bluuebunny/crossref_metadata_2025 huggingface dataset:
Nichtallergische Erkrankungen der oberen und unteren Atemwege
Authors: Rothe Thomas , Menz Günter
Published: February 2008

Bei Erkrankungen der Atemwege sollten die oberen und unteren nicht isoliert betrachtet werden, da der gesamte Atemtrakt eine funktionelle Einheit darstellt. Dies ist sowohl beim allergischen, als auch beim nichtallergischen, dem Intrinsic Asthma, der Fall. Diese Asthmaform ist durch eine eosinophile Entzündung der Mukosa mit Sekret-, teilweise auch Bluteosinophilie, gekennzeichnet, die vielfach nicht nur im Bereich der Bronchien, sondern auch der oberen Atemwege nachweisbar ist. Das Krankheitsbild wird nicht durch eine exogen-allergische Reaktion unterhalten; die Ätiologie ist noch unklar. Die Befunde im Bereich der oberen Atemwege werden unter dem Begriff nichtallergische, eosinophile Rhinitis (NARE-Syndrom) zusammengefasst. In vielen Fällen kommt es nach einer jahrelangen Latenzphase rhinosinusitischer Symptome zur Manifestation des Intrinsic Asthmas. Finden sich auch Nasenpolypen, besteht ein erhebliches Risiko, dass sich im Gefolge eine nicht IgE-vermittelte Intoleranzreaktion auf Aspirin und NSAR entwickelt. Eine «Desensibilisierung» mit Aspirin in aufsteigenden Dosen (adaptive Desaktivierung) führt oft zu einer nachhaltigen Verbesserung der Symptome des oberen Atemtraktes, teilweise auch der eines parallel bestehenden Intrinsic Asthmas.
Asthma und Rhinitis beim Kind
Authors: Sennhauser Felix H.
Published: February 2008

Das Asthma bronchiale ist die häufigste chronische Krankheit im Kindesalter mit einer kumulativen Prävalenz in der Schweiz zwischen 7–15%. Die Diagnose wird klinisch gestellt, da besonders im Säuglings- und Vorschulalter objektiv beweisende Kriterien fehlen. Allen Asthmaformen gemeinsam ist ein ursächlicher Entzündungsprozess der respiratorischen Schleimhaut der intrathorakalen Atemwege. Im Schulalter lassen sich in bis zu 80% allergische Mechanismen klinisch vermuten respektive testphysiologisch dokumentieren. Im Zentrum der Asthma-Therapie steht die Inhalation mit symptomatisch wirkenden Bronchodilatatoren respektive mit entzündungshemmenden topischen Steroiden. Die Rhinitis im Vorschulalter ist mehrheitlich viral-infektiös, im Schulalter oft allergisch bedingt. In der Regel sind die ausgebildeten Nasennebenhöhlen am nasalen Entzündungsprozess beteiligt als Rhinosinusitis. Im Säuglingsalter beschränkt sich die Therapie in der Regel auf symptomatische Maßnahmen, bei allergischen Formen bewähren sich besonders die topischen Steroide. Antibiotika sind selten indiziert. Der Säugling mit Nasenobstruktion kann bedrohlich erkranken wegen obligater Nasenatmung in diesem Altersabschnitt. Die oberen und unteren Atemwege bilden funktionell eine Einheit mit gleichartigen Entzündungsmechanismen und oft gleichzeitig bestehenden entzündlichen Veränderungen. Verschiedene pathogenetische Interaktionen zwischen oberen und unteren Atemwegen erklären die symptomatische Interdependez und definieren das sogenannte Rhinobronchiale Syndrom.
Preventing Suicide in Prisons, Part I
Authors: Konrad Norbert , Daigle Marc S. , Daniel Anasseril E. , Dear Greg E. , Frottier Patrick , Hayes Lindsay M. , Kerkhof Ad , Liebling Alison , Sarchiapone Marco
Published: February 2008

Abstract. In 2000 the Department of Mental Health of the World Health Organization (WHO) published a guide named Preventing Suicide. A Resource for Prison Officers as part of the WHO worldwide initiative for the prevention of suicide. In 2007 there are new epidemiological data on prison suicide, a more detailed discussion of risk factors accounting for the generally higher rate of suicide in correctional settings in comparison to the general population, and several strategies for developing screening instruments. As a first step, this paper presents an update of the WHO guide by the Task Force on Suicide in Prisons, created by the International Association for Suicide Prevention. A second paper, by the same Task Force, will present some international comparisons of suicide prevention services in correctional facilities.
Social Modeling in the Transmission of Suicidality
Authors: de Leo Diego , Heller Travis
Published: March 2008

