bluuebunny/crossref_metadata_2025_split huggingface dataset:
Novel splice variants derived from the receptor tyrosine kinase superfamily are potential therapeutics for rheumatoid arthritis
Authors: Jin Pei , Zhang Juan , Sumariwalla Percy F , Ni Irene , Jorgensen Brett , Crawford Damian , Phillips Suzanne , Feldmann Marc , Shepard H Michael , Paleolog Ewa M 
Published: July 2008

AbstractIntroductionDespite the advent of biological therapies for the treatment of rheumatoid arthritis, there is a compelling need to develop alternative therapeutic targets for nonresponders to existing treatments. Soluble receptors occur naturallyin vivo, such as the splice variant of the cell surface receptor for vascular endothelial growth factor (VEGF) – a key regulator of angiogenesis in rheumatoid arthritis. Bioinformatics analyses predict that the majority of human genes undergo alternative splicing, generating proteins – many of which may have regulatory functions. The objective of the present study was to identify alternative splice variants (ASV) from cell surface receptor genes, and to determine whether the novel proteins encoded exert therapeutic activity in anin vivomodel of arthritis.MethodsTo identify novel splice variants, we performed RT-PCR using an mRNA pool representing major human tissue types and tumors. Novel ASV were identified by alignment of each cloned sequence to its respective genomic sequence in comparison with full-length transcripts. To test whether these ASV have biologic activity, we characterized a subset of them for ligand binding, and for efficacy in an animal model of arthritis. Thein vivostudy was accomplished using adenoviruses expressing secreted ASV.ResultsWe cloned 60 novel human ASV from 21 genes, encoding cell surface receptors – many of which are known to be important in the regulation of angiogenesis. The ASV were characterized by exon extension, intron retention and alternative exon utilization. Efficient expression and secretion of selected ASV – corresponding to VEGF receptor type 1, VEGF receptor type 2, VEGF receptor type 3, angiopoietin receptor Tie1, Met (receptor for hepatocyte growth factor), colony-stimulating factor 1 receptor, platelet-derived growth factor receptor beta, fibroblast growth factor receptor 1, Kit, and RAGE – was demonstrated, together with binding to their cognate ligands. Importantly, ASV derived from VEGF receptor type 1 and Tie1, and to a lesser extent from VEGF receptor type 2 and fibroblast growth factor receptor 1, reduced clinical signs of arthritisin vivo. The reduction was paralleled by decreased joint inflammation and destruction.ConclusionThe present study shows that unique ASV derived from receptors that play key roles in angiogenesis – namely, VEGF receptor type 1 and, for the first time, Tie1 – can markedly reduce arthritis severity. More broadly, our results demonstrate that ASV are a source of novel proteins with therapeutic potential in diseases in which angiogenesis and cellular hyperplasia play a central role, such as rheumatoid arthritis.
Over-expression of Skp2 is associated with resistance to preoperative doxorubicin-based chemotherapy in primary breast cancer
Authors: Davidovich Shirly , Ben-Izhak Ofer , Shapira Ma'anit , Futerman Boris , Hershko Dan D 
Published: July 2008

Abstract
Introduction
Preoperative chemotherapy is often used in patients with locally advanced breast cancer. However, commonly used clinical and pathological parameters are poor predictors of response to this type of therapy. Recent studies have suggested that altered regulation of the cell cycle in cancer may be involved in resistance to chemotherapy. Over-expression of the ubiquitin ligase Skp2 results in loss of the cell cycle inhibitor p27Kip1 and is associated with poor prognosis in early breast cancer. The purpose of the present study was to examine the role of these proteins as predictors of clinical outcome and response to chemotherapy in locally advanced breast cancer.

Methods
The expression levels of Skp2 and p27Kip1 were determined by immunohistochemistry both before and after preoperative chemotherapy in 40 patients with locally advanced breast cancer. All patients were treated with cyclophosphamide/doxorubicin (adriamycin)/5-fluorouracil (CAF) and some patients received additional treatment with docetaxel. Expression data were compared with patients' clinical and pathological features, clinical outcome, and response to chemotherapy.

Results
Skp2 expression before preoperative chemotherapy was inversely related to p27Kip1 levels, tumor grade, and expression of estrogen and progesterone receptors. Both Skp2 and p27Kip1 were found to be accurate prognostic markers for disease-free and overall survival. High preoperative expression of Skp2 was associated with resistance to CAF therapy in 94% of patients (P < 0.0001) but not with resistance to docetaxel.

Conclusion
Skp2 expression may be a useful marker for predicting response to doxorubicin-based preoperative chemotherapy and clinical outcome in patients with locally advanced breast cancer.
Plastic architecture of bacterial genome revealed by comparative genomics of Photorhabdus variants
Authors: Gaudriault Sophie , Pages Sylvie , Lanois Anne , Laroui Christine , Teyssier Corinne , Jumas-Bilak Estelle , Givaudan Alain 
Published: July 2008

Abstract
Background
The phenotypic consequences of large genomic architecture modifications within a clonal bacterial population are rarely evaluated because of the difficulties associated with using molecular approaches in a mixed population. Bacterial variants frequently arise among Photorhabdus luminescens, a nematode-symbiotic and insect-pathogenic bacterium. We therefore studied genome plasticity within Photorhabdus variants.

