bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Fluorescence of Diacetyl
Authors: Almy G. M. , Fuller H. Q. , Kinzer G. D. 
Published: January 2005

Diacetyl, in the vapor phase or in water solution, exhibits a bright green fluorescence when excited with light within its absorption band in the violet and near ultraviolet. A detailed measurement of the structure shows that the spectrum is the same as is shown in the fluorescence of acetone vapor when excited with λ3130. The fluorescence spectrum is insensitive to changes in diacetyl pressure (0.1 mm to 50 mm), temperature (10°C to 100°C), exciting wave-length (3650A to 4358A) or amount of added oxygen, which quenches the fluorescence strongly. The intensity of fluorescence, measured with photo-cell and amplifier, is constant in time, with weak excitation. The ratio of intensity of fluorescence to light absorbed is independent of the pressure and the intensity of the fluorescence is linearly proportional to the exciting intensity, at constant pressure. The fluorescence is quenched by oxygen, the intensity falling to one-half at 0.013 mm oxygen. The Stern-Volmer law is followed over a range of oxygen pressures in which the fluorescence drops to 20 percent of the intensity without oxygen; at higher pressures the intensity falls more rapidly than expected. The oxygen is consumed, presumably in the quenching process, and the fluorescence returns to full intensity. From the quenching curve and from an experiment on the diffusion of the excited molecules into shadow the lifetime of the fluorescing molecule is estimated to be about 10—5 sec.
These results can be understood on the assumption that the diacetyl molecule emits the fluorescence after excitation and redistribution (spontaneous and through collisions) of the vibrational energy. In the case of acetone the fluorescence builds up gradually from practically zero intensity, as expected if diacetyl is accumulating; it is excited, not by light, but probably by collisions with excited acetone or with combining radicals. The diffusion experiments can scarcely be reconciled with the assumption that the observed emission in pure diacetyl is a recombination spectrum.
Dispersion and Absorption in Dielectrics I. Alternating Current Characteristics
Authors: Cole Kenneth S. , Cole Robert H. 
Published: January 2005

The dispersion and absorption of a considerable number of liquid and dielectrics are represented by the empirical formula ε*−ε∞=(ε0−ε∞)/[1+(iωτ0)1−α]. In this equation, ε* is the complex dielectric constant, ε0 and ε∞ are the ``static'' and ``infinite frequency'' dielectric constants, ω=2π times the frequency, and τ0 is a generalized relaxation time. The parameter α can assume values between 0 and 1, the former value giving the result of Debye for polar dielectrics. The expression (1) requires that the locus of the dielectric constant in the complex plane be a circular arc with end points on the axis of reals and center below this axis.
If a distribution of relaxation times is assumed to account for Eq. (1), it is possible to calculate the necessary distribution function by the method of Fuoss and Kirkwood. It is, however, difficult to understand the physical significance of this formal result.
If a dielectric satisfying Eq. (1) is represented by a three-element electrical circuit, the mechanism responsible for the dispersion is equivalent to a complex impedance with a phase angle which is independent of the frequency. On this basis, the mechanism of interaction has the striking property that energy is conserved or ``stored'' in addition to being dissipated and that the ratio of the average energy stored to the energy dissipated per cycle is independent of the frequency.
Statistical Mechanics of Nearest Neighbor Systems
Authors: Montroll Elliott W. 
Published: January 2005

In many solids the intermolecular forces are sufficiently short ranged so that practically the entire potential energy of the system results from interactions between nearest neighbors. The thermodynamic properties of a solid with respect to a given coordinate, α, (for example, in a ferromagnetic system α might represent the excess unpaired electron spin at a given lattice point; or in a substitutional binary alloy α might denote which of the two possible kinds of atoms are at a given lattice point) can be found from the factor of the partition function which averages over all possible configurations of α at all lattice points.
Here the evaluation of such a factor of the partition function is reduced to the calculation of the largest characteristic value of a linear homogeneous operator equation involving the potential energy between two adjacent layers of lattice points in the solid. By assuming that all possible configurations of a layer are equally probable, a lower bound for the partition function for a simple cubic lattice is found in terms of the partition function of a cube of eight molecules.
The operator equation for a real crystal becomes quite complex, but in some problems it is possible to obtain characteristic vectors and characteristic values (and thus the partition function) at high and low temperatures. For intermediate temperatures a theory of resonance between the low temperature ``almost ordered'' characteristic vectors and the high temperature ``almost disordered'' characteristic vectors is developed. In cases where the operator equation can be solved for microcrystals a few layers thick, a perturbation method is discussed in which interactions between the individual microcrystals are treated as perturbations.
Some remarks are made concerning phase transitions and finally the general theory is applied to a superficial treatment of two-dimensional ferromagnetic plates.
The H2A.Z/H2B dimer is unstable compared to the dimer containing the major H2A isoform
Authors: Placek Brandon J. , Harrison L. Nicole , Villers Brooke M. , Gloss Lisa M. 
Published: January 2005

