bluuebunny/crossref_metadata_2025 huggingface dataset:
Preoperative single-slab 3D time-of-flight magnetic resonance angiography predicts development of new cerebral ischemic events after carotid endarterectomy
Authors: Suzuki Taro , Ogasawara Kuniaki , Hirooka Ryonoshin , Sasaki Makoto , Kobayashi Masakazu , Ishigaki Daiya , Fujiwara Shunro , Yoshida Kenji , Otawara Yasunari , Ogawa Akira
Published: March 2009

Object

Preoperative impairment of cerebral hemodynamics predicts the development of new cerebral ischemic events after carotid endarterectomy (CEA), including neurological deficits and cerebral ischemic lesions on diffusion weighted MR imaging. Furthermore, the signal intensity of the middle cerebral artery (MCA) on single-slab 3D time-of-flight MR angiography (MRA) can assess hemodynamic impairment in the cerebral hemisphere. The purpose of the present study was to determine whether, on preoperative MR angiography, the signal intensity of the MCA can be used to identify patients at risk for development of cerebral ischemic events after CEA.

Methods

The signal intensity of the MCA ipsilateral to CEA on preoperative MR angiography was graded according to the ability to visualize the MCA in 106 patients with unilateral internal carotid artery stenosis (≥ 70%). Diffusion weighted MR imaging was performed within 3 days of and 24 hours after surgery. The presence or absence of new postoperative neurological deficits was also evaluated.

Results

Cerebral ischemic events after CEA were observed in 16 patients. Reduced signal intensity of the MCA on preoperative MR angiography was the only significant independent predictor of postoperative cerebral ischemic events. When the reduced MCA signal intensity on preoperative MR angiography was defined as an impairment in cerebral hemodynamics, MR angiography grading resulted in an 88% sensitivity and 63% specificity, with a 30% positive- and a 97% negative-predictive value for the development of postoperative cerebral ischemic events.

Conclusions

Signal intensity of the MCA on preoperative single-slab 3D time-of-flight MR angiography is useful for identifying patients at risk for cerebral ischemic events after CEA.
Structural Fingerprints of Transcription Factor Binding Site Regions
Authors: Gardiner Eleanor J. , Hunter Christopher , Willett Peter
Published: March 2009

Fourier transforms are a powerful tool in the prediction of DNA sequence properties, such as the presence/absence of codons. We have previously compiled a database of the structural properties of all 32,896 unique DNA octamers. In this work we apply Fourier techniques to the analysis of the structural properties of human chromosomes 21 and 22 and also to three sets of transcription factor binding sites within these chromosomes. We find that, for a given structural property, the structural property power spectra of chromosomes 21 and 22 are strikingly similar. We find common peaks in their power spectra for both Sp1 and p53 transcription factor binding sites. We use the power spectra as a structural fingerprint and perform similarity searching in order to find transcription factor binding site regions. This approach provides a new strategy for searching the genome data for information. Although it is difficult to understand the relationship between specific functional properties and the set of structural parameters in our database, our structural fingerprints nevertheless provide a useful tool for searching for function information in sequence data. The power spectrum fingerprints provide a simple, fast method for comparing a set of functional sequences, in this case transcription factor binding site regions, with the sequences of whole chromosomes. On its own, the power spectrum fingerprint does not find all transcription factor binding sites in a chromosome, but the results presented here show that in combination with other approaches, this technique will improve the chances of identifying functional sequences hidden in genomic data.
Improvement of Morphine-Mediated Analgesia by Inhibition of β-Arrestin 2 Expression in Mice Periaqueductal Gray Matter
Authors: Li Yuting , Liu Xing , Liu Chang , Kang Jiuhong , Yang Jingyu , Pei Gang , Wu Chunfu
Published: March 2009

Morphine is a well-known μ-opioid receptor (MOR) agonist and an efficient analgesic, but its long-term use inevitably leads to drug addiction and tolerance. Here, we show that specific inhibition of β-arrestin2 with its siRNA lentivirus microinjected in mice periaqueductal gray matter (PAG) significantly improved both acute and chronic morphine analgesia and delayed the tolerance in the hotplate test. The specific effect of β-arrestin2 was proven by overexpression or knockdown of its homology β-arrestin1 in PAG, which showed no significant effects on morphine analgesia. These findings suggest that specific siRNA targeting β-arrestin2 may constitute a new approach to morphine therapy and other MOR agonist-mediated analgesia and tolerance.
Structural Changes of Malt Proteins During Boiling
Authors: Jin Bei , Li Lin , Liu Guo-Qin , Li Bing , Zhu Yu-Kui , Liao Liao-Ning
Published: March 2009

Changes in the physicochemical properties and structure of proteins derived from two malt varieties (Baudin and Guangmai) during wort boiling were investigated by differential scanning calorimetry, SDS-PAGE, two-dimensional electrophoresis, gel filtration chromatography and circular dichroism spectroscopy. The results showed that both protein content and amino acid composition changed only slightly during boiling, and that boiling might cause a gradual unfolding of protein structures, as indicated by the decrease in surface hydrophobicity and free sulfhydryl content and enthalpy value, as well as reduced α-helix contents and markedly increased random coil contents. It was also found that major component of both worts was a boiling-resistant protein with a molecular mass of 40 kDa, and that according to the two-dimensional electrophoresis and SE-HPLC analyses, a small amount of soluble aggregates might be formed via hydrophobic interactions. It was thus concluded that changes of protein structure caused by boiling that might influence beer quality are largely independent of malt variety.
Ultra-Fast Low Concentration Detection of Candida Pathogens Utilizing High Resolution Micropore Chips
Authors: Mulero Rafael , Lee Dong Heun , Kutzler Michele A. , Jacobson Jeffrey M. , Kim Min Jun
Published: March 2009

