanedionato)platinum(II) were isolated, and molecular structure of the cis isomer of the first complex was determined by X-ray analysis.
Adsorption of N-Dodecyl-β-alanine to the Spread Monolayer of Lecithin or Dilaurin
Authors: Tajima Kazuo , Tsutsui Takao 
Published: July 2006

Abstract
The adsorption of N-dodecyl-β-alanine (NDA) was studied at the air–solution interface with the spread film of l-α,β-dimyristoyllecithin (DML) or α,α′-dilaurin (DIL). The adsorbed amounts were measured by radiometry using tritium-labelled NDA, combined with surface pressure measurements. Measurements of IR, DSC, and NMR were made in order to determine the bulk properties of amphoteric moieties in the mixture of DML and NDA. For the mixed monolayer of NDA and DML or DIL, the surface composition vs. area curves were obtained at various surface pressures. The molecular interaction in monolayer was discussed on the basis of the excess free energy of mixing, which was calculated at various surface pressures and compositions. As a result, the mixing of DIL and NDA in monolayer was ideal at surface pressures less than 5 mN m−1, whereas the mixed monolayer of DML and NDA showed a remarkable condensation in surface molecular area. Such a large condensation at low surface pressure was concluded to be due to the formation of ion pairs between the choline and alanine moieties on the water surface, by referring to the findings obtained by studying the lipid properties in the bulk phase. It was also found that the DML–NDA monolayer near close packing exhibited various types of complicated behavior, depending on the surface compositions. The appreciable differences in the nature of the amphoteric moieties in DML and NDA molecules can explain these findings.
Dynamic Structure of the Potent Uncoupler SF 6847 (3,5-Di-t-butyl-4-hydroxybenzylidenemalononitrile) and Its Derivatives
Authors: Yoshikawa Kenichi , Kumazawa Noriyuki , Terada Hiroshi , Ju-ichi Motoharu 
Published: July 2006

Abstract
The steric and electronic structures of the most potent uncoupler of oxidative phosphorylation known, SF 6847, and its derivatives were studied. 1H and 13C NMR measurements showed that the malononitrile moiety is not planar with the benzene ring and that its intramolecular motional freedom is reduced on acid dissociation of the phenolic proton. The activation energies of the tumbling motion of the malononitrile moiety in the anionic forms of SF 6847 and its derivatives were also determined from their 1H NMR measured at various temperatures. The CNDO/2 and ab initio MO calculations of the model compounds of SF 6847 showed that the planar form is quite unstable and that the malononitrile moiety is twisted considerably relative to the benzene ring. The effect of the dynamic structure on the acidity of SF 6847 was discussed based on the above results.
Preparation of Several 1,5,5,11-Pentamethyltricyclo[6.2.1.02,6]undecane Derivatives
Authors: Inouye Yoshinobu , Fukaya Chikara , Kakisawa Hiroshi 
Published: July 2006

Abstract
1,6-Diketone, available in eight steps from homocamphorquinone, was converted into 1,5,5,11,11-pentamethyltricyclo[6.2.1.02,6]undecan-7-one by treatment with potassium t-butoxide and then lithium dimethylcuprate, while α,α-dimethyl-γ-valerolactone, prepared in five steps from homocamphor, was converted into 1,5,5,11,11-pentamethyltricyclo[6.2.1.02,6]undec-2-en-4-one by treatment with diphosphorus pentoxide–methanesulfonic acid.
The Nitration of Acylpentamethylbenzenes and 1,3-Diacyltetramethylbenzenes Bearing, as the Acyl Components, Pivaloyl, Trichloroacetyl, and Tribromoacetyl Groups. Exclusive Attack on the Methyl Group at the Most Crowded Site
Authors: Suzuki Hitomi , Hashihama Mitsuyuki , Mishina Tadashi 
Published: July 2006

Abstract
When treated with concentrated nitric acid in dichloromethane at room temperature, the title compounds undergo an exclusive attack on the methyl group at the most crowded site, giving 6-acyl-2,3,4,5-tetramethylbenzyl nitrates, and 2,6-diacyl-3,4,5-trimethylbenzyl nitrates and/or (2,6-diacyl-3,4,5-trimethylphenyl)nitromethanes respectively, as the major products. While the predominant mode of the side-chain substitution reactions is nitrooxylation for acylpentamethylbenzenes and 1,3-dipivaloyl-2,4,5,6-tetramethylbenzene, it shifts to nitration for 1,3-bis(trihalogenoacetyl)-2,4,5,6-tetramethylbenzenes. Nitrodeacylation is seen to some extent for pivaloylbenzenes, but not for trihalogenoacetylbenzenes. The exclusive attack on the methyl group at the most hindered position can be explained by a sequence involving the attachment of a nitronium ion at the site meta to the acyl group, followed by a proton release from the resulting arenium ion to form a nitromethylenecyclohexadiene intermediate, which is then transformed into the benzylic compounds via a benzyl cation/nitrite anion pair.
Synthesis and Reactions of Perylenecarboxylic Acid Derivatives. VIII. Synthesis of N-Alkyl-3,4:9,10-Perylenetetracarboxylic Monoanhydride Monoimide
Authors: Nagao Yukinori , Misono Takahisa 
Published: July 2006