AbstractThe nucleosome, the basic fundamental repeating unit of chromatin, contains two H2A/H2B dimers and an H3/H4 tetramer. Modulation of the structure and dynamics of the nucleosome is an important regulation mechanism of DNA‐based chemistries in the eukaryotic cell, such as transcription and replication. One means of altering the properties of the nucleosome is by incorporation of histone variants. To provide insights into how histone variants may impact the thermodynamics of the nucleosome, the stability of the heterodimer between the H2A.Z variant and H2B was determined by urea‐induced denaturation, monitored by far‐UV circular dichroism, intrinsic Tyr fluorescence intensity, and anisotropy. In the absence of stabilizing agents, the H2A.Z/H2B dimer is only partially folded. The stabilizing cosolute, trimethylamine‐N‐oxide (TMAO) was used to promote folding of the unstable heterodimer. The equilibrium stability of the H2A.Z/H2B dimer is compared to that of the H2A/H2B dimer. The equilibrium folding of both histone dimers is highly reversible and best described by a two‐state model, with no detectable equilibrium intermediates populated. The free energies of unfolding, in the absence of denaturant, of H2A.Z/H2B and H2A/H2B are 7.3 kcal mol−1 and 15.5 kcal mol−1, respectively, in 1 M TMAO. The H2A.Z/H2B dimer is the least stable histone fold characterized to date, while H2A/H2B appears to be the most stable. It is speculated that this difference in stability may contribute to the different biophysical properties of nucleosomes containing the major H2A and the H2A.Z variant.
NMR structure of HI0004, a putative essential gene product from Haemophilus influenzae, and comparison with the X‐ray structure of an Aquifex aeolicus homolog
Authors: Yeh Deok Cheon , Parsons Lisa M. , Parsons James F. , Liu Fang , Eisenstein Edward , Orban John 
Published: January 2005

AbstractThe solution structure of the 154‐residue conserved hypothetical protein HI0004 has been determined using multidimensional heteronuclear NMR spectroscopy. HI0004 has sequence homologs in many organisms ranging from bacteria to humans and is believed to be essential in Haemophilus influenzae, although an exact function has yet to be defined. It has a α–β–α sandwich architecture consisting of a central four‐stranded β‐sheet with the α2‐helix packed against one side of the β‐sheet and four α‐helices (α1, α3, α4, α5) on the other side. There is structural homology with the eukaryotic matrix metalloproteases (MMPs), but little sequence similarity except for a conserved region containing three histidines that appears in both the MMPs and throughout the HI0004 family of proteins. The solution structure of HI0004 is compared with the X‐ray structure of an Aquifex aeolicus homolog, AQ_1354, which has 36% sequence identity over 148 residues. Despite this level of sequence homology, significant differences exist between the two structures. These differences are described along with possible functional implications of the structures.
The mechanism of inhibition of the cyclin‐dependent kinase‐2 as revealed by the molecular dynamics study on the complex CDK2 with the peptide substrate HHASPRK
Authors: Bártová Iveta , Otyepka Michal , KřÍž Zdeněk , Koča Jaroslav 
Published: January 2005

AbstractMolecular dynamics (MD) simulations were used to explain structural details of cyclin‐dependent kinase‐2 (CDK2) inhibition by phosphorylation at T14 and/or Y15 located in the glycine‐rich loop (G‐loop). Ten‐nanosecond‐long simulations of fully active CDK2 in a complex with a short peptide (HHASPRK) substrate and of CDK2 inhibited by phosphorylation of T14 and/or Y15 were produced. The inhibitory phosphorylations at T14 and/or Y15 show namely an ATP misalignment and a G‐loop shift (∼5 Å) causing the opening of the substrate binding box. The biological functions of the G‐loop and GxGxxG motif evolutionary conservation in protein kinases are discussed. The position of the ATP γ‐phosphate relative to the phosphorylation site (S/T) of the peptide substrate in the active CDK2 is described and compared with inhibited forms of CDK2. The MD results clearly provide an explanation previously not known as to why a basic residue (R/K) is preferred at the P2 position in phosphorylated S/T peptide substrates.
Regulation of protein activity with small‐molecule‐controlled inteins
Authors: Skretas Georgios , Wood David W. 
Published: January 2005