Although Candida species are the fourth most common cause of nosocomial blood stream infections in the United States, early diagnostic tools for invasive candidemia are lacking. Due to an increasing rate of candidemia, a new screening system is needed to detect the Candida species in a timely manner. Here we describe a novel method of detection using a solid-state micro-scale pore similar to the operational principles of a Coulter counter. With a steady electrolyte current flowing through the pore, measurements are taken of changes in the current corresponding to the shape of individual yeasts as they translocate or travel through the pore. The direct ultra-fast low concentration electrical addressing of C. albicans has established criteria for distinguishing individual yeast based on their structural properties, which may reduce the currently used methods’ complexity for both identification and quantification capabilities in mixed blood samples
Porcine Endogenous Retrovirus (PERV) and its Transmission Characteristics: A Study of the New Zealand Designated Pathogen-Free Herd
Authors: Garkavenko O. , Wynyard S. , Nathu D. , Simond D. , Muzina M. , Muzina Z. , Scobie L. , Hector R. D. , Croxson M. C. , Tan P. , Elliott B. R.
Published: March 2009

Previously a strategy for monitoring of pigs intended for cell transplantation was developed and successfully applied to several representative herds in New Zealand. A designated pathogen-free (DPF) herd has been chosen as a good candidate for xenotransplantation. This herd has previously tested free of infectious agents relevant to xenotransplantation and we present here an in depth study of porcine endogenous retrovirus (PERV) transmission. A panel of assays that describes the constraints for the transmission of PERV has been suggested. It includes a) infectivity test in coculture of DPF pig primary cells with both human and pig target cell lines; b) RT activity in supernatant of stimulated primary cells from DPF pigs; c) viral load in donor's blood plasma; d) PERV proviral copy number in DPF pig genome; e) PERV class C prevalence in the herd and its recombination potential. There was no evidence of PERV transmission from DPF pig tissue to either pig or human cells. Additionally, there was no evidence of PERV RNA present in pig blood plasma. PERV copy number differs in individual pigs from as low as 3 copies to 30 copies and the presence of PERV-C varied between animals and breeds. In all DPF pigs tested, a specific locus for PERV-C potentially associated with the recombination of PERV in miniature swine was absent. Presented data on the PERV transmission allows us to classify the DPF potential donors as “null” or noninfectious pigs.
Combined Treatment of Intrapancreatic Autologous Bone Marrow Stem Cells and Hyperbaric Oxygen in Type 2 Diabetes Mellitus
Authors: Estrada Esteban J. , Valacchi Fabian , Nicora Eduardo , Brieva Sergio , Esteve Claudio , Echevarria Laura , Froud Tatiana , Bernetti Karina , Cayetano Shari Messinger , Velazquez Omaida , Alejandro Rodolfo , Ricordi Camillo
Published: March 2009

The objective of this study was to determine whether the combination therapy of intrapancreatic autologous stem cell infusion (ASC) and hyperbaric oxygen treatment (HBO) before and after ASC can improve islet function and metabolic control in patients with type 2 diabetes mellitus (T2DM). This prospective phase 1 study enrolled 25 patients with T2DM who received a combination therapy of intrapancreatic ASC and periinfusion HBO between March 2004 and October 2006 at Stem Cells Argentina Medical Center Buenos Aires, Argentina. Clinical variables (body mass index, oral hypoglycemic drugs, insulin requirement) and metabolic variables (fasting plasma glucose, C-peptide, HbA1c, and calculation of C-peptide/glucose ratio) were assessed over quartile periods starting at baseline and up to 1 year follow-up after intervention. Means were calculated in each quartile period and compared to baseline. Seventeen male and eight female patients were enrolled. Baseline variables expressed as means ± SEs were: age 55 ± 2.14 years, diabetes duration 13.2 ± 1.62 years, insulin dose 34.8 ± 2.96 U/day, and BMI 27.11 ± 0.51. All metabolic variables showed significant improvement when comparing baseline to 12 months follow-up, respectively: fasting glucose 205.6 ± 5.9 versus 105.2 ± 14.2 mg/dl, HbA1c 8.8 ± 0.2 versus 6.0 ± 0.4%, fasting C-peptide 1.5 ± 0.2 versus 3.3 ± 0.3 ng/ml, C-peptide/glucose ratio 0.7 ± 0.2 versus 3.5 ± 0.3, and insulin requirements 34.8 ± 2.9 versus 2.5 ± 6.7 U/day. BMI remained constant over the 1-year follow-up. Combined therapy of intrapancreatic ASC infusion and HBO can improve metabolic control and reduce insulin requirements in patients with T2DM. Further randomized controlled clinical trials will be required to confirm these findings.
SUSTAINABLE ECOLOGICAL DEVELOPMENT REDUCING NEGATIVE EFFECTS OF ROAD MAINTENANCE SALTS
Authors: Baltrėnas Pranas , Kazlauskienė Agnė
Published: March 2009

