bluuebunny/crossref_metadata_2025 huggingface dataset:
Enhancement of field effect mobility of poly(3-hexylthiophene) thin film transistors by soft-lithographical nanopatterning on the gate-dielectric surface
Authors: Park Jeong-Ho , Kang Seok-Ju , Park Jeong-Woo , Lim Bogyu , Kim Dong-Yu
Published: November 2007

The submicroscaled octadecyltrichlorosilane (OTS) line patterns on gate-dielectric surfaces were introduced into the fabrication of organic field effect transistors (OFETs). These spin-cast regioregular poly(3-hexylthiophene) films on soft-lithographically patterned SiO2 surfaces yielded a higher hole mobility (∼0.072cm2∕Vs) than those of unpatterned (∼0.015cm2∕Vs) and untreated (∼5×10−3cm2∕Vs) OFETs. The effect of mobility enhancement as a function of the patterned line pitch was investigated in structural and geometric characteristics. The resulting improved mobility is likely attributed to the formation of efficient π-π stacking as a result of guide-assisted, local self-organization-involved molecular interactions between the poly(3-hexylthiophene) polymer and the geometrical OTS patterns.
Crystalline Ge3N4 on Ge(111)
Authors: Lieten R. R. , Degroote S. , Kuijk M. , Borghs G.
Published: November 2007

The exposure of Ge(111) to a nitrogen plasma at temperatures above which Ge3N4 is thermally stable leads to the formation of a thin, monocrystalline Ge3N4 layer. At these temperatures, equilibrium is established between the formation and dissociation of Ge3N4, limiting its thickness to 0.7nm at ∼800°C. The thermal stability of a crystalline Ge3N4 layer is comparable to an amorphous one. It starts to evaporate at temperatures above 600°C. Crystalline Ge3N4 allows the growth of III-nitrides on top of Ge(111) substrates and possibly the passivation of Ge-based field effect transistors.
Generation and detection of broadband airborne ultrasound with cellular polymer ferroelectrets
Authors: Dansachmüller Mario , Minev Ivan , Bartu Petr , Graz Ingrid , Arnold Nikita , Bauer Siegfried
Published: November 2007

Cellular polypropylene ferroelectrets are useful for broadband airborne ultrasound generation and detection up to the fundamental thickness extension resonance. The authors show that the coupling of ferroelectrets to air alters the electromechanical resonance of the foam. In an acoustical cavity, Fabry-Perot resonances are obtained, which is in excellent agreement with the plane wave model calculations. For material assessment in airborne ultrasound applications, a figure of merit is used based on the electromechanical coupling factor and acoustical impedance of the material. The good coupling of ferroelectrets to gases results from the small acoustical impedance of the material.
Direct piezoelectric response of piezopolymer polyvinylidene fluoride under high mechanical strain and stress
Authors: Wang Yong , Ren Kailiang , Zhang Q. M.
Published: November 2007

We show that the nonlinear piezoelectric response of polyvinylidene fluoride (PVDF) exhibits quite different behavior compared with the piezoceramics. Instead of increasing linearly with the stress amplitude Tac, d31 coefficient raises with Tac2. Furthermore, the nonlinear effect does not set in until the strain increases beyond 0.3%, indicating very strong barriers to the domain wall motions in PVDF. The electromechanical coupling factor k31 also exhibits an increase with stress. Furthermore, the piezopolymer can withstand more than 3% strain without degrading the piezoelectric responses.
Epidermal growth factor receptor juxtamembrane region regulates allosteric tyrosine kinase activation
Authors: Thiel Kristina W. , Carpenter Graham
Published: November 2007

Structural studies of the extracellular and tyrosine kinase domains of the epidermal growth factor receptor (ErbB-1) provide considerable insight into facets of the receptor activation mechanism, but the contributions of other regions of ErbB-1 have not been ascertained. This study demonstrates that the intracellular juxtamembrane (JM) region plays a vital role in the kinase activation mechanism. In the experiments described herein, the entire ErbB-1 intracellular domain (ICD) has been expressed in mammalian cells to explore the significance of the JM region in kinase activity. Deletion of the JM region (ΔJM) results in a severe loss of ICD tyrosine phosphorylation, indicating that this region is required for maximal activity of the tyrosine kinase domain. Coexpression of ΔJM and dimerization-deficient kinase domain ICD mutants revealed that the JM region is indispensable for allosteric kinase activation and productive monomer interactions within a dimer. Studies with the intact receptor confirmed the role of the JM region in kinase activation. Within the JM region, Thr-654 is a known protein kinase C (PKC) phosphorylation site that modulates kinase activity in the context of the intact ErbB-1 receptor; yet, the mechanism is not known. Whereas a T654A mutation promotes increased ICD tyrosine phosphorylation, the phosphomimetic T654D mutant generates a 50% reduction in ICD tyrosine phosphorylation. Similar to the ΔJM mutants, the T654D mutant ICD failed to interact with a wild-type monomer. This study reveals an integral role for the intracellular JM region of ErbB-1 in allosteric kinase activation.
CD4+CD25+Foxp3+regulatory T cells induce alternative activation of human monocytes/macrophages
Authors: Tiemessen Machteld M. , Jagger Ann L. , Evans Hayley G. , van Herwijnen Martijn J. C. , John Susan , Taams Leonie S.
Published: November 2007

