bluuebunny/crossref_metadata_2025_split huggingface dataset:
A simple approach for improving the hybrid MMVB force field: Application to the photoisomerization of s‐cis butadiene
Authors: Garavelli Marco , Ruggeri Fabrizio , Ogliaro Francois , Bearpark Michael J. , Bernardi Fernando , Olivucci Massimo , Robb Michael A. 
Published: June 2003

AbstractMMVB is a QM/MM hybrid method, consisting of a molecular mechanics force field coupled to a valence bond Heisenberg Hamiltonian parametrized from ab initio CASSCF calculations on several prototype molecules. The Heisenberg Hamiltonian matrix elements Qij and Kij, whose expressions are partitioned here into a primary contribution and second‐order correction terms, are calculated analytically in MMVB. When the original MMVB force field fails to produce potential energy surfaces accurate enough for dynamics calculations, we show that significant improvements can be made by refitting the second‐order correction terms for the particular molecule(s) being studied. This “local” reparametrization is based on values of Kij extracted (using effective Hamiltonian techniques) from CASSCF calculations on the same molecule(s). The method is demonstrated for the photoisomerization of s‐cis butadiene, and we explain how the correction terms that enabled a successful MMVB dynamics study [Garavelli, M.; Bernardi, F.; Olivucci, M.; Bearpark, M. J.; Klein, S.; Robb, M. A. J Phys Chem A 2001, 105, 11496] were refitted. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1357–1363, 2003
Theoretical studies on the molecular dependence of bond dissociation after core excitations II: CH3CO(CH2)nCN, n = 0–3
Authors: Takahashi Osamu , Joyabu Masanori , Mitani Masaki , Saito Ko , Iwata Suehiro 
Published: June 2003

AbstractApproximate theoretical normal and resonant Auger spectra for a series of methylcyano ketones were calculated. Compared with our previous procedure, a set of initial molecular orbitals (MOs) for Auger decay probability calculations of the normal Auger process was modified by changing from a set of ground state MOs to a set of core‐holed MOs. For the resonant Auger process, a set of MOs was also modified in the same manner. Furthermore, the bond dissociation factor, which we introduced in the previous article, was also calculated to estimate the bond strength after Auger decay. The site‐selectivity for a series of methylcyano ketones was qualitatively explained, but a significant state‐specificity was not observed. Molecular size dependence after Auger decay was also discussed. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1329–1335, 2003
An ab initio study of microsolvation of LiF in water: Structures and properties of LiF–Wn, n = 1–9 complexes
Authors: Upadhyay D. M. , Mishra P. C. 
Published: June 2003

AbstractGeometries of clusters of water molecules (Wn) and those of the LiF–Wn (n = 1–9) complexes were optimized using the B3LYP/6‐31+G** method. Geometries of the complexes up to n = 7 were also optimized using the MP2/6‐31+G** approach. Only one structure of each of Wn, n = 1–5 was considered to generate the complexes with LiF while two structures, one of a cage type and the other of a prism type, were considered for n = 6–9. The LiF–W2 complex is found to be most stable among the various complexes. The LiF–W6 complex, where W6 is of a cage type, is predicted to be substantially less stable than that where W6 is of a prism type. Certain existing ambiguities regarding the most stable structures of the LiF–Wn (n = 1–3) complexes have been resolved. The LiF molecule seems to divide the Wn clusters in the LiF–Wn (n = 3–6) complexes into different fragments where at least one W2‐like fragment is present. In LiF–W6 (cage), there is one W2‐like fragment while in LiF–W6 (prism), there are three W2‐like fragments. The LiF bond length is substantially increased in going from the gas phase to the different complexes, this increase being most prominent in LiF–W6, where W6 is of the cage or prism type. The LiF molecule, however, does not acquire the ionic structure Li+F− in any of the complexes studied here. An appreciable amount of electronic charge is transferred from LiF to the water molecules involved in the different complexes. In this process, the Li atom gains electronic charge in some cases, while the F atom considered separately, as well as the Li and F atoms taken together, lose the same in most cases. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1336–1347, 2003
A theoretical ab initio study on the H2NO + O3 reaction
Authors: Peiró–García Julio , Ramírez–Ramírez Víctor M. , Nebot–Gil Ignacio 
Published: June 2003