To ensure traffic safety in winter, large amounts of technical salts (chlorides) are applied on roads. De‐icing salts directly or indirectly contaminate the road environment and have a negative effect on the components of road environment. The analysis of the situation raises a question: how to ensure traffic safety in wintertime applying salts and achieve sustainable development. The article presents the investigations of chloride concentrations on the roadsides of a highway. In 5 recent years, complex environmental laboratory investigations and investigations under natural conditions of the effect of salts on the components of the road environment have been carried out proving their toxic effect. Consequently, to reduce a negative effect of salts on the road environment, measures of sustainable ecological development have to be taken. To achieve a balanced use of salts, the proposal is to apply alternative materials (formiates, molasses‐based material). The introduction of biotechnical measures (an infiltration‐grassy ditch, biological and chemical indication on roadsides) is expedient to eliminate the consequences but not the reasons of salt use. Santrauka Žiemos sezonu eismo saugumui užtikrinti naudojami dideli kiekiai techninių druskų (chloridų). Slidumui šalinti barstomosios druskos tiesiogiai ir netiesiogiai užteršia kelio aplinką ir neigiamai veikia kelio aplinkos komponentus. Todėl kyla klausimas – kaip užtikrinti eismo saugumą žiemą naudojant druskas bei įgyvendinti darnaus vystymosi nuostatas. Straipsnyje pateikti chloridų koncentracijų tyrimai magistralinio kelio, kertančio saugomas teritorijas, pakelių dirvožemyje. Pastaruosius penkerius metus vykdomi kompleksiniai aplinkosaugos laboratoriniai ir natūriniai druskų poveikio kelio aplinkos komponentams tyrimai įrodo nuodingą jų poveikį. Todėl būtina imtis darnaus ekologinio vystymo priemonių, mažinant neigiamą druskų įtaką kelio aplinkai. Siekiant nepadidinti naudojamų druskų kiekio, siūlomos alternatyvios medžiagos (formiatai, melasos pagrindu pagaminta medžiaga). Druskų sukeliamoms pasekmėms (ne priežastims) pašalinti tikslinga įdiegti biotechnines priemones (infiltracinis-žolinis griovys, biologinė ir cheminė indikacija pakelėse).
L'assignation identitaire des unités de visites familiales
Authors: Rambourg Cécile
Published: March 2009

Cet article est issu d’une recherche consacrée à l’analyse de la mise en œuvre des Unités de Visites Familiales (UVF) en France. Il montre comment les personnes détenues se positionnent face à un dispositif nouveau qui bouleverse les repères instaurés durant le temps de la détention et se réinscrivent dans une autre symbolique sociale, affective et relationnelle: autant d’éléments majeurs du parcours intime du détenu qui peuvent influer sur son processus identitaire et lui permettre de s’envisager en tant qu’être à soi et aux autres, dans un temps carcéral qui ne suspend pas tout avenir. L’assignation identitaire des UVF est plus variée et valorisante que celle de la détention mais elle est également source de tension et de conflit pour les détenus qui ont vécu plusieurs années de détention et ceux qui sont condamnés à de longues peines.
La représentation de l'impôt dans l'analyse économique de l'impôt et dans l'économie des dispositifs fiscaux
Authors: Koleva Kalina , Monnier Jean-Marie
Published: March 2009

Résumé Considérant l’impôt comme l’application d’un pouvoir de contrainte et l’expression d’une autorité étatique, l’objectif de l’article est d’examiner comment l’analyse économique de l’impôt prend en compte cette dimension des prélèvements obligatoires. Pour cela, on rappelle, d’abord, la position de l’ancienne économie financière publique française. On souligne ensuite les défaillances de l’économie publique et particulièrement de la théorie de la taxation optimale. Puis, on présente le cadre d’analyse de l’économie des dispositifs fiscaux qui prétend précisément rendre compte de la complexité du droit fiscal et des institutions dévolues à la collecte de l’impôt. La troisième partie permet d’en tirer un premier bilan critique, ainsi qu’un programme de recherche, argumentés selon trois axes principaux. Dès lors, un véritable renouvellement méthodologique s’impose.
Les marchés dérivés sont-ils dangereux ?
Authors: Capelle-Blancard Gunther
Published: March 2009

Résumé Depuis le début des années 1970-1980, la sphère financière connaît un flot intense d’innovations et il existe un certain consensus aujourd’hui pour affirmer qu’elles ont globalement une incidence positive. Malgré tout, à chaque crise financière, le débat est relancé. En particulier, les produits dérivés, qui sont certainement les innovations financières les plus importantes des trente dernières années, suscitent de vives inquiétudes : les qualificatifs de « bête sauvage » ou d’« armes de destruction massive » leur collent à la peau. On a d’abord craint que les produits dérivés favorisent la volatilité, mais les études empiriques ne semblent pas valider ces soupçons. En revanche, la complexité des produits et la concentration des risques sont sources d’instabilité : augmentation de l’incertitude, de la fréquence et de l’ampleur des risques extrêmes, possibilité accrue de risque systémique.
Students' Perceptions of Learning Mathematics With Cellular Phones and Applets
Authors: Daher Wajeeh M.
Published: March 2009