Results
We used a combination of macrorestriction and DNA microarray experiments to perform a comparative genomic study of different P. luminescens TT01 variants. Prolonged culturing of TT01 strain and a genomic variant, collected from the laboratory-maintained symbiotic nematode, generated bacterial lineages composed of primary and secondary phenotypic variants and colonial variants. The primary phenotypic variants exhibit several characteristics that are absent from the secondary forms. We identify substantial plasticity of the genome architecture of some variants, mediated mainly by deletions in the 'flexible' gene pool of the TT01 reference genome and also by genomic amplification. We show that the primary or secondary phenotypic variant status is independent from global genomic architecture and that the bacterial lineages are genomic lineages. We focused on two unusual genomic changes: a deletion at a new recombination hotspot composed of long approximate repeats; and a 275 kilobase single block duplication belonging to a new class of genomic duplications.

Conclusion
Our findings demonstrate that major genomic variations occur in Photorhabdus clonal populations. The phenotypic consequences of these genomic changes are cryptic. This study provides insight into the field of bacterial genome architecture and further elucidates the role played by clonal genomic variation in bacterial genome evolution.
Organizational determinants of boundary spanning activity in outpatient substance abuse treatment programmes
Authors: Alexander Jeffrey A , Wells Rebecca , Jiang Lan , Pollack Harold 
Published: July 2008

Objectives Substance abuse treatment programmes depend on boundary spanning to identify opportunities and threats, and represent their interests to stakeholders such as licensing entities and regulators. This study sought to identify director, client, unit and market factors associated with active director boundary spanning. Methods Using data from the 1995, 1999–2000 and 2005 waves of a national survey of outpatient substance abuse treatment units, generalized estimating equation regression models tested associations between predictors and five aspects of directors' self-reported boundary spanning. Results Directors licensed as substance abuse treatment counsellors spent more time than average consulting with other treatment providers and making presentations in the community. Older directors spent less time consulting with other treatment providers, making community presentations and liaisoning with monitoring organizations. The few associations between client unemployment and director boundary spanning were positive; the two associations between the percentage of clients who were African-American and boundary spanning were negative. Private ownership and being based in larger organizations were negatively associated with some types of boundary spanning. Perceived competition for public support was positively associated with all measures of boundary spanning. Conclusion Directors of treatment organizations may improve treatment practices and political leverage by directly, but selectively, interacting with key external stakeholders.
Associations between peer victimization, fear of future victimization and disrupted concentration on class work among junior school pupils
Authors: Boulton Michael J. , Trueman Mark , Murray Lindsay 
Published: July 2008

Background. Studies have shown that peer victimization is associated with psychological maladjustment, and have implicated such maladjustment in disrupted ability to concentrate.Aims. To investigate the levels of, and associations between, physical, verbal, and social exclusion victimization, fear of future victimization, and disrupted classroom concentration.Sample. Participants consisted of 485 pupils aged 10–11 drawn from 11 junior schools in the UK.Method. Peer‐ and self‐nominations of physical, verbal, and social exclusion victimization were collected in individual interviews. Self‐reports of other variables were collected either individually or in small groups.Results. A substantial minority of pupils reported high levels of fear of future victimization and disrupted concentration on class work, and girls reported higher levels of fear of future victimization than boys. All three types of self‐reported victimization, all three types of peer‐reported victimization, and fear of all three types of future victimization predicted disrupted concentration on class work. Fear of future social exclusion moderated the association between peer‐reported social exclusion and disrupted concentration on class work.Conclusions. In addition to tackling victimization per se, allaying pupils' fears of it happening to them in the future is called for in order to address a hitherto largely overlooked correlate, and possible source, of disrupted classroom concentration.
Hydrothermal dissolution of mixed southern hardwoods
Authors: Tunc Mehmet Sefik , van Heiningen Adriaan R.P. 
Published: July 2008

Abstract
A hydrothermal dissolution profile of wood components cellulose, hemicelluloses, and lignin of hardwood during autohydrolysis for 100 min at temperatures from 130 to 170°C in a modified accelerated solid extraction system (Dionex ASE-100) is described. The content of cellulose, hemicelluloses, lignin, acetyl, and uronic acid groups remaining in the extracted wood were determined. The extract was analyzed for oligosaccharides and monosaccharides, lignin, acetic acid, uronic acid, furfural, and hydroxymethylfurfural. Xylo-oligomers are the predominant component in the extract at temperatures higher than 150°C. At temperatures higher than 160°C, small amounts of furfural and hydroxymethylfurfural are generated. Most of the arabinan and galactan are removed from the wood at 160°C. The xylan remaining in the wood is acetylated at the same degree as in the original wood. In the extract, the ratio of acetyl groups bound to xylo-oligosaccharides decreases with increasing temperature. The content of uronic acid groups found in the extract obtained after autohydrolysis at T≥150°C is significantly smaller than that calculated from the decrease in uronic content of the wood.
Randomized Trial of Endotracheal Tube Versus Laryngeal Mask Airway in Simulated Prehospital Pediatric Arrest
Authors: Chen Lei , Hsiao Allen L. 
Published: July 2008