AbstractThe deviation of the NH2 pseudo‐first‐order decay Arrhenius plots of the NH2 + O3 reaction at high ozone pressures measured by experimentalists, has been attributed to the regeneration of NH2 radicals due to the subsequent reactions of the products of this reaction with ozone. Although these products have not yet been characterized experimentally, the radical H2NO has been postulated, because it can regenerate NH2 radicals through the reactions: H2NO + O3 → NH2 + O2 and H2NO + O3 → HNO + OH + O2. With the purpose of providing a reasonable explanation from a theoretical point of view to the kinetic observed behaviour of the NH2 + O3 system, we have carried ab initio electronic structure calculations on both H2NO + O3 possible reactions. The results obtained in this article, however, predict that of both reactions proposed, only the H2NO + O3 → NH2 + O2 reaction would regenerate indeed NH2 radicals, explaining thus the deviation of the NH2 pseudo‐first‐order decay observed experimentally. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1321–1328, 2003
Isomers of C20: An energy profile II
Authors: Beran Kyle A. 
Published: June 2003

AbstractSemi‐empirical calculations, at the PM3 level provided within the Winmopac v2.0 software package, are used to geometrically optimize and determine the absolute energies (heats of formation) of a variety of C20 isomers that are predicted to exist in and around the bowl and cage isomers. Using the optimized Cartesian coordinates for the bowl and the cage isomers, a saddle‐point calculation was performed. The output file generated, containing energy, distance, and geometry information, is then organized into a graphical format. The resulting graph, which plots the energy of the 20‐atom system as a function of the distance from the geometric midpoint, is a two‐dimensional energy profile. This profile illustrates an estimation of the contours on the potential energy surface, showing energy minima and maxima that are encountered as the bowl evolves into the cage structure, or vice‐versa. To expand the surface into three dimensions, geometry optimizations were performed on the sets of Cartesian coordinates that correspond to energy minima in the bowl‐cage profile. Based on these optimizations, eight additional isomers of C20 have been identified and are predicted to be energetically stable. These additional isomers were subsequently subjected to saddle‐point calculations in order to identify those isomers that lie adjacent to one another on the three‐dimensional surface. Two isomers that are adjacent to each other will exhibit an energy profile that progresses smoothly from the potential well of each isomer up to the saddle point separating them. Consequently, these adjacent pairs of isomers establish a step‐wise transformation between the bowl and the cage. This process, which extends out over the three‐dimensional surface, is predicted to require less energy than that of the direct, two‐dimensional transformation predicted in the bowl‐cage profile. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1287–1290, 2003
Design and training of a neural network for predicting the solvent accessibility of proteins
Authors: Ahmad Shandar , Gromiha M. Michael 
Published: June 2003

AbstractA feed‐forward neural network has been developed to predict the solvent accessibility/accessible surface area (ASA) of proteins using improved design and training methods. Several network issues ranging from the coding of ASA states to the problem of local minima of learning curve, have been addressed. Successful new approaches to overcome these problems are presented. Set of trained network weights for each ASA threshold is provided. It has been established that the prediction accuracy results with neural network are better than other reported results of ASA prediction, despite a high test to training data ratio. © 2003 Wiley Periodicals, Inc. J Comput Chem 11: 1313–1320, 2003
Wing‐locking mechanisms in aquatic Heteroptera
Authors: Gorb Stanislav N. , Goodwyn P.J. Perez 
Published: June 2003

AbstractThis account provides a detailed morphological and ultrastructural study of wing‐locking mechanisms (LM) in some aquatic Heteroptera. Scanning and transmission electron microscopy were used to describe the functional significance of macro‐ and microstructures holding wings tightly against the body at rest and those involved in functional diptery in flight. There are two types of LM holding the forewings (hemelytra) at rest: 1) wing‐to‐wing LM, and 2) wing‐to‐body LM. The first type includes the brush‐to‐brush LM, the clavus–clavus clamp and the clavus–clavus locking ridge. The second type includes devices locking the hemelytra to the body: the subcostal border of the hemelytra to the lateral border of mesepimeron, the knob‐and‐socket locking mechanism of the hemelytra, and the clavus‐locking mechanism to the scutellum groove. The hindwing is locked by a pair of microtrichial fields situated on the hindwing‐articulated pad at the basal area of the hindwing and on the thoracic pad in the vicinity of the wing articulation. Morphological and ultrastructural data suggest that different LM are parts of one mechanism holding wings to the body at rest. An additional locking mechanism, connecting the hemelytra with the hindwing, is the only LM providing functional diptery in flight. J. Morphol. 257:127–146, 2003. © 2003 Wiley‐Liss, Inc.
Anatomy of the middle ear of the japanese crane Grus japonensis (gruidae: Aves)
Authors: Vorster Willie , Starck J. Matthias 
Published: June 2003

