bluuebunny/crossref_metadata_2025 huggingface dataset:
The development of a side effect risk assessment tool (ASyMS©-SERAT) for use in patients with breast cancer undergoing adjuvant chemotherapy
Authors: Maguire Roma , Cowie Julie , Leadbetter Clare , McCall Kathryn , Swingler Kevin , McCann Lisa , Kearney Nora
Published: January 2009

Abstract

Patients with breast cancer receiving chemotherapy are at risk of developing toxicities which can be severe or life threatening. The aim of this study was to develop and test a side effect risk modeling tool (ASyMS©-SERAT) for use in patients with breast cancer undergoing adjuvant chemotherapy. The study was conducted in two phases. Phase 1 entailed the development of the ASyMS©-SERAT tool using a secondary data set and in collaboration with an expert group of clinicians and an advisory group of patients. In phase 2, the predictive accuracy of the tool was measured using a prospective data set of 24 patients with breast cancer undergoing adjuvant chemotherapy. A high level of accuracy was reported for four of the six symptoms measured (>70%) supporting the future development and application of ASyMS©-SERAT in the prediction of chemotherapy-related toxicity. For patients, such information can be used to target information on side effects that they are likely to experience thereby facilitating the provision of tailored information based on their individual needs. For clinicians, knowing the likelihood of potential side effects can assist them in identifying patients who are at greater risk of developing certain toxicities, facilitating more targeted and cost-effective interventions.
An exploration of the internet as a self-management resource
Authors: Foster Claire , Roffe Liz
Published: January 2009

Abstract

In this paper, we explore the role of the internet as a resource for self-managing problems experienced by people affected by cancer. To do this, we draw on our observations of a UK online discussion forum used by people affected by cancer. We explored online contributions to the online discussion forum to identify examples of how people used the internet to seek and share information and support in the context of cancer to support their self-management of problems. Our findings show that of those registering on an online discussion forum only a minority (18%) contributed posts. Few people contributed to the online discussion forum more than five times although a minority of contributors participated numerous times. Examples of emotional and informational support exchanged in the online discussions are described. Benefits of contributing to the online discussions were noted. In conclusion, the online discussion forum can provide a useful resource for people to seek and share experiences, information and support with others in similar situations.
Surveying the experience of living with metastatic breast cancer: comparing face-to-face and online recruitment
Authors: Reed Elizabeth , Simmonds Peter , Corner Jessica
Published: January 2009

Abstract

With its growing use, the Internet offers researchers a novel approach in reaching those they seek to study locally, nationally or globally. The purpose of this paper is to describe our experience of using the Internet as one means of recruiting to a research study exploring the experience of women with metastatic breast cancer and to compare the methodological issues of using face-to-face and online approaches to survey recruitment. The survey incorporated the Functional Assessment of Cancer Therapy-Breast (FACT-B) quality of life measure, a patient experience with care measure and open ended text questions about respondents’ physical, emotional and practical needs. Recruitment was done face-to-face in two cancer centres and on the Breast Cancer Care (it is the UK’s leading provider of information, practical assistance and emotional support for anyone affected by breast cancer) Website, recruiting 110 people in the cancer centres and 125 from the Website. The age range was 25–84. Website respondents were significantly younger than cancer centre respondents (<0.000). They also had significantly lower social well-being on the FACT-B scale and were less satisfied with information and advice (<0.000) and their personal experience of care (<0.010). Finally, we consider the role of the Internet in research and the methodological and ethical challenges this presents both now and in the future.
Expression of the oncofetal ED-B–containing fibronectin isoform in hematologic tumors enables ED-B–targeted 131I-L19SIP radioimmunotherapy in Hodgkin lymphoma patients
Authors: Sauer Stefanie , Erba Paola A. , Petrini Mario , Menrad Andreas , Giovannoni Leonardo , Grana Chiara , Hirsch Burkhard , Zardi Luciano , Paganelli Giovanni , Mariani Giuliano , Neri Dario , Dürkop Horst , Menssen Hans D.
Published: January 2009

Current treatment of hematologic malignancies involves rather unspecific chemotherapy, frequently resulting in severe adverse events. Thus, modern clinical research focuses on compounds able to discriminate malignant from normal tissues. Being expressed in newly formed blood vessels of solid cancers but not in normal mature tissues, the extradomain B of fibronectin (ED-B FN) is a promising target for selective cancer therapies. Using immunohistology with a new epitope retrieval technique for paraffin-embedded tissues, ED-B FN expression was found in biopsies from more than 200 Hodgkin and non-Hodgkin lymphoma patients of nearly all entities, and in patients with myeloproliferative diseases. ED-B FN expression was nearly absent in normal lymph nodes (n = 10) and bone marrow biopsies (n = 9). The extent of vascular ED-B FN expression in lymphoma tissues was positively correlated with grade of malignancy. ED-B FN expression was enhanced in lymph nodes with severe lymphadenopathy and in some hyperplastic tonsils. The in vivo accessibility of ED-B FN was confirmed in 3 lymphoma patients, in whom the lymphoma lesions were visualized on scintigraphy with 131I-labeled L19 small immunoprotein (131I-L19SIP). In 2 relapsed Hodgkin lymphoma patients131I-L19SIP radioimmunotherapy induced a sustained partial response, qualifying ED-B FN as a promising target for antibody-based lymphoma therapies.
Haptoglobin preserves the CD163 hemoglobin scavenger pathway by shielding hemoglobin from peroxidative modification
Authors: Buehler Paul W. , Abraham Bindu , Vallelian Florence , Linnemayr Charlotte , Pereira Claudia P. , Cipollo John F. , Jia Yiping , Mikolajczyk Malgorzata , Boretti Felicitas S. , Schoedon Gabriele , Alayash Abdu I. , Schaer Dominik J.
Published: January 2009

