bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structure alignment based on coding of local geometric measures
Authors: Chang Peter L , Rinne Andrew W , Dewey T Gregory 
Published: July 2006

AbstractBackgroundA structure alignment method based on a local geometric property is presented and its performance is tested in pairwise and multiple structure alignments. In this approach, the writhing number, a quantity originating from integral formulas of Vassiliev knot invariants, is used as a local geometric measure. This measure is used in a sliding window to calculate the local writhe down the length of the protein chain. By encoding the distribution of writhing numbers across all the structures in the protein databank (PDB), protein geometries are represented in a 20-letter alphabet. This encoding transforms the structure alignment problem into a sequence alignment problem and allows the well-established algorithms of sequence alignment to be employed. Such geometric alignments offer distinct advantages over structural alignments in Cartesian coordinates as it better handles structural subtleties associated with slight twists and bends that distort one structure relative to another.ResultsThe performance of programs for pairwise local alignment (TLOCAL) and multiple alignment (TCLUSTALW) are readily adapted from existing code for Smith-Waterman pairwise alignment and for multiple sequence alignment using CLUSTALW. The alignment algorithms employed a blocked scoring matrix (TBLOSUM) generated using the frequency of changes in the geometric alphabet of a block of protein structures. TLOCAL was tested on a set of 10 difficult proteins and found to give high quality alignments that compare favorably to those generated by existing pairwise alignment programs. A set of protein comparison involving hinged structures was also analyzed and TLOCAL was seen to compare favorably to other alignment methods. TCLUSTALW was tested on a family of protein kinases and reveal conserved regions similar to those previously identified by a hand alignment.ConclusionThese results show that the encoding of the writhing number as a geometric measure allow high quality structure alignments to be generated using standard algorithms of sequence alignment. This approach provides computationally efficient algorithms that allow fast database searching and multiple structure alignment. Because the geometric measure can employ different window sizes, the method allows the exploration of alignments on different, well-defined length scales.
Interaction between Mycobacterium avium subsp. paratuberculosis and environmental protozoa
Authors: Whan Lynne , Grant Irene R , Rowe Michael T 
Published: July 2006

Abstract

Background
Interactions between Mycobacterium avium subsp. paratuberculosis (Map) and free-living protozoa in water are likely to occur in nature. The potential impact of ingestion of Map by two naturally occurring Acanthamoeba spp. on this pathogen's survival and chlorine resistance was investigated.

Results
Between 4.6 and 9.1% of spiked populations of three Map strains (NCTC 8578, B2 and ATCC 19698), which had been added at a multiplicity of infection of 10:1, were ingested by Acanthamoeba castellanii CCAP 1501/1B and A. polyphaga CCAP 1501/3B during co-culture for 3 h at 25°C. Map cells were observed to be present within the vacuoles of the amoebae by acid-fast staining. During extended co-culture of Map NCTC 8578 at 25°C for 24 d with both A. castellanii and A. polyphaga Map numbers did not change significantly during the first 7 days of incubation, however a 1–1.5 log10 increase in Map numbers was observed between days 7 and 24 within both Acanthamoeba spp. Ingested Map cells were shown to be more resistant to chlorine inactivation than free Map. Exposure to 2 μg/ml chlorine for 30 min resulted in a log10 reduction of 0.94 in ingested Map but a log10 reduction of 1.73 in free Map (p < 0.001).

Conclusion
This study demonstrated that ingestion of Map by and survival and multiplication of Map within Acanthamoeba spp. is possible, and that Map cells ingested by amoebae are more resistant to inactivation by chlorine than free Map cells. These findings have implications with respect to the efficacy of chlorination applied to Map infected surface waters.
Reduced neuronal cell death after experimental brain injury in mice lacking a functional alternative pathway of complement activation
Authors: Leinhase Iris , Holers V Michael , Thurman Joshua M , Harhausen Denise , Schmidt Oliver I , Pietzcker Malte , Taha Mohy E , Rittirsch Daniel , Huber-Lang Markus , Smith Wade R , Ward Peter A , Stahel Philip F 
Published: July 2006