CD4+CD25+Foxp3+regulatory T cells (Tregs) are potent suppressors of the adaptive immune system, but their effects on innate immune cells are less well known. Here we demonstrate a previously uncharacterized function of Tregs, namely their ability to steer monocyte differentiation toward alternatively activated macrophages (AAM). AAM are cells with strong antiinflammatory potential involved in immune regulation, tissue remodeling, parasite killing, and tumor promotion. We show that, after coculture with Tregs, monocytes/macrophages display typical features of AAM, including up-regulated expression of CD206 (macrophage mannose receptor) and CD163 (hemoglobin scavenger receptor), an increased production of CCL18, and an enhanced phagocytic capacity. In addition, the monocytes/macrophages have reduced expression of HLA-DR and a strongly reduced capacity to respond to LPS in terms of proinflammatory mediator production (IL-1β, IL-6, IL-8, MIP-1α, TNF-α), NFκB activation, and tyrosine phosphorylation. Mechanistic studies reveal that CD4+CD25+CD127lowFoxp3+Tregs produce IL-10, IL-4, and IL-13 and that these cytokines are the critical factors involved in the suppression of the proinflammatory cytokine response. In contrast, the Treg-mediated induction of CD206 is entirely cytokine-independent, whereas the up-regulation of CD163, CCL18, and phagocytosis are (partly) dependent on IL-10 but not on IL-4/IL-13. Together these data demonstrate a previously unrecognized function of CD4+CD25+Foxp3+Tregs, namely their ability to induce alternative activation of monocytes/macrophages. Moreover, the data suggest that the Treg-mediated induction of AAM partly involves a novel, cytokine-independent pathway.
HDAC inhibitor PCI-24781 decreases RAD51 expression and inhibits homologous recombination
Authors: Adimoolam Shanthi , Sirisawad Mint , Chen Jun , Thiemann Patti , Ford James M. , Buggy Joseph J.
Published: November 2007

Histone deacetylase (HDAC) inhibitors such as the phenyl hydroxamic acid PCI-24781 have emerged recently as a class of therapeutic agents for the treatment of cancer. Recent data showing synergy of HDAC inhibitors with ionizing radiation and other DNA-damaging agents have suggested that HDAC inhibitors may act, in part, by inhibiting DNA repair. Here we present evidence that HDAC enzymes are important for homologous recombinational repair of DNA double-strand breaks. Combination studies of PCI-24781 with the poly(ADP-ribose) polymerase inhibitor PJ34, an agent thought to produce lesions repaired by homologous recombination (HR), resulted in a synergistic effect on apoptosis. Immunofluorescence analysis demonstrated that HDAC inhibition caused a complete inhibition of subnuclear repair foci in response to ionizing radiation. Mechanistic investigations revealed that inhibition of HDAC enzymes by PCI-24781 led to a significant reduction in the transcription of genes specifically associated with HR, including RAD51. RAD51 protein levels were significantly decreased after 24 h of drug exposure bothin vitroandin vivo. Consistent with inhibition of HR, treatment with PCI-24781 resulted in a decreased ability to perform homology directed repair of I-SceI-induced chromosome breaks in transfected CHO cells. In addition, an enhancement of cell killing was observed in Ku mutant cells lacking functional nonhomologous end joining compared with WT cells. Together these results demonstrate that HDAC enzymes are critically important to enable functional HR by controlling the expression of HR-related genes and promoting the proper assembly of HR-directed subnuclear foci.
B7-H3 and B7x are highly expressed in human prostate cancer and associated with disease spread and poor outcome
Authors: Zang Xingxing , Thompson R. Houston , Al-Ahmadie Hikmat A. , Serio Angel M. , Reuter Victor E. , Eastham James A. , Scardino Peter T. , Sharma Padmanee , Allison James P.
Published: November 2007

B7-H3 and B7x are recently discovered members of the B7-CD28 family thought to dampen peripheral immune responses via negative costimulation. We evaluated their potential expression in human prostate cancer using a large cohort of patients with 7 years of follow-up. We identified 823 patients with tissue available treated with radical prostatectomy between 1985 and 2003. Immunohistochemistry was performed on tissue microarray sections using anti-B7-H3 and -B7x. The percentage and intensity of immunoreactivity by tumor cells were blindly evaluated by two urological pathologists, and outcome analyses were conducted. Both B7-H3 and B7x were highly expressed; 93% and 99% of tumors had aberrant expression, respectively. The median percentage of tumor cells staining positive was 80% for each molecule. Strong intensity for B7-H3 and B7x was noted in 212 (26%) and 120 (15%) patients, respectively. Patients with strong intensity for B7-H3 and B7x were significantly more likely to have disease spread at time of surgery (
P
< 0.001 and
P
= 0.005, respectively). Additionally, patients with strong intensity for B7-H3 and B7x were at significantly increased risk of clinical cancer recurrence (
P
< 0.001 and
P
= 0.005) and cancer-specific death (
P
= 0.004 and
P
= 0.04, respectively). To our knowledge, we present the largest investigation of B7 family molecules in a human malignancy and a previously undescribed evaluation of B7x in prostate cancer. B7-H3 and B7x are abundantly expressed in prostate cancer and associated with disease spread and poor outcome. Given the proposed immune-inhibitory mechanisms of B7-H3 and B7x, these molecules represent attractive targets for therapeutic manipulation in prostate cancer.
Specific subgroups of Fru
M
neurons control sexually dimorphic patterns of aggression in
Drosophila melanogaster
Authors: Chan Yick-Bun , Kravitz Edward A.
Published: November 2007

