bluuebunny/crossref_metadata_2025_split huggingface dataset:
Preparation of different forms of titanium oxide on titanium surface: Effects on apatite deposition
Authors: Rohanizadeh R. , Al‐Sadeq M. , LeGeros R. Z. 
Published: September 2004

AbstractMethods of preparing different types of titanium oxide (TiO2) and their effects on apatite deposition and adhesion on titanium surfaces were investigated. Forty‐eight commercially pure titanium (Ti) discs were divided into four groups (12 per group) and each group was subjected to the following treatments: Group 1, heat treatment at 750°C; Group 2, oxidation in H2O2 solution followed by heat treatment; Group 3, dipping in rutile/gelatin slurry; and Group 4, dipping in anatase/gelatin slurry. Surface‐treated Ti discs were immersed in a supersaturated calcium phosphate solution to allow apatite deposition. Results showed that the percentage of area covered by deposited apatite was highest in Group 4 compared to the other groups. Apatite deposited on Ti discs pretreated in H2O2 solution (Group 2) demonstrated the highest adhesion to the titanium substrate. Results from this study indicated that surface treatment method affects the type of TiO2 layer formed (anatase or rutile) and affects apatite deposition and adhesion on the Ti surface. © 2004 Wiley Periodicals, Inc. J Biomed Mater Res 71A: 343–352, 2004
Properties of crosslinked protein matrices for tissue engineering applications synthesized by multiphoton excitation
Authors: Basu Swarna , Campagnola Paul J. 
Published: September 2004

AbstractWe demonstrate the fabrication of model scaffolds and extracellular matrices using multiphoton excited photochemistry. This method is three‐dimensional in nature and has excellent biocompatibility. Crosslinked matrices were fabricated from the proteins fibrinogen, fibronectin, and concanavalin A using two‐photon rose bengal photoactivation and the relatives rates were determined. Immunofluorescence labeling of fibrinogen and fibronectin indicated retention of bioactivity following the multiphoton crosslinking process. Using the fluorescence recovery after photobleaching method, we measured the lateral mobility of fluorescent dyes of different mass and chemistry in order to model the behavior of therapeutic agents and bioactive molecules and found diffusion coefficients within these fabricated structures to be on the order of 10−9–10−10 cm2/s, or approximately three to four orders of magnitude slower than in free solution. The precise diffusion coefficients can be smoothly tuned by varying the laser exposure during the fabrication of the matrix, which results in both an increase in crosslink density as well as protein concentration in the matrix. Terminal crosslink density is achieved at integrated high exposure dose and the relative fabrication rates were determined for these proteins. For all the proteins, the range of diffusion coefficients between the threshold for fabrication and the terminal limit is correlated with the change in matrix mesh size as determined by Flory‐Rehner swelling analysis. Both normal Fickian as well as hindered anomalous diffusion is observed depending on specific molecular interactions of the tracer dyes and protein host. © 2004 Wiley Periodicals, Inc. J Biomed Mater Res 71A: 359–368, 2004
Using quaternions to calculate RMSD
Authors: Coutsias Evangelos A. , Seok Chaok , Dill Ken A. 
Published: September 2004

AbstractA widely used way to compare the structures of biomolecules or solid bodies is to translate and rotate one structure with respect to the other to minimize the root‐mean‐square deviation (RMSD). We present a simple derivation, based on quaternions, for the optimal solid body transformation (rotation‐translation) that minimizes the RMSD between two sets of vectors. We prove that the quaternion method is equivalent to the well‐known formula due to Kabsch. We analyze the various cases that may arise, and give a complete enumeration of the special cases in terms of the arrangement of the eigenvalues of a traceless, 4 × 4 symmetric matrix. A key result here is an expression for the gradient of the RMSD as a function of model parameters. This can be useful, for example, in finding the minimum energy path of a reaction using the elastic band methods or in optimizing model parameters to best fit a target structure. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1849–1857, 2004
Prediction of pKa shifts in proteins using a combination of molecular mechanical and continuum solvent calculations
Authors: Kuhn Bernd , Kollman Peter A. , Stahl Martin 
Published: September 2004