AbstractBackgroundNeuroprotective strategies for prevention of the neuropathological sequelae of traumatic brain injury (TBI) have largely failed in translation to clinical treatment. Thus, there is a substantial need for further understanding the molecular mechanisms and pathways which lead to secondary neuronal cell death in the injured brain. The intracerebral activation of the complement cascade was shown to mediate inflammation and tissue destruction after TBI. However, the exact pathways of complement activation involved in the induction of posttraumatic neurodegeneration have not yet been assessed. In the present study, we investigated the role of the alternative complement activation pathway in contributing to neuronal cell death, based on a standardized TBI model in mice with targeted deletion of the factor B gene (fB-/-), a "key" component required for activation of the alternative complement pathway.ResultsAfter experimental TBI in wild-type (fB+/+) mice, there was a massive time-dependent systemic complement activation, as determined by enhanced C5a serum levels for up to 7 days. In contrast, the extent of systemic complement activation was significantly attenuated infB-/- mice (P< 0.05,fB-/-vs.fB+/+;t= 4 h, 24 h, and 7 days after TBI). TUNEL histochemistry experiments revealed that posttraumatic neuronal cell death was clearly reduced for up to 7 days in the injured brain hemispheres offB-/- mice, compared tofB+/+ littermates. Furthermore, a strong upregulation of the anti-apoptotic mediator Bcl-2 and downregulation of the pro-apoptotic Fas receptor was detected in brain homogenates of head-injuredfB-/- vs.fB+/+ mice by Western blot analysis.ConclusionThe alternative pathway of complement activation appears to play a more crucial role in the pathophysiology of TBI than previously appreciated. This notion is based on the findings of (a) the significant attenuation of overall complement activation in head-injuredfB-/- mice, as determined by a reduction of serum C5a concentrations to constitutive levels in normal mice, and (b) by a dramatic reduction of TUNEL-positive neurons in conjunction with an upregulation of Bcl-2 and downregulation of the Fas receptor in head-injuredfB-/- mice, compared tofB+/+ littermates. Pharmacological targeting of the alternative complement pathway during the "time-window of opportunity" after TBI may represent a promising new strategy to be pursued in future studies.
Different profiles of immune reconstitution in children and adults with HIV-infection after highly active antiretroviral therapy
Authors: Resino Salvador , Seoane Elena , Pérez Alicia , Ruiz-Mateos Ezequiel , Leal Manuel , Muñoz-Fernández Maria Á 
Published: July 2006

Abstract

Background
Recent advances in characterizing the immune recovery of HIV-1-infected people have highlighted the importance of the thymus for peripheral T-cell diversity and function. The aim of this study was to investigate differences in immune reconstitution profiles after highly active antiretroviral therapy (HAART) between HIV-children and adults.

Methods
HIV patients were grouped according to their previous clinical and immunological status: 9 HIV-Reconstituting-adults (HIV-Rec-adults) and 10 HIV-Reconstituting-children (HIV-Rec-children) on HAART with viral load (VL) ≤400 copies/ml and CD4+ ≥500 cells/μL at least during 6 months before the study and CD4+ ≤300 cells/μL anytime before. Fifteen healthy-adults and 20 healthy-children (control subjects) were used to calculate Z-score values to unify value scales between children and adults to make them comparable.

Results
HIV-Rec-children had higher T-cell receptor excision circles (TREC) and lower interleukin (IL)-7 levels than HIV-Rec-adults (p < 0.05). When we analyzed Z-score values, HIV-Rec-children had higher TREC Z-score levels (p = 0.03) than HIV-Rec-adults but similar IL-7 Z-score levels. Regarding T-cell subsets, HIV-Rec-children had higher naïve CD4+ (CD4+CD45RA hi+CD27+), naïve CD8+ (CD8+CD45RA hi+CD27+), and memory CD8+ (CD8+CD45RO+) cells/μl than HIV-Rec-adults, but similar memory CD4+ (CD4+CD45RO+) counts. HIV-Rec-children had lower naïve CD8+ Z-score values than HIV-Rec-adults (p = 0.05).

Conclusion
Our data suggest that HIV-Rec-children had better thymic function than HIV-Rec-adults and this fact affects the peripheral T-cell subsets. Thus, T-cell recovery after HAART in HIV-Rec-adults could be the consequence of antigen-independent peripheral T-cell expansion while in HIV-Rec-children thymic output could play a predominant role in immune reconstitution.
Dimensional analysis of MINMOD leads to definition of the disposition index of glucose regulation and improved simulation algorithm
Authors: Nittala Aparna , Ghosh Soumitra , Stefanovski Darko , Bergman Richard , Wang Xujing 
Published: July 2006

Abstract

Background
Frequently Sampled Intravenous Glucose Tolerance Test (FSIVGTT) together with its mathematical model, the minimal model (MINMOD), have become important clinical tools to evaluate the metabolic control of glucose in humans. Dimensional analysis of the model is up to now not available.