A great challenge facing neuroscience is to understand how genes, molecules, cells, circuits, and systems interact to generate social behavior. Fruit flies (
Drosophila melanogaster
) offer a powerful model system to address questions of this magnitude. These animals display genetically specified, sexually dimorphic patterns of fighting behavior via sex-specific splicing of the
fruitless
gene. Here, we show that sexually dimorphic behavioral patterns displayed during aggression are controlled by specific subgroups of neurons expressing male forms of
fruitless
proteins (Fru
M
). Using the GAL4/UAS system to manipulate
transformer
expression, we feminized or masculinized different populations of neurons in fly nervous systems. With a panneuronal
elav-GAL4
driver, male patterns of fighting behavior were transferred into females and female patterns into males. We screened 60 Gal4 lines that express the yeast transcription factor in different patterns in fly central nervous systems and found five that showed abnormal same-sex courtship behavior. The sexually dimorphic fighting patterns, however, were completely switched only in one and partially switched in a second of these lines. In the other three lines, female patterns of aggression were seen despite a switch in courtship preference. A tight correspondence was seen between Fru
M
expression and how flies fight in several subgroups of neurons usually expressing these proteins: Expression is absent when flies fight like females and present when flies fight like males, thereby beginning a separation between courtship and aggression among these neurons.
A biochemical approach to identifying microRNA targets
Authors: Karginov Fedor V. , Conaco Cecilia , Xuan Zhenyu , Schmidt Bryan H. , Parker Joel S. , Mandel Gail , Hannon Gregory J.
Published: November 2007

Identifying the downstream targets of microRNAs (miRNAs) is essential to understanding cellular regulatory networks. We devised a direct biochemical method for miRNA target discovery that combined RNA-induced silencing complex (RISC) purification with microarray analysis of bound mRNAs. Because targets of miR-124a have been analyzed, we chose it as our model. We honed our approach both by examining the determinants of stable binding between RISC and synthetic target RNAs
in vitro
and by determining the dependency of both repression and RISC coimmunoprecipitation on miR-124a seed sites in two of its well characterized targets
in vivo
. Examining the complete spectrum of miR-124 targets in 293 cells yielded both a set that were down-regulated at the mRNA level, as previously observed, and a set whose mRNA levels were unaffected by miR-124a. Reporter assays validated both classes, extending the spectrum of mRNA targets that can be experimentally linked to the miRNA pathway.
Blocking LIF action in the uterus by using a PEGylated antagonist prevents implantation: A nonhormonal contraceptive strategy
Authors: White Christine A. , Zhang Jian-Guo , Salamonsen Lois A. , Baca Manuel , Fairlie W. Douglas , Metcalf Donald , Nicola Nicos A. , Robb Lorraine , Dimitriadis Evdokia
Published: November 2007

Blastocyst implantation is a critical stage in the establishment of pregnancy. Leukemia inhibitory factor (LIF) is essential for mouse blastocyst implantation and also plays a role in human pregnancy. We examined the effect of a potent LIF antagonist (LA) on mouse implantation. In mice, LIF expression peaks on day 3.5 of pregnancy (D3.5) (D0.5 = day of mating plug detection) in the uterine glandular epithelium. LA (7 mg/kg per day) administered from D2.5 to D4.5 via four hourly i.p. injections plus continuous administration via miniosmotic pump resulted in complete implantation failure. To improve its pharmacokinetic properties, we conjugated LA to polyethylene glycol (PEG), achieving a significant increase in serum levels. PEGylated LA (PEGLA) (37.5 mg/kg per day) administered via three i.p. injections between D2.5 and D3.5 also resulted in complete implantation failure. PEGLA immunolocalized to the uterine luminal epithelium at the time of blastocyst implantation. Both LA and PEGLA reduced phosphorylation of the downstream signaling molecule STAT3 in luminal epithelial cells on D3.5. The effects of PEGLA were found to be endometrial, with no embryo-lethal effects observed. These data demonstrate that administration of a PEGylated LIF antagonist is an effective method of targeting LIF signaling in the endometrium and a promising novel approach in the development of nonhormonal contraceptives for women.
Identification of differentially expressed gene categories in microarray studies using nonparametric multivariate analysis
Authors: Nettleton Dan , Recknor Justin , Reecy James M.
Published: November 2007

Motivation: The field of microarray data analysis is shifting emphasis from methods for identifying differentially expressed genes to methods for identifying differentially expressed gene categories. The latter approaches utilize a priori information about genes to group genes into categories and enhance the interpretation of experiments aimed at identifying expression differences across treatments. While almost all of the existing approaches for identifying differentially expressed gene categories are practically useful, they suffer from a variety of drawbacks. Perhaps most notably, many popular tools are based exclusively on gene-specific statistics that cannot detect many types of multivariate expression change.

Results: We have developed a nonparametric multivariate method for identifying gene categories whose multivariate expression distribution differs across two or more conditions. We illustrate our approach and compare its performance to several existing procedures via the analysis of a real data set and a unique data-based simulation study designed to capture the challenges and complexities of practical data analysis. We show that our method has good power for differentiating between differentially expressed and non-differentially expressed gene categories, and we utilize a resampling based strategy for controling the false discovery rate when testing multiple categories.

Availability: R code (www.r-project.org) for implementing our approach is available from the first author by request.