Abstract. Evidence from twin, adoption, and family studies suggests that there is strong aggregation of suicidal behaviors in some families. By comparison, the role of social modeling through peers has yet to be convincingly established. This paper uses data from four large studies (the WHO/EURO Multicentre Study on Suicidal Behaviour, the WHO/SUPRE-MISS, the CASE study, and the Queensland Suicide Register) to compare the effects of exposure to fatal and nonfatal suicidal behavior in family members and nonfamilial associates on the subsequent suicidal behavior of male and female respondents of different ages. Across all studies, we found that prior suicidal behaviors among respondents' social groups were more important predictors of suicidal behavior in the respondents themselves than previous research had indicated. Community-based suicide attempters in the WHO SUPRE-MISS had higher rates of exposure to prior suicide in nonfamilial associates than in family members. In an adolescent population, exposure to prior fatal suicidal behavior did not predict deliberate self-harm when exposure to nonfatal suicidal behavior (both familial and social) were controlled for, but exposure to nonfatal suicidal behaviors in family and friends was predictive of deliberate self-harm and suicide ideation, even after controlling for exposure to fatal suicidal behavior. The potential impact of “containment” of information regarding suicidal behaviors as a prevention initiative is discussed, in light of information behavior principles of social marketing.
Deliberate Self-Harm
Authors: Zakiullah Nida , Saleem Sadia , Sadiq Sameea , Sani Nadia , Shahpurwala Munira , Shamim Afroz , Yousuf Atif , Khan Murad M. , Nayani Parvez
Published: March 2008

Abstract. Introduction: Previous deliberate self-harm (DSH) is the strongest predictor of suicide. Although several studies exist in other countries, characteristics of DSH have not been well-studied in Pakistan. Aims: To identify characteristics of deliberate self-harm in a hospital population, building on previous work carried out on this subject at this center. Methods: 284 cases admitted to the Aga Khan University Hospital, Karachi, between January 1997 and August 2003 were studied by analyzing medical records. Information was collected regarding demographics, family history, personal history, suicidal ideation, current stressors, the act of DSH and its management. Results: The most common age group was 21-25 years of age. The majority were females (60.3%). 95.1% of patients used self-poisoning as a method of deliberate self-harm. 47.3% used benzodiazepines for self-poisoning. Precipitating factors included conflict with family, marital problems, chronic illnesses, and unemployment. Comorbid psychiatric disorders were present in 76.4% patients. Discussion: Despite the difference in socio-cultural background of our patients, many of our results were found to be consistent with Western data. Our findings suggest that problem-solving therapy, stress management and improved mental health care may be effective interventions in preventing DSH. Prescription of medications should be regulated. Further studies are suggested at the community level.
The Impact of Suicide on the Family
Authors: Cerel Julie , Jordan John R. , Duberstein Paul R.
Published: March 2008

Abstract. Little research has examined the consequences of a suicide for social or family networks. Because suicide occurs within families, the focus on the aftermath of suicide within families is an important next step to determine exactly how to help survivors. In this article, we review and summarize the research on the impact of suicide on individuals within families and on family and social networks. We begin with a discussion of family changes following suicide. Next, we discuss the effects of suicide on social networks overall and responses of children and the elderly to a suicide in the family. Finally, we identify key issues that remain to be resolved in family survivor research and make recommendations for future studies.
The Changing Gender Ratio in Occurrence of Deliberate Self-Harm Across the Lifecycle
Authors: Hawton Keith , Harriss Louise
Published: March 2008

Abstract. Background: Overall gender ratios are often quoted in studies of deliberate self-harm (DSH) patients, almost always with higher rates in females than males. Reporting a ratio across all ages may conceal important variations in the gender ratio across the life cycle. Method: Analysis was done of the gender ratio by age groups in rates of DSH in a consecutive sample of DSH patients presenting to a general hospital over a 10-year period. The patients were identified through a well-established monitoring system. Results: The study sample included 2,189 female and 1,439 male patients. While the overall gender rate ratio was 1.5 females to each male, the ratio varied considerably by age group: 8:1 in 10-14-year-olds, 3.1:1 in 15-19-year-olds, 1.6:1 in 20-24-year-olds, approximately 1.3:1 in 25-49-year-olds, and 0.8:1 in people aged 50 years and over. Conclusion: Statements about overall gender ratios for DSH conceal important changes in the ratio across the life cycle. These changes probably reflect differences in development and problems faced in adolescence, changes in motivation for DSH with age, and the closer resemblance of DSH to suicide in older age groups.
Suicide among Indigenous Peoples
Authors: Lester David
Published: March 2008

Abstract. The present note describes the resource for studying suicide in indigenous peoples provided by the Human Relations Area Files and describes three ways in which these files can illuminate suicidal behavior: testing theories of suicide, exploring the linguistics of suicide, and challenging myths about suicide.
Measurements of target compressive and tensile strength for application to impact cratering on ice‐silicate mixtures
Authors: Hiraoka Kensuke , Arakawa Masahiko , Setoh Masato , Nakamura Akiko M.
Published: February 2008

Small icy bodies in the outer solar system have been shown to consist of ice‐silicate mixtures. The results of previous impact cratering experiments on ice‐silicate mixture targets showed that a crater volume decreases with increasing silicate content. Surface strength controls craterings in laboratory experiments and on small bodies with a certain degree of strength. In this study we measured the uniaxial compressive and tensile strength of the targets used in previous impact cratering experiments by uniaxial compression and Brazilian tests, respectively, at 263 K and calculated the shear strength from the measured values. We found the uniaxial compressive and tensile strength increased with silicate content, which explains why the crater volume decreases with increasing silicate content. Since the gradient of increase of the uniaxial compressive and the tensile strength was different, the difference between the tensile strength and the uniaxial compressive strength becomes smaller with the increase of silicate content up to 50 wt %. We show that the crater spall diameter is better scaled by the tensile strength to compensate the difference of the silicate content than by the uniaxial compressive strength.
The role of OXA-1 β-lactamase Asp66 in the stabilization of the active-site carbamate group and in substrate turnover
Authors: Leonard David A. , Hujer Andrea M. , Smith Brian A. , Schneider Kyle D. , Bethel Christopher R. , Hujer Kristine M. , Bonomo Robert A.
Published: February 2008

