bluuebunny/crossref_metadata_2025 huggingface dataset:
Carbon budget of tropical forests in Southeast Asia and the effects of deforestation: an approach using a process-based model and field measurements
Authors: Adachi M. , Ito A. , Ishida A. , Kadir W. R. , Ladpala P. , Yamagata Y.
Published: March 2011

Abstract. More reliable estimates of carbon (C) stock within forest ecosystems and C emission induced by deforestation are urgently needed to mitigate the effects of emissions on climate change. A process-based terrestrial biogeochemical model (VISIT) was applied to tropical primary forests of two types (a seasonal dry forest in Thailand and a rainforest in Malaysia) and one agro-forest (an oil palm plantation in Malaysia) to estimate the C budget of tropical ecosystems, including the impacts of land-use conversion, in Southeast Asia. Observations and VISIT model simulations indicated that the primary forests had high photosynthetic uptake: gross primary production was estimated at 31.5–35.5 t C ha−1 yr−1. In the VISIT model simulation, the rainforest had a higher total C stock (plant biomass and soil organic matter, 301.5 t C ha−1) than that in the seasonal dry forest (266.5 t C ha−1) in 2008. The VISIT model appropriately captured the impacts of disturbances such as deforestation and land-use conversions on the C budget. Results of sensitivity analysis implied that the ratio of remaining residual debris was a key parameter determining the soil C budget after deforestation events. The C stock of the oil palm plantation was about 46% of the rainforest's C at 30 yr following initiation of the plantation, when the ratio of remaining residual debris was assumed to be about 33%. These results show that adequate forest management is important for reducing C emission from soil and C budget of each ecosystem must be evaluated over a long term using both the model simulations and observations.
A regional ocean circulation model for the mid-Cretaceous North Atlantic Basin: implications for black shale formation
Authors: Topper R. P. M. , Trabucho Alexandre J. , Tuenter E. , Meijer P. Th.
Published: March 2011

Abstract. High concentrations of organic matter accumulated in marine sediments during Oceanic Anoxic Events (OAEs) in the Cretaceous. Model studies examining these events invariably make use of global ocean circulation models. In this study, a regional model for the North Atlantic Basin during OAE2 at the Cenomanian-Turonian boundary has been developed. A first order check of the results has been performed by comparison with the results of a recent global Cenomanian CCSM3 run, from which boundary and initial conditions were obtained. The regional model is able to maintain tracer patterns and to produce velocity patterns similar to the global model. The sensitivity of the basin tracer and circulation patterns to changes in the geometry of the connections with the global ocean is examined with three experiments with different bathymetries near the sponges. Different geometries turn out to have little effect on tracer distribution, but do affect circulation and upwelling patterns. The regional model is also used to test the hypothesis that ocean circulation may have been behind the deposition of black shales during OAEs. Three scenarios are tested which are thought to represent pre-OAE, OAE and post-OAE situations. Model results confirm that Pacific intermediate inflow together with coastal upwelling could have enhanced primary production during OAE2. A low sea level in the pre-OAE scenario could have inhibited large scale black shale formation, as could have the opening of the Equatorial Atlantic Seaway in the post-OAE scenario.
Influence of the compiler on multi-CPU performance of WRFv3
Authors: Langkamp T.
Published: March 2011

Abstract. The Weather Research and Forecasting system version 3 (WRFv3) is an open source and state of the art numerical regional climate model used in climate related sciences. Over the years the model has been successfully optimized on a wide variety of clustered compute nodes connected with high speed interconnects. This is currently the most used hardware architecture for high-performance computing. As such, understanding WRFs dependency on the various hardware elements like the CPU, its interconnects, and the software is crucial for saving computing time. This is important because computing time in general is rare, resource intensive, and hence very expensive. This paper evaluates the influence of different compilers on WRFs performance, which was found to differ up to 26%. The paper also evaluates the performance of different message passing interface library versions, a software which is needed for multi CPU runs, and of different WRF versions. Both showed no significant influence on the performance for this test case on the used High Performance Cluster (HPC) hardware. Some emphasis is also laid on the applied non-standard method of performance measuring, which was required because of performance fluctuations between identical runs on the used HPC. Those are caused by contention for network resources, a phenomenon examined for many HPCs.
Excitation of low frequency oscillations in a planetary magnetosheath by supersonic shear flow
Authors: Borisov N. , Fränz M.
Published: March 2011

Abstract. We show that the slow magnetosonic (SM) perturbations generated in the vicinity of the magnetopause, due to the excitation of the Kelvin-Helmholtz (K.-H.) instability in the case of a supersonic flow velocity, are transformed into fast magnetosonic (FM) waves which can propagate into the magnetosheath. Under the conditions discussed in this paper, the FM wave has negative energy in the stationary (magnetospheric) coordinate frame. Due to this the outgoing FM wave increases the growth rate of the K.-H. instability excited at the magnetopause. Within the linear theory, we investigate the influence of the excited FM wave on the growth rate of the K.-H. instability. Simultaneously we predict the transformation of the SM mode into kinetic Alfvén (KA) mode. Thus, in general, two types of waves with different polarizations (the KA wave and the FM wave) should appear in the magnetosheath due to the excitation of the K.-H. instability. At the same time, the SM perturbations are only present in the localized region where the K.-H. instability is excited. To correctly describe the excitation of waves, we use two-fluid (for electrons and ions) magnetohydrodynamics. This approach is more general than the ideal magnetohydrodynamics and allows us to take into account the effects associated with the finite Larmor radius of ions. Also it can be used to investigate the K.-H. instability in a multi-component plasma, or in the case where the frequency of perturbations is of the order of the gyrofrequency of oxygen ions which may occur, for example, at the magnetosheath of Mars.
The "tipping" temperature within Subglacial Lake Ellsworth, West Antarctica and its implications for lake access
Authors: Thoma M. , Grosfeld K. , Mayer C. , Smith A. M. , Woodward J. , Ross N.
Published: March 2011

