bluuebunny/crossref_metadata_2025 huggingface dataset:
A reactive force field simulation of liquid–liquid phase transitions in phosphorus
Authors: Ballone P. , Jones R. O.
Published: October 2004

A force field model of phosphorus has been developed based on density functional (DF) computations and experimental results, covering low energy forms of local tetrahedral symmetry and more compact (simple cubic) structures that arise with increasing pressure. Rules tailored to DF data for the addition, deletion, and exchange of covalent bonds allow the system to adapt the bonding configuration to the thermodynamic state. Monte Carlo simulations in the N-P-T ensemble show that the molecular (P4) liquid phase, stable at low pressure P and relatively low temperature T, transforms to a polymeric (gel) state on increasing either P or T. These phase changes are observed in recent experiments at similar thermodynamic conditions, as shown by the close agreement of computed and measured structure factors in the molecular and polymer phases. The polymeric phase obtained by increasing pressure has a dominant simple cubic character, while the polymer obtained by raising T at moderate pressure is tetrahedral. Comparison with DF results suggests that the latter is a semiconductor, while the cubic form is metallic. The simulations show that the T-induced polymerization is due to the entropy of the configuration of covalent bonds, as in the polymerization transition in sulfur. The transition observed with increasing P is the continuation at high T of the black P to arsenic (A17) structure observed in the solid state, and also corresponds to a semiconductor to metal transition.
Nucleation near the spinodal: Limitations of mean field density functional theory
Authors: Wilemski Gerald , Li Jin-Song
Published: October 2004

We investigate the diverging size of the critical nucleus near the spinodal using the gradient theory (GT) of van der Waals and Cahn and Hilliard and mean field density functional theory (MFDFT). As is well known, GT predicts that at the spinodal the free energy barrier to nucleation vanishes while the radius of the critical fluctuation diverges. We show numerically that the scaling behavior found by Cahn and Hilliard for these quantities holds quantitatively for both GT and MFDFT. We also show that the excess number of molecules Δg satisfies Cahn-Hilliard scaling near the spinodal and is consistent with the nucleation theorem. From the latter result, it is clear that the divergence of Δg is due to the divergence of the mean field isothermal compressibility of the fluid at the spinodal. Finally, we develop a Ginzburg criterion for the validity of the mean field scaling relations. For real fluids with short-range attractive interactions, the near-spinodal scaling behavior occurs in a fluctuation dominated regime for which the mean field theory is invalid. Based on the nucleation theorem and on Wang’s treatment of fluctuations near the spinodal in polymer blends, we infer a finite size for the critical nucleus at the pseudospinodal identified by Wang.
Lattice-Boltzmann simulation of coalescence-driven island coarsening
Authors: Başağaoğlu Hakan , Green Christopher T. , Meakin Paul , McCoy Benjamin J.
Published: October 2004

A two-dimensional lattice-Boltzmann model (LBM) with fluid-fluid interactions was used to simulate first-order phase separation in a thin fluid film. The intermediate asymptotic time dependence of the mean island size, island number concentration, and polydispersity were determined and compared with the predictions of the distribution-kinetics model. The comparison revealed that the combined effects of growth, coalescence, and Ostwald ripening control the phase transition process in the LBM simulations. However, the overall process is dominated by coalescence, which is independent of island mass. As the phase transition advances, the mean island size increases, the number of islands decrease, and the polydispersity approaches unity, which conforms to the predictions of the distribution-kinetics model. The effects of the domain size on the intermediate asymptotic island size distribution, scaling form of the island size distribution, and the crossover to the long-term asymptotic behavior were elucidated.
Hydrogen bond mediated rotor-ring coupling in acetic acid–benzoic acid mixed dimer
Authors: Nandi Chayan K. , Hazra Montu K. , Chakraborty Tapas
Published: October 2004

In this work we demonstrate that a doubly hydrogen-bonded interface of two carboxylic acid groups behaves as efficient conduit to transmit the rotor effects for IVR acceleration in a phenyl ring. The phenomenon has been demonstrated by measuring the resolved emission spectra following SVL excitations in S1 of a 1:1 mixed dimer between acetic acid and benzoic acid. The role of the methyl rotor has been ascertained by comparing the results with those obtained for an analogous dimeric system between formic acid and benzoic acid.
Coexistence of two different anion states in polyacene nanocluster anions
Authors: Mitsui Masaaki , Kokubo Shinsuke , Ando Naoto , Matsumoto Yukino , Nakajima Atsushi , Kaya Koji
Published: October 2004

Two types of anion states are shown to coexist in nanometer-scale polyacene cluster anions. Naphthalene and anthracene nanoclusters having a single excess electron were produced in the gas-phase. Photoelectron spectra of size-selected cluster anions containing 2 to 100 molecules revealed that rigid “crystal-like” cluster anions emerge, greater than ∼2 nanometers in size, and coexist with the “disordered” cluster anion in which the surrounding neutral molecules are reorganizing around the charge core. These two anion states appear to be correlated to negative polaronic states formed in the corresponding crystals.
Most species are not driven to extinction before genetic factors impact them
Authors: Spielman Derek , Brook Barry W. , Frankham Richard
Published: October 2004