The OXA-1 β-lactamase is one of the few class D enzymes that has an aspartate residue at position 66, a position that is proximal to the active-site residue Ser67. In class A β-lactamases, such as TEM-1 and SHV-1, residues adjacent to the active-site serine residue play a crucial role in inhibitor resistance and substrate selectivity. To probe the role of Asp66 in substrate affinity and catalysis, we performed site-saturation mutagenesis at this position. Ampicillin MIC (minimum inhibitory concentration) values for the full set of Asp66 mutants expressed in Escherichia coli DH10B ranged from ≤8 μg/ml for cysteine, proline and the basic amino acids to ≥256 μg/ml for asparagine, leucine and the wild-type aspartate. Replacement of aspartic acid by asparagine at position 66 also led to a moderate enhancement of extended-spectrum cephalosporin resistance. OXA-1 shares with other class D enzymes a carboxylated residue, Lys70, that acts as a general base in the catalytic mechanism. The addition of 25 mM bicarbonate to Luria–Bertani-broth agar resulted in a ≥16-fold increase in MICs for most OXA-1 variants with amino acid replacements at position 66 when expressed in E. coli. Because Asp66 forms hydrogen bonds with several other residues in the OXA-1 active site, we propose that this residue plays a role in stabilizing the CO2 bound to Lys70 and thereby profoundly affects substrate turnover.
Molecular identification of three Arabidopsis thaliana mitochondrial dicarboxylate carrier isoforms: organ distribution, bacterial expression, reconstitution into liposomes and functional characterization
Authors: Palmieri Luigi , Picault Nathalie , Arrigoni Roberto , Besin Evelyne , Palmieri Ferdinando , Hodges Michael
Published: February 2008

Screening of the Arabidopsis thaliana genome revealed three potential homologues of mammalian and yeast mitochondrial DICs (dicarboxylate carriers) designated as DIC1, DIC2 and DIC3, each belonging to the mitochondrial carrier protein family. DIC1 and DIC2 are broadly expressed at comparable levels in all the tissues investigated. DIC1–DIC3 have been reported previously as uncoupling proteins, but direct transport assays with recombinant and reconstituted DIC proteins clearly demonstrate that their substrate specificity is unique to plants, showing the combined characteristics of the DIC and oxaloacetate carrier in yeast. Indeed, the Arabidopsis DICs transported a wide range of dicarboxylic acids including malate, oxaloacetate and succinate as well as phosphate, sulfate and thiosulfate at high rates, whereas 2-oxoglutarate was revealed to be a very poor substrate. The role of these plant mitochondrial DICs is discussed with respect to other known mitochondrial carrier family members including uncoupling proteins. It is proposed that plant DICs constitute the membrane component of several metabolic processes including the malate–oxaloacetate shuttle, the most important redox connection between the mitochondria and the cytosol.
Post-transcriptional regulation of CLMP mRNA is controlled by tristetraprolin in response to TNFα via c-Jun N-terminal kinase signalling
Authors: Sze Kit-Ling , Lui Wing-Yee , Lee Will M.
Published: February 2008

During spermatogenesis, extensive restructuring of blood–testis barrier takes place to facilitate the migration of preleptotene/leptotene spermatocytes from the basal to the adluminal compartment in the seminiferous epithelium. However, the biochemical mechanisms involved in this event remain elusive. Recent studies have shown that pro-inflammatory cytokine TNFα (tumour necrosis factor α) plays a crucial role in this event by inhibiting the expression of tight junction proteins in Sertoli cells. In the present study, we sought to examine the detailed mechanism on how TNFα affects the expression of CLMP (coxsackie- and adenovirus-receptor-like membrane protein), a newly identified tight junction transmembrane protein, in the testis. Addition of TNFα (10 ng/ml) to Sertoli cell culture (TM4 cells) significantly reduced the steady-state CLMP mRNA and protein levels. In an mRNA stability assay, it was shown that the rate of CLMP mRNA degradation was significantly increased when cells treated with TNFα were compared with vehicle. Blockage of the JNK (c-Jun N-terminal kinase) signalling pathway by SP600125 significantly abolished the TNFα-mediated destabilization of CLMP mRNA. Activation of the JNK signalling pathway by TNFα up-regulated the expression of an RNA-binding protein, TTP (tristetraprolin). TTP was present in the RNA–protein complex in the RNA EMSA (electrophoretic mobility shift assay) and decreased the CLMP 3′-UTR (untranslated region)-dependent luciferase activity. Taken together, these results suggest that the TNFα-mediated mRNA degradation of the CLMP gene is controlled by TTP through the JNK signalling cascade.
A broadband method to measure magnetic spectra of thin films
Authors: Starostenko S. N. , Rozanov K. N. , Osipov A. V.
Published: February 2008

Conventional single-port strip-line techniques to measure permeability of thin films are based on the quasistationary approximation. In this paper, wave phenomena in the measurement cell are taken into account. Particularly, the dielectric response of the sample may be accounted for and removed by the consideration of the geometry of the cell and the sample. An additional measurement with a reference sample with known constitutive parameters allows the directivity error and the frequency response error to be removed from the experimental reflectivity data; accounting for the field inhomogeneity inside the strip cell is also introduced. A proper selection of the reference sample is shown to be critical for the measurement accuracy. The measurement results may also be affected by the demagnetization of the sample. With these corrections introduced, the operating frequency range of the technique is extended up to 8GHz. The measurement results are validated by the data obtained with either standard materials or by conventional techniques.
Satellite generation during bubble coalescence
Authors: Zhang F. H. , Thoroddsen S. T.
Published: February 2008