Methods
A formal dimensional analysis of MINMOD was carried out and the degree of freedom of MINMOD was examined. Through re-expressing all state variable and parameters in terms of their reference scales, MINMOD was transformed into a dimensionless format. Previously defined physiological indices including insulin sensitivity, glucose effectiveness, and first and second phase insulin responses were re-examined in this new formulation. Further, the parameter estimation from FSIVGTT was implemented using both the dimensional and the dimensionless formulations of MINMOD, and the performances were compared utilizing Monte Carlo simulation as well as real human FSIVGTT data.

Results
The degree of freedom (DOF) of MINMOD was found to be 7. The model was maximally simplified in the dimensionless formulation that normalizes the variation in glucose and insulin during FSIVGTT. In the new formulation, the disposition index (Dl), a composite parameter known to be important in diabetes pathology, was naturally defined as one of the dimensionless parameters in the system. The numerical simulation using the dimensionless formulation led to a 1.5–5 fold gain in speed, and significantly improved accuracy and robustness in parameter estimation compared to the dimensional implementation.

Conclusion
Dimensional analysis of MINMOD led to simplification of the model, direct identification of the important composite factors in the dynamics of glucose metabolic control, and better simulations algorithms.
Six year disease free survival after liver transplantation in a patient with T3 gallbladder carcinoma: case presentation and review of the literature
Authors: Ortiz Jorge , Reich David , Joon Hoon Bae , Martinez Oscar , Manzarbeitia Cosme 
Published: July 2006

Abstract

Background
The incidence of gallbladder carcinoma in cirrhotics is unknown. Known risk factors are primary sclerosing cholangitis and polypoid masses.

Case presentation
A sixty year old with primary sclerosing cholangitis, cirrhosis, and gallbladder polyps underwent liver transplantation. A polypoid lesion measuring 1.5 × 0.5 cm was found on the fundus of the gallbladder. Histological examination revealed moderately differentiated adenocarcinoma with full thickness penetration of the gallbladder encroaching liver parenchyma. Angiolymphatic invasion was noted. The lymph nodes, the cystic duct and the common duct were free of tumor (T3N0M0). Extensive evaluation did not demonstrate metastasis. No chemotherapy was given. He is currently six years post procedure and free of disease.

Conclusion
"Incidentally" discovered stage IIA gallbladder carcinoma may not negatively affect long term survival after liver transplantation.
Persistent Expression of Notch2 Delays Gonadotrope Differentiation
Authors: Raetzman Lori T. , Wheeler Bayly S. , Ross Shelley A. , Thomas Paul Q. , Camper Sally A. 
Published: July 2006

AbstractNormal pituitary gland development requires coordination between maintenance of progenitor cell pools and selection of progenitors for differentiation. The spatial and temporal expression of Notch2 during pituitary development suggested that it could control progenitor cell differentiation in the pituitary. Consistent with this idea, Notch2 is not expressed in Prop1 mutants, and anterior pituitary progenitors in Prop1 mutants appear to be unable to transition from proliferation to differentiation properly, resulting in anterior lobe failed cell specification and evolving hypoplasia. To test the function of Notch2 directly, we used the αGSU subunit promoter to express activated NOTCH2 persistently in pre-gonadotropes and pre-thyrotropes of transgenic mice. At birth, there is a small reduction in the population of fully differentiated thyrotropes and almost no fully differentiated gonadotropes. The temporal and spatial expression of Hey1 suggests that it could be a mediator of this effect. Gonadotropes complete their differentiation program eventually, although expression of LH and FSH is mutually exclusive with NOTCH2 transgene expression. This demonstrates that activated Notch2 is sufficient to delay gonadotrope differentiation, and it supports the hypothesis that Notch2 regulates progenitor cell differentiation in the pituitary gland.
Molecular Orbital Considerations on Interaction of 2-Aminopyridine with Formic Acid in the Ground State
Authors: Inuzuka Kozo , Fujimoto Akira 
Published: July 2006

Abstract
In order to ascertain the formation processes of the tautomer and proton-transferred complexes in the 2-aminopyridine–acetic acid system in the ground state, a molecular orbital calculation was carried out for the 2-aminopyridine–formic acid system by the ab initio STO-3G method with full-geometry optimization of the complex. The following conclusions were drawn from the present calculation: (1) The amino–imino tautomerization in the 2-aminopyridine–formic acid system proceeds through a double proton transfer process between 2-aminopyridine and formic acid. (2) The formation of a proton-transferred complex in the 2-aminopyridine–formic acid system is difficult in the ground state. This conclusion may be applicable to the 2-aminopyridine–acetic acid system. (3) In the case of the ab initio STO-3G calculation a full-geometry optimization of the complex plays an important role in elucidating the stabilization energies and geometries of the tautomer and proton-transferred complexes. (4) A full-geometry optimization of the complex model is not so important for evaluating the hydrogen bond energy of the stable hydrogen-bonded complex, but is necessary for elucidating the effect of hydrogen bond formation on the molecular geometry of the complex. (5) The bisectal angle of the NH2 group, calculated by the ab initio STO-3G method, becomes much larger than the experimental value. Further, the energy difference between the planar and pyramidal 2-aminopyridine with respect to the NH2 group is much larger than the experimental value.
Synthesis and Properties of Diamino-Substituted Dipyrido [3,2-a: 2′,3′-c]phenazine
Authors: Yamada Masaki , Tanaka Yoshihito , Yoshimoto Yasuyuki , Kuroda Shigeyasu , Shimao Ichiro 
Published: July 2006