Abstract. We present results from new geophysical data allowing 3-D modelling of the water flow within Subglacial Lake Ellsworth (SLE), West Antarctica. Our simulations indicate that this lake has a novel temperature distribution due to significantly thinner ice than other surveyed subglacial lakes. The critical pressure boundary (tipping depth), established from the semi-empirical Equation of State, defines whether the lake's flow regime is convective or stratified. It passes through SLE and separates different temperature (and flow) regimes on either side of the lake. Our results have implications for the location of proposed access holes into SLE, the choice of which will depend on scientific or operational priorities. If an understanding of subglacial lake water properties and dynamics is the priority, holes are required in a basal freezing area at the North end of the lake. This would be the preferred priority suggested by this paper, requiring temperature and salinity profiles in the water column. A location near the Southern end, where bottom currents are lowest, is optimum for detecting the record of life in the bed sediments; to minimise operational risk and maximise the time span of a bed sediment core, a location close to the middle of the lake, where the basal interface is melting and the lake bed is at its deepest, remains the best choice. Considering potential lake-water salinity and ice-density variations, we estimate the critical tipping depth, separating different temperature regimes within subglacial lakes, to be in about 2900 to 3045 m depth.
Role of road traffic accidents and other traumatic events in the onset of chronic widespread pain: Results from a population‐based prospective study
Authors: Jones Gareth T. , Nicholl Barbara I. , McBeth John , Davies Kelly A. , Morriss Richard K. , Dickens Chris , Macfarlane Gary J.
Published: March 2011

Objective

To determine the relationship between physically traumatic events and the onset of chronic widespread pain (CWP).

Methods

This was a case–control study nested within a large prospective cohort. CWP was determined, by questionnaire, as per the American College of Rheumatology fibromyalgia classification criteria. Data were also collected on psychological health, health behavior, and sleep problems. Participants without CWP were then followed up at 4 years, and (new‐onset) CWP was determined in the same manner. At followup, participants were also asked to report whether they had experienced any of a series of physically traumatic events between baseline and followup.

Results

A total of 2,069 individuals (46.6%) participated at followup, and 241 of these individuals (11.6%) reported CWP. More than one‐third of the study population reported at least 1 physically traumatic event; although these individuals were more likely to develop CWP, this relationship was completely attenuated after adjustment for confounding (odds ratio 1.01, 95% confidence interval 0.73–1.40). However, there was some evidence to suggest that involvement in a road traffic accident, specifically, may confer an increase in the risk of CWP onset.

Conclusion

This study provides support for the “at risk” phenotype hypothesis, where individuals characterized by poorer health and psychological variables may be predisposed to develop CWP following a traumatic trigger. However, although this has been seen with road traffic accidents, it is not the case with other events. Future research should examine what is peculiar about an accident, or about one's reaction to it, that confers this increase in the risk of CWP onset.
Domains of health‐related quality of life important and relevant to multiethnic English‐speaking Asian systemic lupus erythematosus patients: A focus group study
Authors: Ow Yen Ling Mandy , Thumboo Julian , Cella David , Cheung Yin Bun , Yong Fong Kok , Wee Hwee Lin
Published: March 2011

Objective

To identify health‐related quality of life (HRQOL) domains of importance to multiethnic Asian systemic lupus erythematosus (SLE) patients, to identify content gaps in existing SLE‐specific HRQOL measures, and to determine whether the Patient‐Reported Outcomes Measurement Information System (PROMIS) item banks could serve as a core set of questions for HRQOL assessment among SLE patients.

Methods

English‐speaking patients with physician‐diagnosed SLE from a specialist clinic in a tertiary care hospital in Singapore and a patient support group were recruited. Thematic analysis was performed to distill themes from transcripts through open coding by 2 independent coders and axial coding for refinement of categories. Items from 3 existing SLE‐specific measures and PROMIS Version 1.0 Item Banks were compared with identified subthemes.

Results

Twenty‐seven female and 2 male participants (21 Chinese, 4 Malay, 3 Indian, 1 other) ages 23–62 years participated in 6 focus groups and 2 individual interviews, respectively. Twenty‐one domains and 92 subthemes were identified. Domains of family, relationships, stigma and discrimination, and freedom were unaddressed by existing SLE‐specific measures. Forty subthemes from 14 domains were addressed by the PROMIS Version 1.0 Item Banks (Physical Function, Pain, Fatigue, Sleep Disturbance, Sleep‐Related Impairment, Anger, Anxiety, and Depression banks).