We experimentally study the formation of a satellite bubble, during the coalescence of two larger bubbles. The daughter bubble is generated by capillary waves which propagate from the growing neck, connecting the two bubbles and focus on the opposite apex. As the successive waves converge on the top, their amplitude grows until a small daughter bubble is pinched off. The mechanism is robust over a large range of parameters. We have observed it in water for bubble diameters from 5.2mm down to 175μm. For equally sized parent bubbles, the size of the daughter bubble is 0.10±0.03 times that of the mother bubble, but the daughter size also depends weakly on the approach velocity of the two initial bubbles. The effects of viscosity is to dampen the capillary waves, preventing the pinch-off for Ohnesorge number >6.5×10−3, which is significantly smaller than the critical value observed for the coalescence cascade of a drop. The relative size of the parent bubbles has a large influence on the pinch-off, suppressing it when the size difference is too large. Linear wave-theory can reproduce the overall wave phenomenon and the amplitude evolution of the capillary waves, with the dominant mode number n≃20.
Electron acceleration in vacuum by subcycle laser pulse
Authors: Liu Ming-Ping , Wu Hai-Cheng , Xie Bai-Song , Yu M. Y.
Published: February 2008

An analytical expression based on the paraxial approximation describing the propagation of a subcycle axicon Gaussian laser pulse in vacuum is obtained. The broad spectrum of the ultrashort pulse is given in terms of a Taylor series in the main wave frequency. The spatial and temporal characteristics of the pulse are strongly coupled. The model is used to consider electron acceleration by the light pressure of an intense subcycle laser pulse. The pulse model can also be applied to other short pulse profiles.
Excitation of Alfvén eigenmodes by low energy beam ions in the DIII-D and JET tokamaks
Authors: Nazikian R. , Gorelenkov N. N. , Alper B. , Berk H. L. , Borba D. , Budny R. V. , Fu G. Y. , Heidbrink W. W. , Kramer G. J. , Makowski M. A. , Pinches S. D. , Sharapov S. E. , Solomon W. M. , Strait E. J. , White R. B. , Van Zeeland M. A. ,   JET-EFDA contributors
Published: February 2008

Core localized Alfvén eigenmodes in DIII-D [J. L. Luxon, Nucl. Fusion 42, 614 (2002)] and Joint European Torus (JET) [P. H. Rebut and B. E. Keen, Fusion Technol. 11, 13 (1987)] plasmas are driven by deuterium neutral beam ions traveling well below the Alfvén speed. Modes are observed in reverse magnetic shear discharges with deuterium ion velocities as low as 0.23 and 0.16 of the Alfvén speed parallel to the magnetic field in DIII-D and JET plasmas, respectively. Ellipticity-induced Alfvén eigenmodes in DIII-D and toroidicity-induced Alfvén eigenmodes in JET are excited by deuterium ions traveling well below the fundamental passing ion resonance condition, indicating the role of high-order resonances in driving these modes. NOVA-K analysis reveals many high-order resonances as contributing to the mode drive at high central safety factor due to the correspondingly large poloidal orbit width and the decrease in the perpendicular scale length of the modes.
Epitaxial assembly and ordering of two-dimensional colloidal crystals
Authors: Xie Rongguo , Liu Xiang-Yang
Published: February 2008

An epitaxial assembly method is described to direct the crystallization of two-dimensional colloidal crystals under an alternating electric field (AEF). By using a colloidal line as an epitaxial template, the colloidal crystals with a predefined orientation have been assembled at specified position of an electrode. The epitaxial correlation between the colloidal crystals and the template can be tuned by varying the frequency of the AEF. By control of the template and the frequency, well-defined linear defects have been incorporated into the colloidal crystals, whereas the unwanted defects can be in situ eliminated through a template-guided annealing process.
Confirmation of a large density variation along the magnetic axis of the Columbia Non-neutral Torus
Authors: Hahn Michael , Pedersen Thomas Sunn , Marksteiner Quinn , Berkery John W.
Published: February 2008

Significant variations in the density and potential along the axis of a pure electron plasma in the Columbia Non-neutral Torus (CNT) stellarator have now been measured. Large variations along the magnetic field are predicted by three-dimensional equilibrium reconstructions of CNT plasmas and by simple electrostatic and geometric arguments [Lefrancois and Pedersen, Phys. Plasmas 13, 120702 (2006)]. The density variation, naxis,ϕ=0°∕naxis,ϕ=90°, is measured directly for several different plasma equilibria, and has a median value of 7.8, consistent with the predicted density variation of 4.4, because the error bars are large. The associated variation in potential predicted from the Boltzmann relation, eΔΦ∕Te=ln(4.4)=1.5, was also measured experimentally. The median measured, eΔΦ∕Te, was 1.1, which is of the predicted sign and in rough agreement with the measurements, but smaller than predicted. The difference is statistically significant, but might be related to the imperfect numerical modeling of the complicated electrostatic boundary conditions in CNT. The measured variations reconfirm that the Debye lengths of these plasmas are small.
Dimensional reduction for generalized Poisson brackets
Authors: Acatrinei Ciprian Sorin
Published: February 2008