Contact:  dnett@iastate.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
Direct method to construct integrals for
N
th-order autonomous ordinary difference equations
Authors: Sahadevan R , Uma Maheswari C
Published: November 2007

A direct method to construct integrals for an
N
th-order autonomous ordinary difference equation (
O
Δ
E
):
w

n
+
N

=
F
(
w

n

, …, 
w

n
+
N
−1

) is presented. As an illustration we first consider third-order autonomous
O
Δ
E w

n
+3

=
F
(
w

n

, 
w

n
+1

, 
w

n
+2

) and identify the forms of
F
for which two independent integrals exist. The effectiveness of the method to construct two or more integrals for fourth- and fifth-order
O
Δ
E
s is also demonstrated. The question of integrability of each of the identified difference equations with more than one integral is also discussed.
Ixolaris binding to factor X reveals a precursor state of factor Xa heparin‐binding exosite
Authors: Monteiro Robson Q. , Rezaie Alireza R. , Bae Jong‐Sup , Calvo Eric , Andersen John F. , Francischetti Ivo M.B.
Published: November 2007

Ixolaris is a two‐Kunitz tick salivary gland tissue factor pathway inhibitor (TFPI). In contrast to human TFPI, Ixolaris specifically binds to factor Xa (FXa) heparin‐binding exosite (HBE). In addition, Ixolaris interacts with zymogen FX. In the present work we characterized the interaction of Ixolaris with human FX quantitatively, and identified a precursor state of the heparin‐binding exosite (proexosite, HBPE) as the Ixolaris‐binding site on the zymogen. Gel‐filtration chromatography demonstrated 1:1 complex formation between fluorescein‐labeled Ixolaris and FX. Isothermal titration calorimetry confirmed that the binding of Ixolaris to FX occurs at stoichiometric concentrations in a reaction which is characteristically exothermic, with a favorable enthalpy (ΔH) of −10.78 kcal/mol. ELISA and plasmon resonance experiments also indicate that Ixolaris binds to plasma FX and FXa, or to recombinant Gla domain‐containing FX/FXa with comparable affinities (∼1 nM). Using a series of mutants on the HBPE, we identified the most important amino acids involved in zymogen/Ixolaris interaction—Arg‐93 >>> Arg‐165 ≥ Lys‐169 > Lys‐236 > Arg‐125—which was identical to that observed for FXa/Ixolaris interaction. Remarkably, Ixolaris strongly inhibited FX activation by factor IXa in the presence but not in the absence of factor VIIIa, suggesting a specific interference in the cofactor activity. Further, solid phase assays demonstrated that Ixolaris inhibits FX interaction with immobilized FVIIIa. Altogether, Ixolaris is the first inhibitor characterized to date that specifically binds to FX HBPE. Ixolaris may be a useful tool to study the physiological role of the FX HBPE and to evaluate this domain as a target for anticoagulant drugs.
Amyloid—a state in many guises: Survival of the fittest fibril fold
Authors: Pedersen Jesper S. , Otzen Daniel E.
Published: November 2007

Under appropriate conditions, essentially all proteins are able to aggregate to form long, well‐ordered and β‐sheet‐rich arrays known as amyloid‐like fibrils. These fibrils consist of varying numbers of intertwined protofibrils and can for any given protein exhibit a wealth of different forms at the ultrastructural level. Traditionally, this structural variability or polymorphism has been attributed to differences in the assembly of a common protofibril structure. However, recent work on glucagon, insulin, and the Aβ peptide suggests that this polymorphism can occur at the level of secondary structure. Simple variations in either solvent conditions such as temperature, protein concentration, and ionic strength or external mechanical influences such as agitation can lead to formation of fibrils with markedly different characteristics. In some cases, these characteristics can be passed on to new fibrils in a strain‐specific manner, similar to what is known for prions. The preferred structure of fibrils formed can be explained in terms of selective pressure and survival of the fittest; the most populated types of fibrils we observe at the end of an experiment are those that had the fastest overall growth rate under the given conditions. Fibrillar polymorphism is probably a consequence of the lack of structural restraints on a nonfunctional conformational state.
Crystal structure of Mycobacterium tuberculosis LrpA, a leucine‐responsive global regulator associated with starvation response
Authors: Reddy Manchi C.M. , Gokulan Kuppan , Jacobs William R. , Ioerger Thomas R. , Sacchettini James C.
Published: November 2007

The bacterial leucine‐responsive regulatory protein (Lrp) is a global transcriptional regulator that controls the expression of many genes during starvation and the transition to stationary phase. The Mycobacterium tuberculosis gene Rv3291c encodes a 150‐amino acid protein (designated here as Mtb LrpA) with homology with Escherichia coli Lrp. The crystal structure of the native form of Mtb LrpA was solved at 2.1 Å. The Mtb LrpA structure shows an N‐terminal DNA‐binding domain with a helix‐turn‐helix (HTH) motif, and a C‐terminal regulatory domain. In comparison to the complex of E. coli AsnC with asparagine, the effector‐binding pocket (including loop 100–106) in LrpA appears to be largely preserved, with hydrophobic substitutions consistent with its specificity for leucine. The effector‐binding pocket is formed at the interface between adjacent dimers, with an opening to the core of the octamer as in AsnC, and an additional substrate‐access channel opening to the outer surface of the octamer. Using electrophoretic mobility shift assays, purified Mtb LrpA protein was shown to form a protein–DNA complex with the lat promoter, demonstrating that the lat operon is a direct target of LrpA. Using computational analysis, a putative motif is identified in this region that is also present upstream of other operons differentially regulated under starvation. This study provides insights into the potential role of LrpA as a global regulator in the transition of M. tuberculosis to a persistent state.
Energetic rationale for an unexpected and abrupt reversal of guanidinium chloride‐induced unfolding of peptide deformylase
Authors: Berg Alexander K. , Manokaran Sumathra , Eiler Daniel , Kooren Joel , Mallik Sanku , Srivastava D.K.
Published: November 2007

