bluuebunny/crossref_metadata_2025 huggingface dataset:
Positive selection optimizes the number and function of MHCII-restricted CD4+T cell clones in the naive polyclonal repertoire
Authors: Chu H. Hamlet , Moon James J. , Takada Kensuke , Pepper Marion , Molitor Jerry A. , Schacker Timothy W. , Hogquist Kristin A. , Jameson Stephen C. , Jenkins Marc K.
Published: June 2009

T cell receptors (TCRs) on T lymphocytes in an individual bind foreign peptides bound to major histocompatibility complex (MHC) molecules expressed in that individual (designated MHCA). Results from radiation bone marrow chimeras and TCR transgenic mice indicate that this complex form of antigen recognition is the result of positive selection of clones with low affinity for self peptide:MHCAcomplexes during development. Here we used a sensitive peptide:MHC tetramer enrichment method to quantify the role of positive selection in the generation of the preimmune polyclonal T cell repertoire in normal individuals. We made the surprising observation that mouse and human naive T cells capable of binding to foreign peptide:MHCAwere present at the same frequency in hosts that expressed MHCAor a different MHC isoform (MHCB). However, most of the clones in MHCBhosts also recognized self peptide:MHCAcomplexes. When these “alloreactive” T cells were removed from the MHCBrepertoire via negative selection in an MHCAhost, the number of foreign peptide:MHCA-binding T cells was reduced to one fifth and many of the remaining cells did not respond to the peptide. Therefore, although positive selection on MHCAwas not required to produce foreign peptide:MHCA-binding clones, it had a large effect on selecting responsive clones.
Structure of a serine protease poised to resynthesize a peptide bond
Authors: Zakharova Elena , Horvath Martin P. , Goldenberg David P.
Published: June 2009

The serine proteases are among the most thoroughly studied enzymes, and numerous crystal structures representing the enzyme–substrate complex and intermediates in the hydrolysis reactions have been reported. Some aspects of the catalytic mechanism remain controversial, however, especially the role of conformational changes in the reaction. We describe here a high-resolution (1.46 Å) crystal structure of a complex formed between a cleaved form of bovine pancreatic trypsin inhibitor (BPTI) and a catalytically inactive trypsin variant with the BPTI cleavage site ideally positioned in the active site for resynthesis of the peptide bond. This structure defines the positions of the newly generated amino and carboxyl groups following the 2 steps in the hydrolytic reaction. Comparison of this structure with those representing other intermediates in the reaction demonstrates that the residues of the catalytic triad are positioned to promote each step of both the forward and reverse reaction with remarkably little motion and with conservation of hydrogen-bonding interactions. The results also provide insights into the mechanism by which inhibitors like BPTI normally resist hydrolysis when bound to their target proteases.
Computing generalized Langevin equations and generalized Fokker–Planck equations
Authors: Darve Eric , Solomon Jose , Kia Amirali
Published: June 2009

The Mori–Zwanzig formalism is an effective tool to derive differential equations describing the evolution of a small number of resolved variables. In this paper we present its application to the derivation of generalized Langevin equations and generalized non-Markovian Fokker–Planck equations. We show how long time scales rates and metastable basins can be extracted from these equations. Numerical algorithms are proposed to discretize these equations. An important aspect is the numerical solution of the orthogonal dynamics equation which is a partial differential equation in a high dimensional space. We propose efficient numerical methods to solve this orthogonal dynamics equation. In addition, we present a projection formalism of the Mori–Zwanzig type that is applicable to discrete maps. Numerical applications are presented from the field of Hamiltonian systems.
Traceless protein splicing utilizing evolved split inteins
Authors: Lockless Steve W. , Muir Tom W.
Published: June 2009

Split inteins are parasitic genetic elements frequently found inserted into reading frames of essential proteins. Their association and excision restore host protein function through a protein self-splicing reaction. They have gained an increasingly important role in the chemical modification of proteins to create cyclical, segmentally labeled, and fluorescently tagged proteins. Ideally, inteins would seamlessly splice polypeptides together with no remnant sequences and at high efficiency. Here, we describe experiments that identify the branched intermediate, a transient step in the overall splicing reaction, as a key determinant of the splicing efficiency at different splice-site junctions. To alter intein specificity, we developed a cell-based selection scheme to evolve split inteins that splice with high efficiency at different splice junctions and at higher temperatures. Mutations within these evolved inteins occur at sites distant from the active site. We present a hypothesis that a network of conserved coevolving amino acids in inteins mediates these long-range effects.
Molecular mechanism of membrane constriction and tubulation mediated by the F-BAR protein Pacsin/Syndapin
Authors: Wang Qi , Navarro Marcos V. A. S. , Peng Gary , Molinelli Evan , Lin Goh Shih , Judson Bret L. , Rajashankar Kanagalaghatta R. , Sondermann Holger
Published: June 2009