We discuss dimensional reduction for Hamiltonian systems which possess nonconstant Poisson brackets between pairs of coordinates and between pairs of momenta. The associated Jacobi identities imply that the dimensionally reduced brackets are always constant. Some examples are given alongside the general theory.
Investigation of the V-pit related morphological and optical properties of InGaN∕GaN multiple quantum wells
Authors: Lin F. , Xiang N. , Chen P. , Chow S. Y. , Chua S. J.
Published: February 2008

In this work, the effects of large V-pits on the morphological and optical properties of InGaN∕GaN multiple quantum wells (MQWs) were studied using scanning electron microscopy, transmission electron microscopy, and photoluminescence. InGaN∕GaN MQWs with high-density large V-pits were grown by metal organic chemical vapor deposition. In addition to the regular c-plane MQWs, the MQWs grown on the {101¯1} faceted sidewalls of the V-pits were also observed, which gave much higher emission energies than those of the c-plane MQWs. Furthermore, when the low-temperature GaN buffer was very thin, the {112¯m} (m⩾2) faceted sidewalls of the V-pits were observed. It was then found that MQWs grown on such sidewalls had emission energies between those of the c-plane MQWs and those of the {101¯1} faceted sidewall MQWs.
Density and size of reef fishes in and around a temperate marine reserve
Authors: Kleczkowski Matt , Babcock Russ C. , Clapin Geordie
Published: February 2008

The effects of marine reserve protection on the density, size, biomass, sex-ratio and overall assemblage structure of reef fishes were investigated at Kingston Reef Sanctuary, Rottnest Island, Western Australia. Significant trends in response to reserve protection were found for two species of top predators and several serially protogynous labrid species. The relative density and biomass of the heavily targeted Glaucosoma hebraicum was 10 and five times greater within the sanctuary respectively. Similarly, the biomass of the serranid, Epinephelides armatus, was 3.2 times greater in the sanctuary, although this difference was owing to a greater mean length not relative density. The male : female sex ratio for the labrid, Ophthalmolepis lineolatus, was significantly different between sanctuary and non-sanctuary sites, with the density of male O. lineolatus significantly greater within the sanctuary. Rottnest Island waters are largely restricted to recreational fishing, therefore these results suggest that a range of fish species around Rottnest Island are affected by recreational fishing, and that these effects are found in taxa beyond the primary target species. The patterns in the effects on bycatch species suggest that fishing-related mortality may be exerting a greater control on these populations than that exerted by natural predation.
Mushroom fruiting and climate change
Authors: Kauserud Håvard , Stige Leif Christian , Vik Jon Olav , Økland Rune H. , Høiland Klaus , Stenseth Nils Chr.
Published: March 2008

Many species of fungi produce ephemeral autumnal fruiting bodies to spread and multiply. Despite their attraction for mushroom pickers and their economic importance, little is known about the phenology of fruiting bodies. Using ≈34,500 dated herbarium records we analyzed changes in the autumnal fruiting date of mushrooms in Norway over the period 1940–2006. We show that the time of fruiting has changed considerably over this time period, with an average delay in fruiting since 1980 of 12.9 days. The changes differ strongly between species and groups of species. Early-fruiting species have experienced a stronger delay than late fruiters, resulting in a more compressed fruiting season. There is also a geographic trend of earlier fruiting in the northern and more continental parts of Norway than in more southern and oceanic parts. Incorporating monthly precipitation and temperature variables into the analyses provides indications that increasing temperatures during autumn and winter months bring about significant delay of fruiting both in the same year and in the subsequent year. The recent changes in autumnal mushroom phenology coincide with the extension of the growing season caused by global climate change and are likely to continue under the current climate change scenario.
Cleavage mechanism of human Mus81–Eme1 acting on Holliday-junction structures
Authors: Taylor Ewan R. , McGowan Clare H.
Published: March 2008

Recombination-mediated repair plays a central role in maintaining genomic integrity during DNA replication. The human Mus81–Eme1 endonuclease is involved in recombination repair, but the exact structures it acts on
in vivo
are not known. Using kinetic and enzymatic analysis of highly purified recombinant enzyme, we find that Mus81–Eme1 catalyzes coordinate bilateral cleavage of model Holliday-junction structures. Using a self-limiting, cruciform-containing substrate, we demonstrate that bilateral cleavage occurs sequentially within the lifetime of the enzyme–substrate complex. Coordinate bilateral cleavage is promoted by the highly cooperative nature of the enzyme and results in symmetrical cleavage of a cruciform structure, thus, Mus81–Eme1 can ensure coordinate, bilateral cleavage of Holliday junction-like structures.
Targeting the carbohydrates on HIV-1: Interaction of oligomannose dendrons with human monoclonal antibody 2G12 and DC-SIGN
Authors: Wang Sheng-Kai , Liang Pi-Hui , Astronomo Rena D. , Hsu Tsui-Ling , Hsieh Shie-Liang , Burton Dennis R. , Wong Chi-Huey
Published: March 2008