This paper describes the perceptions of middle school students regarding learning mathematics with cellular phones and web applets, their perceptions regarding the differences between these two electronic devices and their preferences regarding using the devices in learning mathematics. To analyze these perceptions I used the grounded theory approach which involves: open coding, axial coding, and selective coding, where the unit of analysis was the sentence in each of the interviews. The research findings imply that the participants perceived different aspects of both of the electronic devices: the availability of the device, the collaboration aspect, the communication aspect, the size of the device, and the swiftness of working with the device. These aspects influenced the participantsâ?? decisions when, where and how to use each of the devices for the learning of mathematics. More participants preferred the cellular phone over the applet primarily for its small size which makes easy its portability as well as for its communication facilities.
MOSEP – More Self-Esteem With My E-Portfolio Development of a Train-the-Trainer Course for E-Portfolio Tutors
Authors: Hilzensauer Wolf , Buchberger Gerlinde
Published: March 2009

E-portfolios are known as a technology- supported learning method for the documentation of competency development. In this article the didactic approach, the course design and the results of the Leonardo da Vinci project MOSEP (More self-esteem with my e-portfolio) are described. The main objective of the project was to develop, test and evaluate a new e-portfolio training concept for teachers and tutors in order to support learners during their competence development phase.
E-Portfolio Implementations and Experiences: Didactical Functionalities of E-Portfolio in Interdisciplinary Contexts
Authors: Mănucă Elena , Alexandru Sevastian , Gavrilaş Roxana
Published: March 2009

We propose to emphasize the opportunities of using e-learning instruments of teaching/learning in the high school education and to prove, from the perspective both of the teacher and of the trainer who offers courses of continuous education to adults, referring to this theme, the way in which there can be conceived and evaluated some digital curriculum products/e-portfolios, starting from a set of characteristics articulated on a series of criteria, such as relevance, accessibility, availability, atractivity, flexibility, the open/generative character, participation/socialization
New Stability Approach for Offshore Construction Vessels
Authors: van Wijngaarden A.M. , Heemskerk R.J.
Published: March 2009

Offshore construction vessels are a special breed that differs substantiallyfrom conventional cargo ships. Although these offshore units have some physicalsimilarities with passenger ships, the nature of their construction andoperation is quite different.

Therefore, offshore construction vessels should not be subjected to the samerange of stability requirements as passenger vessels. Application of SOLASpassenger ship type stability regulations for a construction vessel in intactand damaged condition may well lead to a G'M requirement that causes anunfavourable motion response. This does not serve the purpose of enhancing thesafety of crew and vessel at sea. Stability requirements based on the IMO MODUCode, such as HSE and NMD, are deemed more appropriate to offshore constructioncraft than SOLAS.

The assumed extent of damage prescribed in stability regulations oftengoverns the watertight subdivision. The internal arrangement of cargo spacesand tanks, however, should also satisfy operational requirements. In thepresent design practice one is obliged to run many optimisation loops ofdeterministic stability calculations, with the sole purpose of achievingcompliance of the unit's subdivision with all the specific criteriaimposed.

If one subjects one and the same watertight subdivision to many differentrequirements, this leads to closer spacing of transverse bulkheads. Safety isnot served with this, since each of the penetrations and closing appliances ofthese extra bulkheads introduces additional flooding risks. The rigorousapplication of extreme stability requirements during short periods ofcontrolled offshore operations may be debated.

Offshore vessels are weight critical, in terms of payload and compliance tostability requirements. Therefore, an accurate weight estimate should beavailable at an early stage of the design, and weight control should beexercised throughout construction. Frequent verification of the weight controlprogress through a displacement test is recommended. It may be wise to allowfor operational contingencies on the lightweight and its vertical centre ofgravity. Offshore craft tend to grow at deckhouse level during theiroperational lifetime. Whenever there is a small discrepancy between alightweight calculation and the lightweight as deduced from a measureddisplacement, most Authorities require that a full inclining experiment needsto be redone.
An Integrated Geoscience and Reservoir Simulation Study of The Liuhua 11-1 Field: South China Sea
Authors: Story Chip , Peng Pat , Heubeck Christoph , Sullivan Claire , Dong Lin Jian
Published: March 2009

The Liuhua 11-1 Field, located 130 miles southeast of Hong Kong in 1000 feetof water, is a vuggy carbonate reservoir at shallow depths (3850 feet subsea), producing 16-22 degree oil under a very strong bottom-water drive. The fieldwas discovered in 1987 and is currently being developed with twenty-fivelong-radius horizontal wells drilled from a floating production system tied toa modular sub-sea structure. Project success is dependent on limiting waterproduction and on well productivity, which in turn makes an accurate reservoirdescription critically important.

To better define reservoir heterogeneity, a 3-D seismic survey of the Liuhuafield was acquired in July 1997. A very highresolution dataset (200+ Hz) wasobtained, and has been used in an integrated field study to evaluate the futureexploitation potential of the reservoir.

Drilling and seismic data were integrated to obtain detailed maps ofreservoir structure and stratigraphy. Petrophysical data and modeling coupledwith seismic inversion were used to obtain a 3D spatial distribution ofreservoir properties (porosity, permeability, and saturation). Coherencetechnology was used to map faults, fractures, and karst dissolution phenomenonin the reservoir. Complex attribute analysis added an additional understandingof rock matrix continuity in different parts of the reservoir. This informationhas been used to build reservoir characterization and simulation models viaseveral commercial and proprietary software systems. These models were tunedand validated using history matching and used to predict future reservoirperformance.