Peripheral membrane proteins of the Bin/amphiphysin/Rvs (BAR) and Fer-CIP4 homology-BAR (F-BAR) family participate in cellular membrane trafficking and have been shown to generate membrane tubules. The degree of membrane bending appears to be encoded in the structure and immanent curvature of the particular protein domains, with BAR and F-BAR domains inducing high- and low-curvature tubules, respectively. In addition, oligomerization and the formation of ordered arrays influences tubule stabilization. Here, the F-BAR domain-containing protein Pacsin was found to possess a unique activity, creating small tubules and tubule constrictions, in addition to the wide tubules characteristic for this subfamily. Based on crystal structures of the F-BAR domain of Pacsin and mutagenesis studies, vesiculation could be linked to the presence of unique structural features distinguishing it from other F-BAR proteins. Tubulation was suppressed in the context of the full-length protein, suggesting that Pacsin is autoinhibited in solution. The regulated deformation of membranes and promotion of tubule constrictions by Pacsin suggests a more versatile function of these proteins in vesiculation and endocytosis beyond their role as scaffold proteins.
Phase matching of high harmonic generation in the soft and hard X-ray regions of the spectrum
Authors: Popmintchev Tenio , Chen Ming-Chang , Bahabad Alon , Gerrity Michael , Sidorenko Pavel , Cohen Oren , Christov Ivan P. , Murnane Margaret M. , Kapteyn Henry C.
Published: June 2009

We show how bright, tabletop, fully coherent hard X-ray beams can be generated through nonlinear upconversion of femtosecond laser light. By driving the high-order harmonic generation process using longer-wavelength midinfrared light, we show that, in theory, fully phase-matched frequency upconversion can extend into the hard X-ray region of the spectrum. We verify our scaling predictions experimentally by demonstrating phase matching in the soft X-ray region of the spectrum around 330 eV, using ultrafast driving laser pulses at 1.3-μm wavelength, in an extended, high-pressure, weakly ionized gas medium. We also show through calculations that scaling of the overall conversion efficiency is surprisingly favorable as the wavelength of the driving laser is increased, making tabletop, fully coherent, multi-keV X-ray sources feasible. The rapidly decreasing microscopic single-atom yield, predicted for harmonics driven by longer-wavelength lasers, is compensated macroscopically by an increased optimal pressure for phase matching and a rapidly decreasing reabsorption of the generated X-rays.
The structure of alanyl-tRNA synthetase with editing domain
Authors: Sokabe Masaaki , Ose Toyoyuki , Nakamura Akiyoshi , Tokunaga Keita , Nureki Osamu , Yao Min , Tanaka Isao
Published: June 2009

Alanyl-tRNA synthetase (AlaRS) catalyzes synthesis of Ala-tRNA
Ala
and hydrolysis of mis-acylated Ser- and Gly-tRNA
Ala
at 2 different catalytic sites. Here, we describe the monomer structures of C-terminal truncated archaeal AlaRS, with both activation and editing domains in the apo form, in complex with an Ala-AMP analog, and in a high-resolution lysine-methylated form. The structures show docking of the editing domain to the activation domain opposite from the predicted tRNA-binding surface. Thus, the editing site is positioned >35 Å from the activation site, prompting us to model 2 different tRNA complexes: one binding tRNA at the activation site, and the other binding tRNA at the editing site. Interestingly, a gel-shift assay also implies the presence of 2 types of tRNA complex with different mobility. These results suggest that tRNA translocation via a canonical CCA flipping is unlikely to occur in AlaRS. The structure also demonstrated the binding of zinc in the editing site, in which the specific coordination of zinc would be facilitated by a conserved GGQ motif, implying that the editing mechanism may not be the same as in ThrRS. As Asn-194 in eubacterial AlaRS important for Ser misactivation is replaced by Thr-213 in archaeal AlaRS, a different Ser accommodation mechanism is proposed.
A model of the cell-autonomous mammalian circadian clock
Authors: Mirsky Henry P. , Liu Andrew C. , Welsh David K. , Kay Steve A. , Doyle Francis J.
Published: June 2009

Circadian timekeeping by intracellular molecular clocks is evident widely in prokaryotes and eukaryotes. The clockworks are driven by autoregulatory feedback loops that lead to oscillating levels of components whose maxima are in fixed phase relationships with one another. These phase relationships are the key metric characterizing the operation of the clocks. In this study, we built a mathematical model from the regulatory structure of the intracellular circadian clock in mice and identified its parameters using an iterative evolutionary strategy, with minimum cost achieved through conformance to phase separations seen in cell-autonomous oscillators. The model was evaluated against the experimentally observed cell-autonomous circadian phenotypes of gene knockouts, particularly retention of rhythmicity and changes in expression level of molecular clock components. These tests reveal excellent de novo predictive ability of the model. Furthermore, sensitivity analysis shows that these knockout phenotypes are robust to parameter perturbation.
Tyrosine kinase nerve growth factor receptor switches from prosurvival to proapoptotic activity via Abeta-mediated phosphorylation
Authors: Matrone C. , Marolda R. , Ciafrè S. , Ciotti M. T. , Mercanti D. , Calissano P.
Published: June 2009

