bluuebunny/crossref_metadata_2025 huggingface dataset:
Lessons learned in the implementation of an innovative consultation and liaison service for children of cancer patients in various hospital settings
Authors: Romer Georg , Saha Rina , Haagen Miriam , Pott Martina , Baldus Christiane , Bergelt Corinna
Published: October 2006

Objective: To evaluate the process of implementing a family‐oriented consultation and liaison service in various hospital‐based settings, with special regard to problems and obstacles encountered.

Method: Qualitative content analysis using categorization and sequential, phenomenological analysis of descriptive progress notes during the implementation period. The team members of the liaison service were defined as participant observers. Interpretations of the material were derived in previously defined, sequential steps in team discussions.

Results: Despite a consistent concept behind the new service, the degree to which it was able to be integrated into different medical settings varied to a remarkable degree. Obstacles encountered were often linked to a lack of consideration being given to divergent concepts of care. It was necessary to give special attention to providing physicians with practical evidence of the value of the intervention. The new service was most readily utilized by families when physicians personally communicated the referrals as a standard procedure to their patients and when the referrals were not made too quickly after the parent's initial diagnosis.

Conclusions: Hospital‐based services for cancer patients with children under the age of 18 should carefully address patients' fears of psychiatric stigmatization. Furthermore, they should include modules for acute crisis intervention. Implications for future implementation activities in this field are discussed. Copyright © 2006 John Wiley & Sons, Ltd.
Evidence for a novel domain of bacterial outer membrane ushers
Authors: Capitani Guido , Eidam Oliv , Grütter Markus G.
Published: October 2006

Many pathogenic bacteria possess adhesive surface organelles (called pili), anchored to their outer membrane, which mediate the first step of infection by binding to host tissue. Pilus biogenesis occurs via the “chaperone–usher” pathway: the usher, a large outer membrane protein, binds complexes of a periplasmic chaperone with pilus subunits, unloads the subunits from the chaperone, and assembles them into the pilus, which is extruded into the extracellular space. Ushers comprise an N‐terminal periplasmic domain, a large transmembrane β‐barrel central domain, and a C‐terminal periplasmic domain. Since structural data are available only for the N‐terminal domain, we performed an in‐depth bioinformatic analysis of bacterial ushers. Our analysis led us to the conclusion that the transmembrane β‐barrel region of ushers contains a so far unrecognized soluble domain, the “middle domain”, which possesses a β‐sandwich fold. Two other bacterial β‐sandwich domains, the TT0351 protein from Thermus thermophilus and the carbohydrate binding module CBM36 from Paenibacillus polymyxa, are possible distant relatives of the usher “middle domain”. Several mutations reported to abolish in vivo pilus formation cluster in this region, underlining its functional importance. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Direct folding simulation of α‐helices and β‐hairpins based on a single all‐atom force field with an implicit solvation model
Authors: Jang Soonmin , Kim Eunae , Pak Youngshang
Published: October 2006

Recently, we have shown that a modified energy model based on the param99 force field with the generalized Born (GB) solvation model produces reliable free energy landscapes of mini‐proteins with a ββα motif (BBA5, 1FSD, and 1PSV), with the native structures of the mini‐proteins located in their lowest free energy minimum states. One of the main features in the modified energy model is a significant improvement for more balanced treatments of α and β strands in proteins. In this study, using the replica exchange molecular dynamics (REMD) simulation method with this new force field, we have carried out extensive ab initio folding studies of several well‐known peptides with α or β strands (C‐peptide, EK‐peptide, le0q, and gbl). Starting from fully extended conformations as the initial conditions, all of the native‐like structures of the target peptides were successfully identified by REMD, with reasonable representations of free energy surfaces. The present simulation results with the modified energy model are consistent with experiments, demonstrating an extended applicability of the energy model to folding studies of a variety of α‐helices, β‐strands, and α/β proteins. Proteins 2007. © 2006 Wiley‐Liss, Inc.
The gap between the concept and definitions in the Evolutionarily Significant Unit: the need to integrate neutral genetic variation and adaptive variation
Authors: de Guia Anna Pauline O. , Saitoh Takashi
Published: October 2006

The Evolutionarily Significant Unit (ESU) was conceptualized in 1986 as a conservation unit below the species level, theoretically applicable to a wide range of taxa. The concept has gained support, and various definitions or criteria, some of which are inconsistent with each other, have since been proposed. Recent critiques of the ESU have pointed out the dominance of definitions biased to the identification of long‐term isolation or neutral genetic variation, which has largely ignored the adaptive components. We present here the validity of such claims and show how the ESU definitions have actually been applied in research. We surveyed scientific journals for original papers supporting ESU designations and determined who among the proponents of ESU definitions have gained wider support. Our results indicate that indeed there are inconsistencies with the original concept and with the existing definitions. Although the original concept recommended both ecological and genetic data as the basis for identification of ESUs, which reflect true evolutionary variation, recent definitions have become biased to either neutral genetic variation or adaptive variation. The definition which uses genetic data to assess neutral genetic variation (long‐term isolation) has gained major support, and therefore validates the earlier claims. To bridge the gap between the original concept and the practical application, we propose the use of partial ESU and full ESU designations. The application of full ESU should be limited solely to when both information about neutral genetic variation and adaptive variation are available. In other cases, in which only a part of the variation is examined, we should use the term partial ESU (e.g., molecular‐based ESU) and continue to investigate focal populations from other aspects of variations to designate full ESU.
Transformation by RAS oncogene decreases the width of substrate‐spread fibroblasts but not their length
Authors: Kharitonova Margarita A. , Kopnin Pavel B. , Vasiliev Jury M.
Published: October 2006