Introduction

The Liuhua reef complex, of which only the western part of the central corearea has been developed, has 1.2 billion barrels of highly viscous crude inplace. The reservoir carbonates are composed largely of shallow-waterforam-agal packstones and boundstones in a common agal-ball matrix.

After the initial production in 1996, it became clear that the reservoir ismuch more petrophysically heterogeneous than originally thought. In addition, many unexpected internal faults and fractures have been identified by drillingand inferred from production performance.
Flow Management: Steady-State and Transient Multiphase Pipeline Simulation
Authors: Danielson Thomas J. , Brown Lloyd D. , Bansal Kris M.
Published: March 2009

Multiphase production systems are quite complex; however, a prioriprediction of their behavior is essential for successful design and operationof offshore facilities. Steady-state and transient simulators can be viewed ascomplementary rather than competitive, and there are specific situations whereeach would be greatly favored over the other. This paper will examine thestrengths and weaknesses of both steady-state and transient simulators, andrecommend best practices for when and how each should be applied, based uponvalidation against laboratory data and field experience. The ultimate objectiveis reliable flow management design and operation through the complementary useof both steady-state and transient multiphase simulations.

Introduction

Both steady-state and transient multiphase flow simulators have found wideuse in the design and operation of offshore facilities. However, informedapplication of these tools is made difficult both by the wide variety ofsteady-state correlations available, and by the complexities arising from fullytransient simulation. Also, there is little guidance as to when steady-statecorrelations will suffice, and when transient simulations will be required. This paper attempts to address itself to these issues, and provide reasonableguidelines for the use of both steady-state and transient models, based onvalidation against laboratory data and field experience. Benchmarking studiesof steady state and transient models was done against the SINTEF large-diameter(8"), high-pressure (20 to 90 bar) Tjiller flow loop database, used to develop OLGA. The focus of this paper is on horizontal and near-horizontalpipelines.

At first glance, the decision whether to use steady-state or transient modelsmight seem a simple one. Clearly, there are many events that are inherentlytime-dependent, e.g., pipeline start-up and shutdown; obviously, in order toproperly capture these events, a transient model must be employed. Likewise, there are multiphase flows that are clearly steady-state, for example, steadyannular or bubble flow, for which a steady-state correlation would suffice.
Application of PIPESIM-FPT Link to Eclipse 100 to Evaluate Field Development Options
Authors: Venkataraman Ramachandran , Mueller J.B.
Published: March 2009

Until recently, reservoir simulation engineers have been modelingsub-surface flow of reservoir with simulators that concentrate mainly on theimpact of subsurface parameters on the production profiles. The influence ofsurface facilities on the sub-surface performance was at best included as lifttables for wells with constraints on the flowing well-head pressures etc.. Theanalysis of the performance of the surface network was left to the facilityengineers. Unfortunately this could be a serious approximation. With change influid ratios (water cuts, gas liquid ratios etc.) the surface network couldimpose significantly different well head pressures as the field gets depleted. The performance made with constant well-head pressure constraints willtherefore be very approximate. There is thus a need to develop a tool that willallow the simulation of surface networks to be linked to subsurface simulationmodels.

BHP Petroleum and Baker Jardine have developed a tool for linking Geoquest's Eclipse-100 simulator to the Baker Jardine's network simulator PIPESIM-Net. Thelinkage is achieved through the PIPESIM-FPT tool of Baker Jardine. The combined Eclipse-PIPESIM-Net model can be run in either of two modes:the model canbe run to obey the Eclipse limits orit can be run under a maximum deliverability mode.

This allows maximum flexibility in the use of the tool tostudy the performance of the models.

The software solves the network on the fly as opposed to the network modeloption in Eclipse-200 which uses tables to interpolate the pressure differencesbetween the various nodes. Thus the solutions are more accurate.

This paper describes the application of the software to study thedevelopment options of two fields. The first is an offshore oil field and thesecond is an onshore condensate reservoir. The examples bring out the utilityof the software in field development planning.
Flow Assurance for Subsea Wells
Authors: Hudson J.D. , Dykhno L.A. , Lorimer S.E. , Schoppa W. , Wilkens R.J.
Published: March 2009

The focus of flow assurance analysis and design has often been from flowlineentry to the initial separator at the production facility. This paper focuseson the flow assurance issues that pertain to the well, with emphasis on thesubsea well located in cold environments. Consideration is given to design andoperational issues that result from management of flow assurance related tohydrates, with a brief discussion of other issues, such as wax, asphaltenes, and chemical compatibility issues.

Introduction

Oil production from the deep water Gulf of Mexico has increased dramaticallyover the past several years. Similar increases are expected in the coming yearsin several locations worldwide. While development of new facilitiesinfrastructure continues in these environments, production from subsea wells indeep water regions is increasingly common. Even in cases where newinfrastructure is included in the development, often a substantial portion ofthe production is derived from subsea wells.