Peptide deformylase (PDF) catalyzes the removal of formyl group from the N‐terminal methionine residues of nascent proteins in prokaryotes, and this enzyme is a high priority target for antibiotic design. In pursuit of delineating the structural–functional features of Escherichia coli PDF (EcPDF), we investigated the mechanistic pathway for the guanidinium chloride (GdmCl)‐induced unfolding of the enzyme by monitoring the secondary structural changes via CD spectroscopy. The experimental data revealed that EcPDF is a highly stable enzyme, and it undergoes slow denaturation in the presence of varying concentrations of GdmCl. The most interesting aspect of these studies has been the abrupt reversal of the unfolding pathway at low to moderate concentrations of the denaturant, but not at high concentration. An energetic rationale for such an unprecedented feature in protein chemistry is offered.
Optimization of baking parameters of part‐baked and rebaked Irish brown soda bread by evaluation of some quality characteristics
Authors: Leuschner Renata G. K. , O'Callaghan Michael J. A. , Arendt Elke K.
Published: November 2007

Summary  Part‐baked Irish brown soda bread loaves with bicarbonate levels from 0 to 2.8 % were baked, packed and stored for up to 11 days at 5 d̀C then second‐baked at 180 or 200 d̀C for various times to give an oven‐fresh end product. The quality of the rebaked bread was dependent on characteristics of the part‐baked bread, its storage conditions and the processing parameters of the second baking phase. Quality parameters evaluated were bread volume yield, crumb and crust firmness, moisture content and colour. Staling of the part‐baked bread during storage at 5 d̀C and the reversion of this process at 59 d̀C was investigated with regard to rebaking time and temperature. Rebaking conditions were optimized by evaluating the core temperature increase in the centre of the bread. Immediately after the second baking phase a post‐baking temperature increase was measured which allowed reduction of the in‐oven rebaking time. The data were modelled mathematically using least squares analyses.
Tomato purèe quality from transgenic processing tomatoes
Authors: Porretta Sebastiano , Poli Giovanna
Published: November 2007

Summary  The quality of tomato purèe prepared from transgenic fruits (Lycopersicon esculentum) which had reduced amounts of polygalacturonase (PG) activity, were evaluated. The application of genetic modification yields products which have lower Bostwick consistency values (from 35 to 55%), reduced serum separation (c. 40%) and better sensory appearance and acceptability in comparison with their conventional counterparts. A new way of producing high quality tomato products using genetically modified fruits together with mild heat treatments is described.
The use of microbial metabolites against post‐harvest diseases of longan fruit
Authors: Jiang Yueming
Published: November 2007

Summary  The effect of different concentrations of polyoxin and culture supernatant of Bacillus subtilis was tested against rot fungi on longan cv. Shixia fruit. Both have good control of rot caused by Botryodiplodia. Control of the fungus was better at the higher concentrations of the two treatments. Control of fruit decay, treated with the culture supernatant of Bacillus subtilis, polyoxin, or a combination of both, was good up to 30 days at 5 d̀C after treatment, but markedly decreased when fruit was stored for a longer time. The combination was better than either treatment alone, and resulted in 96.3% good fruit in cold storage after 30 days compared with only 66.3% for the control.
Some physicochemical and antinutritional properties of raw flours and protein isolates from Mucuna pruriens (velvet bean) and Canavalia ensiformis (jack bean)
Authors: Betancur‐Ancona David , Gallegos‐Tintoré Santiago , Delgado‐Herrera América , Pérez‐Flores Virginia , Castellanos Ruelas Arturo , Chel‐Guerrero Luis
Published: November 2007

The legumes Canavalia ensiformis and Mucuna pruriens are underexploited in tropical Mexico. Their seeds have good nutritional potential, but contain antinutritional factors. Physicochemical and antinutritional properties were determined for raw flours (RF) and protein isolates (PI) produced from these legumes. Protein content in the PI was 737 g kg–1 for C. ensiformis and 666 g kg–1 for M. pruriens. Protein isolation improved in vitro digestibility, while maintaining high lysine levels and adequate sulphur amino acids content. Antinutritional factors such as cyanogenic glucosides, cyanide precursors from hydrolysis, tannins and trypsin inhibitors were lower in the PIs than in the RFs. The reduction in canavanine levels, a structural analogue of arginine, in the C. ensiformis PI was noteworthy. These PIs thus have potential applications in the development of new food ingredients in tropical regions using processes that improve nutritional value.
Broad-line Balmer decrements in blue active galactic nuclei
Authors: Dong Xiaobo , Wang Tinggui , Wang Jianguo , Yuan Weimin , Zhou Hongyan , Dai Haifeng , Zhang Kai
Published: November 2007