AbstractThe prediction of pKa shifts of ionizable groups in proteins is of great relevance for a number of important biological phenomena. We present an implementation of the MM‐GBSA approach, which combines molecular mechanical (MM) and generalized Born (GB) continuum solvent energy terms, to the calculation of pKa values of a panel of nine proteins, including 69 individual comparisons with experiment. While applied so far mainly to the calculation of biomolecular binding free energies, we show that this method can also be used for the estimation of protein pKa shifts, with an accuracy around 1 pKa unit, even for strongly shifted residues. Our analysis reveals that the nonelectrostatic terms that are part of the MM‐GBSA free energy expression are important contributors to improved prediction accuracy. This suggests that most of the previous approaches that focus only on electrostatic interactions could be improved by adding other nonpolar energy terms to their free energy expression. Interestingly, our method yields best accuracy at protein dielectric constants of εint = 2–4, which is in contrast to previous approaches that peak at higher εint ≥ 8. An important component of our procedure is an intermediate minimization step of each protonation state involving different rotamers and tautomers as a way to explicitly model protein relaxation upon (de)protonation. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1865–1872, 2004
Systematic study of vibrational frequencies calculated with the self‐consistent charge density functional tight‐binding method
Authors: Witek Henryk A. , Morokuma Keiji 
Published: September 2004

AbstractWe present a detailed study of harmonic vibrational frequencies obtained with the self‐consistent charge density functional tight‐binding (SCC‐DFTB) method. Our testing set comprises 66 molecules and 1304 distinct vibrational modes. Harmonic vibrational frequencies are computed using an efficient analytical algorithm developed and coded by the authors. The obtained results are compared to experiment and to other theoretical findings. Scaling factor for the SCC‐DFTB method, determined by minimization of mean absolute deviation of scaled frequencies, is found to be 0.9933. The accuracy of the scaled SCC‐DFTB frequencies is noticeably better than for other semiempirical methods (including standard DFTB method) and approximately twice worse than for other well established scaled ab initio quantum chemistry methods (e.g., HF, BLYP, B3LYP). Mean absolute deviation for the scaled SCC‐DFTB frequencies is 56 cm−1, while standard deviation is 82 cm−1, and maximal absolute deviation is as large as 529 cm−1. Using SCC‐DFTB allows for substantial time savings; computational time is reduced from hours to seconds when compared to standard ab initio techniques. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1858–1864, 2004
Brood care in freshwater crayfish and relationship with the offspring's sensory deficiencies
Authors: Vogt Günter , Tolley Laura 
Published: September 2004

AbstractProlonged brood care is one of the evolutionary clues for the successful colonization of freshwater habitats by freshwater crayfish (Astacida). By means of macrophotography, light microscopy, and scanning electron microscopy we investigated all phases of brood care in freshwater crayfish, with particular emphasis on the morphological structures involved. We selected the recently discovered parthenogenetic marbled crayfish (species identity not yet known) as a model organism due to its fast reproduction and high resistance to handling stress. In order to examine if there is a causal relationship between brood care and the developmental status of the offspring's sensory apparatus, we additionally investigated major sense organs of juvenile Stages 1–5 in comparison with those of the adults. Brood care in the marbled crayfish is characterized by initial and final “active” phases dominated by specific maternal or juvenile behavior and a medial “passive” phase based more on the action of temporarily developed structures rather than on behavior. The most remarkable feature of this period, which includes permanent carrying of the eggs and the first two juvenile stages under the mother's abdomen, is safeguarding of hatching by a telson thread that keeps the helpless newborn hatchlings linked to the egg cases on the maternal pleopods and thus prevents them from being lost. Further important transient structures are the recurved hooks on the first pereiopods of Stage 1 and 2 juveniles that are used to firmly attach these nonfeeding stages to the mother's abdomen. In hatchlings all sense organs necessary for an independent life, such as eyes, olfactory aesthetascs, gustatory fringed setae, hydrodynamic receptor hairs, and statocysts are not developed or are underdeveloped, making brood care indispensable. Most of these sense organs appear in Stage 2 juveniles, but only from Stage 3, the first freelancing and feeding stage, are all sense organs well developed and operating, thus reducing brood care in this final period to temporary provisioning of shelter. Brooding of the eggs and postembryonic brood care are to some extent also found in other freshwater Decapoda like freshwater crabs and aeglid anomurans, but safeguarding of hatching is confined to the Astacida only. This sophisticated mode of passive brood care is unique in the animal kingdom and is apparently related to the sensory deficiencies of the first juvenile stage. J. Morphol. 262:566–582, 2004. © 2004 Wiley‐Liss, Inc.
Morphology of the kidney in the West African caecilian, Geotrypetes seraphini (Amphibia, Gymnophiona, Caeciliidae)
Authors: Møbjerg N. , Jespersen Å. , Wilkinson M. 
Published: September 2004