We compared morphometric parameters of the contours of cells in four pairs of non‐transformed mouse and rat lines and of the same lines transformed by oncogenes of the RAS family. As expected, the mean areas of all RAS‐transformed lines were much smaller than those of their non‐transformed counterparts. At the same time the average length of cell projection did not regularly decrease after transformation. These results show that transformation induced by expression of RAS oncogene selectively affect only one component of spreading, namely transversal spreading and not longitudinal spreading; these changes result in an increase of antero‐posterior polarity of transformed fibroblasts.
Pfnek3: An atypical activator of a MAP kinase in Plasmodium falciparum
Authors: Lye Yu Min , Chan Maurice , Sim Tiow-Suan
Published: October 2006

The canonical mitogen‐activated protein kinase (MAPK) signal cascade was previously suggested to be atypical in the malaria parasite. This raises queries on the existence of alternative mediators of plasmodial MAPK pathways. This study describes, Pfnek3, a malarial protein kinase belonging to the NIMA (Never in Mitosis, Aspergillus) family. Endogenous Pfnek3 is expressed during late asexual to gametocyte stages and lacks some classical protein kinase sequence motifs. Moreover, Pfnek3 is phylogenetically distant from mammalian NIMA‐kinases. Recombinant Pfnek3 was able to phosphorylate and stimulate a malarial MAPK (Pfmap2). Contrastingly, this was not observed with two other kinases, Pfmap1 and human MAPK1, suggesting that the Pfnek3–Pfmap2 interaction may be specific for Pfmap2 regulation. In summary, our data reveal a malarial NIMA‐kinase with the potential to regulate a MAPK. Possessing biochemical properties divergent from classical mammalian NIMA‐kinases, Pfnek3 could potentially be an attractive target for parasite‐selective anti‐malarials.
Yonton Revisited: A Case Study in the Reception of Hellenistic Science within Early Judaism
Authors: Toepel Alexander
Published: October 2006

In the Syriac Book of the Cave of Treasures, which in a general way we may reckon among the rewritten Bible texts, in ch. 27.6–11, an apocryphal fourth son of Noah appears, Yōnṭōn by name. This figure resides near the seashorein a far-easternland and possesses oracular and astrological wisdom. In 1980, Stephen Gero interpreted this figure against a Jewish background. Recently, however, Clemens Leonhard, following Witold Witakowski, has questioned this approach and denied any prehistory to Yōnṭōn; he regards him as an “invention” of the Syriac author of the Cave of Treasures. In the present article I aim to investigate whether it is possible indeed to trace a Jewish origin of Yōnṭōn's appearance in the Cave of Treasures. Taking Gero's interpretation as a starting point, I will first investigate the setting in which a figure like Yōnṭōn could have evolved within a Jewish context. Secondly, I will attempt to actually identify Yōnṭōn in earlier Jewish sources. In this I will follow a recent assertion of Su-Min Ri, that Yōnṭōn originates in the Biblical person of Yoqṭān (Gen 10:25). While Ri's assumption derives from the possibility of a misspelling, I will produce internal evidence which renders the identification of Yōnṭōn and Yoqṭān very probable, thus justifying the direction of thought taken by both Gero and Ri over against the allegations of Leonhard and Witakowski. Moreover, the following discussion will shed light on how Jews received influences from Hellenistic astronomy and astrology and how they read these concepts into, or set them in opposition to, the Bible.
Essene Sectarianism and Social Differentiation in Judaea After 70 C.E.
Authors: Burns Joshua Ezra
Published: October 2006

What happened to the Essenes after the first Jewish revolt? The answer to this seemingly simple question has proven elusive. Prior to the war, the Essenes stood alongside the Pharisees and Sadducees as one of the most prominent social factions in Judaea. Josephus and Philo allege that they numbered in the thousands and that they could be found in cities and towns throughout the country.
A Proposed Rereading of P.Oxy. 654 line 41 (Gos. Thom. 7)
Authors: Gathercole Simon
Published: October 2006

The Coptic text of the Gospel of Thomas is paralleled in three sections by Greek fragments from Oxyrhynchus. P.Oxy. 655, in the Houghton Library at Harvard, consists of small amounts of text, which correspond to sayings 24 and 36–39. P.Oxy. 1, in the Bodleian Library in Oxford, is a fragment of a codex containing sayings 26–33 (cf. also saying 77). This latter exemplar in particular shows that—with some exceptions—there is a good deal of correspondence between the Greek and Coptic versions, and therefore that it is quite possible that substantial portions of the Coptic version of Thomas go back to a Greek original.
Hearing preservation after classical translabyrinthine removal of a vestibular schwannoma: case report and literature review
Authors: Springborg L K , Springborg J B , Thomsen J
Published: October 2006

The translabyrinthine approach is one of the favoured access routes for removal of vestibular schwannomas; however, total hearing loss in the operated ear is a predictable consequence. Here, we report a case in which a patient maintained serviceable hearing almost six years after classic translabyrinthine surgery. Possible explanations for the hearing preservation are discussed, as well as the feasibility of a modified translabyrinthine approach in attempting preservation of hearing following vestibular schwannoma surgery.
Platysma myofascial flap for reconstruction of oropharyngeal defects after transoral laser microsurgery of locally advanced carcinomas
Authors: Jäckel M C
Published: October 2006

Introduction: Transoral laser microsurgery of locally advanced carcinomas of the lateral oropharynx often results in exposure of major vessels of the neck and may be accompanied by a substantial risk of intra- and post-operative bleeding.