Conclusion

Family and stigma and discrimination (identified as content gaps) may be accentuated in the Asian sociocultural context. PROMIS item banks have tremendous potential to serve as a core set of items for HRQOL assessment in SLE patients. Additional items may be written to fill the gaps in existing PROMIS item banks.
Multilevel strategies for the retrofit of large‐scale industrial water system: A brewery case study
Authors: Tokos Hella , Pintarič Zorka Novak , Yang Yongrong , Kravanja Zdravko
Published: March 2011

This article presents an approach to designing a large‐scale water system, which integrates water‐using operations and wastewater treatment units in different production sections within the same network. This approach uses a mixed‐integer nonlinear programming (MINLP) model for water reuse and regeneration reuse in batch and semicontinuous processes. The application of this mathematical formulation to large‐scale industrial problems with changing daily production schedule leads to huge and complex mathematical models. Two alternative multilevel strategies are proposed to solve such problems by means of temporal decomposition. The approach is illustrated with a brewery case study that integrates water consumers in two production sections. The results obtained show that, despite the high piping cost, integration of both sections yields better result than the separate water network design in each section. © 2011 American Institute of Chemical Engineers AIChE J, 2012
Partial and total monosomal karyotypes in myelodysplastic syndromes: Comparative prognostic relevance among 421 patients
Authors: Belli Carolina B. , Bengió Raquel , Aranguren Pedro Negri , Sakamoto Francisco , Flores María G. , Watman Nora , Nucifora Elsa , Prates María V. , Arbelbide Jorge , Larripa Irene
Published: March 2011

Myelodysplastic syndromes (MDS) include a group of heterogeneous hematological disorders with a variable risk of leukemic evolution and short survival. Around 40–50% of patients show abnormal karyotypes that are mostly characterized by monosomies or deletions. Cytogenetic findings are an independent prognostic factor and the International prognostic scoring system (IPSS) differentiates three cytogenetic categories, despite the Intermediate one being heterogeneous. The aim of this study, including 421 Argentinean patients with primary MDS, is to characterize the cytogenetic profile, to test its prognostic value and to compare partial and monosomal karyotypes against other cytogenetic findings. An abnormal karyotype (median survival: 26 months) was observed in 176 patients. The presence of complex karyotypes, number of alterations, and the IPSS cytogenetic groups showed significant differences for predicting outcome. Behavior of patients with isolated deletions (median survival: 49 months) did not differ from those with normal karyotype (56 months, P = 0.654) or Good prognostic findings (43 months, P = 0.371). However, a worse prognosis was observed when another alteration was added (31 months, P = 0.043). Karyotypes with autosomal monosomies (median survival: 16 months) had a prognostic impact similar to other Poor cytogenetic findings (17 months, P = 0.626). In our population classified according to French‐American‐British (FAB) or World Health Organization (WHO), this new categorization of cytogenetic abnormalities, recognizing three different risk groups, showed an independent prognostic impact and a better discriminating power than the IPSS categories. It can be concluded that all isolate deletions (excluding 7q‐) are good prognostic findings and all monosomies (excluding Y chromosome loss) are bad indicators. Am. J. Hematol., 2011. © 2011 Wiley‐Liss, Inc.
Observations of hand preference in wild groups of white‐faced sakis (Pithecia pithecia) in Suriname
Authors: Smith H.M. , Thompson C.L.
Published: March 2011

Hand preference is well observed in humans and some primates. Unlike many other primates, however, humans show a consistent hand preference across a variety of tasks, and a distinct right‐handed skew at the population level. Although there are a moderate number of published studies, primate hand preference literature is unbalanced by the large number of studies on only a few species. No previous studies have addressed hand preference in white‐faced sakis (WFS;Pithecia pithecia). We followed three habituated groups of wild WFS in Suriname and recorded individual hand preference for six different manual behaviors. There was no consistent hand preference across a range of uni‐manual behaviors for any individual. Likewise, there were significantly more ambidextrous individuals in the population than expected (χ2(df = 2) = 11.2,P= 0.004) and thus, no population level hand preference. Our findings contribute baseline data to the debate of primate hand lateralization, and support the notion that lateralization of hand function does not characterize all species. Am. J. Primatol. 73:655–664, 2011. © 2011 Wiley‐Liss, Inc.
Preparation of poly(ethylene terephthalate)‐based proton‐exchange membranes through the ultraviolet‐induced graft copolymerization of allyl methacrylate for applications in fuel cells
Authors: Khan Mohammad B. , Ahmed Mostak , Khan Mubarak A. , Alam Syed S. , Khan M. Anwar H.
Published: March 2011

The ultraviolet‐induced graft copolymerization of allyl methacrylate into poly(ethylene terephthalate) films and the subsequent sulfonation of the grafted film were performed to prepare a polymer electrolyte membrane (PEM). The sulfonation reaction occurred at the grafted chain under mild conditions; that is, the grafted film was easily transformed into a PEM. The mechanical, chemical, and thermal properties of the prepared PEM (i.e., the ion‐exchange capacity, water uptake, tensile strengths at different water uptakes and temperatures, stability in hydrogen peroxide solutions, and proton conductivity) were measured with titrimetric and gravimetric analyses; most were found to be better than those of Nafion. The maximum ion‐exchange capacity and proton conductivity of the PEM were observed to be 0.072 mmol/g and 0.0458 S/cm, respectively. Because this PEM is inexpensive to prepare with available raw materials and has the properties required for fuel cells, it could be an attractive and suitable device for use in fuel‐cell technology. © 2011 Wiley Periodicals, Inc. J Appl Polym Sci, 2011
Zinc‐based catalyst for the ring‐opening polymerization of cyclic esters
Authors: Yuan Yuping , Jing Xiabin , Xiao Haihua , Chen Xuesi , Huang Yubin
Published: March 2011