Detoxification and clearance of extracellular hemoglobin (Hb) have been attributed to its removal by the CD163 scavenger receptor pathway. However, even low-level hydrogen peroxide (H2O2) exposure irreversibly modifies Hb and severely impairs Hb endocytosis by CD163. We show here that when Hb is bound to the high-affinity Hb scavenger protein haptoglobin (Hp), the complex protects Hb from structural modification by preventing α-globin cross-links and oxidations of amino acids in critical regions of the β-globin chain (eg, Trp15, Cys93, and Cys112). As a result of this structural stabilization, H2O2-exposed Hb-Hp binds to CD163 with the same affinity as nonoxidized complex. Endocytosis and lysosomal translocation of oxidized Hb-Hp by CD163-expressing cells were found to be as efficient as with nonoxidized complex. Hp complex formation did not alter Hb's ability to consume added H2O2 by redox cycling, suggesting that within the complex the oxidative radical burden is shifted to Hp. We provide structural and functional evidence that Hp protects Hb when oxidatively challenged with H2O2 preserving CD163-mediated Hb clearance under oxidative stress conditions. In addition, our data provide in vivo evidence that unbound Hb is oxidatively modified within extravascular compartments consistent with our in vitro findings.
Human Rad51 mediated DNA unwinding is facilitated by conditions that favour Rad51-dsDNA aggregation
Authors: Balakrishnan Kamakshi , Krishnan Neeraja M , Kulkarni Anagha , Rao Basuthkar J
Published: January 2009

Background

Human Rad51 (RAD51), analogous to its bacterial homolog, RecA, binds and unwinds double stranded DNA (dsDNA) in the presence of certain nucleotide cofactors. ATP hydrolysis is not required for this process, because even ATP non hydrolysable analogs like AMP-PNP and ATPγS, support DNA unwinding. Even ADP, the product of ATP hydrolysis, feebly supports DNA unwinding.

Results

We find that human Rad52 (RAD52) stimulates RAD51 mediated DNA unwinding in the presence of all Adenine nucleotide cofactors, (except in AMP and no nucleotide conditions that intrinsically fail to support unwinding reaction) while enhancing aggregation of RAD51-dsDNA complexes in parallel. Interestingly, salt at low concentration can substitute the role of RAD52, in facilitating aggregation of RAD51-dsDNA complexes, that concomitantly also leads to better unwinding.

Conclusion

RAD52 itself being a highly aggregated protein perhaps acts as scaffold to bring together RAD51 and DNA molecules into large co-aggregates of RAD52-RAD51-DNA complexes to promote RAD51 mediated DNA unwinding reaction, when appropriate nucleotide cofactors are available, presumably through macromolecular crowding effects. Our work highlights the functional link between aggregation of protein-DNA complexes and DNA unwinding in RAD51 system.
Phone and e-mail counselling are effective for weight management in an overweight working population: a randomized controlled trial
Authors: van Wier Marieke F , Ariëns Geertje AM , Dekkers J Caroline , Hendriksen Ingrid JM , Smid Tjabe , van Mechelen Willem
Published: January 2009

Background

The work setting provides an opportunity to introduce overweight (i.e., Body Mass Index ≥ 25 kg/m2) adults to a weight management programme, but new approaches are needed in this setting. The main purpose of this study was to investigate the effectiveness of lifestyle counselling by phone or e-mail on body weight, in an overweight working population. Secondary purposes were to establish effects on waist circumference and lifestyle behaviours, and to assess which communication method is the most effective.

Methods

A randomized controlled trial with three treatments: intervention materials with phone counselling (phone group); a web-based intervention with e-mail counselling (internet group); and usual care, i.e. lifestyle brochures (control group). The interventions used lifestyle modification and lasted a maximum of six months. Subjects were 1386 employees, recruited from seven companies (67% male; mean age 43 (SD 8.6) y; mean BMI 29.6 (SD 3.5) kg/m2). Body weight was measured by research personnel and by questionnaire. Secondary outcomes fat, fruit and vegetable intake, physical activity and waist circumference were assessed by questionnaire. Measurements were done at baseline and after six months. Missing body weight was multiply imputed.

Results

Body weight reduced 1.5 kg (95% CI -2.2;-0.8, p < 0.001) in the phone group and 0.6 kg (95% CI -1.3; -0.01, p = 0.045) in the internet group, compared with controls. In completers analyses, weight and waist circumference in the phone group were reduced with 1.6 kg (95% CI -2.2;-1.0, p < 0.001) and 1.9 cm (95% CI -2.7;-1.0, p < 0.001) respectively, fat intake decreased with 1 fatpoint (1 to 4 grams)/day (95% CI -1.7;-0.2, p = 0.01) and physical activity increased with 866 METminutes/week (95% CI 203;1530, p = 0.01), compared with controls. The internet intervention resulted in a weight loss of 1.1 kg (95% CI -1.7;-0.5, p < 0.001) and a reduction in waist circumference of 1.2 cm (95% CI -2.1;-0.4, p = 0.01), in comparison with usual care. The phone group appeared to have more and larger changes than the internet group, but comparisons revealed no significant differences.