Abstract
A heteroaromatic compound 3,6-diaminodipyrido[3,2-a: 2′,3′-c]phenazine was synthesized with an improved method to convert 1,10-phenanthroline derivatives to the corresponding 5,6-diones. It was shown that the electron-donating effects of amino substituents were extended not only to pyridine rings but also to the phenazine ring.
Re-evaluation of the Acid Dissociation Constants of the Hydroxyl Groups in Tetrasodium 25,26,27,28-Tetrahydroxycalix[4]arene-5,11,17,23-tetrasulfonate
Authors: Yoshida Isao , Yamamoto Nobuhiro , Sagara Fumio , Ishii Daido , Ueno Keihei , Shinkai Seiji 
Published: July 2006

Abstract
The acid dissociation constants of the hydroxyl groups in tetrasodium 25,26,27,28-tetrahydroxycalix[4]arene-5,11,17,23-tetrasulfonate (CALX-S4) were determined at 25 °C by potentiometric and spectrophotometric titration methods. The first acid dissociation constant(pKa1) was found to be 3.26 ± 0.02 (μ = 0.1 with KNO3), which demonstrated a remarkable pKa shift due to intramolecular hydrogen-bonding interactions among the hydroxyl groups in CALX-S4. On the other hand, considerably weak acidities were observed on the residual three hydroxyl groups of CALX-S4 (pKa2 = 11.8 ± 0.3 (μ = 0.1 with KNO3), 11.3 ± 0.3 (μ = 2.0 with KCl), pKa3 = 12.8 ± 0.3 (μ = 2.0 with KCl), and pKa4= ca. 14 (μ = 2.0 with KCl)).
Preparation and Characterization of Palladium(I) and Platinum(I) Dinuclear Complexes Bridged by 2-(Dimethylphosphino)pyridine
Authors: Suzuki Takayoshi , Fujita Junnosuke 
Published: July 2006

Abstract
A series of dinuclear complexes containing Me2Ppy ( = 2-(dimethylphosphino)pyridine) as a bridging ligand, [MM′X2(μ-Me2Ppy)2] (M, M′ = Pd(I), Pt(I); X = Cl, Br, and I), have been prepared by reactions between [MX2(Me2Ppy-P)2] and [M′2(dba)3] (dba = 1,5-diphenyl-1,4-pentadien-3-one). In these reactions it has been found by 31P{1H} NMR studies that a dimeric head-to-head isomer was formed in the first place and then isomerized to a head-to-tail isomer. The reactions for analogous Ph2Ppy ( = 2-(diphenylphosphino)pyridine) complexes have been also examined in the same manner. The monomeric Pd(II) complexes reacted more rapidly than did the corresponding Pt(II) complexes in these dimerization and isomerization reactions. For each halogeno series of the Me2Ppy and Ph2Ppy complexes, it seems that the dimerization occurs faster in the order of Cl &lt; Br &lt; I, while the order is reversed in the isomerization, Cl &gt; Br &gt; I. The Me2Ppy complexes isomerized to a head-to-tail isomer more rapidly than did the Ph2Ppy complexes, indicating a larger trans effect of Me2Ppy than Ph2Ppy.
Solid State Oscillatory Reaction. I. Thermal Decomposition Studies of [Co(NH3)6]Br3 and CoBr2·2H2O
Authors: Patil Murlidhar D , Natu Gopal N , Kulkarni Shantaram B 
Published: July 2006