A zinc‐based catalyst zinc bis[bis(trimethylsilyl)amide] was used for the polymerization of cyclic esters including L‐lactide (L‐LA) and 2‐methyl‐2‐carboxyl‐propylene carbonate (MBC). The polymerization of L‐lactide in THF could be carried out successfully under mild conditions in very short time by using the zinc catalyst and alcohols as the initiators. Kinetic study in solution polymerization prooved the polymerization has high monomer conversion degree close to 100% and the molecular weight of the resulting polyester has linear increase with the increase of [M]0 /[I] (molar ratio of monomer to initiator). Sequential polymerization of L‐LA and MBC in THF also showed high MBC conversion of 94% with a narrow molecualr weight maintained, indicating a living nature of this polymerization. The zinc catalyst system has also been used for the L‐LA bulk polymerization with a high monomer conversion. 13C NMR indicated the polymer possesses high regioregularity and the minor regioirregular component was owing to the D‐LA in the monomer inserted into the polymer mainchain during the transesterifcation. Interaction between monomer and zinc catalyst has been found to be a key factor to sustain a homogenous solution during the initiating procedure. © 2011 Wiley Periodicals, Inc. J Appl Polym Sci, 2011
Application of the X‐shooter physical model to flexure analysis
Authors: Bristow P. , Vernet J. , Modigliani A.
Published: March 2011

We use the large number of available X‐shooter automatic flexure compensation exposures that have accumulated in the archive to constrain parameters of the instrument physical model. This enables us to establish which physical model parameters vary with instrument orientation and hence directly identify physical mechanisms that give rise to flexure effects in the spectral format (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
X‐shooting Herbig Ae/Be stars: Accretion probed by near‐infrared He I emission
Authors: Oudmaijer R.D. , van den Ancker M.E. , Baines D. , Caselli P. , Drew J.E. , Hoare M.G. , Lumsden S.L. , Montesinos B. , Sim S. , Vink J.S. , Wheelwright H.E. , de Wit W.J.
Published: March 2011

The Herbig Ae/Be stars are intermediate mass pre‐main sequence stars that bridge the gap between the low mass T Tauri stars and the Massive Young Stellar Objects. In this mass range, the acting star forming mechanism switches from magnetically controlled accretion to an as yet unknown mechanism, but which is likely to be direct disk accretion onto the star. We observed a large sample of Herbig Ae/Be stars with X‐shooter to address this issue from a multi‐wavelength perspective. It is the largest such study to date, not only because of the number of objects involved, but also because of the large wavelength coverage from the blue to the near‐infrared. This allows many accretion diagnostics to be studied simultaneously. By correlating the various properties with mass, temperature and age, we aim to determine where and whether the magnetically controlled mass accretion mechanism halts and the proposed direct disk accretion takes over. Here, we will give an overview of the background, present some observations and discuss our initial results. We will introduce a new accretion diagnostic for the research of Herbig Ae/Be stars, the HeI 1.083 μm line (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
X‐shooter GTO observations and chemical tagging of two main‐sequence stars in the globular cluster NGC 2808
Authors: Bragaglia A. , Carretta E. , Gratton R.G. , Lucatello S. , Milone A. , Piotto G. , D'Orazi V. , Cassisi S. , Sneden C. , Bedin R.L.
Published: March 2011

We observed two main sequence stars in the globular cluster NGC 2808, using X‐shooter. We selected one of the targets on the blue main sequence (bMS) and one on the red main sequence (rMS) and measured abundances for several light elements that are expected to be different in stars of first and second generations in globular clusters. The differences between the bMS and the rMS stars amply exceed the errors and is in agreement with a difference in products of hydrogen burning at high temperature. More data are required to put the findings on more solid basis and to try to distinguish between the different models proposed to explain the formation of globular clusters (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Interacting binaries: Science cases where simultaneous multicolor medium‐resolution spectroscopy makes a difference
Authors: Mason E. , Gandhi P.
Published: March 2011

This contribution to “The 1st year of science with X‐shooter” conference illustrates 2 different applications of the new ESO multi‐waveband spectrograph to the study of interacting binaries. In particular we present spectra collected during the late decline of U Sco 2010 outburst and during a low/hard X‐ray phase of the black hole candidate GX339‐4. In both cases the unprecedented spectral coverage and resolution offered by X‐shooter have unveiled unexpected features (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
GRB‐selected galaxies
Authors: Jakobsson P. , Malesani D. , Hjorth J. , Fynbo J.P.U. , Milvang‐Jensen B.
Published: March 2011

We describe the current status and recent results from our Swift/VLT legacy survey, a VLT Large Programme aimed at characterizing the host galaxies of a homogeneously selected sub‐sample of Swift gamma‐ray bursts (GRBs). The immediate goals are to determine the host luminosity function, study the effects of reddening, determine the fraction of Lyα emitters in the hosts, and obtain redshifts for targets without a reported one. We have defined a very carefully selected sample, obeying strict and well‐defined criteria: 68 targets in total. Among the preliminary results is a large optical detection rate, the lack of extremely red objects (only one possible case in the sample), and 10 new GRB redshifts with the mean redshift of the host sample assessed to be 〈z 〉 ≳ 2 (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
The high redshift intergalactic and interstellar media with X‐shooter
Authors: Petitjean P.
Published: March 2011