Conclusion

Lifestyle counselling by phone and e-mail is effective for weight management in overweight employees and shows potential for use in the work setting.

Trial registration

ISCRTN04265725.
The prevalence of chronic diseases and major disease risk factors at different ages among 150 000 men and women living in Mexico City: cross-sectional analyses of a prospective study
Authors: Kuri-Morales Pablo , Emberson Jonathan , Alegre-Díaz Jesús , Tapia-Conyer Roberto , Collins Rory , Peto Richard , Whitlock Gary
Published: January 2009

Background

While most of the global burden from chronic diseases, and especially vascular diseases, is now borne by low and middle-income countries, few large-scale epidemiological studies of chronic diseases in such countries have been performed.

Methods

From 1998–2004, 52 584 men and 106 962 women aged ≥35 years were visited in their homes in Mexico City. Self reported diagnoses of chronic diseases and major disease risk factors were ascertained and physical measurements taken. Age- and sex-specific prevalences and means were analysed.

Results

After about age 50 years, diabetes was extremely common – for example, 23.8% of men and 26.9% of women aged 65–74 reported a diagnosis. By comparison, ischaemic heart disease was reported by 4.8% of men and 3.0% of women aged 65–74, a history of stroke by 2.8% and 2.3%, respectively, and a history of cancer by 1.3% and 2.1%. Cancer history was generally more common among women than men – the excess being largest in middle-age, due to breast and cervical cancer. At older ages, the gap narrowed because of an increasing prevalence of prostate cancer. 51% of men and 25% of women aged 35–54 smoked cigarettes, while 29% of men and 41% of women aged 35–54 were obese (i.e. BMI ≥30 kg/m2). The prevalence of treated hypertension or measured blood pressure ≥140/90 mmHg increased about 50% more steeply with age among women than men, to 66% of women and 58% of men aged 65–74. Physical inactivity was highly prevalent but daily alcohol drinking was relatively uncommon.

Conclusion

Diabetes, obesity and tobacco smoking are highly prevalent among adults living in Mexico City. Long-term follow-up of this and other cohorts will establish the relevance of such factors to the major causes of death and disability in Mexico.
Use of task-shifting to rapidly scale-up HIV treatment services: experiences from Lusaka, Zambia
Authors: Morris Mary B , Chapula Bushimbwa Tambatamba , Chi Benjamin H , Mwango Albert , Chi Harmony F , Mwanza Joyce , Manda Handson , Bolton Carolyn , Pankratz Debra S , Stringer Jeffrey SA , Reid Stewart E
Published: January 2009

The World Health Organization advocates task-shifting, the process of delegating clinical care functions from more specialized to less specialized health workers, as a strategy to achieve the United Nations Millennium Development Goals. However, there is a dearth of literature describing task shifting in sub-Saharan Africa, where services for antiretroviral therapy (ART) have scaled up rapidly in the face of generalized human resource crises. As part of ART services expansion in Lusaka, Zambia, we implemented a comprehensive task-shifting program among existing health providers and community-based workers. Training begins with didactic sessions targeting specialized skill sets. This is followed by an intensive period of practical mentorship, where providers are paired with trainers before working independently. We provide on-going quality assessment using key indicators of clinical care quality at each site. Program performance is reviewed with clinic-based staff quarterly. When problems are identified, clinic staff members design and implement specific interventions to address targeted areas. From 2005 to 2007, we trained 516 health providers in adult HIV treatment; 270 in pediatric HIV treatment; 341 in adherence counseling; 91 in a specialty nurse "triage" course, and 93 in an intensive clinical mentorship program. On-going quality assessment demonstrated improvement across clinical care quality indicators, despite rapidly growing patient volumes. Our task-shifting strategy was designed to address current health care worker needs and to sustain ART scale-up activities. While this approach has been successful, long-term solutions to the human resource crisis are also urgently needed to expand the number of providers and to slow staff migration out of the region.
Seasonal prevalence of malaria in West Sumba district, Indonesia
Authors: Syafruddin Din , Krisin  , Asih Puji , Sekartuti  , Dewi Rita M , Coutrier Farah , Rozy Ismail E , Susanti Augustina I , Elyazar Iqbal RF , Sutamihardja Awalludin , Rahmat Agus , Kinzer Michael , Rogers William O
Published: January 2009

Background

Accurate information about the burden of malaria infection at the district or provincial level is required both to plan and assess local malaria control efforts. Although many studies of malaria epidemiology, immunology, and drug resistance have been conducted at many sites in Indonesia, there is little published literature describing malaria prevalence at the district, provincial, or national level.

Methods

Two stage cluster sampling malaria prevalence surveys were conducted in the wet season and dry season across West Sumba, Nusa Tenggara Province, Indonesia.