AbstractInteins are the protein analogs of self‐splicing RNA introns, as they post‐translationally excise themselves from a variety of protein hosts. Intein insertion abolishes, in general, the activity of its host protein, which is subsequently restored upon intein excision. These protein elements therefore have the potential to be used as general molecular “switches” for the control of arbitrary target proteins. Based on rational design, an intein‐based protein switch has been constructed whose splicing activity is conditionally triggered in vivo by the presence of thyroid hormone or synthetic analogs. This modified intein was used in Escherichia coli to demonstrate that a number of different proteins can be inactivated by intein insertion and then reactivated by the addition of thyroid hormone via ligand‐induced splicing. This conditional activation was also found to occur in a dose‐dependent manner. Rational protein engineering was then combined with genetic selection to evolve an additional intein whose activity is controlled by the presence of synthetic estrogen ligands. The ability to regulate protein function post‐translationally through the use of ligand‐controlled intein splicing will most likely find applications in metabolic engineering, drug discovery and delivery, biosensing, molecular computation, as well as many additional areas of biotechnology.
When an epithelium ceases to exist – an ultrastructural study on the fate of the embryonic coelom in Epiperipatus biolleyi (Onychophora, Peripatidae)
Authors: Mayer Georg , Ruhberg Hilke , Bartolomaeus Thomas 
Published: January 2005

AbstractIt is an accepted fact that fusion between the coelomic cavities and the primary body cavity occurs during development in the Arthropoda. However, such a fusion is much disputed in the Onychophora. In order to clarify this subject, the fate of embryonic coelomic cavities has been studied in an onychophoran. Ultrastructural investigations in this paper provide evidence that embryonic coelomic cavities fuse with spaces of the primary body cavity in Epiperipatus biolleyi. During embryogenesis, the somatic and splanchnic portions of the mesoderm separate and the former coelomic linings are transformed into mesenchymatic tissue. The resulting body cavity therefore represents a mixture of primary and secondary (coelomic) body cavities, i.e. the ‘mixocoel’. The nephridial anlage is already present, when the ‘mixocoel’ is formed, although there is no trace of a sacculus yet. The lumen of the nephridial anlage, thus, communicates with the newly formed ‘mixocoel’. Accordingly, the lumen of the nephridial sacculus cannot be regarded as a kind of ‘persisting coelomic cavity’ in E. biolleyi. Our findings support the hypothesis that the ‘mixocoel’ was already present in the common stem species of the Onychophora and Euarthropoda.
Ultrastructural study of the jaw structures in two species of Ampharetidae (Annelida: Polychaeta)
Authors: Tzetlin Alexander B. 
Published: January 2005

AbstractTwo species of jaw bearing Ampharetidae (Adercodon pleijeli (Mackie 1994) and Ampharete sp. B) were investigated in order to describe the microanatomy of the mouth parts and especially jaws of these enigmatic polychaetes. The animals of both studied species have 14–18 mouth tentacles that are about 30 µm in diameter each. In both species, the ventral pharyngeal organ is well developed and situated on the ventral side of the buccal cavity. It is composed of a ventral muscle bulb and investing muscles. The bulb consists of posterior and anterior parts separated by a deep median transversal groove. In both species, the triangular teeth or denticles are arranged in a single transversal row on the surface of the posterior part of the ventral bulb just in front of its posterior edge. There are 36 denticles in Adercodon pleijeli and 50 in Ampharete sp. B. The height of the denticles (6–12 µm) is similar in both species. Each tooth is composed of two main layers. The outer one (dental) is the electron‐dense sclerotized layer that covers the tooth. The inner one consists of long microvilli with a collagen matrix between them. The thickness of the dental layer ranges from 0.95 to 0.6 µm. The jaws of the studied worms may play a certain role in scraping off microfouling. The fine structure of the jaws in Ampharetidae is very similar to that of the mandibles of Dorvilleidae, the mandibles and the maxillae of Lumbrineridae, Eunicidae and Onuphidae, and the jaws of other Aciculata. This type of jaw is characterized by unlimited growth and the absence of replacement. The occurrence of jaws in a few smaller Ampharetidae is considered as an apomorphic state.
Ultrastructure of the digestive tract of Diacyclops thomasi (Cyclopoida, Copepoda) during different stages of encystment during a summer diapause
Authors: Baud Alexandra , Cuoc C. , Alekseev V. 
Published: January 2005