Procedure: Six patients with tonsillar cancers radiologically infiltrating the parapharyngeal space underwent ipsilateral neck dissection with temporary protection of neck vessels. While the neck remained open, transoral laser resection of the primary tumour was performed. Pharyngeal defects were subsequently closed by a superiorly based platysma myofascial flap.

Results: All tumours were completely resected. Intra- and post-operative bleeding complications requiring blood transfusion or surgical revision did not occur. None of the patients developed a cervical fistula. During a mean follow-up time of 24.8 months, no local and/or regional recurrence was observed.

Conclusion: The described approach is oncologically safe and seems to ensure reliable protection of neck vessels during and after transoral laser resection of locally advanced oropharyngeal carcinomas, as well as to prevent fistula formation.
Perspectives on spirituality at the end of life: A
meta-summary
Authors: WILLIAMS ANNA-LEILA
Published: October 2006

Objective: A meta-summary of the qualitative literature on
spiritual perspectives of adults who are at the end of life was undertaken
to summarily analyze the research to date and identify areas for future
research on the relationship of spirituality with physical, functional,
and psychosocial outcomes in the health care setting.

Methods: Included were all English language reports from 1966
to the present catalogued in PubMed, Medline, PsycInfo, and CINAHL,
identifiable as qualitative investigations of the spiritual perspectives
of adults at the end of life. The final sample includes 11 articles,
collectively representing data from 217 adults.

Results: The preponderance of participants had a diagnosis of
cancer; those with HIV/AIDS, cardiovascular disease, and ALS were also
represented. Approximately half the studies were conducted in the United
States; others were performed in Australia, Finland, Scotland, and Taiwan.
Following a process of theme extraction and abstraction, thematic patterns
emerged and effect sizes were calculated. A spectrum of spirituality at
the end of life encompassing spiritual despair (alienation, loss of self,
dissonance), spiritual work (forgiveness, self-exploration, search for
balance), and spiritual well-being (connection, self-actualization,
consonance) emerged.

Significance: The findings from this meta-summary confirm the
fundamental importance of spirituality at the end of life and highlight
the shifts in spiritual health that are possible when a terminally ill
person is able to do the necessary spiritual work. Existing end-of-life
frameworks neglect spiritual work and consequently may be deficient in
guiding research. The area of spiritual work is fertile ground for further
investigation, especially interventions aimed at improving spiritual
health and general quality of life among the dying.
Psychological intervention in fluid management
Authors: FISHER LINDA , CAIRNS HUGH S. , AMIR-ANSARI BEHZAD , SCOBLE JOHN E. , CHALDER TRUDIE , TREASURE JANET
Published: October 2006

Background: Hemodialysis is a palliative treatment for
patients with established renal failure (ERF), and volume overload is a
common problem for hemodialysis patients with low urinary output. Volume
overload is thought to be mostly attributable to interdialytic fluid
intake by the patient and is associated with an increased symptom burden
and the development of serious medical complications. Repeated episodes of
volume overload may adversely affect staff–patient relationships and
the perception of care in this patient population. The aim of this case
series study was to evaluate the effect and experience of a psychological
intervention on interdialytic weight gain in a small group of
patients.

Methods: Five patients were treated. The intervention
involved using techniques derived from both cognitive behavior therapy and
motivational interviewing. The main outcome measures were interdialytic
weight gain and patient perception of the intervention.

Results: Three of the five patients reduced both mean
interdialytic weight gain and the frequency with which they gained in
excess of 3% of their dry weight during the intervention phase. The
intervention was found to be acceptable to patients.

Significance of results: The intervention was effective in
helping three of the five patients to reduce both the frequency and the
severity of volume overload, and two of these patients maintained this for
at least 6 months post intervention. The intervention used actively
engaged the patients and appeared to be experienced positively. The
methods used to mobilize patient resources and optimize
staff–patient relationships as vehicles of change are discussed.
Both may have implications for treatment concordance and the perception of
care delivered.
PAIN WILTS AWAY
Authors: RAINGRUBER BONNIE
Published: October 2006

Pain wilts away.
LEAVING THINGS TIDY
Authors: RAINGRUBER BONNIE
Published: October 2006

Leaving things tidy.
DREAM CARCASS
Authors: RAINGRUBER BONNIE
Published: October 2006

Dream carcass.
Meningokokkeninfektion: Zwei Fälle zur Breite des klinischen Spektrums
Authors: Boscacci  , Leib
Published: October 2006