I review here a few important questions that X‐shooter can help tackle and answer in the field of quasar absorption lines. This includes (i) determine the ionizing background and the physical state of the inter‐galactic medium (IGM) by analysing the characteristics of the Lyman‐α forest and the proximity effect; (ii) investigate the metal content of the high redshift IGM; (iii) study the small scale transverse correlation in the IGM by observing pairs of quasars with small separation in the sky; (iv) study the galaxy‐IGM relations by detecting the counterpart of damped Lyman‐α systems (DLAs) or determining the correlation between the properties of galaxies and absorption lines; (v) detect and characterize the long‐sought cold diffuse molecular (H2 and CO) interstellar medium (ISM) of high redshift galaxies and study its dust content (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Embryos as targets of endocrine disrupting contaminants in wildlife
Authors: Hamlin Heather J. , Guillette Louis J.
Published: March 2011

Environmental contaminants are now a ubiquitous part of the ecological landscape, and a growing literature describes the ability of many of these chemicals to alter the developmental trajectory of the embryo. Because many environmental pollutants readily bioaccumulate in lipid rich tissues, wildlife can attain considerable body burdens. Embryos are often exposed to these pollutants through maternal transfer, and a growing number of studies report long‐term or permanent developmental consequences. Many biological mechanisms are reportedly affected by environmental contaminants in the developing embryo and fetus, including neurodevelopment, steroidogenesis, gonadal differentiation, and liver function. Embryos are not exposed to one chemical at a time, but are chronically exposed to many chemicals simultaneously. Mixture studies show that for some developmental disorders, mixtures of chemicals cause a more deleterious response than would be predicted from their individual toxicities. Synergistic responses to low dose mixtures make it difficult to estimate developmental outcomes, and as such, traditional toxicity testing often results in an underestimate of exposure risks. In addition, the knowledge that biological systems do not necessarily respond in a dose‐dependent fashion, and that very low doses of a chemical can prove more harmful than higher doses, has created a paradigm shift in studies of environmental contaminant‐induced dysfunction. Although laboratory studies are critical for providing dose‐response relationships and determining specific mechanisms involved in disease etiology, wildlife sentinels more accurately reflect the genetic diversity of real world exposure conditions, and continue to alert scientists and health professionals alike of the consequences of developmental exposures to environmental pollutants. Birth Defects Research (Part C) 93:19–33, 2011. © 2011 Wiley‐Liss, Inc.
Stimulation of human embryonic stem cell‐derived cardiomyocytes on thin‐film microelectrodes
Authors: Viitanen Jouko , Heimala Päivi , Hokkanen Ari , Iljin Kristiina , Kerkelä Erja , Kolari Kai , Kattelus Hannu
Published: March 2011

We describe successful long‐term stimulation of human embryonic stem cell‐derived cardiomyocyte clusters on thin‐film microelectrode structures in vitro. Interdigitated electrode structures were constructed using plain titanium on glass as the electrode material. Titanium rapidly oxidizes in atmospheric conditions to produce an insulating TiOχ layer with high relative permittivity. Capacitive coupling to the incubation medium and to the cells adherent to the electrodes was still efficient, and the dielectric layer prevented electrolysis, allowing a wider window of possible stimulation amplitudes to be used, relative to conducting surfaces. A common hypothesis suggests that to achieve proper differentiation of electroactive cells from the stem cells electrical stimuli are also needed. Spontaneously beating cardiomyocyte clusters were seeded on the glass‐electrode surfaces, and we successfully altered and resynchronized a clearly different beat interval. The new pace was reliably maintained for extended periods of several tens of minutes.
Enhanced productivity of NS0 cells in fed‐batch culture with cholesterol nanoparticle supplementation
Authors: Wu Yun , Ma Ningning , Wyslouzil Barbara E. , Chalmers Jeffrey J. , McCormick Ellen , Casnocha Susan A.
Published: March 2011

NS0 cells are an important industrial cell line for the production of therapeutic monoclonal antibodies. Culturing these cells is challenging because they are cholesterol auxotrophs, and providing cholesterol to the cells is hampered by the low solubility of lipids in aqueous medium. Limited loading capacity, precipitation, instability, and toxicity are associated with traditional delivery methods that involve solvents or carrier molecules. In this work, nanoparticle cholesterol mixtures (NCM) were produced by electrohydrodynamic spraying and added directly to a cholesterol auxotroph NS0 cell line. Compared to a cholesterol‐cyclodextrin solution and a commercial proprietary cholesterol solution, SyntheChol™ NS0 supplement, NCM is significantly less cytotoxic. In the fed batch cell culture process, product titer was increased by 32% when the NCM supplement replaced SyntheChol™ NS0 supplement. An even greater product titer improvement, 64%, was achieved when both NCM and SyntheChol™ NS0 supplements were used in the fed‐batch process. © 2011 American Institute of Chemical Engineers Biotechnol. Prog., 2011
Engineering an Allosteric Binding Site for Aminoglycosides into TEM1‐β‐Lactamase
Authors: Volkov Alexander N. , Barrios Humberto , Mathonet Pascale , Evrard Christine , Ubbink Marcellus , Declercq Jean‐Paul , Soumillion Patrice , Fastrez Jacques
Published: March 2011