AbstractBaud, A., Cuoc, C. and Alekseev, V. 222_. Ultrastructure of the digestive tract of Diacyclops thomasi (Cyclopoida, Copepoda) during different stages of encystment during a summer diapause. — Acta Zoologica (Stockholm) 85: 181–189 Diacyclops thomasi (Forbes, 1882) has a life cycle comprising a summer diapause with whole‐body encystment at the copepodid IV stage. Formed progressively, the cyst can indicate the extent of entry into diapause. In this study the ultrastructure of the midgut epithelium during encystment of CIV was compared with that of active CIV and females.In active individuals two well‐differentiated epithelial cell types were observed: vacuolar cells (B‐cells), and cells without vacuoles but with more densely packed microvilli and abundant rough endoplasmic reticulum and mitochondria (F/R cells). In encysted specimens a striking transformation of the midgut epithelial layer was noted. Only inactive nuclei with highly concentrated euchromatin and encircled by a thin rim of hyaloplasm were observed. Compartments of both urosome and especially cephalothorax displayed large lipid‐rich lacunae. At the beginning of encystment, the midgut epithelium showed an intermediate state.Changes in ultrastructure observed in the midgut epithelium of D. thomasi clearly reflect different stages of diapause, and represent clear evidence of profound reorganization, which is progressively induced by diapause in the organism.
Stomach expression of histo‐blood group antigens A and B in some vertebrates
Authors: Sarafian Victoria S. , Tomova Elena S. , Kalaydjiev Svetoslav K. 
Published: January 2005

AbstractHisto‐blood group antigens (HBGA) are genetically determined glycoproteins and glycolipids expressed not only on human erythrocytes but also in vertebrate tissues. Direct evidence for the immunobiological importance of their tissue localization in the evolutionary aspect is still lacking.The present study examines the expression of A and B HBGA in the stomach of free‐living vertebrates belonging to: Chondrichthyes, Actinopterygii, Amphibia, Reptilia, Aves, and Mammalia.HBGA were detected immunohistochemically on stomach paraffin sections from 11 species. In all classes from Actinopterygii to Mammalia HBGA expression was confined to stomach mucosa only. Antigenic heterogeneity in the pattern of expression and localization was observed. Smooth muscle tissue, endothelial and red blood cells were immunonegative, except for the reptileEmys orbicularis.Our results present the first comparative evidence for the expression of HBGA in the stomach of 11 free‐living vertebrate species from six classes, some of which have never been studied so far. It could be assumed that A and B antigens are constant and conservative structures with almost similar tissue localization. Their immunobiological role in the animal gastrointestinal tract might be possibly related to cell differentiation and homeostasis maintenance which would contribute to sustain the evolutionary stable ABH antigen cellular expression.
Identification of different bacterial DNAs in human coronary arteries
Authors: Lehtiniemi J. , Karhunen P. J. , Goebeler S. , Nikkari S. , Nikkari S. T. 
Published: January 2005

AbstractBackground  Various studies have suggested a link between infection, atherosclerosis and coronary artery disease. We studied whether bacterial DNA is present in coronary specimens obtained from left anterior descending coronary arteries of subjects having sudden deaths of cardiovascular and other causes, as verified by an autopsy.Materials and methods  Coronary specimens were obtained from five subjects who died of sudden coronary causes and five controls. Broad‐range 16‐s rDNA PCR (Br‐PCR) amplification, cloning and sequencing were used to detect bacterial rDNA.Results  Bacterial rDNA sequences of oral pathogens were detected from the coronary samples in all cases regardless of the cause of death.Conclusions  Br‐PCR is a powerful method to detect bacterial rDNA. By this method we were able to detect wide palette of oral bacteria from coronary tissues. Our findings suggest that atheromas may act as mechanical sieves collecting bacteria from the circulation.
Alpha‐Gal on bioprostheses: xenograft immune response in cardiac surgery
Authors: Z. Konakci K. , Bohle B. , Blumer R. , Hoetzenecker W. , Roth G. , Moser B. , Boltz‐Nitulescu G. , Gorlitzer M. , Klepetko W. , Wolner E. , Ankersmit H. J. 
Published: January 2005