While flow assurance issues can have relevance in shallow water environmentsand with Direct-Vertical-Access (DVA) wells, the advent of subsea production indeeper waters has increased the importance of these concerns to system designand operations. In addition to flow assurance-related impacts on systemavailability, deep water developments may be susceptible to dramatically higherintervention costs associated with flow assurance related failures orimpairments. The importance of these issues is demonstrated to some extent bythe industry's significant investment in these technologies in the past severalyears (e.g., by Deepstar and by Petrobras).

The impact of these issues must always be seen in terms of the overallproject economics, where tradeoffs between initial capital expenses andoperating costs are considered. To do this effectively, the hardware/systemdesign and operations planning must integrate flow assurance at each stage ofdevelopment.

The need for flow assurance methodology in multiphase production lines(flowlines) is well established and some information on methodology isavailable in the literature. To date, there has been limited attention given toflow assurance concerns that are specific to subsea wells. This paper attemptsto define the flow assurance objectives for subsea wells, to indicate some ofthe design issues and operational constraints that may be inferred from theseobjectives, and to give a couple of examples of the analysis process used todefine design and operational parameters.
TRIM21 Is Essential to Sustain IFN Regulatory Factor 3 Activation during Antiviral Response
Authors: Yang Kai , Shi He-Xin , Liu Xin-Yi , Shan Yu-Fei , Wei Bo , Chen She , Wang Chen
Published: March 2009

Virus infection induces host antiviral responses including induction of type I IFNs. Transcription factor IFN regulatory factor 3 (IRF3) plays an essential role and is tightly regulated in this process. Herein we report that TRIM21 (tripartite motif-containing 21) is significantly induced and interacts with IRF3 upon RNA virus infection. Ectopic expression or knockdown of TRIM21 could respectively enhance or impair IRF3-mediated gene expression. Mechanistically, TRIM21 interferes with the interaction between Pin1 (peptidyl-prolyl cis/trans isomerase, NIMA-interacting 1) and IRF3, thus preventing IRF3 ubiquitination and degradation. A conserved motif in the B 30.2 domain of TRIM21 is critical for its modulation of IRF3 function, while the RING finger is dispensable. Host antiviral responses are significantly boosted or crippled in the presence or absence of TRIM21. Our results identify TRIM21 as an essential modulator of IRF3 stability and demonstrate that it positively regulates the strength and duration of primary antiviral response, thus further strengthening the notion that the TRIM family is evolutionarily integrated with innate immunity.
Histone Modifications: Chemistry and Structural Consequences
Authors: Andrews Andrew J. , Luger Karolin
Published: March 2009

The fate of a multicellular organism, in every developmental stage of its life cycle, depends on the timed and coordinated readout of its genes. At the molecular level, this requires the accurate transcription of a subset of genes from the total complement that is present in each cell. The DNA of a single eukaryotic cell is over 2 m in length, but it compacts in the cell nucleus over 100,000 times by a hierarchical scheme of folding and compaction into a histone‐DNA assembly termed chromatin, which has profound effects on the accessibility of the DNA template. Thus, many activities that impact the level of DNA compaction are likely to be key players in the regulation of transcription, replication, repair, and recombination. The incorporation of histone variants and posttranslational modifications (PTMs) of histones (and their variants) have emerged as the primary mechanisms by which the chemical composition of chromatin may be altered, with wide‐ranging implications for chromatin structure and its interaction with other nuclear components. Currently, the known PTMs of histones can be grouped into two classes: 1) addition or modification of only a few atoms, such as acetylation, methylation, phosphorylation, and arginine deimination (and the special case of proline isomerazation) and 2) addition of higher molecular weight modifications, such as poly‐ADP ribosylation, ubiquitylation, and sumoylation. Here, we review the known effects of histone PTMs on chromatin structure and dynamics from a chemical and structural perspective.
Ion Channels: Computational Analysis
Authors: Kurnikova Maria
Published: March 2009

Ion channels are proteins that are embedded in the lipid bilayer and open water filled pores for ion conduction. This article briefly discusses applications of the methods of computational chemistry to model structure and properties of ion channels. Molecular dynamics simulations are applied to study structure–function relationships in ion channels, their interaction with the lipid bilayer, as well as some aspects of gating and selectivity. Ion permeation properties of the channels are typically modeled using coarse‐grained theories based on continuum representation of water, protein and sometimes permeating ions. In such models, interaction of ions with the environment is governed by the Poisson equation of classic electrostatics. Dynamic flow of ions is modeled by using either Brownian Dynamics (BD) [or alternatively Dynamic Monte Carlo methods (DMC)] or by using continuum diffusion formalism. A model that combines continuum diffusion formalism with the Poisson equation is termed Poisson–Nernst–Planck (PNP) theory. A generalized continuum flow theory that accounts for a single ion interaction with the environment is termed Potential of Mean Force PMP (PMFPNP). The main limitation of both BD and PNP theories stems from the rigid representation of the protein and the membrane. In many hybrid models, this limitation has been overcome.
Mass Spectrometry for Lipid Analyses
Authors: Mesaros Clementina , Blair Ian A.
Published: March 2009