There is controversy concerning the role of genetic factors in species extinctions. Many authors have asserted that species are usually driven to extinction before genetic factors have time to impact them, but few studies have seriously addressed this issue. If this assertion is true, there will be little difference in genetic diversity between threatened and taxonomically related nonthreatened species. We compared average heterozygosities in 170 threatened taxa with those in taxonomically related nonthreatened taxa in a comprehensive metaanalysis. Heterozygosity was lower in threatened taxa in 77% of comparisons, a highly significant departure from the predictions of the no genetic impact hypothesis. Heterozygosity was on average 35% lower (median 40%) in threatened taxa than in related nonthreatened ones. These differences in heterozygosity indicate lowered evolutionary potential, compromised reproductive fitness, and elevated extinction risk in the wild. Independent evidence from stochastic computer projections has demonstrated that inbreeding depression elevates extinction risk for threatened species in natural habitats when all other threatening processes are included in the models. Thus, most taxa are not driven to extinction before genetic factors affect them adversely.
A rapid bioassay for single bacterial cell quantitation using bioconjugated nanoparticles
Authors: Zhao Xiaojun , Hilliard Lisa R. , Mechery Shelly John , Wang Yanping , Bagwe Rahul P. , Jin Shouguang , Tan Weihong
Published: October 2004

The rapid and sensitive determination of pathogenic bacteria is extremely important in biotechnology, medical diagnosis, and the current fight against bioterrorism. Current methods either lack ultrasensitivity or take a long time for analysis. Here, we report a bioconjugated nanoparticle-based bioassay forin situpathogen quantification down to single bacterium within 20 min. The bioconjugated nanoparticle provides an extremely high fluorescent signal for bioanalysis and can be easily incorporated with biorecognition molecules, such as antibody. The antibody-conjugated nanoparticles can readily and specifically identify a variety of bacterium, such asEscherichia coliO157:H7, through antibody–antigen interaction and recognition. The single-bacterium-detection capability within 20 min has been confirmed by the plate-counting method and realized by using two independent optical techniques. The two detection methods correlated extremely well. Furthermore, we were able to detect multiple bacterial samples with high throughput by using a 384-well microplate format. To show the usefulness of this assay, we have accurately detected 1–400E. coliO157 bacterial cells in spiked ground beef samples. Our results demonstrate the potential for a broad application of bioconjugated nanoparticles in practical biotechnological and medical applications in various biodetection systems. The ultimate power of integrating bionanotechnology into complex biological systems will emerge as a revolutionary tool for ultrasensitive detection of disease markers and infectious agents.
Stimulatory G protein directly regulates hypertrophic differentiation of growth plate cartilage
in vivo
Authors: Bastepe Murat , Weinstein Lee S. , Ogata Naoshi , Kawaguchi Hiroshi , Jüppner Harald , Kronenberg Henry M. , Chung Ung-il
Published: October 2004

Stimulatory heterotrimeric G protein (Gs) transduces signals from various cell-surface receptors to adenylyl cyclases, which generate cAMP. The α subunit of Gs (Gsα) is encoded by
GNAS
(
Gnas
in mice), and heterozygous Gsα inactivating mutations lead to Albright hereditary osteodystrophy. The
in vivo
role of Gsα in skeletogenesis is largely unknown, because of early embryonic lethality of mice with disruption of
Gnas
exon 2 (

Gnas
E2

–
/E2
–

) and the absence of easily detectable phenotypes in growth plate chondrocytes of heterozygous mutant mice (
Gnas

+
/E2
–

). We generated chimeric mice containing wild-type cells and either

Gnas
E2

–
/E2
–

or
Gnas

+
/E2
–

cells.

Gnas
E2

–
/E2
–

chondrocytes phenocopied
PTH
/
PTHrP receptor
(
PPR
)
–/–
cells by prematurely undergoing hypertrophy. Introduction of a transgene expressing Gsα, one of several gene products that include
Gnas
exon 2, into

Gnas
E2

–
/E2
–

cells prevented premature hypertrophy. Gsα mRNA expression detected by real-time RT-PCR analysis was reduced to approximately half that of the wild-type in both paternal and maternal
Gnas

+
/E2
–

growth plate chondrocytes, indicating biallelic expression of Gsα in these cells. Hypertrophy of
Gnas

+
/E2
–

chondrocytes was modestly but significantly premature in chimeric growth plates of mice containing wild-type and
Gnas

+
/E2
–

cells. These data suggest that Gsα is the primary mediator of the actions of PPR in growth plate chondrocytes and that there is haploinsufficiency of Gsα signaling in
Gnas

+
/E2
–

chondrocytes.
Growth retardation and abnormal maternal behavior in mice lacking testicular orphan nuclear receptor 4
Authors: Collins Loretta L. , Lee Yi-Fen , Heinlein Cynthia A. , Liu Ning-Chun , Chen Yei-Tsung , Shyr Chih-Rong , Meshul Charles K. , Uno Hideo , Platt Kenneth A. , Chang Chawnshang
Published: October 2004