Results

Eight thousand eight hundred seventy samples were collected from 45 sub-villages in the surveys. The overall prevalence of malaria infection in the West Sumba District was 6.83% (95% CI, 4.40, 9.26) in the wet season and 4.95% (95% CI, 3.01, 6.90) in the dry. In the wet season Plasmodium falciparum accounted for 70% of infections; in the dry season P. falciparum and Plasmodium vivax were present in equal proportion. Malaria prevalence varied substantially across the district; prevalences in individual sub-villages ranged from 0–34%. The greatest malaria prevalence was in children and teenagers; the geometric mean parasitaemia in infected individuals decreased with age. Malaria infection was clearly associated with decreased haemoglobin concentration in children under 10 years of age, but it is not clear whether this association is causal.

Conclusion

Malaria is hypoendemic to mesoendemic in West Sumba, Indonesia. The age distribution of parasitaemia suggests that transmission has been stable enough to induce some clinical immunity. These prevalence data will aid the design of future malaria control efforts and will serve as a baseline against which the results of current and future control efforts can be assessed.
New Insights into the Role of Androgens in Wolffian Duct Stabilization in Male and Female Rodents
Authors: Welsh Michelle , Sharpe Richard M. , Walker Marion , Smith Lee B. , Saunders Philippa T. K.
Published: January 2009

Androgen-mediated wolffian duct (WD) development is programmed between embryonic d 15.5 (e15.5) and 17.5 in male rats, and WD differentiation has been shown to be more susceptible to reduced androgen action than is its initial stabilization. We investigated regulation of these events by comparing fetal WD development at e15.5–postnatal d0 in male and female androgen receptor knockout mice, and in rats treated from e14.5 with flutamide (100 mg/kg/d) plus di-n(butyl) phthalate (500 mg/kg/d) to block both androgen action and production, testosterone propionate (20 mg/kg/d) to masculinize females, or vehicle control. In normal females, WD regression occurred by e15.5 in mice and e18.5 in rats, associated with a lack of epithelial cell proliferation and increased apoptosis, disintegration of the basement membrane, and reduced epithelial cell height. Exposure to testosterone masculinized female rats including stabilization and partial differentiation of WDs. Genetic or chemical ablation of androgen action in males prevented masculinization and induced WD regression via similar processes to those in normal females, except this occurred 2–3 d later than in females. These findings provide the first evidence that androgens may not be the only factor involved in determining WD fate. Other factors may promote survival of the WD in males or actively promote WD regression in females, suggesting sexually dimorphic differences in the preprogrammed setup of the WD.
Kinetic Complexity of the Global Response to Glucocorticoid Receptor Action
Authors: John Sam , Johnson Thomas A. , Sung Myong-Hee , Biddie Simon C. , Trump Saskia , Koch-Paiz Christine A. , Davis Sean R. , Walker Robert , Meltzer Paul S. , Hager Gordon L.
Published: January 2009

We have characterized the kinetic response of gene targets throughout the murine genome to transcriptional modulation by the glucocorticoid receptor (GR). In contrast to a model in which multiple genes are either repressed or activated during the GR response, the vast majority of responsive genes are subject to complex regulation profiles, frequently with alternate activation and repression phases. We also observe that GR binding at response elements does not always correlate with the target gene response profile. Thus, the cellular response to GR stimulation involves a highly orchestrated series of regulatory actions and not simply a binary response to hormone.
GnRH-Regulated Expression of Jun and JUN Target Genes in Gonadotropes Requires a Functional Interaction between TCF/LEF Family Members and β-Catenin
Authors: Salisbury Travis B. , Binder April K. , Grammer Jean C. , Nilson John H.
Published: January 2009

GnRH regulates gonadotrope function through a complex transcriptional network that includes three members of the immediate early gene family: Egr1, Jun, and Atf3. These DNA-binding proteins act alone or in pairs to confer hormonal responsiveness to Cga, Lhb, Fshb, and Gnrhr. Herein we suggest that the transcriptional response of Jun requires a functional interaction between the T-cell factor (TCF)/lymphoid enhancer factor (LEF) family of DNA-binding proteins and β-catenin (officially CTNNB1), a coactivator of TCF/LEF. Supporting data include demonstration that GnRH increases activity of TOPflash, a TCF/LEF-dependent luciferase reporter, in LβT2 cells, a gonadotrope-derived cell line. Additional cotransfection experiments indicate that a dominant-negative form of TCF7L2 (TCFDN) that binds DNA, but not β-catenin, blocks GnRH induction of TOPflash. Overexpression of AXIN, an inhibitor of β-catenin, also reduces GnRH stimulation of TOPflash. Transduction of LβT2 cells with TCFDN adenoviruses diminishes GnRH stimulation of Jun mRNA without altering expression of Egr1 and Atf3, two other immediate early genes that confer GnRH responsiveness. Reduction of β-catenin in LβT2 cells, through stable expression of short hairpin RNA, also selectively compromises GnRH regulation of Jun expression and levels of JUN protein. Finally, overexpression of TCFDN attenuates GnRH regulation of Cga promoter activity, a known downstream target of JUN. Together, these results indicate that GnRH regulation of Jun transcription requires a functional interaction between TCF/LEF and β-catenin and that alteration of either impacts expression of JUN downstream targets such as Cga.
Theoretical characterization of stability in axial-flow compressor rotors
Authors: Benavides E M
Published: January 2009