AbstractComparative anatomical studies of the avian middle ear provide structural data from which functional models can be derived. Subsequent phylogenetic analyses may reveal the phylogenetic history of taxon and the evolution of the functional model of the middle ear. We studied serial sections of a nestling of Grus japonensis. The microscopic anatomy of the middle ear (including skeletal parts, nerves, blood vessels, tendons, and tympanic recesses) was described with the help of a polystyrene plate reconstruction. These results were compared to those from skulls of adult cranes. Structural peculiarities of the crane middle ear are: 1) the ventral and anterior closure of the middle ear cavity by a dense plate of connective tissue, which ossifies during posthatching development; 2) the S‐shaped infracolumellar process of the columella, of which the distal end forms a horizontal bar, and abuts against the ventral wall of the middle ear cavity; and 3) the absence of an intracolumellar hinge between the stapes and extracolumella. The crane middle ear shows the plesiomorphic pattern of middle ear structures of neognathous birds. We propose a one‐lever‐arm functional model for the middle ear of the crane, similar to that of paleognathous birds. J. Morphol. 257:260–269, 2003. © 2003 Wiley‐Liss, Inc.
Hemocytes of the centipede Scutigera coleoptrata (Chilopoda, Notostigmophora) with notes on their interactions with the tracheae
Authors: Hilken Gero , Brockmann Claudia , Nevermann Lutz 
Published: June 2003

AbstractThe hemocytes of Scutigera coleoptrata were investigated by light and electron microscopy. Four types of hemocytes were identified: prohemocytes, plasmatocytes, granulocytes, and spherulocytes. Only granulocytes could be distinguished from the three other types by May‐Grünwald staining, as this is the only hemocyte type demonstrating an eosinophilic reaction. Shape and size give further indications for distinguishing the cell types. In addition, differentiation is possible on the basis of their ultrastructure. However, only a combination of all three methods (staining and light and electron microscopy) allows clear separation of the cell types. As transitional stages between the cell types occur in S. coleoptrata, it is likely that prohemocytes, plasmatocytes, and granulocytes are ontogenetic stages of a single cell lineage. Special cell components and their possible functions are described. Plasmatocytes exocytose tubular structures that probably play a role in coagulation processes. These tubular structures develop in the grana of plasmatocytes. Also, a special arrangement of microtubules and microfilaments was demonstrated. For the first time interactions between hemocytes and tracheae are documented within the Chilopoda. It is assumed that the hemocytes meet their oxygen requirements directly from the tracheae. Phylogenetic implications of the results are discussed. J. Morphol. 257:181–189, 2003. © 2003 Wiley‐Liss, Inc.
Ventral neurons in the anterior nerve cord of amphioxus larvae. I. An inventory of cell types and synaptic patterns
Authors: Lacalli T.C. , Kelly S.J. 
Published: June 2003

AbstractSerial sections were used to map the ventrally positioned neurons of the anterior nerve cord of a 12.5‐day amphioxus larva from the infundibular region to the end of somite 2. Synaptic patterns reveal five categories of descending pathways, four of which are associated with the ventral compartment (VC) motoneurons responsible for escape swimming. 1) Pre‐, para‐, and postinfundibular (tegmental) neurons with large varicosities and mixed vesicle populations provide both synaptic and paracrine input to various components of the tegmental neuropile and primary motor center. Four categories of these neurons are distinguished on the basis of their vesicles. 2) Multiple anterior sensory pathways converge on the large paired neurons (LPNs) located near the junction of somites 1 and 2. LPN synaptic output is almost exclusively contralateral. This, together with the evidence for cross‐innervation between the third pair of LPNs, is consistent with the latter acting as locomotory pacemakers. 3) Axons from several classes of tegmental neurons converge in the paraxial region on each side of the cord where they form distinct tracts, the upper paraxial bundles. The right bundle is larger than the left, which suggests a role during early development when myotome contractions are biased to one side. 4) Fibers in the ventral tracts from ipsilateral projection neurons, sensory neurons, and additional ascending fibers synapse repeatedly with VC motoneurons. This may be how the overall level of excitation of the latter is controlled so as to modulate their response to pacemaker input. The fifth pathway consists of fibers involved in controlling the dorsal compartment (DC) motoneurons responsible for slow swimming, which are largely isolated from inputs to the VC locomotory system. The ventral neurons of the primary motor center form a more or less continuous file on either side of the floor plate, with certain cell types showing a tendency to cluster. There are, however, few obvious patterns of the kind expected if development were controlled by a rigid, lineage‐based mechanism. The evolutionary implications of the involvement of a midbrain‐level pacemaker in controlling larval swimming in amphioxus is discussed. J. Morphol. 257:190–211, 2003. © 2003 Wiley‐Liss, Inc.
Postembryonic development of the wing imaginal discs in the female wingless bagworm moth Eumeta variegata (Lepidoptera, Psychidae)
Authors: Niitsu Shuhei 
Published: June 2003