Testicular orphan nuclear receptor 4 (TR4) is a member of the nuclear receptor superfamily for which a ligand has not yet been found.
In vitro
data obtained from various cell lines suggest that TR4 functions as a master regulator to modulate many signaling pathways, yet the
in vivo
physiological roles of TR4 remain unclear. Here, we report the generation of mice lacking TR4 by means of targeted gene disruption (TR4
–/–
). The number of TR4
–/–
pups generated by the mating of TR4
+/–
mice is well under that predicted by the normal Mendelian ratio, and TR4
–/–
mice demonstrate high rates of early postnatal mortality, as well as significant growth retardation. Additionally, TR4
–/–
females show defects in reproduction and maternal behavior, with pups of TR4
–/–
dams dying soon after birth with no indication of milk intake. These results provide
in vivo
evidence that TR4 plays important roles in growth, embryonic and early postnatal pup survival, female reproductive function, and maternal behavior.
Exploring the potential of variola virus infection of cynomolgus macaques as a model for human smallpox
Authors: Jahrling Peter B. , Hensley Lisa E. , Martinez Mark J. , LeDuc James W. , Rubins Kathleen H. , Relman David A. , Huggins John W.
Published: October 2004

Smallpox virus (variola) poses a significant threat as an agent of bioterrorism. To mitigate this risk, antiviral drugs and an improved vaccine are urgently needed. Satisfactory demonstration of protective efficacy against authentic variola will require development of an animal model in which variola produces a disease course with features consistent with human smallpox. Toward this end, cynomolgus macaques were exposed to several variola strains through aerosol and/or i.v. routes. Two strains, Harper and India 7124, produced uniform acute lethality when inoculated i.v. in high doses (10
9
plaque-forming units). Lower doses resulted in less fulminant, systemic disease and lower mortality. Animals that died had profound leukocytosis, thrombocytopenia, and elevated serum creatinine levels. After inoculation, variola was disseminated by means of a monocytic cell-associated viremia. Distribution of viral antigens by immunohistochemistry correlated with the presence of replicating viral particles demonstrated by electron microscopy and pathology in the lymphoid tissues, skin, oral mucosa, gastrointestinal tract, reproductive system, and liver. These particles resembled those seen in human smallpox. High viral burdens in target tissues were associated with organ dysfunction and multisystem failure. Evidence of coagulation cascade activation (D dimers) corroborated histologic evidence of hemorrhagic diathesis. Depletion of T cell-dependent areas of lymphoid tissues occurred, probably as a consequence of bystander apoptotic mechanisms initiated by infected macrophages. Elaboration of cytokines, including IL-6 and IFN-γ, contribute to a cytokine storm formerly known as “toxemia.” A more precise understanding of disease pathogenesis should provide targets for therapeutic intervention, to be used alone or in combination with inhibitors of variola virus replication.
Remote Liver Injury is Attenuated by Adenovirus‐Mediated Gene Transfer of Heme Oxygenase‐1 During the Systemic Inflammatory Response Syndrome
Authors: MCCARTER SARAH D. , BADHWAR AMIT , SCOTT JEFFREY R. , AKYEA THELMA G. , BIHARI AURELIA , DUNGEY ALISON A. , HARRIS KENNETH A. , POTTER RICHARD F.
Published: October 2004

Objectives: Adenovirus‐mediated gene therapy is being investigated with increasing success for future treatment of autoimmune diseases. However, the use of adenoviruses is still limited by inflammatory and immune responses in the target organ. Previous work by the authors' laboratory established that the adenovirus encoding inducible heme oxygenase (Ad‐HO‐1) does not elicit the acute hepatic inflammation normally caused by adenoviruses, inviting further investigation in models of severe inflammation. Concurrently, there is increasing evidence for an endogenous protective role for heme oxygenase (HO) in the liver during the systemic inflammatory response syndrome (SIRS). Building on our previous results, this study investigated the effect of Ad‐HO‐1 pretreatment on remote liver injury during normotensive SIRS, induced by bilateral hind limb ischemia and reperfusion.

Methods: Microvascular perfusion and hepatocyte death were quantified using established intravital videomicroscopy techniques. Hepatocellular injury and liver function were assessed using blood‐borne indicators.

Results: Microvascular perfusion deficits and increased hepatocyte death occurred following limb ischemia and 3 h of reperfusion in vehicle‐pretreated animals; however, Ad‐HO‐1 pretreatment prevented these deficits. In contrast, the increase in serum alanine transaminase levels was unaffected by Ad‐HO‐1 pretreatment. Serum bilirubin levels were increased during systemic inflammation, predominantly in the conjugated form; and, this increase was prevented by administration of Ad‐HO‐1.

Conclusions: These data indicate that gene transfer of inducible HO is an effective method to protect the liver during SIRS, providing incentive for further investigation into gene therapy strategies exploiting this anti‐inflammatory enzyme.
In Vivo Properties of Potassium Channels in Cerebral Blood Vessels During Diabetes Mellitus
Authors: MAYHAN WILLIAM G. , MAYHAN JILL F. , SUN HONG , PATEL KAUSHIK P.
Published: October 2004

Objective: While potassium (K+) channels are important in basal tone and dilatation of large and small cerebral vessels, the effect of diabetes mellitus on K+ channels remains unclear. The goal of this study was to identify the influence of diabetes on responses of cerebral vessels to inhibition/activation of K+ channels.

Methods: The authors measured in vivo responses of pial arterioles and the basilar artery to inhibition/activation of K+ channels in nondiabetic and diabetic rats using intravital microscopy.