AbstractThis study deals with the morphology and ultrastructure of the mesonephros in adult caecilians of the species Geotrypetes seraphini. Based on serial sections in paraffin and araldite, nephrons are reconstructed and the cellular characteristics of different nephron segments described. The long and slender mesonephric kidneys of G. seraphini are broadest caudally and taper toward the front, where the organs are divided into smaller segmental divisions. Two nephron types can be distinguished on the basis of their connections to the coelom and their position within the nephric tissue: ventral nephrons connect to the coelom via a ciliated peritoneal funnel, whereas medial nephrons lack this connection. Both nephron types are composed of a filtration unit, the Malpighian corpuscle, and a renal tubule, which can be divided into six morphologically distinct segments: neck segment, proximal tubule, intermediate segment, early distal tubule, late distal tubule, and collecting tubule. Collecting tubules merge and form a branch system that opens into collecting ducts. Collecting ducts empty into the Wolffian duct. Proximal tubules of nephrons in the frontal divisions are morphologically different from the proximal tubules of more caudal kidney regions. Distal tubule subdivision is only clearly recognizable at the electron microscopic level. The length of each nephron segment is calculated from a ventral nephron with a total length of ∼3.8 mm, and the course of the segments within the nephric tissue is reported. The number of nephrons was estimated at 1,700 units in each kidney. The segmentation and ultrastructure of the mesonephric nephrons in G. seraphini are discussed in relation to nephron descriptions from other caecilians and we further discuss the evolutionary origin of the amphibian nephron. J. Morphol. 262:583–607, 2004. © 2004 Wiley‐Liss, Inc.
Renal organs of cephalopods: A habitat for dicyemids and chromidinids
Authors: Furuya Hidetaka , Ota Mitsunori , Kimura Ritsuko , Tsuneki Kazuhiko 
Published: September 2004

AbstractThe renal organs of 32 species of cephalopods (renal appendage of all cephalopods, and renal and pancreatic appendages in decapods) were examined for parasite fauna and for histological comparison. Two phylogenetically distant organisms, dicyemid mesozoans and chromidinid ciliates, were found in 20 cephalopod species. Most benthic cephalopods (octopus and cuttlefish) were infected with dicyemids. Two pelagic cephalopod species, Sepioteuthis lessoniana and Todarodes pacificus, also harbored dicyemids. Chromidinid ciliates were found only in decapods (squid and cuttlefish). One dicyemid species was found in branchial heart appendages of Rossia pacifica. Dicyemids and chromidinids occasionally occurred simultaneously in Euprymna morsei, Sepia kobiensis, S. peterseni, and T. pacificus. The small‐sized cephalopod species, Idiosepius paradoxus and Octopus parvus, harbored no parasites. Comparative histology revealed that the external surface of renal organs varies morphologically in various cephalopod species. The small‐sized cephalopod species have a simple external surface. In contrast, the medium‐ to large‐sized cephalopod species have a complex external surface. In the medium‐ to large‐sized cephalopod species, their juveniles have a simple external surface of the renal organs. The external surface subsequently becomes complicated as they grow. Dicyemids and chromidinids attach their heads to epithelia or insert their heads into folds of renal appendages, pancreatic appendages, and branchial heart appendages. The rugged and convoluted external surface provides a foothold for dicyemids and chromidinids with a conical head. They apparently do not harm these tissues of their host cephalopods. J. Morphol. 262:629–643, 2004. © 2004 Wiley‐Liss, Inc.
Ontogeny of the palatoquadrate and adjacent lateral cranial wall of the endocranium in prehatching Alligator mississippiensis (Archosauria: Crocodylia)
Authors: Klembara Jozef 
Published: September 2004