AbstractThe process of wing disc development and degeneration in the bagworm moth Eumeta variegata was investigated histologically. Morphological differences between two sexes first appear in the penultimate (eighth) larval instar. In the male, wing discs proliferate rapidly in the penultimate larval instar and continue proliferating; a conspicuous peripodial epithelium forms in the last (ninth) larval instar. The hemopoietic organs break down in this stage and disappear completely by the prepupal stage. In the female, in contrast, the wing discs remain as in the previous (seventh) instar, without proliferation of cells inside. No peripodial epithelium forms in the penultimate instar or later. Hemopoietic organs are still attached to the wing discs in the last larval instar and the entire wing discs transform into a plain, thick epidermis in the prepupal period. It is suggested that the hemopoietic organs may prevent the wing discs from developing in E. variegata. J. Morphol. 257:164–170, 2003. © 2003 Wiley‐Liss, Inc.
Male genital system and spermiogenesis of Nanorchestes amphibius (Acari: Endeostigmata: Nanorchestidae): Anatomy, histology, and evolutionary implications
Authors: Müller Gunnar 
Published: June 2003

AbstractIn the present article the anatomy and histology of the male genital system of an endeostigmatid mite are described for the first time. The Endeostigmata probably are a paraphyletic group supposed to include the most primitive actinotrichid mites. In Nanorchestes amphibius, the testis comprises a paired germinal region connected with an unpaired glandular region. In the germinal region, spermiogenesis takes place in cysts of a somatic cell containing germ cells representing the same developmental stage. In the lumen of the glandular region, the spermatozoa are stored together with secretions of the glandular epithelium. These secretions are probably involved in the formation of spermatophores. From the glandular region, spermatozoa and secretions are released into the vasa deferentia that histologically can be divided into three sections, beginning with a short paired region with strong circular muscles serving as a sphincter, continuing with a paired proximal zone, followed by a short unpaired distal section. The distal vas deferens leads into the chitinous, unpaired ductus ejaculatorius which is followed by the progenital chamber. The ductus ejaculatorius is composed of a proximal section and a proximal, central, and anterior chamber. It is accompanied by a complex system of muscles and sclerites probably involved in the formation and ejaculation of the spermatophore. A similar organization can also be found in Prostigmata, but not in Oribatida. Anterior to the progenital chamber is located a paired accessory gland that probably produces a lipid secretion. Spermiogenesis is characterized by disintegration of the nuclear envelope, condensation of chromatin, and extensive reduction of the amount of sperm cell cytoplasm. The mature aflagellate, U‐shaped spermatozoa are simple in structure and lack mitochondria and an acrosome complex. The results do not support the current view that Nanorchestidae are more closely related to Sarcoptiformes, i.e., Oribatida and Astigmata, than to Prostigmata. J. Morphol. 257:171–180, 2003. © 2003 Wiley‐Liss, Inc.
Developmental transformations in a normal series of embryos of the sea lamprey Petromyzon marinus (linnaeus)
Authors: Richardson Michael K. , Wright Glenda M. 
Published: June 2003