The present study shows that increased Abeta production in hippocampal neurons, due to a failure of NGF signal, induces an unexpected phosphorylation of tyrosine kinase receptor A (TrkA), followed by activation of the phospholipase C γ (PLCγ) pathway and neuronal death. Such phosphorylation seems causally connected with 2 kinases known be involved in amyloidogenesis, Src and CDK5, and associated with α and γ secretase–mediated p75 processing. Pharmacologic inhibition of TrkA phosphorylation and partial silencing of TrkA and/or p75 receptors prevent PLCγ activation and protect neurons from death. Concomitantly with these events, TrkA, p75, Abeta peptides, and PS1 protein coimmunoprecipitate, suggesting their direct interplay in the subsequent onset of apoptotic death. Together, these findings depict a cellular mechanism whereby the same cellular transducing system may invert its intracellular message from trophic and antiapoptotic to a death signaling, which could also have relevance in the onset of Alzheimer's disease.
Tentacled snakes turn C-starts to their advantage and predict future prey behavior
Authors: Catania Kenneth C.
Published: June 2009

Fish are elusive prey with a short-latency escape behavior—the C-start—initiated to either the left or right by a “race” between 2 giant Mauthner neurons in the fish brainstem. Water disturbances usually excite the ipsilateral neuron, which massively excites contralateral motor neurons, resulting in a rapid turn away from striking predators. Here, it is reported that tentacled snakes (
Erpeton tentaculatus
) exploit this normally adaptive circuitry by feinting with their body, triggering the Mauthner cell that is furthest from their head milliseconds before a ballistic strike is initiated. As a result, fish that were oriented parallel to the long axis of the snake's head most often turned toward the approaching jaws, sometimes swimming directly into the snake's mouth. When strikes were instead directed at fish oriented at a right angle to the snake's head, snakes anticipated future fish behavior by striking to where fish would later be if they escaped from the snake's body feint, which fish usually did. The results provide an example of a rare predator taking advantage of a prey's normally adaptive escape circuitry and suggest that the snake's sensory-motor system is adapted to predict future behavior.
Derivation of induced pluripotent stem cells from pig somatic cells
Authors: Ezashi Toshihiko , Telugu Bhanu Prakash V. L. , Alexenko Andrei P. , Sachdev Shrikesh , Sinha Sunilima , Roberts R. Michael
Published: June 2009

For reasons that are unclear the production of embryonic stem cells from ungulates has proved elusive. Here, we describe induced pluripotent stem cells (iPSC) derived from porcine fetal fibroblasts by lentiviral transduction of 4 human (h) genes, hOCT4, hSOX2, hKLF4, and hc-MYC, the combination commonly used to create iPSC in mouse and human. Cells were cultured on irradiated mouse embryonic fibroblasts (MEF) and in medium supplemented with knockout serum replacement and FGF2. Compact colonies of alkaline phosphatase-positive cells emerged after ≈22 days, providing an overall reprogramming efficiency of ≈0.1%. The cells expressed porcine OCT4, NANOG, and SOX2 and had high telomerase activity, but also continued to express the 4 human transgenes. Unlike human ESC, the porcine iPSC (piPSC) were positive for SSEA-1, but negative for SSEA-3 and -4. Transcriptional profiling on Affymetrix (porcine) microarrays and real time RT-PCR supported the conclusion that reprogramming to pluripotency was complete. One cell line, ID6, had a normal karyotype, a cell doubling time of ≈17 h, and has been maintained through >220 doublings. The ID6 line formed embryoid bodies, expressing genes representing all 3 germ layers when cultured under differentiating conditions, and teratomas containing tissues of ectoderm, mesoderm, and endoderm origin in nude mice. We conclude that porcine somatic cells can be reprogrammed to form piPSC. Such cell lines derived from individual animals could provide a means for testing the safety and efficacy of stem cell-derived tissue grafts when returned to the same pigs at a later age.
Typological diversity in New Englishes
Authors: Sharma Devyani
Published: June 2009

Recent research has aimed to integrate the investigation of vernacular universals in native English dialects with variation in postcolonial varieties of English and cross-linguistic typology (Chambers 2004; Kortmann 2004). This article assumes that any search for universals in bilingual varieties must include an assessment of the grammatical conditioning of features and a comparison with the relevant substrates. Comparing Indian English and Singapore English, I examine three proposed candidates for English universals (Kortmann and Szmrecsanyi 2004), all of which show some presence in the two varieties — past tense omission, over-extension of the progressive, and copula omission. Past tense omission is found to be genuinely similar in the two varieties and accounted for by typological parallels in the substrates, whereas progressive morphology use and copula omission are found to be divergent in the two varieties and accounted for by typological differences in the substrates. All three variable systems are explicable as substrate-superstrate interactions, tempering claims of universality in both distribution and explanation.
Depicting gestures
Authors: Streeck Jürgen
Published: June 2009

In “Depicting by gestures” (Gesture, 8 (3)), I have explored the methods by which hand gestures depict the world. Here I explore how gestures themselves are depicted. Many paintings and sculptures show human bodies in motion or showcase traces of body movements, including gestures of the hand. The issue is how the artists succeeded in depicting or insinuating movement in media that are inherently still, and how such arrested gestures function in pictures of social life so that these are perceived as “legible interactions” (Gombrich). By scrutinizing the changing logic of representation of embodied communication in the visual arts, gesture researchers can gain insights into the relationships between movement, form, meaning, and context, and recontextualize their own analytic methodologies within the broader discourse in the humanities on human behavior and its interpretation (Streeck, 2003).  In the following, I examine a number of characteristic attempts, made during different periods of Western art-history, to solve this problem: in Egyptian, Greek, and Hellenistic art; in some medieval illuminations; in the early and late Renaissance; and in the 20th century styles of “écriture automatique” and Abstract Expressionism. Each of the strategies involved is predicated on three types of analysis: of ways in which body motion communicates meaning, of visual perception, and of the nature of pictorial representation.
Comparative analysis of children’s narratives at different ages
Authors: Colletta Jean-Marc
Published: June 2009