Allosteric regulation of enzyme activity is a remarkable property of many biological catalysts. Up till now, engineering an allosteric regulation into native, unregulated enzymes has been achieved by the creation of hybrid proteins in which a natural receptor, whose conformation is controlled by ligand binding, is inserted into an enzyme structure. Here, we describe a monomeric enzyme, TEM1‐β‐lactamase, that features an allosteric aminoglycoside binding site created de novo by directed‐evolution methods. β‐Lactamases are highly efficient enzymes involved in the resistance of bacteria against β‐lactam antibiotics, such as penicillin. Aminoglycosides constitute another class of antibiotics that prevent bacterial protein synthesis, and are neither substrates nor ligands of the native β‐lactamases. Here we show that the engineered enzyme is regulated by the binding of kanamycin and other aminoglycosides. Kinetic and structural analyses indicate that the activation mechanism involves expulsion of an inhibitor that binds to an additional, fortuitous site on the engineered protein. These analyses also led to the defining of conditions that allowed an aminoglycoside to be detected at low concentration.
Tungsten(0)‐ and Rhenium(I)‐Catalyzed Tandem Cyclization of Acetylenic Dienol Silyl Ethers Based on Geminal Carbo‐Functionalization of Alkynes
Authors: Kusama Hiroyuki , Karibe Yusuke , Imai Rie , Onizawa Yuji , Yamabe Hokuto , Iwasawa Nobuharu
Published: March 2011

Tungsten(0)‐ and rhenium(I)‐catalyzed reactions of acetylenic dienol silyl ethers based on the concept of geminal carbo‐functionalization of alkynes are reported. Treatment of 3‐siloxy‐1,3‐diene‐7‐ynes with catalytic amounts of [W(CO)6] or [ReCl(CO)5] under photoirradiation conditions gives synthetically useful bicyclo[3.3.0]octane derivatives in good yields. Extremely high catalytic activity is noted for the rhenium(I) complex. The reaction has been extended to substrates containing a nitrogen atom in their tethers. In this case, two kinds of synthetically useful heterocyclic compounds—the 2‐azabicyclo[3.3.0]octane derivatives 9 and the monocyclic dihydropyrroles 10, with allenyl substituents—are obtained, and selective preparation of either product can be achieved through the use of an appropriate combination of the nitrogen substituent and the type of the rhenium(I) catalyst. The 2‐azabicyclo[3.3.0]octane derivatives 9 are obtained selectively by carrying out treatment of NNs derivatives in the presence of [ReCl(CO)4(PPh3)], whereas the dihydropyrrole derivatives 10 are obtained by treatment of NMbs derivatives with [ReCl(CO)5]/AgSbF6. Finally, we have applied this geminal carbo‐functionalization to one‐carbon‐elongated substrates containing NTs moieties in their tethers. Selective 5‐exo cyclization is achieved in the presence of gold(I) or rhenium(I) catalysts, whereas 6‐endo cyclization is observed on use of [W(CO)6].
IL4I1: an inhibitor of the CD8+ antitumor T‐cell response in vivo
Authors: Lasoudris Fanette , Cousin Céline , Prevost‐Blondel Armelle , Martin‐Garcia Nadine , Abd‐Alsamad Issam , Ortonne Nicolas , Farcet Jean‐Pierre , Castellano Flavia , Molinier‐Frenkel Valérie
Published: March 2011

The L‐phenylalanine oxidase IL4I1 inhibits T‐cell proliferation in vitro through H2O2 production, and is highly expressed in tumor‐associated macrophages. IL4I1 is also detected by immunohistochemistry in neoplastic cells from several B‐cell lymphomas and some non‐lymphoid tumors. To evaluate IL4I1's effect on tumor growth, we developed a mouse melanoma model constitutively coexpressing IL4I1 and the GP33 epitope. After GP33 vaccination, tumors developed more frequently in mice injected with IL4I1‐expressing cells in comparison with mice receiving control cells. Tumor escape was preceded by a rapid diminution of IFN‐γ‐producing cytotoxic antitumor CD8+ T cells. Moreover, tumor incidence was already increased when only 20% of the injected cells expressed IL4I1. The minimal IL4I1 activities leading to tumor escape were close to those detected in human melanoma and mesothelioma. Thus, we demonstrate the immunosuppressive functions of IL4I1 in vivo and suggest that IL4I1 facilitates human tumor growth by inhibiting the CD8+ antitumor T‐cell response.
Catalytic Synthesis of Triaryl Phosphates from White Phosphorus
Authors: Armstrong Kenneth M. , Kilian Petr
Published: March 2011

Triaryl phosphates were synthesized from white phosphorus and phenols under aerobic conditions and in the presence of iron catalysts and iodine. Full conversion to phosphates was achieved without the use of chlorine, and the reactions do not produce acid waste. Triphenyl phosphate, tritolyl phosphate and tris(2,4‐di‐tert‐butyl)phenyl phosphate were synthesized by this method with high selectivities. Various iron(III) diketonates were used to catalyze the conversion. Mechanistic studies showed that the reaction proceeds by formation of PI3, then O=PI(OPh)2 before the final formation of the phosphate. The nucleophilic substitution of O=PI(OPh)2 with phenol to form O=P(OPh)3 was found to be the rate‐limiting step.
Separation of nickel catalyst by microfiltration
Authors: Subrahmanyam C. V. , Rao M. Venkateswara , Bhowmick D. N.
Published: March 2011