We have investigated the broad-line Balmer decrements (Hα/Hβ) for a large, homogeneous sample of Seyfert 1 galaxies and quasi-stellar objects (QSOs) using spectroscopic data obtained in the Sloan Digital Sky Survey. The sample, drawn from the Fourth Data Release, comprises 446 low-redshift (z≲ 0.35) active galactic nuclei (AGN) that have blue optical continua as indicated by the spectral slopes in order to minimize the effect of dust extinction. We find that (i) the distribution of the intrinsic broad-line Hα/Hβ ratio can be well described by log-Gaussian, with a peak at Hα/Hβ= 3.06 and a standard deviation of about 0.03 dex only; (ii) the Balmer decrement does not correlate with AGN properties such as luminosity, accretion rate and continuum slope, etc.; (iii) on average, the Balmer decrements are found to be only slightly larger in radio-loud sources (3.37) and sources having double-peaked emission-line profiles (3.27) compared to the rest of the sample. We therefore suggest that the broad-line Hα/Hβ ratio can be used as a good indicator for dust extinction in the AGN broad-line region; this is especially true for radio-quiet AGN with regular emission-line profiles, which constitute the vast majority of the AGN population.
Is the modulation of retinoid and retinoid‐associated signaling a future therapeutic strategy in neurological trauma and neurodegeneration?
Authors: Malaspina Andrea , Michael‐Titus Adina T.
Published: November 2007

The complex molecular pathways that mediate the effects of vitamin A and its derivatives, are increasingly recognized as a component of the repair capacity that could be activated to induce protection and regeneration in the mature nervous tissue. Retinoid and retinoid‐associated signaling plays an essential role in normal neurodevelopment and appears to remain active in the adult CNS. In this paper, we review evidence which supports the hypothesis of an activation of retinoid‐associated signaling molecular pathways in the mature nervous tissue and its significance in the context of neurodegenerative, trauma‐induced and psychiatric disorders, at spinal and supra‐spinal levels. Finally, we summarize the potential therapeutic avenues based on the modulation of retinoid targets undergoing reactivation under conditions of acute injury and chronic degeneration in the central nervous system, and discuss some of the unresolved issues linked to this treatment strategy.
Nitrated alpha‐synuclein‐activated microglial profiling for Parkinson’s disease
Authors: Reynolds Ashley D. , Glanzer Jason G. , Kadiu Irena , Ricardo‐Dukelow Mary , Chaudhuri Anathbandhu , Ciborowski Pawel , Cerny Ronald , Gelman Benjamin , Thomas Mark P. , Mosley R. Lee , Gendelman Howard E.
Published: November 2007

J. Neurochem. (2008) 104, 1504–1525.

Microglial neuroinflammatory processes play a primary role in dopaminergic neurodegeneration for Parkinson’s disease (PD). This can occur, in part, by modulation of glial function following activation by soluble or insoluble modified alpha‐synuclein (α‐syn), a chief component of Lewy bodies that is released from affected dopaminergic neurons. α‐Syn is nitrated during oxidative stress responses and in its aggregated form, induces inflammatory microglial functions. Elucidation of these microglial function changes in PD could lead to new insights into disease mechanisms. To this end, PD‐associated inflammation was modeled by stimulation of microglia with aggregated and nitrated α‐syn. These activated microglia were ameboid in morphology and elicited dopaminergic neurotoxicity. A profile of nitrated, aggregated α‐syn‐stimulated microglia was generated using combinations of genomic (microarrays) and proteomic (liquid chromatography‐tandem mass spectrometry, differential gel electrophoresis, and protein array) assays. Genomic studies revealed a substantive role for nuclear factor‐kappa B transcriptional activation. Qualitative changes in the microglial proteome showed robust increases in inflammatory, redox, enzyme, and cytoskeletal proteins supporting the genomic tests. Autopsy brain tissue acquired from substantia nigra and basal ganglia of PD patients demonstrated that parallel nuclear factor‐kappa B‐related inflammatory processes were, in part, active during human disease. Taken together, the transcriptome and proteome of nitrated α‐syn activated microglia, shown herein, provide new potential insights into disease mechanisms.
Differential expression of duplicated VAL‐opsin genes in the developing zebrafish
Authors: Kojima Daisuke , Torii Masaki , Fukada Yoshitaka , Dowling John E.
Published: November 2007

Non‐visual opsins mediate various light‐dependent physiological events. Our previous search for non‐visual opsin genes in zebrafish led to the discovery of VAL‐opsin (VAL‐opsinA) in deep brain cells and retinal horizontal cells of the adult fish. In this study, we report the identification and characterization of its duplicated gene, VAL‐opsinB, in zebrafish. A molecular phylogenetic analysis indicates that VAL‐opsinB is orthologous to a previously reported salmon gene and that the duplication of the VAL‐opsin gene occurred in the teleost lineage. The recombinant protein of zebrafish VAL‐opsinB forms a green‐sensitive photopigment when reconstituted with 11‐cis‐retinal. VAL‐opsinB expression was detected in a limited number of cells of the brain and the eye, and the expression pattern is distinct from that of the VAL‐opsinA gene. Such a differential expression pattern suggests that VAL‐opsinA and VAL‐opsinB are involved in different physiological events in zebrafish.
Stand management: a threat or opportunity for birds in British woodland?
Authors: QUINE CHRISTOPHER P. , FULLER ROBERT J. , SMITH KEN W. , GRICE PHILIP V.
Published: November 2007