It is widely accepted that the heavily glycosylated glycoprotein gp120 on the surface of HIV-1 shields peptide epitopes from recognition by the immune system and may promote infection
in vivo
by interaction with dendritic cells and transport to tissue rich in CD4
+
T cells such as lymph nodes. A conserved cluster of oligomannose glycans on gp120 has been identified as the epitope recognized by the broadly HIV-1-neutralizing monoclonal antibody 2G12. Oligomannose glycans are also the ligands for DC-SIGN, a C-type lectin found on the surface of dendritic cells. Multivalency is fundamental for carbohydrate–protein interactions, and mimicking of the high glycan density on the virus surface has become essential for designing carbohydrate-based HIV vaccines and antiviral agents. We report an efficient synthesis of oligomannose dendrons, which display multivalent oligomannoses in high density, and characterize their interaction with 2G12 and DC-SIGN by a glycan microarray binding assay. The solution and the surface binding analysis of 2G12 to a prototype oligomannose dendron clearly demonstrated the efficacy of dendrimeric display. We further showed that these glycodendrons inhibit the binding of gp120 to 2G12 and recombinant dimeric DC-SIGN with IC
50
in the nanomolar range. A second-generation Man
9
dendron was identified as a potential immunogen for HIV vaccine development and as a potential antiviral agent.
HIV-1 matrix protein p17 induces human plasmacytoid dendritic cells to acquire a migratory immature cell phenotype
Authors: Fiorentini Simona , Riboldi Elena , Facchetti Fabio , Avolio Manuela , Fabbri Marco , Tosti Giorgio , Becker Pablo D. , Guzman Carlos A. , Sozzani Silvano , Caruso Arnaldo
Published: March 2008

Numerical and functional defects in plasmacytoid dendritic cells (pDCs) are an important hallmark of progressive HIV-1 infection, yet its etiology remains obscure. HIV-1 p17 matrix protein (p17) modulates a variety of cellular responses, and its biological activity depends on the expression of p17 receptors (p17Rs) on the surface of target cells. In this study, we show that peripheral blood pDCs express p17Rs on their surface and that freshly isolated pDCs are sensitive to p17 stimulation. Upon p17 treatment, pDCs undergo phenotypic differentiation with up-regulation of CCR7. A chemotaxis assay reveals that p17-treated pDCs migrate in response to CCL19, suggesting that these cells may acquire the ability to migrate to secondary lymphoid organs. In contrast, p17 does not induce release of type I IFN nor does it enhance pDC expression of CD80, CD86, CD83, or MHC class II. Microarray gene expression analysis indicated that p17-stimulated pDCs down-regulate the expression of molecules whose functions are crucial for efficient protein synthesis, protection from apoptosis, and cell proliferation induction. Based on these results, we propose a model where p17 induces immature circulating pDCs to home in lymph nodes devoid of their ability to serve as a link between innate and adaptative immune systems.
Automated image alignment for 2D gel electrophoresis in a high-throughput proteomics pipeline
Authors: Dowsey Andrew W. , Dunn Michael J. , Yang Guang-Zhong
Published: March 2008

Motivation: The quest for high-throughput proteomics has revealed a number of challenges in recent years. Whilst substantial improvements in automated protein separation with liquid chromatography and mass spectrometry (LC/MS), aka ‘shotgun’ proteomics, have been achieved, large-scale open initiatives such as the Human Proteome Organization (HUPO) Brain Proteome Project have shown that maximal proteome coverage is only possible when LC/MS is complemented by 2D gel electrophoresis (2-DE) studies. Moreover, both separation methods require automated alignment and differential analysis to relieve the bioinformatics bottleneck and so make high-throughput protein biomarker discovery a reality. The purpose of this article is to describe a fully automatic image alignment framework for the integration of 2-DE into a high-throughput differential expression proteomics pipeline.

Results: The proposed method is based on robust automated image normalization (RAIN) to circumvent the drawbacks of traditional approaches. These use symbolic representation at the very early stages of the analysis, which introduces persistent errors due to inaccuracies in modelling and alignment. In RAIN, a third-order volume-invariant B-spline model is incorporated into a multi-resolution schema to correct for geometric and expression inhomogeneity at multiple scales. The normalized images can then be compared directly in the image domain for quantitative differential analysis. Through evaluation against an existing state-of-the-art method on real and synthetically warped 2D gels, the proposed analysis framework demonstrates substantial improvements in matching accuracy and differential sensitivity. High-throughput analysis is established through an accelerated GPGPU (general purpose computation on graphics cards) implementation.

Availability: Supplementary material, software and images used in the validation are available at http://www.proteomegrid.org/rain/

Contact:  g.z.yang@imperial.ac.uk

Supplementary information: Supplementary data are available at Bioinformatics online.
In silico Biochemical Reaction Network Analysis (IBRENA): a package for simulation and analysis of reaction networks
Authors: Liu Gang , Neelamegham Sriram
Published: March 2008

Summary: We present In silico Biochemical Reaction Network Analysis (IBRENA), a software package which facilitates multiple functions including cellular reaction network simulation and sensitivity analysis (both forward and adjoint methods), coupled with principal component analysis, singular-value decomposition and model reduction. The software features a graphical user interface that aids simulation and plotting of in silico results. While the primary focus is to aid formulation, testing and reduction of theoretical biochemical reaction networks, the program can also be used for analysis of high-throughput genomic and proteomic data.