Results: Pial arterioles from nondiabetic and diabetic rats constricted to barium chloride (BaCl2) and 4‐aminopyridine (4‐AP). However, the magnitude of vasoconstriction to BaCl2 was greater in nondiabetic than in diabetic rats. Tetraethylammonium (TEA) did not alter diameter of pial arterioles in nondiabetic or diabetic rats. In addition, dilatation of pial arterioles to KCl and NS‐1619 was less in diabetic compared to nondiabetic rats. The basilar artery from nondiabetic and diabetic rats constricted in a similar manner to BaCl2 and 4‐AP. In contrast, vasoconstriction to TEA was greater in diabetic than nondiabetic rats. Similar to that reported for pial arterioles, dilatation of the basilar artery to KCl and NS‐1619 was less in diabetic than nondiabetic rats.

Conclusions: Inward‐rectifier (Kir) and voltage‐dependent (Kv), but not calcium‐activated (Kca), K+ channels are active under basal conditions in pial arterioles, while Kir, Kv, and Kca are active under basal conditions in the basilar artery of nondiabetic and diabetic rats. In addition, activation of Kir and Kca channels produces less cerebral vasodilatation in diabetic compared to nondiabetic rats. These findings provide new and important information regarding the influence of diabetes on the role of K+ channels in the regulation of cerebral vascular diameter.
Inhibitory Effects of TSG‐6 Link Module on Leukocyte–Endothelial Cell Interactions In Vitro and In Vivo
Authors: CAO THONG V. , LA MYLINH , GETTING STEPHEN J. , DAY ANTHONY J. , PERRETTI MAURO
Published: October 2004

Objective: The authors investigated whether the anti‐inflammatory protein tumor necrosis factor (TNF)‐stimulated gene‐6 (TSG‐6) and its Link module (Link_TSG6) could affect the complex multistep process of leukocyte/endothelial cell (EC) interaction.

Methods: Mouse mesenteries were inflamed with interleukin (IL)‐1β and the extent of leukocyte rolling, adhesion, and emigration was determined after 2 h. Link_TSG6 and a single‐point mutant (termed K13E) were given intraperitoneally together with the cytokine. Human neutrophil chemotaxis and transmigration were determined in vitro in response to IL‐8 and/or TNF‐α. TSG‐6, Link_TSG6, and K13E were added to the leukocytes or the EC monolayers.

Results: Co‐injection of Link_TSG6 with IL‐1β selectively inhibited cell flux, adhesion, and emigration as analyzed in mesenteric postcapillary venules. The fewer cells that rolled in the animals treated with Link_TSG6 displayed a velocity similar to that measured in vehicle‐treated mice. In vitro, Link_TSG6 did not affect neutrophil chemotaxis or EC activation but did inhibit neutrophil transmigration across EC monolayers. The latter effect was shared by full‐length TSG‐6 and observed equally in response to IL‐8 or TNF‐α.

Conclusions: These data restrict the site of action for at least some of the anti‐inflammatory effects ascribed to TSG‐6/Link_TSG6 to the microenvironment of the extravasating leukocyte.
Requirement of plakophilin 2 for heart morphogenesis and cardiac junction formation
Authors: Grossmann Katja S. , Grund Christine , Huelsken Joerg , Behrend Martin , Erdmann Bettina , Franke Werner W. , Birchmeier Walter
Published: October 2004

Plakophilins are proteins of the armadillo family that function in embryonic development and in the adult, and when mutated can cause disease. We have ablated the plakophilin 2 gene in mice. The resulting mutant mice exhibit lethal alterations in heart morphogenesis and stability at mid-gestation (E10.5–E11), characterized by reduced trabeculation, disarrayed cytoskeleton, ruptures of cardiac walls, and blood leakage into the pericardiac cavity. In the absence of plakophilin 2, the cytoskeletal linker protein desmoplakin dissociates from the plaques of the adhering junctions that connect the cardiomyocytes and forms granular aggregates in the cytoplasm. By contrast, embryonic epithelia show normal junctions. Thus, we conclude that plakophilin 2 is important for the assembly of junctional proteins and represents an essential morphogenic factor and architectural component of the heart.
The syndecan-1 ectodomain regulates αvβ3 integrin activity in human mammary carcinoma cells
Authors: Beauvais DeannaLee M. , Burbach Brandon J. , Rapraeger Alan C.
Published: October 2004

The αvβ3 integrin participates in cell morphogenesis, growth factor signaling, and cell survival. Activation of the integrin is central to these processes and is influenced by specific ECM components, which engage both integrins and syndecans. This paper demonstrates that the αvβ3 integrin and syndecan-1 (S1) are functionally coupled. The integrin is dependent on the syndecan to become activated and to mediate signals required for MDA-MB-231 and MDA-MB-435 human mammary carcinoma cell spreading on vitronectin or S1-specific antibody. Coupling of the syndecan to αvβ3 requires the S1 ectodomain (ED), as ectopic expression of glycosylphosphatidylinositol-linked S1ED enhances αvβ3 recognition of vitronectin; and treatments that target this domain, including competition with recombinant S1ED protein or anti-S1ED antibodies, mutation of the S1ED, or down-regulation of S1 expression by small-interfering RNAs, disrupt αvβ3-dependent cell spreading and migration. Thus, S1 is likely to be a critical regulator of many cellular behaviors that depend on activated αvβ3 integrins.
Yeast Miro GTPase, Gem1p, regulates mitochondrial morphology via a novel pathway
Authors: Frederick Rebecca L. , McCaffery J. Michael , Cunningham Kyle W. , Okamoto Koji , Shaw Janet M.
Published: October 2004