This study addresses two questions. The first question is about how children integrate linguistic, prosodic and kinesic resources into organised discourse behaviour such as oral narratives. Three event reports produced spontaneously by 9- to 11-year-old French children during interviews with an adult were extracted from a video corpus. A detailed analysis of these on four dimensions (discourse construction, voice and prosody, co-speech gestures and facial expressions, gaze direction) reveals a remarkable ability in children of this age to use prosodic and kinesic resources to frame and structure their narrative, to dramatise and enliven the recounted events, and to comment on them or on the narration. The second question stresses the developmental aspect of multimodal narrative behaviour. 32 event reports extracted from the same corpus and produced by French children aged from 6 to 11 years were analysed in a similar way and rated by two independent coders. This second study leads us to distinguish between three levels of narrative performance which appear to coincide by age. The multimodal study of oral narratives thus shows how and when children gradually become genuine narrators.
L’enseignement de la terminologie juridique française à un public slovène
Authors: Vaupot Sonia
Published: June 2009

Terminology is part of the program of university degree in Slovenia. The purpose of the paper is to study some parameters in terminology teaching within the framework of French legal terminology offered by the Department of Translation at the Faculty of Arts in Ljubljana. The program takes into account multiple aspects, which represent an important issue in translation. Mastering legal terminology is often a source of difficulties, since law, as any specialized discipline, uses its own vocabulary. The present article suggests an analysis of some specificities of legal terminology in particular for the teaching of the French legal system in Slovenian legal education.
First trimester PTX3 levels in women who subsequently develop preeclampsia and fetal growth restriction
Authors: CETIN IRENE , COZZI VERONICA , PAPAGEORGHIOU ARIS T , MAINA VIRGINIA , MONTANELLI ALESSANDRO , GARLANDA CECILIA , THILAGANATHAN BASKY
Published: June 2009

Pentraxin 3 (PTX3) and C‐reactive protein (CRP) levels were measured in the first trimester of pregnancy in women who subsequently developed preeclampsia (PE, n = 16) and fetal growth restriction (FGR, n = 12) requiring iatrogenic delivery before 37 weeks, and those who had uncomplicated pregnancies delivering at term (n = 60). Mean PTX3 levels were significantly higher in women who subsequently developed PE (7.31 ng/ml, SD = 4.12) when compared to those with normal pregnancy outcome (4.92 ng/ml, SD = 1.94, p = 0.0046). There were no significant differences between PTX3 levels in women with FGR (4.82 ng/ml, SD = 2.35) compared to normal pregnancy outcome (p = 0.88). The median CRP levels did not vary significantly between the three groups (p = 0.26). PTX3 levels in women who subsequently develop PE are already elevated in the first trimester, but not in those that develop FGR. This supports the hypothesis of an excessive maternal inflammatory response to pregnancy in the etiology of PE.
Social orientations and adolescent health behaviours in Hungary
Authors: Piko Bettina F. , Skultéti Dóra , Luszczynska Aleksandra , Gibbons Frederick X.
Published: June 2009

Adolescent health behaviours are influenced by a variety of social factors, including social orientations, such as social comparison or competitiveness. The main goal of the present study was to investigate the role that these social orientations might play in health behaviours (both health‐impairing and health‐promoting). Data were collected from high school students (N = 548; ages 14–20 years; 39.9% males) in two counties of the Southern Plain Region of Hungary. The self‐administered questionnaires contained items on sociodemographics, such as age, sex, parental schooling, and socioeconomic status (SES) self‐assessment; school achievement, health behaviours, competitiveness and social comparison. Multiple regression analyses suggest that those who scored higher on competitiveness engaged in more substance use, a pattern that was not present for health‐promoting behaviours. Social comparison, however, was associated with lower levels of substance use. In addition, in relation to health‐impairing behaviours, both competitiveness and social comparison interacted with sex; both social orientation variables proved to be more important for boys. Social comparison also contributed to health‐promoting behaviours among boys. Findings support the idea that the role of social orientations, such as competitiveness and social comparison, can be quite different depending on sex and the nature of the health behaviour. While competitiveness may act as a risk factor for substance use among boys, social comparison may act as a protection. It appears that social orientations play less of a role in girls' health‐related behaviours. More focus is needed on gender differences in influences on adolescents' health‐related behaviours.
Reappraising Communism and Nationalism
Authors: Mevius Martin
Published: June 2009

There are two popular myths concerning the relationship between communism and nationalism. The first is that nationalism and communism are wholly antagonistic and mutually exclusive. The second is the assertion that in communist Eastern Europe nationalism was oppressed before 1989, to emerge triumphant after the Berlin Wall came down. Reality was different. Certainly from 1945 onwards, communist parties presented themselves as heirs to national traditions and guardians of national interests. The communist states of Central and Eastern Europe constructed “socialist patriotism,” a form of loyalty to their own state of workers and peasants. Up to 1989, communists in Eastern Europe sang the national anthem, and waved the national flag next to the red banner. The use of national images was not the exception, but the rule. From Cuba to Korea, all communist parties attempted to gain national legitimacy. This was not incidental or a deviation from Marxist orthodoxy, but ingrained in the theory and practice of the communist movement since its inception.
Nation and Empire: Dilemmas of Legitimacy during Stalinism in Poland (1941–1956)
Authors: Behrends Jan C.
Published: June 2009