Availability: The software package, manual and examples are available at http://www.eng.buffalo.edu/~neel/ibrena

Contact:  neel@eng.buffalo.edu
ISD: a software package for Bayesian NMR structure calculation
Authors: Rieping Wolfgang , Nilges Michael , Habeck Michael
Published: March 2008

Summary: The conventional approach to calculating biomolecular structures from nuclear magnetic resonance (NMR) data is often viewed as subjective due to its dependence on rules of thumb for deriving geometric constraints and suitable values for theory parameters from noisy experimental data. As a result, it can be difficult to judge the precision of an NMR structure in an objective manner. The inferential structure determination (ISD) framework, which has been introduced recently, addresses this problem by using Bayesian inference to derive a probability distribution that represents both the unknown structure and its uncertainty. It also determines additional unknowns, such as theory parameters, that normally need to be chosen empirically. Here we give an overview of the ISD software package, which implements this methodology.

Availability:  http://www.bioc.cam.ac.uk/isd

Contact:  wolfgang.rieping@bioc.cam.ac.uk, michael.habeck@tuebingen.mpg.de
Inhibition of Cell Proliferation and MAP Kinase and Akt Pathways in Oral Squamous Cell Carcinoma by Genistein and Biochanin A
Authors: Johnson Tara L. , Lai Maria B. , Lai James C. K. , Bhushan Alok
Published: March 2008

High morbidity and mortality associated with oral squamous cell carcinoma (OSCC) are largely attributable to late stage diagnosis. Despite significant advances in therapeutic strategies, the five‐year survival rate for oral cancer remains at about 50%. A chemopreventive approach may be an effective alternative or adjunct to current therapies. Previous studies have shown anti‐tumor effects of isoflavones in several cancers, including oral cancer. However, their mechanisms of action are still unclear. We hypothesized that isoflavones inhibit multiple signaling pathways implicated in oral carcinogenesis. To address our hypothesis, we investigated the effects of three isoflavone derivatives, genistein, biochanin A and daidzein, on SCC15 and SCC25 squamous cell carcinoma cell lines. In cell proliferation experiments, we found that genistein and biochanin A inhibited SCC15 and SCC25 cell growth with an IC50 of 50 μM. We also investigated the effect of isoflavones on ERK and Akt pathways. Our results, from western blot analysis, suggest that both genistein and biochanin A induced decreases in phosphorylation of ERK and Akt at treatment concentrations of 20, 50 and 100 μM. Taken together, our results clearly demonstrate a differential regulation of signaling pathways by various isoflavones in OSCC cell lines. Thus, tumor progression models can be utilized to study the preventive and therapeutic roles of isoflavones in oral cancer cell lines.
Physical factors mediate effects of grazing by a non-indigenous snail species on saltmarsh cordgrass (Spartina alterniflora) in New England marshes
Authors: Tyrrell Megan C. , Dionne Michele , Edgerly Jessica A.
Published: February 2008

Tyrrell, M. C., Dionne, M., and Edgerly, J. A. 2008. Physical factors mediate effects of grazing by a non-indigenous snail species on saltmarsh cordgrass (Spartina alterniflora) in New England marshes. – ICES Journal of Marine Science, 65: 746–752. In the southeastern US, grazing by a common indigenous littorinid snail has caused large declines in the biomass of saltmarsh cordgrass (Spartina alterniflora). In northeastern marshes, a closely related but non-indigenous snail may also negatively affect production of this key marsh-building plant. We manipulated densities of the gastropod Littorina littorea at two sites to investigate the effect of its grazing on plant production and sediment accumulation. The effects of the manipulation differed between sites. The site with longer inundation periods, lower elevation, and poorer drainage attributable to smaller sediment grain size had more stressful conditions for S. alterniflora. At that site, protection from snail grazing resulted in higher end-of-season plant biomass than all the other treatments and controls. Rates of sediment accumulation were also lower at that site, and the difference between sites increased as the season progressed. At the site where physical conditions were benign, snail manipulation had no effect on S. alterniflora biomass. The nature of the physical conditions at a site may influence the susceptibility of S. alterniflora to grazing pressure by this ubiquitous snail species. Accelerating anthropogenic impacts, such as sea-level rise, could further stress saltmarsh plants, leaving them increasingly susceptible to herbivory.
Fluid Shear Stress and Inner Curvature Remodeling of the Embryonic Heart. Choosing the Right Lane!
Authors: Hierck Beerend P. , Van der Heiden Kim , Poelma Christian , Westerweel Jerry , Poelmann Robert E.
Published: March 2008

Cardiovascular development is directed or modulated by genetic and epigenetic factors. The latter include blood flow-related shear stress and blood pressure-related circumferential strain. This review focuses on shear stress and its effects on endothelial cells lining the inner surfaces of the heart and blood vessels. Flow characteristics of the embryonic blood, like velocity, viscosity and periodicity, are taken into account to describe the responses of endothelial cells to shear stress and the sensors for this friction force. The primary cilium, which is an integral part of the shear sensor, connects to the cytoskeletal microtubules and transmits information about the level and direction of blood flow into the endothelial cell. When the heart remodels from a more or less straight into a c-shaped tube the sharp curvature, in combination with the small vessel dimensions and high relative viscosity, directs the highest shear stress to the inner curvature of this pump. This proves to be an important epigenetic modulator of cardiac morphogenesis because when shear stress is experimentally altered inner curvature remodeling is affected which leads to the development of congenital cardiovascular anomalies. The best of both worlds, mechanics and biology, are used here to describe early cardiogenesis.
Transitional Cell Carcinoma of the Upper Ureter Metastatic to the Thoracic Spine Presenting as a Spinal Cord Compression
Authors: Larkin J. O. , Cullen I. M. , Kelleher M. O. , Fitzgibbon J. , Keohane K. , O'Sullivan M. G. J. , Rogers E.
Published: March 2008