Cell signaling events elicit changes in mitochondrial shape and activity. However, few mitochondrial proteins that interact with signaling pathways have been identified. Candidates include the conserved mitochondrial Rho (Miro) family of proteins, which contain two GTPase domains flanking a pair of calcium-binding EF-hand motifs. We show that Gem1p (yeast Miro; encoded by YAL048C) is a tail-anchored outer mitochondrial membrane protein. Cells lacking Gem1p contain collapsed, globular, or grape-like mitochondria. We demonstrate that Gem1p is not an essential component of characterized pathways that regulate mitochondrial dynamics. Genetic studies indicate both GTPase domains and EF-hand motifs, which are exposed to the cytoplasm, are required for Gem1p function. Although overexpression of a mutant human Miro protein caused increased apoptotic activity in cultured cells (Fransson et al., 2003. J. Biol. Chem. 278:6495–6502), Gem1p is not required for pheromone-induced yeast cell death. Thus, Gem1p defines a novel mitochondrial morphology pathway which may integrate cell signaling events with mitochondrial dynamics.
A role for talin in presynaptic function
Authors: Morgan Jennifer R. , Di Paolo Gilbert , Werner Hauke , Shchedrina Valentina A. , Pypaert Marc , Pieribone Vincent A. , De Camilli Pietro
Published: October 2004

Talin, an adaptor between integrin and the actin cytoskeleton at sites of cell adhesion, was recently found to be present at neuronal synapses, where its function remains unknown. Talin interacts with phosphatidylinositol-(4)-phosphate 5-kinase type Iγ, the major phosphatidylinositol-(4,5)-bisphosphate [PI(4,5)P2]–synthesizing enzyme in brain. To gain insight into the synaptic role of talin, we microinjected into the large lamprey axons reagents that compete the talin–PIP kinase interaction and then examined their effects on synaptic structure. A dramatic decrease of synaptic actin and an impairment of clathrin-mediated synaptic vesicle endocytosis were observed. The endocytic defect included an accumulation of clathrin-coated pits with wide necks, as previously observed after perturbing actin at these synapses. Thus, the interaction of PIP kinase with talin in presynaptic compartments provides a mechanism to coordinate PI(4,5)P2 synthesis, actin dynamics, and endocytosis, and further supports a functional link between actin and clathrin-mediated endocytosis.
Membrane biogenesis and the unfolded protein response
Authors: Ron David , Hampton Randolph Y.
Published: October 2004

In addition to serving as the entry point for newly translated polypeptides making their way through the secretory pathway, the endoplasmic reticulum (ER) also synthesizes many lipid components of the entire endomembrane system. A report published in this issue implicates a signaling pathway known to respond to ER unfolded protein load in the control of phospholipid biosynthesis by the organelle (Sriburi et al., 2004). The reasonable notion that demand for ER membrane is integrated with protein processing capacity was initially suggested by genetic analysis of yeast. The new data lend direct support for this idea and imply interesting mechanistic possibilities for how this coupling develops.
CD24 Expression on T Cells Is Required for Optimal T Cell Proliferation in Lymphopenic Host
Authors: Li Ou , Zheng Pan , Liu Yang
Published: October 2004

It is well established that T lymphocytes undergo homeostatic proliferation in lymphopenic environment. The homeostatic proliferation requires recognition of the major histocompatibility complex on the host. Recent studies have demonstrated that costimulation-mediated CD28, 4-1BB, and CD40 is not required for T cell homeostatic proliferation. It has been suggested that homeostatic proliferation is costimulation independent. Here, we report that T cells from mice with a targeted mutation of CD24 have a remarkably reduced rate of proliferation when adoptively transferred into syngeneic lymphopenic hosts. The reduced proliferation cannot be attributed to abnormal survival and homing properties of the CD24-deficient T cells. T cell proliferation in allogeneic hosts is less affected by this mutation. These results demonstrate a novel function of CD24 expressed on T cells. Thus, although distinct costimulatory molecules are involved in antigen-driven proliferation and homeostatic proliferation, both processes can be modulated by costimulatory molecules.
An intermediate grade of finished genomic sequence suitable for comparative analyses
Authors: Blakesley Robert W. , Hansen Nancy F. , Mullikin James C. , Thomas Pamela J. , McDowell Jennifer C. , Maskeri Baishali , Young Alice C. , Benjamin Beatrice , Brooks Shelise Y. , Coleman Bradley I. , Gupta Jyoti , Ho Shi-Ling , Karlins Eric M. , Maduro Quino L. , Stantripop Sirintorn , Tsurgeon Cyrus , Vogt Jennifer L. , Walker Michelle A. , Masiello Catherine A. , Guan Xiaobin ,   NISC Comparative Sequencing Program, Bouffard Gerard G. , Green Eric D.
Published: October 2004