Invasive Infektionen mit Meningokokken zeigen ein breites klinisches Verlaufsbild. Wir berichten über die klinische Präsentation einer fulminanten Meningokokkensepsis und einer Meningokokkenmeningitis und diskutieren die zwei Verlaufsbilder mit unterschiedlicher Prognose. Die fulminante Meningokokkensepsis ist charakterisiert durch eine massive systemische Freisetzung von Endotoxin, welche über eine massive Zytokinantwort des Wirtes innerhalb von Stunden zu einer Schocksymptomatik und einem Multiorganversagen führen kann. Die Mortalität ist trotz intensivmedizinischer Behandlung sehr hoch. Meningitis entsteht im Rahmen einer Bakteriämie als Folge einer Ansiedlung von Meningokokken in den Ventrikulär- und Subarachnoidalraum. Die Mortalität der Meningitis ist niedriger als diejenige der Sepsis. Das Entstehen einer Meningitis kann somit als Hinweis auf eine geringere Pathogenität des Keimes und/oder einer effektiveren Infektkontrolle durch den Wirt als bei der fulminanten Sepsis gewertet werden.
Status asthmaticus mit Rhabdomyolyse der Atemmuskulatur
Authors: Weiss  , Stäubli  , Ursprung  , Reber
Published: October 2006

Ein 40-jähriger Dachdecker alarmierte wegen akuter Dyspnoe und retrosternalem Druckgefühl die Sanität. Er litt unter bekanntem Asthma bronchiale, das wahrscheinlich durch Lösungsmittel-Exposition bei der Arbeit exazerbierte. Bei klinischem Status asthmaticus musste er wegen dramatischer Verschlechterung notfallmässig für zirka zehn Stunden intubiert und beatmet werden. Nach Extubation klagte er über Thoraxschmerzen, die bei Kreatinkinase-Anstieg bis 4368 U/l im Rahmen einer Rhabdomyolyse der Atemmuskulatur infolge extremer Atemarbeit während des Status asthmaticus interpretiert wurden. Als Ursache der Thoraxschmerzen nach schwerem Status asthmaticus muss eine Rhabdomyolyse der Atemmuskulatur in Betracht gezogen werden.
Relevant parameters and finite amplitude effects in estuarine hydrodynamics
Authors: Toffolon Marco , Vignoli Gianluca , Tubino Marco
Published: October 2006

The propagation of the tidal wave in convergent estuaries is investigated through a one‐dimensional numerical model, which allows consideration of the role of finite amplitude effects. The relevant dimensionless parameters characterizing estuarine hydrodynamics are given in terms of independent quantities, namely the geometry of the channel and the tidal forcing. Hence a suitable scale of velocity is derived, which covers both the cases of convergent and dissipative estuaries. Furthermore, the marginal conditions for tidal wave amplification, resulting from a balance between the damping effect of friction and the amplification due to channel convergence, are investigated. We show that the marginal curves can be given the form of power laws whose coefficients depend on the dimensionless tidal amplitude; the linear behavior predicted by analytical solutions is only recovered for vanishing values of the ratio between the tidal amplitude and the tidally averaged water depth. Finally, the proposed scale of velocity and that derived from the model of H. H. G. Savenije and E. J. M. Veling (2005) are tested against numerical results for a wide range of parameters.
p62 mutations, ubiquitin recognition and Paget's disease of bone
Authors: Layfield R. , Cavey J.R. , Najat D. , Long J. , Sheppard P.W. , Ralston S.H. , Searle M.S.
Published: October 2006

Functional analyses of PDB (Paget's disease of bone)-associated mutants of the p62 [also known as SQSTM1 (sequestosome 1)] signalling adaptor protein represent an interesting paradigm for understanding not only the disease mechanism in this skeletal disorder, but also the critical determinants of ubiquitin recognition by an ubiquitin-binding protein. The 11 separate PDB mutations identified to date all affect the C-terminal region of p62 containing the UBA domain (ubiquitin-associated domain), a ubiquitin-binding element. All of these mutations have deleterious effects on ubiquitin binding by p62 in vitro, and there is evidence of an inverse relationship between ubiquitin-binding function and disease severity. The effects on ubiquitin-binding function of most of the mutations can be attributed to either reduced UBA domain stability, and/or the mutations affecting the presumed ubiquitin-binding interface of the UBA domain. However, a subset of the mutations are more difficult to rationalize; several of these affect sequences of p62 outside of the minimal ubiquitin-binding region, providing insights into non-UBA domain sequences within the host protein which mediate ubiquitin-binding affinity. The p62 mutations are presumed to result in activation of (osteoclast) NF-κB (nuclear factor κB) signalling. Understanding how loss of ubiquitin-binding function of p62 impacts on signal transduction events in osteoclasts will undoubtedly further our understanding of the disease mechanism in PDB at the molecular level.
Molecular architecture of the pyruvate dehydrogenase complex: bridging the gap
Authors: Smolle M. , Lindsay J.G.
Published: October 2006

The PDC (pyruvate dehydrogenase complex) is a high-molecular-mass (4–11 MDa) complex of critical importance for glucose homoeostasis in mammals. Its multi-enzyme structure allows for substrate channelling and active-site coupling: sequential catalytic reactions proceed through the rapid transfer of intermediates between individual components and without diffusion into the bulk medium due to its ‘swinging arm’ that is able to visit all PDC active sites. Optimal positioning of individual components within this multi-subunit complex further affects the efficiency of the overall reaction and stability of its intermediates. Mammalian PDC comprises a 60-meric pentagonal dodecahedral dihydrolipoamide (E2) core attached to which are 30 pyruvate decarboxylase (E1) heterotetramers and six dihydrolipoamide (E3) homodimers at maximal occupancy. Stable E3 integration is mediated by an accessory E3-binding protein associated with the E2 core. Association of the peripheral E1 and E3 enzymes with the PDC core has been studied intensively in recent years and has yielded some interesting and substantial differences when compared with prokaryotic PDCs.
The JIP family of MAPK scaffold proteins
Authors: Whitmarsh A.J.
Published: October 2006