The article describes an analytical model to calculate the stability of axial-flow compressor rotors. It illustrates how stability is related to the ratio of two times. The definitions of both times are obtained in a rational way for high-performance rotors subjected to non-small disturbances, and a theoretical stability margin coefficient is established. This coefficient determines the location of the stability line in the rotor map. The range of validity of this theoretical characterization is supported by several lemmas and theorems, whose proofs are given. These proofs also give physical meaning to the final analytical formula, connect the results with the surge and stall phenomena, and provide the widest area in the rotor map where normal operation can be sustained. The analytical results link the loading and flow coefficients, the tangential Mach number, and the basic rotor geometry. The stability model is validated with the actual data of transonic axial-compressor rotors. Errors lie in the 1—7 per cent range for cases accomplishing the premises of the theorems. Other empirical and numerical evidences that support the theory, as well as its limitations, are discussed. Due to its simplicity and robustness, the model can be easily used for multi-objective optimizations, preliminary performance calculations, and first estimations of axial solidity in new designs.
High-speed wear lifetime analysis of instrument ball bearings
Authors: Liu C H , Chen X Y , Gu J M , Jiang S N , Feng Z L
Published: January 2009

The instrument ball bearings often operate with high speed and light load. The common failure mode is wear-out occurring under insufficient lubrication condition. As a result, the vibration/noise and frictional torque will be enlarged, and the bearings lose accuracy and precision. In this article, the wear lifetime model of instrument ball bearings is established based on Archard's theory. A new wear coefficient curve is developed from the relationship of Archard wear coefficients obtained by a ball-plate experiment, which is related to oil type and load, with a certain lubricant film parameter (Λ). Then a computer program has been developed to calculate the location of pure rolling lines on the contact ellipse and obtain the contact stress and sliding speed on both inner and outer ball-raceway contact zones. Hence, the total wear time can be determined by the volume of wear with the allowable radial clearances. A 4000-h censored test of eight group samples, with its subgroup size of two bearings, has been conducted in special high-speed test rigs. The data of the experimental results were statistically analysed and compared with the model of wear lifetime. A consistent trend was found out between the experimental data and the proposed model.
Imprecise reliability by evidential networks
Authors: Simon C , Weber P
Published: January 2009

This article deals with an implementation of probist reliability problems in evidential networks to propagate imprecise probabilities expressed as fuzzy numbers. First, the problem of imprecise knowledge in reliability problems is described concerning system and data representation. Then, the basics of the evidence theory and its use in a directed acyclic graph approach are given. The imprecise probist reliability of a complex system by modelling the component failure probabilities as real, interval, or fuzzy numbers is pointed out. Two numerical studies of systems are carried out. The results are discussed and some comparisons with a Monte-Carlo simulation and a fuzzy fault tree approach are made.
Interruption modelling in electrical power distribution systems using the Weibull—Markov model
Authors: Medjoudj R , Aissani D , Boubakeur A , Haim K D
Published: January 2009

This paper develops an application of the Markov and Weibull—Markov methods to evaluate the effects of maintenance actions on the availability and reliability of electrical distribution systems. It unifies existing models and critically reviews them on their applicability to electrical components. Both methods are applied to investigate the expected performances of underground and overhead circuits. It compares expected performance in terms of failure rates, outage times, and availability. Based an a threshold reliability value and maximum benefit, specific preventive maintenance actions are defined for reliability improvement for each component and therefore for the system. The results obtained by the Weibull—Markov method would seem to be more realistic. A range of recommendations is formulated for practical considerations which may be of interest to operators, as well as to managers of these systems.
Electronic Properties of Charge-Tagged Peptides upon Electron Capture
Authors: Chung Thomas W. , Tureček František
Published: January 2009

We report a computational study of Ala–Lys (AK) and Lys–Ala (KA) dipeptide ions furnished with fixed-charged pyridinium groups that were attached by amide linkers to the N-terminal amino groups. Cation–radicals from one-electron reduction of the doubly charged AK and KA peptide conjugates showed various extents of unpaired electron density being delocalized between the pyridine and peptide moieties. The delocalization depended on the local recombination energies ( REloc) of the charged groups. The REloc of the pyridine moieties were modified by introducing electron-donating substituents (CH3, OCH3, and N(CH3)2). The REloc of the peptide moieties were found to depend on the peptide conformation and internal solvation of the Lys ammonium groups. Substantial electron delocalization was found for combinations of pyridine substituents and peptide conformers with closely matched REloc, such as 4-dimethylaminopyridine and internally solvated Lys ammonium or unsubstituted pyridine and free (unsolvated) Lys ammonium. The dissociation (Δ Hdiss) and transition state energies ( ETS) for the loss of the pyridine ring from the conjugates were found to be Δ Hdiss = 34–36 kJ mol−1 and ETS = 67–69 kJ mol−1 for the unsubstituted pyridine moieties, but did not depend much on the peptide sequence.
Application of Silicon Nanowires and Indium Tin Oxide Surfaces in Desorption Electrospray Ionization
Authors: Pól Jaroslav , Novák Petr , Volný Michael , Kruppa Gary H. , Kostiainen Risto , Lemr Karel , Havlíček Vladimír
Published: January 2009