Introduction

In 1944 Poland was re-established for the second time in the twentieth century. Between the Lublin manifesto of 22 July 1944 and the Potsdam conference of summer 1945 a communist-dominated regime had formed, which was had little in common with the Second Republic that had been founded between the declaration of independence on 9 November 1918 and the peace of Riga with Bolshevik Russia signed in March 1921. Post-war Poland was significantly smaller, geographically further to the west, and ethnically more homogeneous. The Holocaust had destroyed Europe's most sizeable Jewish population, the loss of thekresy(eastern borderlands) to the USSR had reduced the size of eastern-Slavic minorities and the expulsion of the Germans from East Prussia, Pomerania and Silesia further helped to create an ethnically homogeneous country. For the first time in her history, Poland had the structure of a nation-state. Through the destruction and catastrophe of Nazi occupation and genocide the goal of firebrand Polish nationalists such as Roman Dmowski had been achieved: a Poland inhabited by ethnic Poles. Still, the new Poland was less independent than its predecessor; from 1944 onwards it was part of the emerging post-war Soviet Empire. Polish sovereignty had fallen victim to Stalin's “revolutionary-imperial paradigm.” Expansion of Moscow's power was as much a priority of the Soviet leadership as the export of Bolshevik revolution.
Influence of Taoism on teachers’ definitions of guidance and discipline in Hong Kong secondary schools
Authors: Hue Ming Tak
Published: June 2009

This article examines how Hong Kong secondary school teachers define caring and the strategies they adopt for behaviour management. The influence of Taoism, emerging as a theme from the data, was prominent, as its principles were incorporated into the teachers’ knowledge of caring. The findings illuminate the influence of Taoism in local schools. Implications for the promotion of culturally responsive programmes of caring are drawn.
Hepatic falciform ligament artery in patients with chronic liver diseases: detection on computed tomography hepatic arteriography
Authors: Tajima T. , Yoshimitsu K. , Irie H. , Nishie A. , Hirakawa M. , Ishigami K. , Ushijima Y. , Okamoto D. , Honda H.
Published: June 2009

Background: The detection rate of hepatic falciform ligament artery (FLA) has been reported as ranging from 2–25%. The rate of FLA on laparotomy, however, is reported to be higher, at 68%.

Purpose: To compare the detection rate of FLA on computed tomography hepatic arteriography (CTHA) with that on angiography and dynamic CT, and to clarify the clinical significance of FLA in patients with chronic liver disease.

Material and Methods: 126 consecutive patients underwent CTHA angiography and dynamic CT to evaluate suspected liver tumors. Liver function was classified as follows: normal, n=5; Child-Pugh class A, n=94; B, n=21; and C, n=6. All CT images were obtained using multidetector (MDCT) scanners (Aquilion; Toshiba, Tokyo, Japan). For CTHA, CT images were obtained during contrast material injection through the left hepatic, proper, or common hepatic artery. On CT, FLAs were retrospectively identified within the hepatic falciform ligament and the hepatic round ligament by the paging method on a workstation (TWS-5000; Toshiba, Tokyo, Japan). The detection rates were compared among the three modalities (hepatic arterial phase of dynamic CT, CTHA, and angiography). The calibers of FLA were also correlated with the hepatic function of the patients.

Results: The detection rates of FLA by angiography, dynamic CT, and CTHA were 37% (47/126), 10% (13/126), and 77% (97/126), respectively. The calibers of FLA increased as the hepatic function deteriorated ( P=0.001).

Conclusion: The detection rates of FLA with CTHA are far higher than those with angiography and dynamic CT. Careful interpretation with recognition of FLA on CTHA images is important, as inadvertent embolization or chemotherapeutic infusion of the FLA may result in supraumbilical skin rash.
Synthesis, spectral, and thermal studies of organotin(IV) complexes with 4-bromo-2-{[(2-hydroxyphenyl)imino]methyl}phenol
Authors: Sedaghat Tahereh , Shafahi Fatemeh
Published: June 2009

The organotin(IV) chlorides R2SnCl2 (R = Ph and Me) react with a Schiff base (H2L), obtained from the condensation of 5-bromo-2-hydroxybenzaldehyde and ortho-aminophenol. Spectral properties of new complexes were investigated by infrared (IR), 1H NMR, and 119Sn NMR spectroscopy and show that in the two complexes H2L acts as a tridentate dianionic ligand and co-ordinates to the metal via two phenolic oxygens and one imine nitrogen. The 119Sn NMR data are consistent with the presence of five-coordinate tin(IV) in solution. Thermal decomposition of the complexes has been studied by thermogravimetry and the activation energy has been determined by the Horowitz–Metzger method.
Synthesis, physico-chemical investigations, and in vitro microbial, studies of VO(IV) complexes with novel ONON donor Schiff bases
Authors: Bagihalli Gangadhar B. , Patil Sangamesh A.
Published: June 2009