We performed a left nephroureterectomy for a gentleman with transitional cell carcinoma of the upper ureter. Histological analysis revealed it to be a T1 lesion, but to be highly mitotically active. The gentleman defaulted on adjuvant therapy and defaulted on follow-up. He represented with symptoms of acute spinal cord compression and magnetic resonance imaging demonstrated a lesion at T6/7. Neurosurgical resection of the lesion showed it to be a metastatic deposit from the ureteric primary. Despite surgical debulking and subsequent radiotherapy to the lesion, the patient died secondary to metastatic complications. This case report is of interest to the surgeon as it demonstrates both the high metastatic potential of upper tract carcinomas and educates the surgeon on the presentation of acute spinal cord compression.
A Homolog ofScRAD5Is Involved in DNA Repair and Homologous Recombination in Arabidopsis
Authors: Chen I-Peng , Mannuss Anja , Orel Nadiya , Heitzeberg Fabian , Puchta Holger
Published: March 2008

Rad5 is the key component in the Rad5-dependent error-free branch of postreplication repair in yeast (Saccharomyces cerevisiae). Rad5 is a member of the Snf2 ATPase/helicase family, possessing as a characteristic feature, a RING-finger domain embedded in the Snf2-helicase domain and a HIRAN domain. Yeast mutants are sensitive to DNA-damaging agents and reveal differences in homologous recombination. By sequence comparisons we were able to identify two homologs (AtRAD5a and AtRAD5b) in the Arabidopsis thaliana genome, sharing about 30% identity and 45% similarity to yeast Rad5. AtRad5a and AtRad5b have the same kind of domain organization with a higher degree of similarity to each other than to ScRad5. Surprisingly, both genes differ in function: whereas two independent mutants of Atrad5a are hypersensitive to the cross-linking agents mitomycin C and cis-platin and to a lesser extent to the methylating agent, methyl methane sulfonate, the Atrad5b mutants did not exhibit any sensitivity to all DNA-damaging agents tested. An Atrad5a/Atrad5b double mutant resembles the sensitivity phenotype of the Atrad5a single mutants. Moreover, in contrast to Atrad5b, the two Atrad5a mutants are deficient in homologous recombination after treatment with the double-strand break-inducing agent bleomycin. Our results suggest that the RAD5-dependent error-free branch of postreplication repair is conserved between yeast and plants, and that AtRad5a might be functionally homologous to ScRad5.
Academic Status for University Librarians in Tanzania:
Challenges and Prospects
Authors: Newa John M.
Published: March 2008

An account is presented of the struggle for academic status by
university librarians in Tanzania. The literature on the academic status
of university libraries in Africa is reviewed. The arguments for, and
benefits, of, academic status to both librarians and users are discussed
in relation to the general African and specifically Tanzanian situation.
An assessment is made of the challenges and prospects for the
realisation and consolidation of academic status.
Architects about briefing
Authors: Bogers Tetske , van Meel Juriaan J. , van der Voordt Theo J.M.
Published: March 2008

Purpose

This paper aims to provide a better understanding of how architects perceive and use briefing documents. It discusses what type of briefing information architects find relevant for their design process, and how and when briefing information should be presented. It also gives recommendations for clients and consultants that produce the brief.

Design/methodology/approach

The article is based on a review of briefing literature, six exploratory interviews with two clients, two architects and two consultants, 18 in‐depth interviews with Dutch architects, and a workshop with Dutch experts on briefing.

Findings

A brief (or “program of requirements”) is a crucial means of communication in the interaction between clients and architects. A good brief explains what the client needs, desires and expects from a project. This is all crucial information for the design process. In the interviews, however, many architects indicated that, in daily practice, briefing documents are not as useful as they should be. In their opinion, briefs are often too long, containing overly‐detailed specifications, that are not always clear, consistent or complete.

Practical implications

In addition to the analysis of architects' complaints, six recommendations are given with respect to the briefing process, the contents and structure of the brief, and the status of the brief.

Originality/value

Most publications on briefing focus on the client and brief writing at the start of a project. The present paper discusses the opinions and experiences of the architect and the use of the brief in the design process.
Brand familiarity: its effects on satisfaction evaluations
Authors: Tam Jackie L.M.
Published: March 2008

Purpose

The purpose of this paper is to examine the moderating effects of brand familiarity on satisfaction evaluations and behavioral intentions.

Design/methodology/approach

A longitudinal survey involving pre‐purchase measures and post‐purchase measures was conducted with consumers in a restaurant setting. The hypotheses were assessed through LISREL methodology.

Findings

The results showed that there are some similarities and differences among customers with different levels of brand familiarity regarding satisfaction formation and behavioral intentions.

Research limitations/implications

A self‐reported item was used to measure brand familiarity. Although there was some evidence to support that the measure captured what it was intended to measure, it would be desirable to develop a multi‐item scale for this construct. There is also a need to extend the findings to other service industries.

Practical implications

Marketers should familiarize customers with a service while capturing opportunities to create a positive experience to gain customers' future purchases.

Originality/value

The study offers some insights into the effects of brand familiarity on satisfaction evaluations and behavioral intentions. It is particularly relevant for marketing services that are high in experience qualities.