Two nanostructured surfaces are introduced as advantageous substrates for desorption electrospray ionization mass spectrometry (DESI-MS). Nano-assisted laser desorption/ionization (NALDI) plates coated with silicon nanowires (SiNWs) and indium tin oxide (ITO) layers on glass are both conductive non-polar surfaces that were originally designed as superior substrates for matrix-free laser desorption ionization. In this study, NALDI/SiNWs and ITO were tested as potentially useful DESI substrates for selected model analytes (cyclosporine, beauverolide, surfactin and nystatin). Both nanostructured surfaces produced more intense and longer-lasting signals than other tested surfaces (polytetrafluoroethylene, glass, polymethylmethacrylate and chromatography paper).
Analysis of Complex Oligosaccharides Using Graphitized Carbon Liquid Chromatography/Mass Spectrometry
Authors: Budai Lívia , Pollreisz Ferenc , Ozohanics Olivér , Ludányi Krisztina , Drahos László , Vékey Károly
Published: January 2009

The sugar fraction of α-1 acid glycoprotein (AGP) was studied using porous graphitized carbon (PGC) chromatography coupled to mass spectrometry. Electrospray ionization provides efficient control over fragmentation; at low collision energy only molecular species were observed, allowing accurate oligosaccharide profiling. PGC chromatography was useful separating 18 sugars differing in monosaccharide composition. Most of these were separated into several isomeric forms; altogether 49 different oligosaccharides were found in AGP.
Negative Ion Ultraviolet Matrix-Assisted Laser Desorption Ionization Mass Spectrometry and Post Source Decay of Glycosyl Esters of Nucleoside Pyrophosphates
Authors: Heinrich Maria , Schäffer Christina , Messner Paul , Allmaier Günter
Published: January 2009

Six different glycosyl esters of nucleoside pyrophosphates (monosaccharide nucleotides) were analyzed by means of matrix-assisted laser desorption/ionisation reflectron time-of-flight mass spectrometry (MALDI/RToF MS) in the negative ion mode. Several matrices were evaluated and 3-hydroxypicolinic acid as well as α-cyano-4-hydroxycinnamic acid (CHCA) turned out to be the matrices of choice applying the thin layer technique to obtain maximum sensitivity for deprotonated molecular ion detection and maximal fragmentation particular with CHCA. The determination of the molecular mass with a mass accuracy below 0.1% was feasible with sample amounts in the lower femtomole range applying a MALDI desk-top mass spectrometer. A further important refinement of this technique was the use of post source decay (PSD) fragment ion analysis with a curved field reflector (which means no stepping of the reflector voltage). Detailed structural information of the six selected monosaccharide nucleotides could be obtained with PSD and differences in the fragmentation pattern were used to distinguish them. This method (based on molecular mass and PSD fragment ion analysis) has been applied to verify the presence of a glycosyl ester of nucleoside pyrophosphate in samples from Saccharomyces cerevisiae.
Multimarker Circulating DNA Assay for Assessing Blood of Prostate Cancer Patients
Authors: Sunami Eiji , Shinozaki Masaru , Higano Celestia S , Wollman Robert , Dorff Tanya B , Tucker Steven J , Martinez Steve R , Singer Frederick R , Hoon Dave S B
Published: January 2009

Background: Prostate cancer (PCa) detection using serum-based prostate specific antigen (PSA) is limited by frequent false-positive and -negative results. Genetic aberrations such as allelic imbalance (AI) and epigenetic changes such as promoter hypermethylation have been detected in circulating DNA of cancer patients. We hypothesized that circulating multimarker DNA assays detecting both genetic and epigenetic markers in serum would be useful in assessing PCa patients.

Methods: We assayed blood from healthy male donors (n = 40) and 83 patients with American Joint Cancer Committee (AJCC) stage I–IV PCa. DNA was assayed for AI of 6 genome microsatellites. We assessed methylation of RASSF1, RARB2, and GSTP1 using a methylation-specific PCR assay and analyzed the sensitivity of each assay for the detection of genetic or epigenetic changes in circulating DNA. The relation between circulating tumor-related DNA detection and prognostic factors was investigated.

Results: The proportion of patients demonstrating AI for ≥1 marker was 47% (38 of 81 patients). Methylation biomarkers were detected in 24 of 83 patients (28%). By combining 2 DNA assays, the number of PCa patients positive for ≥1 methylated or LOH marker increased (52 of 83; 63%). The combined assays detected PCa in 15 of 24 patients (63%) with normal PSA concentrations. The combination of the DNA assays detected the presence of PCa regardless of AJCC stage or PSA concentration. Combination of the DNA and PSA assays gave 89% sensitivity.