A series of metal complexes of VO(IV) have been synthesized with newly derived biologically active ligands. These ligands were synthesized by the condensation of 3-substituted-4-amino-5-hydrazino-1,2,4-triazole and 8-formyl-7-hydroxy-4-methylcoumarin. The probable structure of the complexes has been proposed on the basis of elemental analyses and spectral (IR, UV–vis, magnetic, ESR, fast atomic bombardment (FAB)-mass, and thermal studies) data. Electrochemical study of the complexes is also reported. All these complexes are non-electrolytes in dimethyl formamide (DMF) and dimethyl sulfoxide (DMSO). All the ligands and their VO(IV) complexes have also been screened for their antibacterial (Escherichia coli, Staphylococcus aureus, Staphylococcus pyogenes, and Pseudomonas aeruginosa) and antifungal activities (Aspergillus niger, Aspergillus flavus, and Cladosporium) using the MIC method.
Dielectric relaxation studies of aqueous sodium dodecyl sulfate with some amines as co-solvents by time domain reflectometry technique
Authors: Kalaivani T. , Undre Prabhakar , Sabesan R. , Krishnan S.
Published: June 2009

Dielectric relaxation studies of aqueous sodium dodecyl sulfate with 1-butanol, benzyl alcohol, aniline, and tributylamine have been carried out for different concentrations at 303 K. Dielectric relaxation spectroscopy (DRS) is a versatile tool to monitor the dynamic process of micellar systems. The time domain dielectric data were obtained in the reflection mode in the frequency range of 10 MHz to 20 GHz using a HP54750A sampling oscilloscope and HP54754A TDR plug-in-module. The sample was held at 303 K in a standard military application (SMA) cell with an effective pin length of 1.35 mm. We have determined the relaxation time (τ) using the Cole–Cole method. The relative viscosity ηr of the micellar solutions was also determined. We find that ηr increases with increasing concentrations of sodium dodecyl sulfate (SDS) and there is a non-linear increase in ηr beyond 80 mM SDS. The observed relaxation time is explained by considering the superposition of two relaxation times. One is due to the rotation of the hydrated water molecule around the micelle ions and the other due to the hydrated water squeezed in the hydrophobic interior of the micelle. Our results are explained on this basis. The results on adding amines are similar to that of adding alcohols but the interaction of the amines with the head group of the micelle is not as effective as hydroxyl group of alcohols.
Effect of substitution on the structures, properties, and aromaticity of 1-H-boratabenzene anion
Authors: Pasdar Hoda , Ghiasi Reza
Published: June 2009

Molecular geometries of 1-H-boratabenzene anion and mono-substituted derivatives were optimized at the B3LYP/6-31+G** level of theory. Energetic results showed that meta isomers have less stability in meta director groups. Basic measurement of aromatic character derived from structure, and nucleus-independent chemical shifts (NICS) has been considered. NICS values show that meta isomers are the most aromatic for meta directors.
ON ‘AN INTROSPECTIVE JOURNEY’
Authors: Bagnoli Anna
Published: June 2009

To what extent can the experience of travel become also a journey of self-discovery leading to a reconstruction of identities? Taking ‘a year out’, inter-railing, going abroad on a language study or an au pair stay: these are some of the most common forms of youth travel in contemporary Europe. As almost ritual ways of moving, they may be likened to initiation journeys. This article explores the significance of travel in young people's lives, and in the process of identity construction. These issues are explored in the travel narratives of a group of young people who took part in an autobiographical and mixed method project on identities which was conducted in England and Italy. The meaning of travel in these young people's lives is appreciated through their own words and written diaries. Young people's agency and role in constructing their travel experiences is analysed, as well as the extent to which fate, in the shape of societal expectations and norms, as well as parental intervention, may actually predefine some forms of travel as ‘institutional’ rites of passage. Travels may offer a scenario for an individualised construction of self, which may also involve the co-participation of significant others. The experiences of young women backpackers in this study point out how travelling can still be a way of defining alternative gender identities.
Speech segmentation is facilitated by visual cues
Authors: Cunillera Toni , Càmara Estela , Laine Matti , Rodríguez-Fornells Antoni
Published: June 2009

Evidence from infant studies indicates that language learning can be facilitated by multimodal cues. We extended this observation to adult language learning by studying the effects of simultaneous visual cues (nonassociated object images) on speech segmentation performance. Our results indicate that segmentation of new words from a continuous speech stream is facilitated by simultaneous visual input that it is presented at or near syllables that exhibit the low transitional probability indicative of word boundaries. This indicates that temporal audio-visual contiguity helps in directing attention to word boundaries at the earliest stages of language learning. Off-boundary or arrhythmic picture sequences did not affect segmentation performance, suggesting that the language learning system can effectively disregard noninformative visual information. Detection of temporal contiguity between multimodal stimuli may be useful in both infants and second-language learners not only for facilitating speech segmentation, but also for detecting word–object relationships in natural environments.
Movements or targets: What makes an action in action–effect learning?
Authors: Hoffmann Joachim , Lenhard Alexandra , Sebald Albrecht , Pfister Roland
Published: June 2009