The components of MAPK (mitogen-activated protein kinase) signalling pathways can assemble into complexes that are co-ordinated by regulatory proteins including scaffold proteins. There is increasing evidence that scaffold proteins (i) maintain signalling specificity and facilitate the activation of pathway components, (ii) localize pathway components to particular subcellular sites or to specific targets, and (iii) serve as a point of signal integration to allow regulation of MAPK pathways by other signalling events in the cell. One family of scaffold proteins that regulate signalling by stress-activated MAPKs are the JIPs [JNK (c-Jun N-terminal kinase)-interacting proteins]. JIP proteins have been demonstrated to form complexes with specific JNK and p38 MAPK signalling modules and to play important roles in brain development, neuronal trafficking, apoptosis, β-cell function and insulin responses. Here, I briefly review our current understanding of the biochemical properties and physiological roles of JIP proteins.
Regulation of RalA GTPase by phosphatidylinositol 3-kinase as visualized by FRET probes
Authors: Yoshizaki H. , Aoki K. , Nakamura T. , Matsuda M.
Published: October 2006

Small GTPases, which are binary switches regulating various signal transduction cascades, function not only to relay signals but also to integrate them from multiple signalling branches. For example, RalA activity is regulated by at least three signalling cascades involving Ras, Rac or PI3K (phosphoinositide 3-kinase). To untangle such complicated regulatory mechanisms, we have been developing probes for GTPases, kinases and phosphatidylinositols based on the principle of FRET (fluorescence resonance energy transfer). We demonstrated previously that, upon EGF (epidermal growth factor) stimulation, Ras activity increases diffusely in the plasma membrane, whereas RalA activity increases predominantly in lamellipodial protrusions. Here, we show that the level of PtdIns(3,4,5)P3 is increased diffusely in the plasma membrane, whereas, in the central region, the level of PtdIns(3,4)P2 is increased more in the nascent lamellipodia than in the plasma membrane. The distribution and time course of Akt activation are similar to those of increased PtdIns(3,4)P2 levels. These observations suggest that the increase in PtdIns(3,4)P2 and the subsequent activation of Akt may be responsible for the localized activation of RalA. Thus the signals from Ras and PI3K converge at the level of Ral GEFs (guanine nucleotide-exchange factors), and this convergence restricts the area of RalA activation.
Structure and trafficking of NMDA and GABAA receptors
Authors: Stephenson F.A.
Published: October 2006

The fidelity of synaptic function is dependent on the expression of the appropriate neurotransmitter receptor subtype, the targeting and trafficking of receptors to synapses as well as the regulation of the actual number of receptors at synapses. GABAA (γ-aminobutyric acid type A) receptors and NMDA (N-methyl-D-aspartate) receptors are both examples of ligand-gated, heteromeric neurotransmitter receptors whose cell-surface expression is dynamic and tightly regulated. NMDA receptors are localized at excitatory synapses. These synapses are highly structured but dynamic, with the interplay between NMDA receptors and NMDA receptor-associated scaffolding proteins regulating the expression of functional cell-surface synaptic and extrasynaptic receptors. Based on current information, inhibitory synapses seem to be less ordered, and a GABAA receptor equivalent of PSD-95 (postsynaptic density-95), the scaffolding molecule pivotal to the organization of NMDA receptor complexes at synapses, is yet to be validated. In the present paper, processes regulating the trafficking, assembly and molecular organization of both NMDA receptors and GABAA receptors will be discussed.
NAADP, a new intracellular messenger that mobilizes Ca2+ from acidic stores
Authors: Galione A.
Published: October 2006

NAADP (nicotinic acid–adenine dinucleotide phosphate) is a recently described Ca2+-mobilizing molecule. First characterized in the sea urchin egg, it has been shown to mobilize Ca2+ from intracellular stores in a wide range of cells from different organisms. It is a remarkably potent molecule, and recent reports show that its cellular levels change in response to a variety of agonists, confirming its role as a Ca2+-mobilizing messenger. In many cases, NAADP appears to interact with other Ca2+-mobilizing messengers such as IP3 (inositol 1,4,5-trisphosphate) and cADP-ribose in shaping cytosolic Ca2+ signals. What is not clear is the molecular nature of the NAADP-sensitive Ca2+ release mechanism and its subcellular localization. This review focuses on the recent progress made in sea urchin eggs, which indicates that NAADP activates a novel Ca2+ release channel distinct from the relatively well-characterized IP3 and ryanodine receptors. Furthermore, in the sea urchin egg, the NAADP-sensitive store appears to be separate from the endoplasmic reticulum and is most likely an acidic store. These findings have also been reinforced by similar findings in mammalian cells, and a unified model for NAADP-induced Ca2+ signalling is presented.
Active zone assembly and synaptic release
Authors: Kittel R.J. , Hallermann S. , Thomsen S. , Wichmann C. , Sigrist S.J. , Heckmann M.
Published: October 2006