Ceramic membranes with pore size of 0.1 and 0.2 µm are used for the separation of nickel catalyst. Effect of trans‐membrane pressure (TMP), linear velocity, temperature and nickel content (solute) on flux and rejection has been investigated. The flux increased with increase in pore size of the membrane. The rejection characteristics were similar for 0.1 and 0.2 µm membranes. The nickel content and iodine value of the membrane‐filtered oil was comparable with that of conventional processes. Permeate flux increased with increase in temperature. Flux increased with increase in linear velocity and a marginal rise was observed above 2.09 m/s. The rejection characteristics were only slightly affected by higher linear velocity. The flux improved after back flushing. The average flux was higher with back flushing as compared to continuous (with out back flushing) filtration process. The results indicated that the secondary layer effect was more pronounced in microfiltration. The flux decreased with increase in solute concentration. The rejection characteristics were not affected by solute concentration. The rejection characteristic of the membranes remained unaltered after membranes were repeatedly cleaned with sodium hydroxide and HCl solutions, however, the flux was decreased marginally.
A field study of mean and turbulent flow characteristics upwind, over and downwind of barchan dunes
Authors: Baddock Matthew C. , Wiggs Giles F. S. , Livingstone Ian
Published: March 2011

Field‐measured patterns of mean velocity and turbulent airflow are reported for isolated barchan dunes. Turbulence was sampled using a high frequency sonic anemometer, deriving near‐surface Reynolds shear and normal stresses. Measurements upwind of and over a crest‐brink separated barchan indicated that shear stress was sustained despite a velocity reduction at the dune toe. The mapped streamline angles and enhanced turbulent intensities suggest the effects of positive streamline curvature are responsible for this maintenance of shear stress. This field evidence supports an existing model for dune morphodynamics based on wind tunnel turbulence measurements.

Downwind, the effect of different dune profiles on flow re‐attachment and recovery was apparent. With transverse incident flow, a re‐attachment length between 2·3 and 5·0h (h is dune brink height) existed for a crest‐brink separated dune and 6·5 to 8·6h for a crest‐brink coincident dune. The lee side shear layer produced elevated turbulent stresses immediately downwind of both dunes, and a decrease in turbulence with distance characterized flow recovery. Recovery of mean velocity for the crest‐brink separated dune occurred over a distance 6·5h shorter than the crest‐brink coincident form.

As the application of sonic anemometers in aeolian geomorphology is relatively new, there is debate concerning the suitability of processing their data in relation to dune surface and streamline angle. This paper demonstrates the effect on Reynolds stresses of mathematically correcting data to the local streamline over varying dune slope. Where the streamline angle was closely related to the surface (windward slope), time‐averaged shear stress agreed best with previous wind tunnel findings when data were rotated along streamlines. In the close lee, however, the angle of downwardly projected (separated) flow was not aligned with the flat ground surface. Here, shear stress appeared to be underestimated by streamline correction, and corrected shear stress values were less than half of those uncorrected. Copyright © 2011 John Wiley & Sons, Ltd.
Impact of coal structural heterogeneity on the nonideal sorption of organic contaminants
Authors: Shi Xin , Fu Heyun , Li Yuan , Mao Jingdong , Zheng Shourong , Zhu Dongqiang
Published: March 2011

Carbonaceous geosorbents (black carbon, coal, and humin/kerogen) play a primary role in the nonideal sorption (isotherm nonlinearity, hysteresis, and multiphasic kinetics) of hydrophobic organic chemicals by soils and sediments. The present study investigated the impact of coal structural heterogeneity on sorption/desorption of two model monoaromatic compounds (1,3-dichlorobenzene and 1,3-dinitrobenzene). Due to the higher degree of aromaticity and condensation, anthracite showed stronger sorption affinity and nonlinearity and slower sorption kinetics than lignite. Removal of humic substances by alkali extraction and/or mineral fraction by acidification did not much affect organic carbon-normalized sorption coefficient to the coal, suggesting nearly complete accessibility of adsorption sites on the condensed organic carbon. However, the treatments greatly increased sorption kinetics and meanwhile alleviated hysteresis of 1,3-dinitrobenzene, as compared with the original lignite. These observations were attributed to the enhanced exposure of high-energy adsorption sites on the condensed organic carbon after exfoliating the surface coverage by humic substances and minerals. An empirical biphasic pseudo-second-order model consisting of a fast sorption phase and a slow sorption phase adequately quantified the overall sorption kinetics for the coal sorbents. The results indicated that the condensed organic carbon, in combination with other structural components, controls the nonideal sorption of unburned coal. Environ. Toxicol. Chem. 2011; 30:1310–1319. © 2011 SETAC
The influence of psychological, social and contextual factors on the expression and measurement of awareness in early‐stage dementia: testing a biopsychosocial model
Authors: Clare Linda , Nelis Sharon M. , Martyr Anthony , Roberts Judith , Whitaker Christopher J. , Markova Ivana S. , Roth Ilona , Woods Robert T. , Morris Robin G.
Published: March 2011

Background

Insufficient attention has been paid to the influence of psychological and social factors on discrepancy‐based measures of awareness.

Objectives

The present study tested a biopsychosocial model of awareness in early‐stage dementia by gathering evidence regarding the relative contributions of neuropsychological, individual psychological and social factors to the level of scoring on measures used to index awareness.