According to ideomotor theory, actions become linked to the sensory feedback they contingently produce, so that anticipating the feedback automatically evokes the action it typically results from. Numerous recent studies have provided evidence in favour of such action–effect learning but left an important issue unresolved. It remains unspecified to what extent action–effect learning is based on associating effect-representations to representations of the performed movements or to representations of the targets at which the behaviour aimed at. Two experiments were designed to clarify this issue. In an acquisition phase, participants learned the contingency between key presses and effect tones. In a following test phase, key–effect and movement–effect relations were orthogonally assessed by changing the hand–key mapping for one half of the participants. Experiment 1 showed precedence for target–effect over movement–effect learning in a forced-choice RT task. In Experiment 2, target–effect learning was also shown to influence the outcome of response selection in a free-choice task. Altogether, the data indicate that both movement–effect and target–effect associations contribute to the formation of action–effect linkages—provided that movements and targets are likewise contingently related to the effects.
The role of timing deviations and target position uncertainty on temporal attending in a serial auditory pitch discrimination task
Authors: Barnes Ralph , Johnston Heather
Published: June 2009

Listeners were presented with sequences of tones that ascended in semitone intervals. On each trial a single target tone in the sequence was displaced in pitch, and listeners were required to indicate whether the target tone was higher or lower than its normal pitch. Task constraints, specifically target serial position uncertainty and the probabilistic relationship between time deviations and target tones, were varied in order to determine the impact of task constraints on temporal attending strategy. When listeners had no advance knowledge of the serial position of the target, and early and late targets provided information regarding target serial position, performance was better for early and late target trials than for on-time target trials (Experiment 1). When listeners had no advance knowledge of the serial position of the target, and early and late temporal deviations provided no information regarding target serial position, performance for late target trials was superior to that for early and on-time target trials (Experiment 2). Finally, when target serial position uncertainty was eliminated, performance was equivalent across all three levels of target timing (early, on time, late). The results indicate that performance profiles based on stimulus timing properties are affected by various task constraints as well as by stimulus properties.
Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly
Authors: Dutilh Bas E. , Huynen Martijn A. , Strous Marc
Published: June 2009

Motivation: Most microbial species can not be cultured in the laboratory. Metagenomic sequencing may still yield a complete genome if the sequenced community is enriched and the sequencing coverage is high. However, the complexity in a natural population may cause the enrichment culture to contain multiple related strains. This diversity can confound existing strict assembly programs and lead to a fragmented assembly, which is unnecessary if we have a related reference genome available that can function as a scaffold.

Results: Here, we map short metagenomic sequencing reads from a population of strains to a related reference genome, and compose a genome that captures the consensus of the population's sequences. We show that by iteration of the mapping and assembly procedure, the coverage increases while the similarity with the reference genome decreases. This indicates that the assembly becomes less dependent on the reference genome and approaches the consensus genome of the multi-strain population.

Contact:  dutilh@cmbi.ru.nl

Supplementary Information:  Supplementary data are available at Bioinformatics online.
ISOLATE: a computational strategy for identifying the primary origin of cancers using high-throughput sequencing
Authors: Quon Gerald , Morris Quaid
Published: June 2009

Motivation: One of the most deadly cancer diagnoses is the carcinoma of unknown primary origin. Without the knowledge of the site of origin, treatment regimens are limited in their specificity and result in high mortality rates. Though supervised classification methods have been developed to predict the site of origin based on gene expression data, they require large numbers of previously classified tumors for training, in part because they do not account for sample heterogeneity, which limits their application to well-studied cancers.

Results: We present ISOLATE, a new statistical method that simultaneously predicts the primary site of origin of cancers and addresses sample heterogeneity, while taking advantage of new high-throughput sequencing technology that promises to bring higher accuracy and reproducibility to gene expression profiling experiments. ISOLATE makes predictions de novo, without having seen any training expression profiles of cancers with identified origin. Compared with previous methods, ISOLATE is able to predict the primary site of origin, de-convolve and remove the effect of sample heterogeneity and identify differentially expressed genes with higher accuracy, across both synthetic and clinical datasets. Methods such as ISOLATE are invaluable tools for clinicians faced with carcinomas of unknown primary origin.

Availability: ISOLATE is available for download at: http://morrislab.med.utoronto.ca/software

Contact:  gerald.quon@utoronto.ca; quaid.morris@utoronto.ca

Supplementary information:  Supplementary data are available at Bioinformatics online.
FancyGene: dynamic visualization of gene structures and protein domain architectures on genomic loci
Authors: Rambaldi Davide , Ciccarelli Francesca D.
Published: June 2009

Summary: FancyGene is a fast and user-friendly web-based tool for producing images of one or more genes directly on the corresponding genomic locus. Starting from a variety of input formats, FancyGene rebuilds the basic components of a gene (UTRs, intron, exons). Once the initial representation is obtained, the user can superimpose additional features—such as protein domains and/or a variety of biological markers—in specific positions. FancyGene is extremely flexible allowing the user to change the resulting image dynamically, modifying colors and shapes and adding and/or removing objects. The output images are generated either in portable network graphics (PNG) or portable document format (PDF) formats and can be used for scientific presentations as well as for publications. The PDF format preserves editing capabilities, allowing picture modification using any vector graphics editor.