Neurotransmitter release at chemical synapses occurs when synaptic vesicles fuse to the presynaptic membrane at a specialized site termed the active zone. The depolarization-induced fusion is highly dependent on calcium ions, and, correspondingly, the transmission characteristics of synapses are thought to be influenced by the spatial arrangement of voltage-gated calcium channels with respect to vesicle release sites. Here, we review the involvement of the Drosophila Bruchpilot (BRP) protein in active zone assembly, a process that is required for the clustering of presynaptic calcium channels to ensure efficient vesicle release.
Molecular characterization of the metabotropic glutamate receptor family in Caenorhabditis elegans
Authors: Dillon J. , Hopper N.A. , Holden-Dye L. , O'Connor V.
Published: October 2006

mGluRs (metabotropic glutamate receptors) are G-protein-coupled receptors that play an important neuromodulatory role in the brain. Glutamatergic transmission itself plays a fundamental role in the simple nervous system of the model organism Caenorhabditis elegans, but little is known about the contribution made by mGluR signalling. The sequenced genome of C. elegans predicts three distinct genes, mgl-1, mgl-2 and mgl-3 (designated Y4C6A.2). We have used in silico and cDNA analyses to investigate the genes encoding mgls. Our results indicate that mgl genes constitute a gene family made up of three distinct subclasses of receptor. Our transcript analysis highlights potential for complex gene regulation with respect to both expression and splicing. Further, we identify that the predicted proteins encoded by mgls harbour structural motifs that are likely to regulate function. Taken together, this molecular characterization provides a platform to further investigate mGluR function in the model organism C. elegans.
Interactions between nitric oxide, oxygen, reactive oxygen species and reactive nitrogen species
Authors: Brown G.C. , Borutaite V.
Published: October 2006

ROS (reactive oxygen species) and RNS (reactive nitrogen species) are central to the innate immunity that protects us from infection, but also contribute to degenerative diseases and possibly aging. However, ROS and RNS are increasingly recognized to contribute to physiological signalling. This review briefly describes the main interactions between ROS and RNS and shows how their origins, chemistry, metabolism and biological actions are intimately linked.
The correction vector method for three-photon absorption: The effects of π conjugation in extended rylenebis(dicarboximide)s
Authors: Yi Yuanping , Zhu Lingyun , Shuai Zhigang
Published: October 2006

A correction vector method within the multireference determinant single and double configuration interaction approximation coupled with the semiempirical intermediate neglect of differential overlap Hamiltonian has been developed for the computation of single and multiphoton absorption spectra of conjugated molecules. We study the effect of π conjugation on these properties in the extended rylenebis(dicarboximide)s. The one-, two-, and three-photon absorption cross sections of the lowest-lying excited states show a power law dependence on the conjugation length, with exponents of about 1.3, 2.6, and 5.6, respectively. The maximum value of the three-photon absorption cross section in these molecules is calculated to be 1.06×10−78cm6s2∕photon2 for photon energy at 0.57eV.
Residual strains in cubic silicon carbide measured by Raman spectroscopy correlated with x-ray diffraction and transmission electron microscopy
Authors: Capano M. A. , Kim B. C. , Smith A. R. , Kvam E. P. , Tsoi S. , Ramdas A. K.
Published: October 2006

Cubic (3C) silicon carbide (SiC) epilayers grown on Si substrates by chemical vapor deposition, characterized using transmission electron microscopy (TEM), high-resolution x-ray diffraction (HRXRD), and Raman spectroscopy, reveal the presence of biaxial in-plane strain. Defect (stacking faults, twins, dislocations) distributions revealed by TEM are correlated with peak widths obtained from HRXRD measurements and Raman shifts of the zone center longitudinal optical phonon line. TEM showed defect densities decreasing with increasing distance from SiC∕Si interface as the lattice mismatch stress is relaxed. Structural defect densities show the most significant reduction within the first 2μm of the epilayer. TEM observations were correlated with a monotonic decrease in HRXRD peak width (full width at half maximum) from 780arcsec (1.5μm thick epilayer) to 350arcsec (10μm thick epilayer). Raman spectroscopy indicates that the residual biaxial in-plane strain decreases with increasing epilayer thickness initially, but becomes essentially constant between 6 and 10μm. Differences in the observed behavior between HRXRD and Raman spectroscopy are discussed in terms of the fundamental interactions of incident radiation with the 3C-SiC epilayers.
Systematic ab initio study of the phase diagram of epitaxially strained SrTiO3
Authors: Lin Chien-Hung , Huang Chih-Meng , Guo G. Y.
Published: October 2006

We use density-functional theory with the local-density approximation to study the structural and ferroelectric properties of SrTiO3 under misfit strains. Both the antiferrodistortive (AFD) and ferroelectric (FE) instabilities are considered by calculating all the phases predicted by Pertsev et al. [Phys. Rev. B 61, R825 (2000)] based on the phenomenological Landau theory. The rotation of the oxygen octahedra and the movement of the atoms are fully relaxed within the constraint of a fixed in-plane lattice constant. We find a rich misfit strain induced phase transition sequence which is in overall agreement with the prediction by Pertsev et al. and is obtained only when the AFD distortion is taken into account. Nevertheless, the calculated locations of the phase boundaries are different from the prediction by Pertsev et al. We also find that compressive misfit strains induce ferroelectricity in the tetragonal low temperature phase only while tensile strains induce ferroelectricity in the orthorhombic phases only. The calculated FE polarization for both the tetragonal and orthorhombic phases increases monotonically with the magnitude of the strains. The AFD rotation angle of the oxygen octahedra in the tetragonal phase increases dramatically as the misfit strain goes from the tensile to compressive strain region while it decreases slightly in the orthorhombic (FO4) phase. This reveals why the polarization in the epitaxially strained SrTiO3 would be larger when the tensile strain is applied, since the AFD distortion is found to reduce the FE instability and even to completely suppress it in the small strain region. Finally, our analysis of the average polar distortion and the charge density distribution suggests that both the Ti–O and Sr–O layers contribute significantly to the FE polarization.
Energies and spatial features for the rotationless bound states of He3+4(Σg+2): A cationic core from helium cluster ionization
Authors: Scifoni Emanuele , Gianturco Franco A. , Grebenshchikov Sergy Yu. , Schinke Reinhard
Published: October 2006