Method

Awareness was assessed in relation to memory, activities of daily living and social functioning in 101 individuals with early‐stage dementia participating in the Memory Impairment and Dementia Awareness (MIDAS) Study. People with dementia (PwD) and carers also completed measures of individual psychological and social variables, and PwD completed measures of neuropsychological functioning.

Results

Scores on discrepancy‐based indices of awareness and on the self‐ratings and informant ratings contributing to these indices were associated with a range of factors including neuropsychological functioning of PwD, individual traits and dispositions and current affective functioning of PwD, socio‐demographic characteristics of PwD and carers, carer well‐being and carer perceptions of PwD and of quality of relationship with PwD. Patterns of association varied across domains of functioning.

Conclusions

The findings support the relevance of a biopsychosocial approach to understanding the factors that influence unawareness of impairment in dementia. Copyright © 2011 John Wiley & Sons, Ltd.
The neuro/PsyGRID calibration experiment
Authors: Suckling John , Barnes Anna , Job Dominic , Brennan David , Lymer Katherine , Dazzan Paola , Marques Tiago Reis , MacKay Clare , McKie Shane , Williams Steve R. , Williams Steven C.R. , Deakin Bill , Lawrie Stephen
Published: March 2011

Calibration experiments precede multicenter trials to identify potential sources of variance and bias. In support of future imaging studies of mental health disorders and their treatment, the Neuro/PsyGRID consortium commissioned a calibration experiment to acquire functional and structural MRI from twelve healthy volunteers attending five centers on two occasions. Measures were derived of task activation from a working memory paradigm, fractal scaling (Hurst exponent) from resting fMRI, and grey matter distributions from T1‐weighted sequences. At each intracerebral voxel a fixed‐effects analysis of variance estimated components of variance corresponding to factors of center, subject, occasion, and within‐occasion order, and interactions of center‐by‐occasion, subject‐by‐occasion, and center‐by‐subject, the latter (since there is no intervention) a surrogate of the expected variance of the treatment effect standard error across centers. A rank order test of between‐center differences was indicative of crossover or noncrossover subject‐by‐center interactions. In general, factors of center, subject and error variance constituted >90% of the total variance, whereas occasion, order, and all interactions were generally <5%. Subject was the primary source of variance (70%–80%) for grey‐matter, with error variance the dominant component for fMRI‐derived measures. Spatially, variance was broadly homogenous with the exception of fractal scaling measures which delineated white matter, related to the flip angle of the EPI sequence. Maps of P values for the associated F‐tests were also derived. Rank tests were highly significant indicating the order of measures across centers was preserved. In summary, center effects should be modeled at the voxel‐level using existing and long‐standing statistical recommendations. Hum Brain Mapp, 2012. © 2011 Wiley Periodicals, Inc.
Mitochondrial antiviral signaling protein defect links impaired antiviral response and liver injury in steatohepatitis in mice
Authors: Csak Timea , Dolganiuc Angela , Kodys Karen , Nath Bharath , Petrasek Jan , Bala Shashi , Lippai Dora , Szabo Gyongyi
Published: March 2011

Mitochondrial dysfunction is a pathogenic feature of nonalcoholic steatohepatitis (NASH). NASH complicates hepatotropic viral disease. The mitochondrial antiviral signaling protein (MAVS) is the adapter of helicase receptors involved in sensing double-stranded RNA (dsRNA). We hypothesized that impaired MAVS function may contribute to insufficient antiviral response and liver damage in steatohepatitis. We identified reduced MAVS protein levels and increased MAVS association with the proteasome subunit alpha type 7 (PSMA7) in livers from mice given a methionine–choline-deficient (MCD) diet. Decreased association of MAVS with mitochondria and increased cytosolic cytochrome c indicated mitochondrial damage in steatohepatitis. In vivo administration of the synthetic dsRNA polyinosinic:polycytidylic acid [poly(I:C)], but not lipopolysaccharide or cytidine–phosphate–guanosine-rich DNA, resulted in impaired induction of type I interferons (IFNs) and proinflammatory cytokines in steatohepatitis. Consistent with a defect in helicase receptor-induced signaling, there was loss of poly(I:C)-induced translocation of MAVS to the cytosol and decreased IFN regulatory factor 3 phosphorylation. Caspases 1 and 8, both of which cleave MAVS, were increased in MCD diet–fed mice. At baseline, steatohepatitis was associated with increased serum alanine aminotransferase (ALT), apoptosis and caspase 3 activation compared with controls. In contrast to apoptosis in controls, necrosis was induced by poly(I:C) stimulation in steatohepatitis. Hepatocyte necrosis was indicated by elevated serum high-mobility group box protein-1 and ALT and was correlated with increased expression of receptor-interacting protein 3 (RIP3), a master regulator of necrosis. Increased expression of MAVS, PSMA7, and RIP3 messenger RNA was also present in human NASH livers. Conclusion: Our novel findings suggest that mitochondrial damage in steatohepatitis extends to MAVS, an adapter of helicase receptors, resulting in inefficient type I IFN and inflammatory cytokine response but increased hepatocyte necrosis and RIP3 induction in response to a dsRNA viral challenge. These mechanisms may contribute to progressive liver damage and impaired viral clearance in NASH. (HEPATOLOGY 2011;)