Although the cost of generating draft-quality genomic sequence continues to decline, refining that sequence by the process of “sequence finishing” remains expensive. Near-perfect finished sequence is an appropriate goal for the human genome and a small set of reference genomes; however, such a high-quality product cannot be cost-justified for large numbers of additional genomes, at least for the foreseeable future. Here we describe the generation and quality of an intermediate grade of finished genomic sequence (termed comparative-grade finished sequence), which is tailored for use in multispecies sequence comparisons. Our analyses indicate that this sequence is very high quality (with the residual gaps and errors mostly falling within repetitive elements) and reflects 99% of the total sequence. Importantly, comparative-grade sequence finishing requires ∼40-fold less reagents and ∼10-fold less personnel effort compared to the generation of near-perfect finished sequence, such as that produced for the human genome. Although applied here to finishing sequence derived from individual bacterial artificial chromosome (BAC) clones, one could envision establishing routines for refining sequences emanating from whole-genome shotgun sequencing projects to a similar quality level. Our experience to date demonstrates that comparative-grade sequence finishing represents a practical and affordable option for sequence refinement en route to comparative analyses.
Dispersal capacity in the Mediterranean corn borer, Sesamia nonagrioides
Authors: Eizaguirre M. , López C. , Albajes R.
Published: October 2004

Corn (Zea mays L.) borers are the primary target of Bacillus thuringiensis Berliner (Bt) transgenic maize. Management of corn borer resistance to Bt requires information on larval and adult dispersal capacities, a feature that is particularly unknown in Sesamia nonagrioides Lefèbvre (Lepidoptera: Noctuidae), the most damaging corn borer in Spain. Larval dispersal was studied over a 3 year period by infesting plants with egg masses and dissecting the neighbouring plants 7, 14, and 32 days later to measure larval dispersal at several ages. The number and age of larvae were recorded in the dissected plants. Only mature larvae dispersed in significant numbers; they moved at least to rows adjacent to those containing the infested plant, and down the row five plants. The percentage of larvae that dispersed from the infested plant was density‐dependent. Adult dispersal was studied with directional light and pheromone uni‐traps over 5 and 3 year periods, respectively. Directional light traps were placed in the margins between Bt and non‐Bt maize fields, half oriented towards each of the two kinds of maize field. Pheromone traps were placed in the Bt and non‐Bt fields at increasing distances (0–100 m) from the border. The numbers of males and females caught in directional light traps were not different in traps oriented towards Bt or non‐Bt fields, but the number of males caught in the third flight in Bt fields was lower than in non‐Bt fields. These results suggest that males from adjacent Bt and non‐Bt fields mate indiscriminately with females emerging in any of the two kinds of maize fields. However, male movement in the third flight may not be sufficient to randomly distribute males between the two fields.
Occurrence of Rhagoletis species in Newfoundland
Authors: Berlocher Stewart H. , Dixon Peggy L.
Published: October 2004

The presence of Rhagoletis fruit flies in Newfoundland, Canada, was investigated by rearing large numbers of the fruits of known and potential host plant species. Three Rhagoletis species, R. tabellaria (Fitch), R. basiola (Osten Sacken), and the cherry pest species R. fausta (Osten Sacken), were found to occur naturally in Newfoundland, representing a range extension of some 500 km for R. tabellaria and R. basiola. Rhagoletis fausta had previously been reported from sticky traps used to monitor R. mendax Curran, which is not known from the province. To investigate the route by which the two new species may have colonized Newfoundland, R. tabellaria adults were sequenced for a mitochondrial genome fragment (COI–tRNA‐Leu–COII–tRNA‐Lys). This sample was genetically identical or similar to samples from other widely distributed sites in North America, suggesting that the presence of R. tabellaria in Newfoundland is the result of postglacial dispersal rather than survival in a glacial refugium. The implications of these findings for Rhagoletis management in Canada are discussed.
Aphid galls accumulate high concentrations of amino acids: a support for the nutrition hypothesis for gall formation
Authors: Koyama Yoshitaka , Yao Izumi , Akimoto Shin‐Ichi
Published: October 2004

The nutrition hypothesis for the adaptive significance of insect gall formation postulates that galls accumulate higher concentrations of nutritive compounds than uninfested plant tissue, resulting in a high performance of the gall former. This hypothesis has been supported by some taxa of gall insects, but not by taxa such as cynipid wasps. Aphid galls are expected to require higher levels of nitrogen than other insects’ galls with a single inhabitant, because aphid galls are required to sustain a number of aphids reproducing parthenogenetically over two generations. The present study tested this hypothesis by evaluating aphid performance and amino acid concentration in phloem sap, using the aphidRhopalosiphum insertum(Walker) (Homoptera: Aphididae), which establishes colonies on leaves ofSorbus commixtaHedlund or in galls of the aphidSorbaphis chaetosiphonShaposhnikov (Homoptera: Aphididae). We prepared the gall and non‐gall treatments on trees ofS. commixta, in whichR. insertumfundatrices were reared and allowed to reproduce. InS. chaetosiphongalls,R. insertumcolonies propagated more rapidly, and the second generation grew larger and more fecund than on ungalled leaves. The amount of amino acids exuding from cut galled leaves was fivefold that in ungalled leaves; however, there was no significant difference in the amino acid composition between galled and ungalled leaves. In the intact leaves, total amino acid concentration in the phloem sap declined rapidly from late April to late May; however, the galls retained this high amino acid concentration in developing leaves for 1 month. These results indicate that the improved performance inR. insertumis ascribed to the increased concentration of amino acids in galled leaves. We suggest thatS. chaetosiphongalls function to promote the breakdown of leaf protein, leading to an increased performance of gall‐inhabiting aphids.
The applicability of the plant vigor and resource regulation hypotheses in explaining Epiblema gall moth–Parthenium weed interactions
Authors: Dhileepan K.
Published: October 2004