AbstractThe purpose of this article is to gain insight into the ossification sequence of the palatoquadrate and the adjacent lateral cranial wall of prehatching Alligator mississippiensis, a process about which there is almost no published information. Results were obtained by studying serial histological sections of the series of ontogenetic stages and enlarged wax‐plate models of several stages. The cartilage of the palatoquadrate starts to ossify endochondrally in the quadrate portion of the pars pterygoquadrata palatoquadrati in Stage 6A. In this stage, a bone, called the lamina palatoquadrati anterior here, appears at and close to the anteromedial wall of the cartilaginous pterygoid portion of the pars pterygoquadrata. The lamina palatoquadrati anterior ossifies in membrane. Later in ontogeny, the lamina palatoquadrati anterior spreads into the cavum epiptericum and sheathes the posterior portion of the trigeminal ganglion laterally. The jaw adductor muscles insert at the outer surface of the lamina palatoquadrati anterior. The lamina palatoquadrati anterior is a new structure not previously recorded in crocodylians or any other Recent reptile. The topology, mode of ossification, and functional anatomy of the lamina palatoquadrati anterior correspond to those of the membranous ossification of the alisphenoid of marsupials. Another bone, called the lamina prootici anterior here, spreads in membrane from the anterolateral wall of the prootic portion of the otic capsule into the prootic fenestra, above the trigeminal ganglion. The lamina prootici anterior represents a structure not recorded previously in crocodylians. It contributes to the orbitotemporal braincase wall. J. Morphol. 262:644–658, 2004. © 2004 Wiley‐Liss, Inc.
Structure of long bones in mammals
Authors: Locke Michael 
Published: September 2004

AbstractTechniques for staining (silver, osmium, metal sulfides, ink) and microphotography (epi‐illumination) of polished bone surfaces have been developed to visualize the three‐dimensional structure of the shafts of mammalian long bones. Bone is a two‐compartment system with capillaries and some kinds of connective tissue in one compartment separated from fibers of bone collagen, often forming lamellae, in the other. Laminar bone consists of stacks of lamellae separated by vascular spaces containing capillary network sheets. It is deposited at the periosteal and endosteal surfaces. Osteonic bone, well described in the literature, consists of cylinders of lamellae with central vascular spaces. The primary structure of the shafts of mammalian long bones is laminar and laminae often remain as the main component. Secondary osteons are a replacement within laminae. As laminar bones mature, some of the irregular longitudinal capillary spaces in the network sheets enlarge and become less crooked to form secondary osteons. Parts of the random networks become ordered longitudinal ones, resulting in collapse of those network spaces not converted to osteons. The residual capillaries become bloodless, making the surviving network spaces difficult to resolve. This may account for them being overlooked in descriptions of bone structure. For example, laminar bone occurs with osteonic bone in the human femur, although it is rarely figured. Nearly mature bones switch the kind of primary bone deposited at the peripheral (periosteal) surface from laminar to primary osteonic. J. Morphol. 262:546–565, 2004. © 2004 Wiley‐Liss, Inc.
Comparative vibrational analysis of thyronine hormones using infrared and Raman spectroscopy and density functional theory calculations
Authors: Álvarez Rosa M. S. , Farías Ricardo N. , Hildebrandt Peter 
Published: September 2004