The increasing recognition that lipids have important biological functions in signal transduction in addition to their structural role in cell membranes has stimulated tremendous activity in the field of lipid research. Their complex structures and the potent biological activity of many individual lipids has necessitated the development of highly specific and sensitive methodology for their analysis. Mass spectrometry (MS)‐based methodology has become the technique of choice because of its ability to conduct analyses on trace amounts of bioactive lipids. Gas chromatography (GC)‐MS was widely used for the early studies on lipid analysis, but the applicability was limited. Development of the new atmospheric pressure ionization (API) techniques and matrix‐assisted laser desorption/ionization (MALDI) has significantly increased the range of lipids that can be analyzed by MS. Methodology based on these ionization techniques will continue to make an important contribution to lipid analysis for the foreseeable future.
Tetrapyrroles in Plants: Chemical Biology of Metal Insertion and Removal
Authors: Saha Kaushik , Moulin Michaël , Smith Alison G.
Published: March 2009

In plants, four types of tetrapyrroles are synthesized: heme, siroheme, chlorophyll, and phytochromobilin, all of which are within the chloroplast. A key feature of these compounds is that the cyclic tetrapyrroles coordinate a central metal ion: Mg2+in chlorophyll, and Fe2+in heme and siroheme. In contrast, bilins are made by ring opening of heme and the concomitant loss of the metal ion. Demetallation of chlorophyll also occurs but during breakdown, and the products, which are the so‐called non‐fluorescent chlorophyll catabolites (NCCs), have no known biological function. Thus, metal insertion and removal is an important aspect of tetrapyrrole metabolism. In this review, we consider how these reactions are achieved and how they are regulated, because many act at key branch points in the tetrapyrrole biosynthetic pathway. The major focus is on the chelatases, which are the insertion enzymes, because recent genetic and structural studies have demonstrated that essentially two classes exist with different evolutionary origins. Class I chelatases include Mg‐chelatase, which is the first enzyme of the chlorophyll branch; it comprises three different subunits and requires adenosine triphosphate (ATP) for activity. In contrast, Class II chelatases are exemplified by the last enzyme of protoheme biosynthesis, ferrochelatase, which is a homodimer and requires no cofactor. This article will discuss the reactions catalysed by the two enzymes, the evolutionary origin of chelatases, and how their activity regulates the flux into either chlorophyll or heme synthesis within the chloroplast.
Polymer Therapeutics
Authors: Miller Keren , Satchi‐Fainaro Ronit
Published: March 2009

Polymer therapeutics is considered the first generation of “nanomedicines.” This family of compounds and drug‐delivery systems are based on water‐soluble polymers that can either be bioactive on their own or an inert functional part of a multifunctional complex, which includes polymer–protein conjugates, polymer–drug conjugates, polymeric micelles, polymeric drugs, and nonviral polyplexes for gene delivery.
Polymerase Chain Reaction (PCR) in Chemical Biology
Authors: Pingoud Alfred , Hahn Meinhard , Wilhelm Jochen
Published: March 2009

The polymerase chain reaction (PCR) is a temperature‐controlled technique for amplifying DNAin vitro. It requires a DNA template; two oligodeoxynucleotide primers, which define the DNA to be amplified; the four deoxynucleoside triphosphates; and a thermostable DNA polymerase. PCR is carried out in a thermocycler, in which the DNA is subjected to cycles of denaturation of the double‐stranded DNA template; annealing of the two primers, which are complementary to the two strands of the DNA template; and DNA polymerization (primer extension). Because the product of one cycle serves as the template for the next cycle, PCR leads to the exponential amplification of the initial DNA template, which produces more than a million copies of a homogenous PCR product in 20 cycles. PCR has become an indispensable technique in all life sciences and is used extensively for research and diagnostic purposes. PCR applications include cloning of genomic DNA, preparing DNA for sequencing, site‐directed mutagenesis and recombination, genetic fingerprinting for forensic purposes, detection and identification of infectious agents, prenatal diagnosis of genetic diseases, identification of allelic sequence variations, and gene‐expression analysis.
Single‐Molecule Studies of Biomolecules
Authors: Blanchard Scott C. , Altman Roger B. , Geggier Peter , Munro James B. , Dave Richa , Feldman Michael B. , Terry Daniel S.
Published: March 2009

Imaging biological processes at the single‐molecule scale enables the direct observation of the temporal and spatial dynamics of cellular processes. This relatively new branch of biophysical investigation, which was founded on a platform of physics and chemistry research, is pushing forward the frontiers of medical science by providing unprecedented new illuminations into the molecular basis of life. Although it is far from comprehensive, this article provides the advanced reader with a review of single‐molecule methods, as well as a discussion of the aims, considerations, achievements, and future directions of this field in the context of ongoing investigations of structure–function relationships inherent to biomolecules.
Stereochemistry of Biological Molecules
Authors: Pereira Mariette M. , Vaz Winchil L. C.
Published: March 2009

The three‐dimensional spatial structure or conformation of biological molecules might be said to be at the root of what we understand as the chemistry of living matter. This conformation is dictated largely by the conformation of the building blocks that constitute the various biopolymers. The study of the three‐dimensional arrangement of atoms in a molecule is part of the area of chemistry known as stereochemistry. In this article, we present a brief history of the development of stereochemistry and discuss the basic principles of diastereoisomerism and enantiomerism. The discussion is extended to the particular cases of amino acids, carbohydrates, and phospholipids. The methodology for stereochemical designation of molecular configuration including drawing Fischer, Newman, and Haworth projections as well as the Cahn–Ingold–Prelog priority rules are discussed in appendices at the end of the article.
The Future of Information Modelling and the End of Theory: Less is Limited, More is Different
Authors: Ottchen Cynthia
Published: March 2009