A basic question in insect–plant interactions is whether the insects respond to, or regulate plant traits, or a complex mixture of the two. The relative importance of the directions of the influence in insect–plant interactions has therefore been articulated through both the plant vigor hypothesis (PVH) and the resource regulation hypothesis (RRH). This study tested the applicability of these hypotheses in explaining the interactions between Parthenium hysterophorus L. (Asteraceae) and its stem‐galling moth, Epiblema strenuana Walker (Lepidoptera: Tortricidae). Parthenium plants exposed to galling were sampled at three sites in north Queensland, Australia, over a 2‐year period, and the relationship between gall abundance and plant vigor (plant height, biomass, flowers per plant, and branches per plant) was studied. To test the predictions of PVH and RRH, the vigor of parthenium plants protected from galling using insecticides was compared to galled plants and plants that escaped from galling. The vigor of ungalled plants was less than the vigor of galled plants. The higher plant vigor in galled plants was not due to galling, as was evident from insecticide exclusion trials. The insect seemed to preferentially gall the more vigorous plants. These findings support the predictions of the PVH and are contrary to those of RRH. Since gall abundance is linked to plant vigor, galling may have only a limited impact on the vigor of parthenium. This has implications for weed biological control. If the objective of biological control is to regulate the population of a plant by a galling insect, a preference for more vigorous plants by the insect is likely to limit its ability to regulate plant populations. This may explain the paucity of successes against biocontrol of annual weeds using gall insects.
Cohabitation in the United States and Britain: Demography, kinship, and the future
Authors: Seltzer Judith A.
Published: October 2004

Cohabitation is a rapidly changing aspect of family life in the United States and Britain. This article describes the demography of cohabitation, considers the place of cohabitation in the kinship system, and speculates on the future of cohabitation. I argue that three processes—cohort replacement, socialization that occurs when children live with cohabiting parents, and social diffusion—will foster continued increases in rates of cohabitation. These processes are also likely to increase variation in the types of cohabiting relationships that couples form. Understanding the meaning of cohabitation in the kinship system requires distinguishing between individuals' attitudes about their own relationships and the composition of cohabiting unions at the population level.
Changes in conjugal life in Canada: Is cohabitation progressively replacing marriage?
Authors: Le Bourdais Céline , Lapierre‐Adamcyk Évelyne
Published: October 2004

This article aims first to contrast the trends of marriage and cohabitation across different regions in Canada, and second, to assess whether cohabitation constitutes a new stage in the progression to marriage, or an alternative to marriage altogether. Based on various empirical demographic indicators, the analysis shows profound differences across the country. In Quebec, cohabiting unions are now widely accepted as forming the basis for family life, whereas they still largely constitute a childless prelude to marriage elsewhere in Canada. The authors discuss the role of different religious and cultural backgrounds, and of recent changes in the relationships between men and women, in accounting for the divergent evolution observed.
The case for (promoting) marriage: The devil is in the details
Authors: Huston Ted L. , Melz Heidi
Published: October 2004

This article considers the quality of the evidence that marriage confers unique benefits, and that, as such, social policies should be enacted to encourage couples, particularly those with few economic resources, to get married and stay together. Public concern about the future of marriage in the United States, we show, is rooted in demographic changes that reflect not so much a turning away from marriage, but an increasing openness to postponing marriage, living together out of wedlock, or divorcing. We examine why people who are motivated to marry hold back from doing so when they see the warning signs of future problems, and what happens when they marry despite them. We argue that marriages are fashioned in the images of the partners and are shaped by the opportunities and constraints of the ecological settings in which they are situated. As such, the promotion of family health and stability will require an approach that attends to couples' psychological, social, and economic needs.
Family, religion, and work among Arab American women
Authors: Ghazal Read Jen'nan
Published: October 2004

Using data from a national survey of 501 Arab American women, this study examines the extent to which family behavior mediates the influence of religion on women's labor force activity. Prior research on families has largely overlooked the role of religion in influencing women's labor force decisions, particularly at different stages of the life cycle. The analysis begins to address this gap by examining whether religious affiliation and religiosity have direct relationships to women's work behaviors, or whether they primarily operate through family behaviors at different phases of the life course. The results show that religiosity exerts a negative influence on women's labor force participation, but only when children are present in the home. Among women with no children, religiosity has no effect on employment.
Reactivity to patch tests with nickel sulfate and fragrance mix in infants
Authors: Jøhnke H. , Norberg L. A. , Vach W. , Bindslev‐Jensen C. , Høst A. , Andersen K. E.
Published: October 2004

The pattern of patch test reactivity to nickel sulfate and fragrance mix was studied with respect to patch test performance, reproducibility and clinical relevance in a population of unselected infants followed prospectively from birth to 18 months of age. TRUE Test™ patches with nickel sulfate in 3 concentrations, 200, 66 and 22 µg/cm2, and fragrance mix 430 µg/cm2 were used. A likely case of nickel sensitivity was defined as a reproducible positive reaction with at least homogeneous erythema and palpable infiltration occurring at least 2× and present at both the 12 and 18 months follow‐up. 543 infants (268 girls and 275 boys) were tested at least 1×, 304 were tested at both 12 and 18 months. The prevalence of a reproducible positive reaction to nickel was 8.6% (20 girls and 6 boys). A transient positive reaction was observed in 111 children. Clinical relevance of nickel sensitivity was found in only 1 child. No reproducible positive reaction to fragrance mix was found. The high proportion of transient patch test reactivity to nickel sulfate 200 µg/cm2 indicates that this standard concentration used for adults cannot be applied to infants. The interpretation of a single positive nickel patch test in infants must be assessed with caution and it is probably of non‐specific or irritant nature.
Benchmarking Audit Committee Effectiveness in Financial Reporting
Authors: Song Jihe , Windram Brian
Published: October 2004