Ab initio quantum calculations have been carried out on the helium ionic trimer. The potential energy surface is accurately fitted, especially in the vicinity of the three equivalent minima. The spectrum of bound states for the zero angular momentum is computed and analyzed in detail. Energies and wave functions reveal several interesting features related to the fact that He3+ represents one of the few homonuclear ionic trimers that are linear in their ground vibrational state. At low energies, the triply degenerate eigenfunctions are localized at the potential minimum. With growing excitation energy, however, the wave functions exhibit stronger spatial delocalization.
The effect of sequence correlation on bubble statistics in double-stranded DNA
Authors: Jeon Jae-Hyung , Park Pyeong Jun , Sung Wokyung
Published: October 2006

DNA exists stably in the double-stranded structure at physiological temperatures, but base pairs are observed to unbind locally, giving way to bubbles (i.e., locally denatured states) due to thermal fluctuation. In this study, we consider the effect of sequence on the bubble statistics. On the basis of the Edwards equation description [W. Sung and J.-H. Jeons, Phys. Rev. E 69, 031902 (2004) ], we develop a stochastic model incorporating the sequence randomness as a dichotomic noise, where the bubble and its size are identified as a returning random walk and its first passage time, respectively. By simulating the model Langevin equation, we obtain the bubble size distribution and show how it is affected by the sequence correlation. We find that the bubble size distribution of DNA with finite sequence correlation deviates from the Poland-Scheraga-type distribution. In particular, the formation of large bubbles is dramatically enhanced as sequence correlation length gets longer.
Quasiclassical trajectories on a finite element density functional potential energy surface: The C++H2O reaction revisited
Authors: Flores Jesús R.
Published: October 2006

A new method for the representation of potential energy surfaces (PESs) based on the p version of the finite element method is presented and applied to the PES of the [COH2]+ system in order to study the C++H2O→[COH]++H reaction through the quasiclassical trajectory method. Benchmark ab initio computations have been performed on the most relevant stationary points of the PES through a procedure that incorporates basis set extrapolations, the contribution of the core correlation energy, and scalar relativistic corrections. The electronic structure method employed to compute the many points needed to construct the PES is a hybrid density functional approach of the B3LYP type with geometry-dependent parameters, which improves dramatically the performance with respect of the B3LYP method. The trajectory computations shed light on the behavior of the COH2+ complex formed in the collision. At a fixed relative translational energy of 0.62eV, which corresponds to the crossed beam experiments [D. M. Sonnenfroh et al., J. Chem. Phys. 83, 3985 (1985)], the complex dissociates significantly into the reactants (37%). However, the behavior for a thermal sampling at T=300K is significantly different because only 9% of the trajectories where capture occurs lead to dissociation into the reactants. The latter kind of behavior is coherent with the view that simple ion-molecule reactions proceed quite often at the capture rate provided it is corrected by the fraction of the electronic states which, being nearly degenerate for the reactants, become attractive at short distances. For both T=300K and crossed beam conditions, the trajectory computations indicate that COH2+ is the critical intermediate, in agreement with a recent work [Y. Ishikawa et al., Chem. Phys. Lett. 370, 490 (2003)] and in contrast with the interpretation of the crossed beam experiments. Besides, virtually all trajectories generate COH++H (>99%), but a significant proportion of the isoformyl cation is formed with enough vibrational energy as to surmount the COH+–HCO+ isomerization barrier, about 37% at T=300K.
Stress dependence of the near-band-gap cathodoluminescence spectrum of GaN determined by spatially resolved indentation method
Authors: Porporati Alessandro Alan , Tanaka Yoshitomo , Matsutani Atsuo , Zhu Wenliang , Pezzotti Giuseppe
Published: October 2006

A microscopic procedure has been proposed for evaluating the stress dependence of the (room-temperature) cathodoluminescence (CL) excitonic band emitted from the (0001) crystallographic plane of GaN in a field-emission-gun scanning electron microscope. The room-temperature near-band-gap emission (generally referred to as the excitonic band) mainly consisted of a band arising from free exciton (FX). However, an asymmetric morphology was found for the band, which thus needed to be deconvoluted into the main FX band and a shoulder. The spectral location at intensity maximum of the overall excitonic band under stress-free conditions was observed at room temperature at around 365nm. Experimentally measured spectral shifts were precisely retrieved nearby the tip of a Vickers indentation microcrack, while CL intensity probe response functions were collected at different acceleration voltages at a sharp interface between a GaN film and its sapphire substrate. Based on these assessments, the magnitude of the piezospectroscopic coefficient (i.e., the spectral shift rate versus the trace of a biaxial stress tensor) Π=1.35±0.01nm∕GPa of the excitonic (cumulative) band of GaN could be evaluated. This study not only emphasizes the importance of microscopic piezospectroscopic calibration procedures for precise residual stress assessments in GaN-based devices, but also the need of deconvoluting the electron probe for minimizing the error involved with its finite size.
A complete active space self-consistent field study of the photochemistry of nitrosamine
Authors: Peláez Daniel , Arenas Juan F. , Otero Juan C. , Soto Juan
Published: October 2006