Recent studies have suggested that the neglect of stand management is having a detrimental effect on the habitat of a number of woodland birds in Britain. The remedy, to reinstate active management, appears to run counter to a number of other conservation recommendations such as re‐wilding and naturalizing of stands. We attempt to unpick this apparent conflict by considering the resource needs of British woodland birds relative to those of birds elsewhere in Europe, and whether these needs differ between those with declining and those with increasing populations. We also consider how these requirements relate to stand management and stand dynamics and consider options for future management. We found that whilst stand stage per se did not discriminate between the declining and increasing species pools, correspondence analysis suggested that there were differences between the groups in their preferred habitat features. Declining woodland birds in Britain appear to be most closely associated with the presence of deciduous trees in the stand, an open canopy, and ecotonal structures. Species present in the near continent, but not in Britain, were associated with deciduous snags, large trees, canopy layer and holes. Species increasing in Britain were located between these groups on an axis of woodland maturity, and most strongly associated with habitat features of canopy layer and holes. Stand management can help provide the structures apparently preferred by many of the declining species and, if targeted, can deliver them at a more rapid rate than development of similar features through natural stand dynamics. However, there are often multiple pathways to particular structures and a single recommendation of active management is likely to be insufficient to secure the necessary features in most situations. In addition, habitat features important in Europe as a whole may not be the most critical at a local or regional scale. The varying requirements of the different species pools suggest that greater recognition of this would be appropriate in developing conservation strategies in different regions, and greater clarity is desirable over conservation objectives and habitat structures for particular woodlands.
The use of GIS in estimating spatial variation in habitat quality: a case study of lay‐date in the Great TitParus major
Authors: WILKIN TEDDY A. , PERRINS CHRISTOPHER M. , SHELDON BEN C.
Published: November 2007

Finding the most biologically meaningful scale at which to describe environmental variation is a persistent problem in ecology. Most studies of forest passerines are conducted at the scale of the habitat or woodland and do not account for environmental variation between individual breeding sites. Here we employ two GIS models, and four spatial scales, to describe environmental variation among 4683 Great TitParus majorbreeding sites occupied over a 32‐year period in Wytham Wood, Oxford, UK, and use these data to help explain variation in an environmentally sensitive trait, first egg date. Model 1 used Thiessen polygons to generate individual spatial scales for each breeding pair, while Model 2 used a range of predetermined radial scales around each breeding site. Environmental variables included local altitude and aspect estimated from a Digital Terrain Model, and the number of OakQuercus roburtrees around each nest‐site, used here as a surrogate for local food (caterpillar) availability. In a Linear Mixed Model, Model 2 explained the most variation in lay‐date at a scale of 25 m from each nestbox. However, the model that returned the lowest Akaike Information Criterion (AIC) contained environmental variables from Model 2, but measured at different fixed spatial scales of between 25 and 75 m. Results from this final model showed that birds breeding in low‐altitude, north‐facing and Oak‐rich areas bred earlier than those in high‐altitude, south‐facing and Oak‐poor areas, at radial scales of 25, 75 and 75 m from each nestbox, respectively. In addition, birds in interior sites bred earlier than those nearer the woodland edge, although this edge effect was only apparent on north‐facing slopes. Thus, the current study demonstrates that a range of GIS models can be effectively used to scale and describe environmental variation between individual breeding sites, and that fine‐scale topographic variation, food availability and edge proximity can affect the breeding date of Great Tits.
SequentiaI RevascuIarization of Intramuscular Left Anterior Descending Coronary Artery
Authors: Suzer Kaya , Yorgancioglu Cem , Gunaydin Serdar , Tokmakoglu Hilmi
Published: November 2007

Abstract We present a new technique for avoiding possible kinking or angulation of the sequential left internal mammary artery to left anterior descending artery (LIMA‐LAD) anastomoses when the LAD follows an intramuscular course. A 3‐ to 5‐mm cusp of saphenous vein segment is interposed between the intramuscular LAD segment and internal mammary artery (IMA) at the sequential anastomotic site, to which the distal portion of the IMA was anastomosed in standard end‐to‐side fashion.
Use of the “Single Suture” Technique to Expose the Anterior Surface of the Heart
Authors: Ricci Marco , Karamanoukian Hratch L. , D'Ancona Giuseppe , Bergsland Jacob , Salerno Tomas A.
Published: November 2007

Abstract The “single suture” technique, which consists of placing a suture in the oblique sinus of the posterior pericardium and connecting it to a vaginal tape, is commonly adopted in off‐pump coronary artery revascularization to obtain elevation of the heart and coronary artery exposure. This report describes the use of this technique to expose the anterior wall of the heart in the setting of ventricular aneurysm repair.
The DNA content of the mycelial nuclei of rust fungi grown on artificial media
Authors: Tetsuka Yasuyuki , Ando Katsuhiko , Yamaoka Yuichi , Katsuya Keizo
Published: November 2007

The nuclear condition of vegetative mycelia of several races of Puccinia recondita f. sp. tritici, P. graminis f. sp. tritici, P. coronata f. sp. avenae, and Gymnosporangium asiaticum was determined by propidium iodide staining. Cultures originating from the uredinial stage of P. recondita f. sp. tritici, from the uredinial stage of P. coronata f. sp. avenae, and from the spermogonial stage of Gymnosporangium asiaticum were all predominantly monokaryotic. The dikaryotic condition was observed in two cultures from the uredinial stage of P. graminis f. sp. tritici and P. recondita f. sp. tritici, in one culture from the aecial stage of Gy. asiaticum, and in germ tubes from uredospores of Puccinia spp. Measurements of the DNA content indicated monokaryotic diploid cultures and dikaryotic haploid cultures in the Puccinia species. In Gy. asiaticum, all nuclei were haploid, but the nuclei had twice as much DNA as haploid nuclei in the Puccinia spp.
Natural intersectional hybridization between North American species of Populus (Salicaceae) in sections Aigeiros and Tacamahaca. III. Paleobotany and evolution
Authors: Eckenwalder James E.
Published: November 2007