The computational design strategist Cynthia Ottchen, who was previously Head of Research and Innovation at OMA, offers insights into the future of building information modelling (BIM). Now in the Petabyte Age of the data deluge, she argues that in our adoption of BIM we have to surpass mere data collection and technical optimisation and open up new ways of thinking with the creative use of ‘soft data’. Copyright © 2009 John Wiley & Sons, Ltd.
Unified Frontiers: Reaching Out with BIM
Authors: Sharples Coren
Published: March 2009

Coren Sharples is a partner of SHoP Architects in New York where building information modelling (BIM) has become integral to the fluid promotion of communication between contractors, consultants and clients on a project. This is exemplified by two projects in the city: the reconstruction of Rector Bridge, where BIM enabled SHoP to work seamlessly with a firm of custom boat builders and other contractors, and the speculative development at 290 Mulberry Street, where it became a significant means of disseminating key data to the client for marketing and financial planning. Copyright © 2009 John Wiley & Sons, Ltd.
Automated Assessment of Early Concept Designs
Authors: Eastman Chuck
Published: March 2009

Building information modelling (BIM) is a powerful tool for clients and architects alike, particularly when clients have ongoing complex programmatic requirements. Chuck Eastman describes how with his team* at the AEC Integration Laboratory at the College of Architecture at the Georgia Institute of Technology he was commissioned by the US federal government's General Service Administration (GSA) to automate the design guidelines for all US courthouses in such a way that preliminary designs by architects could be assessed and checked against specific criteria. Copyright © 2009 John Wiley & Sons, Ltd.
An Enthusiastic Sceptic
Authors: Oppenheimer Nat
Published: March 2009

Nat Oppenheimer, principal of structural engineers Robert Silman Associates, is a dissenting voice among the advocates of building information modelling (BIM) ‐ an enthusiastic sceptic. Could the quest for integration be leading towards oversimplification rather than customisation and differentiation? Even towards the sort of standardisation adopted with LEED ratings in the quest for sustainability? Copyright © 2009 John Wiley & Sons, Ltd.
Pierre Thibault
Authors: Carter Brian
Published: March 2009

At a time when little in architectural design seems like uncharted territory, Brian Carter, Professor and Dean of the School of Architecture and Planning at the University of Buffalo, The State University of New York, goes northeast to Quebec and encounters the work of architectural explorer Pierre Thibault. He describes how Thibault sets out to develop projects in some of the most ‘remote, expansive and sparsely settled’ areas of the region, responding afresh to the landscape and its indigenous culture. Copyright © 2009 John Wiley & Sons, Ltd.
Densification of Oxide Nanoparticle Thin Films by Irradiation with Visible Light
Authors: Bertino Massimo F. , Smarsly Bernd , Stocco Antonio , Stark Arne
Published: March 2009

A technique is presented that allows for altering of the physical characteristics of films of TiO2 nanoparticles by exposure to visible light. In this technique, dye‐sensitized oxide nanoparticles are deposited on a substrate by dip‐coating. Photodissociation of the organic ligand layer leads to cross‐linking of the nanoparticles. Consequently, irradiated films have a decreased porosity, an increased index of refraction and an increased hydrophobicity. Films irradiated with green light are compared to films irradiated with UV light. Within experimental error, visible‐ and UV‐illumination induces the same changes in the films. The mechanism of surfactant elimination in dye‐sensitized oxide particles is discussed, patterning is demonstrated, and prospective applications of the technique are considered.
Solubility‐Induced Ordered Polythiophene Precursors for High‐Performance Organic Thin‐Film Transistors
Authors: Park Yeong Don , Lee Hwa Sung , Choi Yeon Joo , Kwak Donghoon , Cho Jeong Ho , Lee Sichoon , Cho Kilwon
Published: March 2009

With the aim of enhancing the field‐effect mobility of self‐assembled regioregular poly(3‐hexylthiophene), P3HT, by promoting two‐dimensional molecular ordering, the organization of the P3HT in precursor solutions is transformed from random‐coil conformation to ordered aggregates by adding small amounts of the non‐solvent acetonitrile to the solutions prior to film formation. The ordering of the precursor in the solutions significantly increases the crystallinity of the P3HT thin films. It is found that with the appropriate acetonitrile concentration in the precursor solution, the resulting P3HT nanocrystals adopt a highly ordered molecular structure with a field‐effect mobility dramatically improved by a factor of approximately 20 depending on the P3HT concentration. This improvement is due to the change in the P3HT organization in the precursor solution from random‐coil conformation to an ordered aggregate structure as a result of the addition of acetonitrile. In the good solvent chloroform, the P3HT molecules are molecularly dissolved and adopt a random‐coil conformation, whereas upon the addition of acetonitrile, which is a non‐solvent for aromatic backbones and alkyl side chains, 1D or 2D aggregation of the P3HT molecules occurs depending on the P3HT concentration. This state minimizes the unfavorable interactions between the poorly soluble P3HT and the acetonitrile solvent, and maximizes the favorable π–π stacking interactions in the precursor solution, which improves the molecular ordering of the resulting P3HT thin film and enhances the field‐effect mobility without post‐treatment.