AbstractBackground  The α‐Gal (Galα1,3‐Galβ1–4GlcNAc‐R) epitope is the major xenoantigen causing hyperacute rejection of pig organs transplanted into primates. Porcine bioprostheses are utilized in cardiac surgery. However, premature degeneration of bioprostheses has limited utilization in younger patients and the immune response remains elusive. We sought to investigate whether a specific α‐Gal immune response may play a role in this clinical scenario.Materials and methods  We investigated the presence of α‐Gal‐epitope on native and fixed porcine valves by means of confocal laser scanning microscope (CLSM). ELISA was utilized to evidence whether implantation of bioprostheses elicits augmentation of pre‐existing cytotoxic anti α‐Gal IgM antibodies within 10 days of surgery. Patients who underwent coronary artery bypass grafting (CABG) or mechanical valve replacement served as controls (each group, n = 12). To corroborate the clinical relevance of the α‐Gal immune response in vivo, we studied serum obtained before and after implantation of bioprostheses and its potency to lyse porcine α‐Gal‐bearing PK15 cells.Results  We found the immunogenic α‐Gal‐epitope on fibrocytes interspersed in the connective tissue of porcine valves as determined by vimentin/IB4 lectin binding. Moreover, patients who were provided with a bioprostheses had developed a significant increase of naturally occurring cytotoxic IgM antibodies directed towards α‐Gal after surgical intervention as compared with control patients (P < 0·0001, respectively). Sera obtained from the patients after the implantation of bioprostheses demonstrated an increased cytotoxicity against α‐Gal‐bearing PK‐15 cells as compared with preoperative sera (P < 0·001). The specificity of the cytotoxic effects was proven as soluble Galα1–3Galβ1–4GlcNAc markedly inhibited cell death of α‐Gal‐bearing PK15 cells (P < 0·001).Conclusion  Our data suggest that implantation of bioprostheses in cardiac surgery induces a xenograft‐specific immune response. Procedures diminishing the presence of α‐Gal on bioprostheses, such as utilization of genetically manipulated α‐Gal‐deficient xenograft or pretreatment with α‐Galactosidase, might diminuate the immune response against bioprostheses and extend durability.
Neurohormonal risk stratification for sudden death and death owing to progressive heart failure in chronic heart failure
Authors: Berger R. , Huelsmann M. , Strecker K. , Moertl D. , Moser P. , Bojic A. , Pacher R. 
Published: January 2005

AbstractBackground  This study tested various neurohormones for prediction of heart failure death (death owing to progressive deterioration of ventricular function; HFD). Moreover, B‐type natriuretic peptide (BNP) as a predictor of sudden death (SD; as reported previously) and the best predictor of HFD were combined for a simple risk stratification model.Design  BNP, the N‐terminal fragment of BNP (N‐BNP), and of the atrial natriuretic peptide (N‐ANP) and big endothelin levels were obtained from 452 patients with a left ventricular ejection fraction ≤ 35%. Outcome was documented during an observation period up to 3 years.Results  Two hundred and ninety‐eight patients survived without heart transplantation, 65 patients underwent heart transplantation and 89 patients died (SD 44 patients, HFD 31 patients, other causes 14 patients). The only independent predictor of SD was BNP (as reported), and the best independent predictor of HFD was N‐ANP (P = 0·0001). Analyzing 293 survivors and 44 patients with SD, fewer patients with BNP < 130 pg mL−1 (Group A, n = 110) died [1%] as compared with patients with BNP > 130 pg mL−1 and N‐ANP < 6300 fmol mL−1 (Group B, n = 177; 18%; P = 0·0001) and patients with BNP > 130 pg mL−1 and N‐ANP > 6300 fmol mL−1 (Group C, n = 50; 19%; P = 0·0001). Analyzing 293 survivors and 31 patients with HFD, fewer patients died in Group A (n = 109; 0%; P = 0·0001) and Group B (n = 153; 6%; P = 0·0001) as compared with patients of Group C (n = 62; 34%).Conclusion  Prognostic power of neurohormones depends on the mode of death. The combined determination of BNP and N‐ANP identifies patients with minimal risk of death, elevated SD but low HFD risk as well as elevated SD and HFD risk.