Fossilized leaves resembling those of contemporary intersectional hybrids occur together with leaves assignable to sections Tacamahaca Spach and Aigeiros Duby in Miocene and Pliocene sediments in western North America. They are not referable to any particular extant hybrid species and are assigned to the extinct Populus × parcedentata Axelrod. Together with other evidence, these ancient hybrids raise questions concerning the evolutionary role of hybridization between species of the two parent sections. Present evidence about hybridization as a bridge for intersectional gene flow is contradictory. The apparent absence of backcrossed individuals in most studied hybridizing populations is offset by morphological pecularitics shared by sympatric cottonwoods and balsam poplars that are not shared with their cladistic sister species.
Purification and characterization of an acid phosphatase from peanut (Arachis hypogaea) seed
Authors: Basha Sheikh Mehboob
Published: November 2007

An acid phosphatase (EC 3.1.3.2) from peanut (Arachis hypogaea L.) seed has been purified 433-fold by ammonium sulfate fractionation, gel filtration, and ion-exchange chromatography. The purified preparation was found to be homogeneous by electrophoresis and gel filtration. The molecular weight of the enzyme was estimated to be approximately 240 000 and it was found to be composed of six identical subunits, each with an apparent molecular weight of 42 500. Following isoelectric focusing, the isolectric point (pI) of the enzyme was found to be around pH 5.6. The apparent Km value with p-nitrophenyl phosphate as substrate was 2 ? 10−1 μM. The enzyme was inhibited by Hg2+, Fe2+, Cu2+, Zn2+, Pb2+, and F−. Higher concentrations (2–50 μM) and long incubation periods (60–90 min) with Ca2+ and Mg2+ ions were shown to activate the enzyme. This enzyme showed no effect toward phosphorylated sugars but appear to hydrolyze ATP, ADP, AMP, and β-glycerophosphate.
A GROUP GAME OF MULTIPLE ATTRIBUTE DECISION MAKING
Authors: CHEN YUH-WEN
Published: November 2007

Multiple Attribute Decision Making (MADM) problem is a management science technique, which is popularly used to rank the priority of alternatives with respect to their competing attributes. It is popularly used in diverse fields such as engineering management, portfolio selection, transportation planning, and performance evaluation. Weights form the core of MADM: it is obvious that different weights lead to various evaluation results and decisions. Several approaches have been developed for assessing the weights of MADM problems, e.g., the eigenvector method, ELECTRE, and TOPSIS. However, an assessment approach of weights in MADM, which meets both the need of simplicity interface for practitioners and concrete theory for scholars is not easy, and balancing these two aspects is a challenging and tough task. Since the pay-off matrix in game theory could be regarded as a simple interface for data input/output, and very few scholars had ever explored the two-person zero-sum game on MADM problems. In this paper, the weights of a MADM problem are obtained by formulating it as a two-person zero-sum game with multiple decision makers. The group equilibrium solution, i.e., consensus of weights and the resolution steps for such a group MADM game has also been originally developed and validated in this study. Finally, an actual case of selecting the appropriate portfolio decision for a paper company is illustrated.
NOTES ON NONCOMMUTATIVE SUPERSYMMETRIC GAUGE THEORY ON THE FUZZY SUPERSPHERE
Authors: YDRI BADIS
Published: November 2007

In this paper we review Klimčík's construction of noncommutative gauge theory on the fuzzy supersphere. This theory has an exact SUSY gauge symmetry with a finite number of degrees of freedom and thus in principle it is amenable to the methods of matrix models and Monte Carlo numerical simulations. We also write down in this paper a novel fuzzy supersymmetric scalar action on the fuzzy supersphere.
Grenville Arthur James Cole (1859–1924): the cycling geologist
Authors: Jackson P. N. Wyse
Published: November 2007

Grenville Arthur James Cole (1859–1924), Professor of Geology at the Royal College of Science for Ireland, was an avid cyclist and shared this passion with his wife Blanche. Born in London, Cole studied at the Royal School of Mines and lectured for a number of years at Bedford College for Ladies. Largely concurrent with his professorship he served as Director of the Geological Survey of Ireland at a time when it was in moderate decline.

He undertook many cycling tours around continental Europe and Ireland. These trips were recounted in two early travel books.
The Gypsy Road: a Journey from Krakow to Coblentz
, published in 1894, provides a delightful account of a tour undertaken by him on a tricycle and his companion on a penny farthing, across what is now Poland, the Czech Republic, and eastern Germany. In a later slim volume entitled
As We Ride
, co-authored with his wife, a number of expeditions to France and the Balkans are eloquently described. Between 1902 and 1908 he organized a week-long geological excursion to various parts of Ireland for his students, and transport was by train and bicycle.

His cycling trips provided him with the opportunity to collect research materials, make geological observations, and to photograph features of interest. Subsequently much of this material was used in his publications and in teaching. Cole's main academic studies were in igneous and metamorphic petrology. He valued and promoted fieldwork as an essential component of geological training. He was heavily involved with professional and amateur scientific societies, and was a prolific author of both academic and popular geological papers and books.