Photodissociation mechanisms of nitrosamine (NH2NO) have been studied at the complete active space self-consistent field level of theory in conjunction with atomic-natural-orbital-type basis sets. In addition, the energies of all the critical points and the potential energy curves connecting them have been recomputed with the multiconfigurational second-order perturbation method. Ground state minimum of nitrosamine has a C1 nonplanar structure with the hydrogen atoms of the amino moiety out of the plane defined by the N–N–O bonds. Electronic transitions to the three lowest states are allowed by selection rules: (i) S0→S3 (7.41eV) has an oscillator strength of f=0.0006 and it is assigned as an (npO)0→(πNO*)2 transition, (ii) S0→S2 (5.86eV) has an oscillator strength of f=0.14 and it is assigned as an npN→πNO* transition, and (iii) S0→S1 (2.98eV) has an oscillator strength of f=0.002 and it is assigned as an npO→πNO* transition. It is found that N–N bond cleavage is the most likely process in all the photochemical relevant states, namely, S1 (1A″1), S2 (2A′1), and T1 (1A″3). While S1 and T1 yield exclusively homolytic dissociation: NH2NO→NH2 (1B12)+NO(XΠ2), on S2 the latter process constitutes the major path, but two additional minor channels are also available: adiabatic homolytic dissociation: NH2NO→NH2 (1A12)+NO(XΠ2), and adiabatic oxygen extrusion: NH2NO→NH2N (1A13)+O(P3). The excited species NH2 (1A12) experiences a subsequent ultrafast decay to the ground state, the final products in all cases the fragments being in their lowest electronic state. We have not found a unimolecular mechanism connecting excited states with the ground state. In addition, homolytic dissociation in the ground state, tautomerizations to NHNOH and NHNHO, and intersystem crossings to T1 are considered. The most favorable process on this state is the isomerization to NHNOH.
Elementary constituents of microdevices: The Ge2H fragment
Authors: Wang Hongyan , Wang Suyun , Yamaguchi Yukio , Schaefer Henry F.
Published: October 2006

Highly correlated ab initio electronic structure theory has been used to systematically investigate the linear (X̃Π2) GeGeH and H-bridged (X̃B12 and ÃA12) GeHGe structures and the isomerization transition state (ÃA′2) connecting X̃Π2 with ÃA12. The equilibrium structures and physical properties have been predicted employing self-consistent field, configuration interaction with single and double excitations, coupled cluster with single and double excitations (CCSD), and CCSD with perturbative triple excitations [CCSD(T)]. Four correlation-consistent polarized valence-[cc-pVXZ and aug-cc-pVXZ (X=T and Q)] type basis sets were used in the study. For the H-bridged GeHGe isomer, the X̃B12 ground state is predicted to lie only 0.74 [0.95 with zero-point vibrational energy (ZPVE) corrections] kcalmol−1 below the ÃA12 excited state at the CCSD(T) level of theory with the augmented correlation-consistent polarized valence quadruple zeta (aug-cc-pVQZ) basis set. The X̃B12 state of the H-bridged GeHGe isomer lies 8.6kcalmol−1 below the X̃Π2 ground state of the linear GeGeH isomer. The forward isomerization barrier from the linear ground state to the ÃA′2 transition state is predicted to be 3.7kcalmol−1. The reverse isomerization barrier between the ÃA12 GeHGe structure and the X̃Π2 GeGeH structure is predicted to be 11.6 (10.8 with the ZPVE corrections) kcalmol−1 at the aug-cc-pVQZ CCSD(T) level of theory.
Cryogenic graphitization of submicrometer grains embedded in nanostructured tetrahedral amorphous carbon films
Authors: Hu A. , Alkhesho I. , Duley W. W. , Zhou H.
Published: October 2006

A growth mechanism for submicrometer grains in diamondlike carbon films has been investigated. Films were formed by laser deposition on quartz substrates at 20–573K. Atomic force microscopy shows that films deposited at 20–100K consist of a matrix assembled from 40nm nanoparticles that further aggregate into 400–500nm grains which become embedded in the matrix. Nanohardness measurements show that these embedded grains possess a lower hardness than that of the matrix. Electronic structure obtained from resonant Raman spectra shows a remarkable clustering of sp2 bonds in the sp3 bonded matrix. It is believed that the sp2 bonded phase is concentrated in these submicrometer grains. X-ray photoelectron spectra show that this segregated structure has an enhanced affinity for oxygen.
When is negativity not a problem for the ultradiscrete limit?
Authors: Kasman Alex , Lafortune Stéphane
Published: October 2006

The “ultradiscrete limit” has provided a link between integrable difference equations and cellular automata displaying soliton-like solutions. In particular, this procedure generally turns strictly positive solutions of algebraic difference equations with positive coefficients into corresponding solutions to equations involving the “Max” operator. Although it certainly is the case that dropping these positivity conditions creates potential difficulties, it is still possible for solutions to persist under the ultradiscrete limit, even in their absence. To recognize when this will occur, one must consider whether a certain expression, involving a measure of the rates of convergence of different terms in the difference equation and their coefficients, is equal to zero. Applications discussed include the solution of elementary ordinary difference equations, a discretization of the Hirota Bilinear Difference Equation and the identification of integrals of motion for ultradiscrete equations.