Abstract
The condensations of 3,4 : 9,10-perylenetetracarboxylic dianhydride with alkylamines (isobutyl-, pentyl-, hexyl-, and octylamines) were spectroscopically determined. Under all of the reaction conditions employed, N-alkyl-3,4 : 9,10-perylenetetracarboxylic monoanhydride monoimide (2a–d) (alkyl=a; isobutyl, b; pentyl, c; hexyl, d; octyl) were obtained. As the reaction proceeded, the yield of 2a–d increased at an initial stage but decreased gradually after reaching a maximum. This maximum yield of 2a–d was: 2a; 85–88%, 2b; 85–89%, 2c; 78–84%, 2d; 79–85%. The kinetics of the reaction were also examined.
Emission Spectra of Aromatic Hydrocarbons by Controlled Electron Impact
Authors: Ogawa Teiichiro , Yamami Naoki , Tsuji Masaharu , Nishimura Yukio 
Published: July 2006

Abstract
The emission spectra of benzene, toluene, ethylbenzene, xylenes, trimethylbenzenes, cymene, and naphthalene were investigated under controlled electron-impact excitation. These aromatic hydrocarbons showed a characteristic band in the 250–400 nm region and several bands of such excited fragment species as H and CH. The characteristic bands are similar to those of fluorescence spectra obtained by optical excitation and, thus, were assigned to fluorescence emissions of the parent molecules. The intensity of the fluorescence emission of benzene decreased at higher electron energies, and fragment emissions became dominant above 100 eV. However, its vibrational structure did not change for electron energies of 5–60 eV. This indicates that cascade processes from high-lying states are negligible for benzene. The fluorescence emission of naphthalene shifted to a shorter wavelength for low electron energies. Together with a theoretical estimation based on the Born approximation, cascade effects from higher excited states (S2 and S3) are found to be the major source of the fluorescence emission of naphthalene.
The Vacuum Ultraviolet Absorption Spectra of Fatty Acid Multilayers
Authors: Nagahira Yukio , Matsuki Kazunori , Fukutome Hideo 
Published: July 2006

Abstract
The electronic absorption spectra of fatty acid multilayers were measured in the vacuum ultraviolet region with an energy below 10 eV. From the chain length dependence of the spectra, the strong absorption (above 8 eV) was assigned to the σ-σ* transitions in the alkane chain moiety, and the weaker one (below 8 eV), to the transitions in the car boxy lie acid and metal car boxy late moieties. The polarized spectra of the Ba stearate multilayer showed that the band near 8.8 eV was polarized perpendicularly to the alkane chain. The spectra of the stearic acid multilayer without metal ions and the multilayer of the Zn stearate showed that their alkane chains were titled against the normal of the layer plane.
Kinetic Isotope Effect of Chemically Activated Vinyl Radicals
Authors: Kowari Ken-ichi , Sugawara Ko-ichi , Sato Shin , Nagaset Shigeru 
Published: July 2006

Abstract
The apparent decay rates of hydrogen and deuterium atoms in the reactions with acetylene-d0 and -d2 in helium in the pressure range from 100 to 800 Torr (1 Torr=133.3 Pa) have been measured by the pulse radiolysisLyman-α absorption method at 300±2 K. The helium pressure dependence of the rate constants was well interpreted in terms of the RRKM theory including a tunneling effect, using the geometry and force constants of the activated complex and vinyl radical estimated by the ab initio calculation. (S. Nagase and C. W. Kern, J. Am. Chem. Soc., 101, 2544 (1979).)
Chlorination of Polyacrylonitrile and Analysis of Its Products
Authors: Okamoto Masao , Yamada Ry\={o}ji , Ishizuka Osamu 
Published: July 2006

Abstract
Chlorination of polyacrylonitrile (PAN) was carried out by passing dried chlorine gas through a tetrahydrothiophene 1,1-dioxide (sulfolane) solution of PAN or a powdery mixture of PAN with sodium chloride. The chlorinated products were examined by comparison with acrylonitrile-α-chloroacrylonitrile (CAN) copolymers corresponding to α-chlorinated PANs. In solution the reaction proceeded easily below 100 °C, but due to side reactions analysis of the products was difficult. In the powdery mixture hardly any reaction took place below 100 °C, but in the range 120–140 °C, the reaction proceeded smoothly and its rate became ca. 2.7 times in proportion as its temperature was raised by 10 °C. The chlorinated products were investigated by means of infrared and thermal analyses. The chlorinated moiety consists mainly of α,β-dichlorinated units, which seem to result from the addition of chlorine to the double bonds produced by dehydrochlorination after β-chlorination. These chlorinated products were dehydrochlorinated at lower temperature than acrylonitrile-CAN copolymers, but in many respects they resemble each other in the behavior of thermal degradation.