This paper examines the effectiveness of UK audit committees in their primary responsibility of overseeing financial reporting. A logit regression approach is used to benchmark corporate financial reporting quality against financial reporting standards in the period from 1991 to 2000. Using a sample of companies that have been subject to adverse rulings by the Financial Reporting Review Panel (FRRP), we test the impact of board and audit committee characteristics on the probability of compliance with financial reporting standards. Our results show that independent boards promote audit committee effectiveness in financial reporting and suggest that director share ownership and multiple directorships could undermine audit committee effectiveness in financial reporting. We also suggest that director financial literacy and an ‘active’ audit committee may contribute to audit committee effectiveness.
Voluntary Audit Committee Formation and Practices among Belgian Listed Companies
Authors: Willekens Marleen , Bauwhede Heidi Vander , Gaeremynck Ann
Published: October 2004

In this paper we investigate some factors that are associated with voluntary audit committee formation in a non‐Anglo‐Saxon environment (and where audit committee formation is voluntary, even for listed companies). For those companies that voluntarily instaled an audit committee we also present evidence on their working practices. We use data from Belgian listed companies for that purpose. Consistent with previous Anglo‐Saxon research, we find that voluntary audit committee formation is positively correlated with the proportion of independent directors on the board of directors and external audit‐firm size. Contrary to prior studies, we do not find that agency costs and board size are associated with voluntary audit committee formation. As to working practices, we find that a substantial amount of Belgian‐listed companies do not comply with the recommendations of the Brussels Stock Exchange regarding audit committees, as about 50% of these companies has no audit committee. Those companies that do have an audit committee perform quite well according to the Belgian recommendations, but not according to recently formulated (tougher) US requirements, as they typically do not include a financial expert nor disclose the audit committee charter.
Audit Reports on Financial Statements Prepared According to IASB Standards: Empirical Evidence from the European Union
Authors: Garcia‐Benau Maria A. , Zorio Ana
Published: October 2004

This paper examines the audit report of 147 firms from the European Union that prepare their financial statements in compliance with the standards developed by the International Accounting Standards Board. Bearing in mind that the consolidated accounts of listed companies will follow IAS from 2005 onwards, the purpose of this paper is to provide some insight into the current outcome of the statutory audit on this information. Interesting conclusions are drawn from this empirical study with regard to the auditing standards applied, the wording used and the differences observed between reports produced by auditors from the big firms and reports from different European countries. The need to harmonise the auditing field is discussed under the results obtained, with the final aim to contribute to the standard‐setting debate on the creation of a high quality financial reporting system in the European Union.
Does Agency Theory Provide a General Framework for Audit Pricing?
Authors: Nikkinen Jussi , Sahlström Petri
Published: October 2004

This paper examines whether agency theory provides a general framework for audit pricing. It is hypothesized that audit fees are determined by agency theory and a set of other factors identified in the previous literature. To empirically test the hypothesis, audit pricing is analyzed in seven countries representing different kinds of accounting and economic environments. The results of the study confirm that a negative relationship exists between audit fees and manager ownership and that a positive relationship exists between audit fees and free cash flow in several countries. This implies that agency theory can be used, at least to some extent, to explain audit fees internationally. Moreover, agency theory explains audit fees similarly across countries while the control variables have different impact on audit fees.
Effect of antitumour necrosis factor‐α therapy on bone turnover in patients with active Crohn's disease: a prospective study
Authors: Ryan B. M. , Russel M. G. V. M. , Schurgers L. , Wichers M. , Sijbrandij J. , Stockbrugger R. W. , Schoon E.
Published: October 2004

Background and aims:  Patients with Crohn's disease are at increased risk of osteoporosis. Disease activity and circulating proinflammatory cytokines are thought to play a role in this process. Infliximab, a chimaeric antitumour necrosis factor‐α antibody is effective in the treatment of Crohn's disease. The aim of this study was to investigate the impact of treatment with infliximab on bone turnover in Crohn's disease patients.

Methods:  This was a prospective trial. Twenty‐four patients with active Crohn's disease were treated with infliximab (5 mg/kg). Bone markers were assayed pre‐ and post‐treatment. Bone formation was measured using serum bone‐specific alkaline phosphatase and total osteocalcin and bone resorption using serum N‐telopeptide cross‐linked type 1 collagen.

Results:  Infliximab therapy caused a significant increase in both markers of bone formation in patients with active Crohn's disease. No significant change in the bone resorption marker serum N‐telopeptide cross‐linked type 1 was found.

Conclusion:  Infliximab therapy had a significant beneficial effect on bone metabolism in patients with active Crohn's disease. These findings further support the theory that active ongoing inflammation and high levels of circulating cytokines play a pivotal role in the pathogenesis of bone loss in patients with Crohn's disease.