AbstractThe molecular structures of L‐thyroxine (T4), 3,5,3′‐triiodo‐L‐thyronine (T3) and 3,5‐diiodo‐L‐thyronine (T2) were investigated by means of vibrational spectroscopy and density functional theory calculations using the B3LYP hybrid functional and the SDD effective core potential basis set, suitable for heavy atoms. The experimental data were obtained from FT‐IR and Raman spectra of the thyroid hormones in the crystalline state. The combined experimental and theoretical approach allows a consistent assignment for most of the fundamental modes in the range between 100 and 1650 cm−1. It was found that, in general, the modes are largely localized in the individual rings and in the linkage connecting both rings. Hence it was possible to identify bands that are dominated by the internal coordinates of the ether bridge and the CI stretchings. These bands are considered to be sensitive spectral markers for monitoring conformational changes of the hormones after insertion into phospholipid bilayers. Copyright © 2004 John Wiley & Sons, Ltd.
Optimization of a high‐performance liquid chromatography system by artificial neural networks for separation and determination of antioxidants
Authors: Wang Huaiwen , Liu Weimin 
Published: September 2004

AbstractA high‐performance liquid chromatography (HPLC) system was used to determine the antioxidants tert‐butyl‐hydroquinone (TBHQ), tert‐butylhydroxyanisole (BHA), and 3,5‐di‐tert‐butylhydroxytoluene (BHT) simultaneously in oils. The paper presents a new methodology for the optimized separation of antioxidants in oils based on the coupling of experimental design and artificial neural networks. The orthogonal design and the artificial neural networks with extended delta‐bar‐delta (EDBD) learning algorithm were employed to design the experiments and optimize the variables. The response function (Rf) used was a weighted linear combination of two variables related to separation efficiency and retention time, according to which the optimized conditions were obtained. The above‐mentioned antioxidants in rapeseed oils were separated and determined simultaneously under optimized conditions by HPLC with UV detection at 280 nm. Linearity was obtained over the range of 10–200 μg/mL with recoveries of 98.3% (TBHQ), 98.1% (BHT), and 96.2% (BHA).
Preparation and characterization of alkylated polymethacrylate monolithic columns for micro‐HPLC of proteins
Authors: Li Yan , Zhang Jian , Xiang Rong , Yang Yanhui , Horváth Csaba 
Published: September 2004

AbstractProtein separations were carried out by micro‐high performance liquid chromatography (micro‐HPLC) with surface alkylated monolithic columns, which were prepared by in situ copolymerization of glycidyl methacrylate (GMA) and ethylene glycol dimethacrylate (EGDMA) in the presence of dodecanol and toluene as porogens. First, glycidyl groups at the surface of the porous monolith were hydrolyzed with sulfuric acid. The hydroxyl groups thus formed were then reacted with n‐alkyl chloride to form alkylated stationary phase. Separation performance for proteins on columns with C18 and C8 stationary phases was compared. The results showed that a poly(GMA‐EGDMA) support derivatized with octadecyl moieties could achieve much better resolution than one with octyl groups. A protein mixture was separated with the octadecylated poly‐(GMA‐EGDMA) monolithic column, and the effluent peaks were collected and analyzed by matrix‐assisted laser desorption ionization‐time of flight mass spectrometry (MALDI‐TOF MS). The physical properties of the monolithic columns such as column morphology, surface area, mesopore size distribution, and column permeability were further characterized by scanning electron microscopy (SEM), multipoint BET nitrogen adsorption/desorption, and Darcy's law, respectively.
Deterrmination of anthocyanins and related components in red wines by micro‐ and capillary HPLC
Authors: Dugo Paola , Favoino Olinda , Lo Presti Maria , Luppino Rosario , Dugo Giovanni , Mondello Luigi 
Published: September 2004

AbstractAnthocyanins and derived components of red wines were determined by microHPLC using a 1 mm ID HPLC column coupled on‐line with an MS detector equipped with an ESI (ElectroSpray Ionisation) source. The use of microcolumn HPLC greatly enhanced detection performance, allowing direct identification of components present in the fraction. Nineteen anthocyanins were detected. Fifteen were identified, two were tentatively identified, and only the aglycon of the remaining two components was certainly identified. Six anthocyanin‐derived pigments, supposedly formed during wine maturation, were also investigated and found in a wine sample. The analysis of red wine anthocyanins was also carried out by injecting a large sample volume onto a 0.32 mm ID HPLC column, using the column focusing technique, in order to decrease the limit of detection and quantification of components present in a very small amounts.