AbstractLamprey development is of interest to evolutionary biologists because it can inform our understanding of primitive vertebrate developmental patterns. In this study, we describe and illustrate some of the principle landmarks of organogenesis in the embryonic sea lamprey Petromyzon marinus L. at different chronological ages. We examined 63 fixed embryos spanning Piavis developmental stages 11–18+ (5–70 days postfertilization) by gross observation and histology. This period begins at late neurulation stages and ends with the formation of the larva (ammocoete). A significant difference with some previous accounts is that the anus develops not from a persistent blastopore, but by secondary canalization and proctodeum formation at the former site of the blastopore. Further, we show that the ciliated bands of the pharyngeal roof originate in the esophagus, distinguishing it from the intestine. We clarify the epithelialization of the gut, showing that the secondary gut cavity is progressively epithelialized from each end. We identify possible germ cells in the coelomic and cloacal walls. Balfour's “subnotochordal rod” is lacking in our specimens; we suggest that he may have misinterpreted the corpus adiposum. Our study is of potential value to the growing number of biologists interested in lamprey development and provides a character set that will be used : 1) in a phylogenetic study of vertebrate development, and 2) to prepare a staging series for the lamprey based on parsimony analysis. J. Morphol. 257:348–363, 2003. © 2003 Wiley‐Liss, Inc.
Morphological response of a bdelloid rotifer to desiccation
Authors: Ricci Claudia , Melone Giulio , Santo Nadia , Caprioli Manuela 
Published: June 2003

AbstractWe desiccated bdelloid rotifers (Macrotrachela quadricornifera), submitting the animals to four desiccation procedures (protocols A, B, C, D) that differed in the rate of water evaporation, in the time of desiccation, and in the substrates provided. We observed external morphological changes of the rotifer bodies during drying with scanning electron microscopy and, in parallel, assessed rates of recovery after a 7‐day period of dormancy. Two protocols produced disorganized morphologies of the anhydrobiotic animals, with no (A) or very poor (B) recovery. Protocols C and D gave rather high rates of recovery and dry rotifers appeared unaltered and well organized. The different protocols affected rotifer morphology during the 7‐day anhydrobiosis and rates of recovery after the 7‐day anhydrobiosis; high recovery rates corresponded to well‐organized morphologies of anhydrobiotic bdelloids, suggesting that a proper contraction of the body into a tun shape and probably a rigorous packing of internal structures are necessary for survival after anhydrobiosis. These features are affected by the time between water shortage and full desiccation, but also by the surrounding relative humidity and by the nature of the substrate. Possible adaptations of anhydrobiotic rotifers are discussed. J. Morphol. 257:246–253, 2003. © 2003 Wiley‐Liss, Inc.
Original molluscan radula: Comparisons among Aplacophora, Polyplacophora, Gastropoda, and the Cambrian fossil Wiwaxia corrugata
Authors: Scheltema Amélie H. , Kerth Klaus , Kuzirian Alan M. 
Published: June 2003

AbstractAs the original molluscan radula is not known from direct observation, we consider what the form of the original radula may have been from evidence provided by neomenioid Aplacophora (Solenogastres), Gastropoda, Polyplacophora, and the Cambrian fossil Wiwaxia corrugata (Matthews). Conclusions are based on direct observation of radula morphology and its accessory structures (salivary gland ducts, radular sac, anteroventral radular pocket) in 25 species and 16 genera of Aplacophora; radula morphogenesis in Aplacophora; earliest tooth formation in Gastropoda (14 species among Prosobranchia, Opisthobranchia, and Pulmonata); earliest tooth formation in four species of Polyplacophora; and the morphology of the feeding apparatus in W. corrugata. The existence of a true radula membrane and of membranoblasts and odontoblasts in neomenioids indicates that morphogenesis of the aplacophoran radula is homologous to that in other radulate Mollusca. We conclude from p
redness of salivary gland ducts, a divided radular sac, and a pair of anteroventral pockets that the plesiomorphic state in neomenioids is bipartite, formed of denticulate bars that are distichous (two teeth per row) on a partially divided or fused radula membrane with the largest denticles lateral, as occurs in the genus Helicoradomenia. The tooth morphology in Helicoradomenia is similar to the feeding apparatus in W. corrugata. We show that distichy also occurs during early development in several species of gastropods and polyplacophorans. Through the rejection of the null hypothesis that the earliest radula was unipartite and had no radula membrane, we conclude that the original molluscan radula was similar to the radula found in Helicoradomena species. J. Morphol. 257:219–245, 2003. © 2003 Wiley‐Liss, Inc.