Conclusions: This pilot study demonstrates that the combined circulating DNA multimarker assay identifies patients with PCa and may yield information independent of AJCC stage or PSA concentration.
A New Ring Shear Device to Measure the Large Displacement Shearing Behavior of Sands
Authors: Sadrekarimi Abouzar , Olson Scott M.
Published: January 2009

Among devices commonly used to measure the shearing behavior of sands, only the ring shear device can shear a soil to virtually unlimited displacements without creating substantial nonuniformities in stress and strain distributions. However, some limitations have precluded its widespread use. A new ring shear device was constructed at the University of Illinois that has large specimen dimensions to reduce stress and strain nonuniformities, has auxiliary load and torque cells to measure any wall friction that develops along the confining rings, and utilizes quad-rings along the confining rings to prevent soil extrusion. Sample ring shear tests on a dry fine-grained, silty sand specimen demonstrate that the new ring shear device operates properly in both constant volume and drained conditions, providing identical effective stress friction angles at large displacements when shear and effective normal stresses on the shear plane are considered. Parallel drained and undrained triaxial compression tests on saturated specimens illustrate that the new ring shear device provides reasonable values of effective stress friction angle and show that the triaxial test does not shear specimens to sufficient displacement to reach critical state shear strengths for this sand, which was reached at displacements ranging from about 1 to 10 m.
Ethnicity, Conflict, and History in Burma: The Myths of Panglong
Authors: Walton Matthew J.
Published: January 2009

The effects of the 1947 Panglong Agreement on Burma's ethnic minority groups can still be seen today in calls for a return to the spirit of Panglong, but there are conflicting versions of this event and its legacy. In order to grasp the prospects for ethnic unity in Burma, it is necessary to deconstruct the various “myths” of Panglong.
The Impact of U.S. Sanctions on the Myanmar Garment Industry
Authors: Kudo Toshihiro
Published: January 2009

The U.S. imposed trade sanctions against the Myanmar military government in July 2003. This action damaged Myanmar's garment industry in particular. This paper concludes that the sanctions' impact was inflicted disproportionately on small- and medium-sized domestic private firms and their workers.
Re-Wiring Baltimore: The Emotive Power of Systemics, Seriality, and the City
Authors: Kinder Marsha
Published: January 2009

The Wire is distinguished by the depth of its systemic analysis of Baltimore's urban corruption and by the emotional power it elicits. By presenting so many vibrant characters with enormous potential and showing how our culture is wired to destroy them, it creates serial tragedy with a systemic form of suture.
G-protein-coupled receptors, cholesterol and palmitoylation: facts about fats
Authors: Chini Bice , Parenti Marco
Published: January 2009

G-protein-coupled receptors (GPCRs) are integral membrane proteins, hence it is not surprising that a number of their structural and functional features are modulated by both proteins and lipids. The impact of interacting proteins and lipids on the assembly and signalling of GPCRs has been extensively investigated over the last 20–30 years, and a further impetus has been given by the proposal that GPCRs and/or their immediate signalling partners (G proteins) can partition within plasma membrane domains, termed rafts and caveolae, enriched in glycosphingolipids and cholesterol. The high content of these specific lipids, in particular of cholesterol, in the vicinity of GPCR transmembranes can affect GPCR structure and/or function. In addition, most GPCRs are post-translationally modified with one or more palmitic acid(s), a 16-carbon saturated fatty acid, covalently bound to cysteine(s) localised in the carboxyl-terminal cytoplasmic tail. The insertion of palmitate into the cytoplasmic leaflet of the plasma membrane can create a fourth loop, thus profoundly affecting GPCR structure and hence the interactions with intracellular partner proteins. This review briefly highlights how lipids of the membrane and the receptor themselves can influence GPCR organisation and functioning.
Reducing Reservoir Prediction Uncertainty by Updating a Stochastic Model Using Seismic History Matching
Authors: Stephen Karl D. , MacBeth Colin
Published: January 2009

We have developed a method in which spatial and dynamic information offered by time-lapse, or 4D, seismic surveys is used in history matching of reservoir simulations. Improved predictions of both recovery and areal sweep are then obtained by reducing uncertainty. Flow simulations are converted to predictions of seismic-impedance attributes using a petroelastic transform and suitable rescaling. The resulting misfit between the model and observed data is combined with an equivalent measure for well data, and these are used to constrain simulations by iteratively updating the model. Updated-model probabilities can then be used to analyze uncertainty.

The method has been applied to the Schiehallion UK Continental Shelf (UKCS) reservoir. We first found a good match to production and seismic data in the field. From the updated probability distribution of the parameters, we then took the best models from the history-matching process and made predictions to determine the most likely outcomes.

We have found that the 4D data reduces uncertainty in predictions of the areal sweep and the pressure distribution. The seismic response is strongest at the injector wells but also helps in the interwell regions. Conventional history matching often struggles to constrain parameters in these regions because of the inherent nonuniqueness of the problem. The uncertainty of permeability- and fault-transmissibility multipliers was also determined in those areas.
Modeling Low-Salinity Waterflooding
Authors: Jerauld Gary R. , Lin C. Y. , Webb Kevin J. , Seccombe Jim C.
Published: January 2009

Low-salinity waterflooding is an emerging enhanced-oil-recovery (EOR) technique in which the salinity of the injected water is controlled to improve oil recovery vs. conventional, higher-salinity waterflooding. Corefloods and single-well chemical-tracer tests have shown that low-salinity waterflooding can improve basic waterflood performance by 5 to 38%. This paper describes a model of low-salinity flooding that can be used to evaluate projects; shows the implications of that model and demonstrates its use to represent corefloods, single-well tests, and field-scale simulations; and gives insight into the reservoir engineering of low-salinity floods.