Abstract
Thermogravimetric analysis, TGA, of cobalt(II)bromide, [Co(NH3)6]Br3 –henceforth referred to by the shortname HCBR– was carried out using a wide diameter short one and a narrow diameter long sample cups. In the former type of cup the TGA trace was similar to that reported one. However, when the latter cup was used, the TGA showed oscillations in the % weight-loss. Cobalt(II)bromide, CoBr2, is formed as an intermediate product in the thermal decomposition of HCBR. The oscillatory nature of weight-loss curve was studied for both HCBR and CoBr2.
The oscillatory behavior in the present system has been confirmed on the basis of the following experiments:
(a) Dynamic TGA and differential thermal analysis, DTA, of HCBR and CoBr2·2H2O.
(b) Isothermal TGA by weight-loss method for HCBR and CoBr2.
(c) Thermal decomposition studies, in closed system, of (i) CoBr2 and of (ii) CoO in a mixture of O2 and Br2 gases, and of a mixture of (iii) Co3O4 and CoBr2 in dry nitrogen.
The oscillations in the composition of the solid residue were attributed to the formation of CoOBr as an intermediate. Final product of thermal decomposition of CoBr2 in air is Co3O4. Hence it is possible to imagine that the point of CoOBr formation makes branching off point. This sets the reaction to oscillate in the composition domain. Therefore, it was thought that Edelstein mechanism would be operative in this reaction. Alternately, the population growth model may also be used to explain this observation. Formation of CoOBr was thought to be the weight-loss step, i.e. decrease in the ‘population’ of CoBr2, while the formation of CoBr2 was the weight-gain step, i.e. increase in the ‘population’ of CoBr2 under the proposed reaction, CoBr2 + 1/2O2 CoOBr. The purpose of this article is, therefore, to present the interesting facts of this reaction before the readers, and not to ascribe any particular model for its explanation.
Reactivity of the Transient UV-Band Produced in Irradiated Liquid Carbon Tetrachloride with Various Alcohols
Authors: Sumiyoshi Takashi , Katayama Meiseki 
Published: July 2006

Abstract
The reactivities of the transient UV-band with a peak at 330 nm produced in irradiated liquid carbon tetrachloride with various alcohols have been measured using the absolute technique of pulse radiolysis. The obtained bimolecular rate constants have been compared with those previously determined for the reaction of chlorine atoms with various alcohols using the competitive scavenging method. The values of reaction rate constants of the UV-band are nearly twice those of chlorine atoms. Similar kinetic isotope effects were observed for deuterated methanol and 2-methyl-2-propanol. However, the dependence on the structure of the alcohols, which is characteristic for hydrogen abstraction from alcohols by chlorine atoms, has not been established by the reaction of the UV-band. These results strongly suggest that the assignment of the UV-band to chlorine atoms is not plausible, and instead, support the assignment to parent cations.
A Water-Soluble Spin Probe Newly Developed for Liposomal Studies
Authors: Sunamoto Junzo , Akiyoshi Kazunari , Kihara Tetsuji , Endo Masayuki 
Published: July 2006

Abstract
A water-soluble spin probe, disodium 4-[(4,8-sulfonatooxy-2-naphthyl)thioureylene]-2,2,6,6-tetramethyl-1-piperidinyloxyl (TEMPO-T) was newly synthesized and characterized comparing with several different TEMPO derivatives from the view point of a possibility of utilization in the liposomal studies. Of TEMPO derivatives studied, TEMPO-T was the best probe because of the high water solubility, the less lipophilicity, the less leakiness from liposome, and the reliable stability to both temperature and pH changes.
Photochemical Reduction of (η5-Cyclopentadienyl)(1,2-disubstituted 1,2-ethylenedichalcogenolato)cobalt(III) and (η5-Cyclopentadienyl)(1,2-benzenedithiolato)cobalt(III) Complexes in the Presence of Triethanolamine
Authors: Akiyama Takeo , Watanabe Yoshihiro , Miyasaka Akiko , Komai Toru , Ushijima Hirobumi , Kajitani Masatsugu , Shimizu Kunio , Sugimori Akira 
Published: July 2006

Abstract
The title complexes, [Co(cp)(S2C2Y2)](cp = η5-C5H5) (1) (a: Y = Ph, b: Y = 2-pyridyl, c: Y = 4-pyridyl, d: Y = −CO2Me, e: Y = −CN), [Co(cp)(S2C6H4)] (2), [Co(cp)(Se2C2Ph2)] (3), and [Co(cp)(SeSC2Ph2)] (4), are photochemically reduced to give one-electron reduced species, Co(II) complexes, under UV-irradiation in the presence of an electron donor, triethanolamine (TEOA), in acetonitrile solutions. The photoreduction is wavelength dependent. The 313 nm light is the most effective (Φ = 0.002–0.018) for all the complexes used, and the light of wavelength longer than 365 nm is ineffective for the photoreduction of 1–4. The irradiation with 254 nm light brings about decomposition of the complexes.