Availability:  http://bio.ifom-ieo-campus.it/fancygene

Contact:  francesca.ciccarelli@ifom-ieo-campus.it

Supplementary Information: Details, examples and tutorials can be found at http://bio.ifom-ieo-campus.it/fancygene/tutorial.html and http://bio.ifom-ieo-campus.it/fancygene/help.html
Wisdom of Generations: A Pilot Study of the Values Transmitted in Ethical Wills of Nursing Home Residents and Student Volunteers
Authors: Cohen-Mansfield Jiska , Regier Natalie G. , Peyser Hedy , Stanton Joshua
Published: June 2009

Purpose: This is a pilot study that provides a description of the values older persons report in ethical wills and their reasoning for the values they chose, and compares the values in ethical wills of seniors and students. Nursing home residents rarely get the opportunity or venue to discuss these topics and the ethical will enables them to have conversations about issues they feel are important.  Design and Methods: The 22 Questions for Ethical Wills© assessment was administered to 15 residents of a large nursing home in suburban Maryland and to 11 student volunteers. Raters identified recurring themes and independently analyzed the text from the ethical wills based on the themes. Questions that prompted similar responses were combined in the analyses.  Results: The most prevalent theme among both nursing home residents and students was “interpersonal relations.” Differences between groups of respondents were especially evident for the theme of “education,” which was given by over a half of the older persons and none of the students. Greater variability was found in the responses of the older participants, as was a greater likelihood of providing detailed explanations for their relayed values.  Implications: The 22 Questions for Ethical Wills© is a useful methodology to elicit meaningful discussions of values and life lessons in persons both young and old. This process offers an intriguing comparison between the similarities and differences of life views of persons at opposite ends of the age spectrum.
Preventing overexploitation of migratory fish stocks: the efficacy of marine protected areas in a stochastic environment
Authors: West Christopher D. , Dytham Calvin , Righton David , Pitchford Jonathan W.
Published: June 2009

West, C. D., Dytham, C., Righton, D., and Pitchford, J.W. 2009. Preventing overexploitation of migratory fish stocks: the efficacy of marine protected areas in a stochastic environment. – ICES Journal of Marine Science, 66: 1919–1930. Marine protected areas (MPAs) have been widely proposed for protecting overexploited fish populations. It has been suggested that fisheries may be enhanced by spillover of individuals from MPAs into fishing grounds. However, traditional spillover studies fail to account for the seasonal migrations of many populations. Most fisheries models also fail to include the stochasticity inherent in marine environments explicitly. Here we assess MPA efficacy using a simple population model simulating the migration of fish populations between a spawning ground MPA and a fishery. Including realistic environmental stochasticity in our model allows the population to deviate from, and shift between, positive stable equilibria, something that is impossible in a deterministic analysis. This deviation may result in population collapse in cases where deterministic analysis predicts population persistence. We show that, although effective at low migration levels, the ability of MPAs to protect stocks from collapse generally decreases as migration increases. However, an MPA provides greater protection and greater expected fisheries yield than a system without an MPA, irrespective of migration level. Combining MPAs with a harvest control rule may further increase protection and yield. We therefore argue that MPAs can play a role in the protection of migratory species.
Influence of Low Molecular Weight Glutenins on Viscoelastic Properties of Intact Wheat Kernels and Their Relation to Functional Properties of Wheat Dough
Authors: Maucher Tanja , Figueroa J. D. C. , Reule W. , Peña R. J.
Published: June 2009

The mechanical and viscoelastic properties of intact wheat kernels of 36 wheat cultivars differing in low molecular weight glutenin subunit (LMW‐GS) composition (loci Glu‐A3, Glu‐B3, and Glu‐D3) were evaluated using load‐compression tests. Comparison among genotypic groups representing Glu‐3 allelic variants showed that groups representing the alleles Glu‐A3 b, c, and d; Glu‐B3 d, g, and h; and Glu‐D3 a, b, and d, had harder kernel texture, higher kernel elastic work and larger gluten strength‐related parameters than those possessing alleles Glu‐A3 e; Glu‐B3 f, i and j (translocation 1B/1R); and Glu‐D3 d. Modulus of elasticity (stress to strain ratio) showed low values (111.9–168.8 MPa) for allelic groups possessing poor elastic properties (Glu‐A3 e; Glu‐B3 f, i, and j; and Glu‐D3 d), and high values (179.8–222.6 MPa) for allelic groups possessing high kernel elastic properties (Glu‐A3 b c, and d; Glu‐B3 d, g, and h; and Glu‐D3 a, b and c). The highest values for gluten strength‐related parameters (SDS‐sedimentation, dough mixing time, and dough strength [W]) corresponded to allelic groups Glu‐A3 d; Glu‐B3 d and g; and Glu‐D3 d, while the lowest corresponded to Glu‐A3 e and Glu‐B3 j. No significant differences were observed among groups with regard to gluten extensibility parameters; however, the highest P/L value (least extensibility) corresponded to Glu‐B3 j, which indicates presence of 1B/1R translocation. Except for the Glu‐B3 j (translocation 1B/1R) allele, which presented more variation within samples, a general relationship between kernel viscoelastic properties and dough viscoelastic properties was observed; samples showing higher elastic work to plastic work ratio (E/P) tended to possess better gluten strength than cultivars with low E/P ratio.