The model represents low-salinity flooding using salinity-dependent oil/water relative permeability functions resulting from wettability change. This is similar to other EOR modeling, and conventional fractional-flow theory can be adapted to describe the process in 1D for secondary and tertiary low-salinity waterflooding. This simple analysis shows that while some degree of connate-water banking occurs, it need not hinder the process.

Mixing of injected water with in-situ water delays the attainment of low salinity, potentially preventing attainment of low salinity all together if very small slugs of low-salinity water are used. This paper demonstrates the importance of mixing to modeling of low-salinity flooding and suggests addressing it in engineering calculations. Care must be taken in representing mixing appropriately in interpreting data and in constructing models. The use of numerical dispersion to represent physical dispersion in 1D, radial, and pattern simulations of this process is demonstrated (i.e., coarse-grid simulations are shown to give the same result as fine-grid simulations with an appropriately large physical dispersion). In many applications, the fine-grid simulation necessary to represent appropriate levels of dispersion is not practical, and pseudoization is necessary. We demonstrate that this can be achieved by changing the salinity dependence and shapes of relative permeability curves.
Relative Permeability Coupled Saturation-Height Models on the Basis of Hydraulic (Flow) Units in a Gas Field
Authors: Amabeoku Maclean O. , Kersey David G. , BinNasser Rami H. , Al-Belowi Ali R.
Published: January 2009

Saturation/height functions on the basis of unique flow units have been developed as part of an integrated petrophysical analysis of a gas field. Furthermore, coupling the saturation/height functions with appropriate relative permeability models has effectively quantified hydrocarbon saturation, classified producibility of intervals, and defined critical water saturation. The results show that linking depositional and diagenetic rock fabric with flow units and then linking the flow units with zones that have similar core capillary pressure and relative permeability relationships have enhanced the utility of the saturation models. The saturation/height functions provided more-accurate water saturation in the study field, and potentially they can overcome uncertainties associated with log interpretation by use of Archie or shaly-sand models.

The saturation/height models were developed from core capillary pressure (Pc) data to calculate water saturation vs. depth, which is independent of logs. The relative permeability models were obtained from special-core analysis (SCA). Consequently, the core-based saturation/height functions can be useful in the calibration of log-based petrophysical models and with relative permeability can also be used to estimate water/gas ratios (WGRs) and critical water saturation.

Capillary pressure and relative permeability curves from SCA studies were distributed into corresponding flow units, on the basis of the calculated flow-zone indicators(FZIs). Saturation/height functions were then developed for each unit and were used to calculate water saturation in the study field. The most accurate flow-unit-based saturation model that evolved is a function only of porosity and of height above the free-water level; it does not require permeability in its application; and it performed better than the Leverett J-function in this field.

Coupled with hydraulic unit (HU)-based relative permeability curves, the saturation models may provide more comprehensive petrophysical interpretation in gas-bearing formations and may highlight potential differences in reservoir producibility.
Using Laboratory Flow Experiments and Reactive Chemical Transport Modeling for Designing Waterflooding of the Agua Fria Reservoir, Poza Rica-Altamira Field, Mexico
Authors: Birkle P. , Pruess K. , Xu T. , Hernández Figueroa R. A. , Díaz López M. , Contreras López E.
Published: January 2009

Waterflooding for enhanced oil recovery requires that injected waters must be chemically compatible with connate reservoir waters, in order to avoid mineral dissolution-and-precipitation cycles that could seriously degrade formation permeability and injectivity. Formation plugging is a concern especially in reservoirs with a large content of carbonates, such as calcite and dolomite, as such minerals typically react rapidly with an aqueous phase, and have strongly temperature-dependent solubility. Clay swelling also can pose problems. During a preliminary waterflooding pilot project, the Poza Rica-Altamira oil field, bordering the Gulf coast in the eastern part of Mexico, experienced injectivity loss after 5 months of reinjection of formation waters into Well AF-847 in 1999. Acidizing with hydrochloric acid (HCl) restored injectivity.

We report on laboratory experiments and reactive-chemistry modeling studies that were undertaken in preparation for long-term waterflooding at the Agua Fría reservoir. Using analogous core plugs obtained from the same reservoir interval, laboratory core-flood experiments were conducted to examine the sensitivity of mineral-dissolution and -precipitation effects to water composition. Native reservoir water, chemically altered waters, and distilled water were used, and temporal changes in core permeability, mineral quantities, and aqueous concentrations of solutes were monitored. The experiments were simulated with the multiphase, nonisothermal reactive transport code TOUGHREACT™ (Lawrence Berkeley National Laboratory, Berkeley, California, 2004), and reasonable-to-good agreement was obtained for changes in solute concentrations. Clay swelling caused an additional impact on permeability behavior during coreflood experiments, whereas the modeled permeability depends exclusively on chemical processes. TOUGHREACT was then used for reservoir-scale simulation of injecting ambient-temperature water (30°C, 86°F) into a reservoir with initial temperature of 80°C (176°F). Untreated native reservoir water was found to cause serious porosity and permeability reduction because of calcite precipitation, which is promoted by the retrograde solubility of this mineral. Using treated water that performed well in the laboratory flow experiments was found to avoid excessive precipitation and allowed injection to proceed.