OBJECTIVE. Proficiency in airway management in children is difficult to acquire and maintain for prehospital providers. The laryngeal mask airway is a relatively new airway device. Its ease of use makes it an attractive potential alternative to endotracheal tubes in pediatrics. The objective of this study was to investigate whether, in simulated cardiopulmonary arrests in children, the use of laryngeal mask airway, compared with endotracheal tubes, results in shorter time to effective ventilation when performed by prehospital providers.
METHODS. A randomized, crossover study was conducted in a local paramedic training program. Fifty-two emergency medical technicians agreed to participate. After a 2-hour training session, an arrest scenario was presented to each participant by using an infant-sized human patient simulator. The participants were randomly assigned first to use 1 of the 2 devices. Time to successful ventilation was recorded. Number of attempts and results were recorded. After the airway was secured successfully, the scenario was repeated with the alternative device.
RESULTS. The mean ± SD length of time to effective ventilation was 46 seconds when using endotracheal tubes and 23 seconds when using laryngeal mask airway, with a mean difference of 23 seconds. The mean number of attempts to achieve effective ventilation was 1.27 when using endotracheal tubes and 1.1 when using laryngeal mask airway. There were 9 (17%) episodes of esophageal intubations and 14 (27%) episodes of right main-stem intubations in the endotracheal tube group, and there were 5 (9.5%) episodes of malposition in the laryngeal mask airway group.
CONCLUSIONS. In simulated pediatric arrests, the use of laryngeal mask airway, compared with endotracheal tubes, led to more rapid establishment of effective ventilation and fewer complications when performed by prehospital providers.
Gradual or pulsed evolution: when should punctuational explanations be preferred?
Authors: Hunt Gene 
Published: July 2008

The problem of gradual versus punctuated change within phyletic lineages can be understood in terms of the homogeneity of evolutionary dynamics. Hypotheses of punctuated change imply that the rules governing evolutionary change shift over time such that the normal dynamics of stasis are temporarily suspended, permitting a period of net evolutionary change. Such explanations are members of a larger class of models in which evolutionary dynamics are in some way heterogeneous over time. In this paper, I develop a likelihood-based statistical framework to evaluate the support for this kind of evolutionary model. This approach divides evolutionary sequences into nonoverlapping segments, each of which is fit to a separate evolutionary model. Models with heterogeneous dynamics are generally more complex—they require more parameters to specify—than uniform evolutionary models such as random walks and stasis. The Akaike Information Criterion can be used to judge whether the greater complexity of punctuational models is offset by a sufficient gain in log-likelihood for these models to be preferred.I use this approach to analyze three case studies for which punctuational explanations have been proposed. In the first, a model of punctuated evolution best accounted for changes in pygidial morphology within a lineage of the trilobiteFlexicalymene, but the uniform model of an unbiased random walk remains a plausible alternative. Body size evolution in the radiolarianPseudocubus vemawas neither purely gradual nor completely pulsed. Instead, the best-supported explanation posited a single, pulsed increase, followed later by a shift to an unbiased random walk. Finally, for the much-analyzed claim of “punctuated gradualism“ in the foraminiferaGloborotalia, the best-supported model implied two periods of stasis separated by a period of elevated but not inherently directional evolution. Although the conclusions supported by these analyses generally refined rather than overturned previous views, the present approach differs from those prior in that all competing interpretations were formalized into explicit statistical models, allowing their relative support to be unambiguously compared.
A Simulation Study for Planning the Development of la Victoria Field in Western Venezuela
Authors: Joe Cordero Franklin 
Published: July 2008

ABSTRACT
This report presents the results of a case study and development program for the La Victoria field in south-western Venezuela. The La Victoria field was discovered in 1984. Original oil in place is approximately 210 MMSTB (334 × 106 m3 ). To date (Dec. 1989), cumulative production has been 5.3 MMSTB (8.4 × 105 m3).
Excellent reservoir characteristics shown by the Escandalosa and Navay formations, which contain most of the oil in the La Victoria field, exhibit the following unusual oil properties: 35 °API (0.85 g/cm3 ) gravity, low bubble point pressure (285 psia) (1.97 MPa), low solution GOR (136 SCF/STB) (24.5 std m3/m3) and an average oil viscosity of 1 cp (1 × 10−3 Pa.s) at 227 °F (108 °C). These anomalous values make this field one of the most prolific discovered in Venezuela. The producing mechanism is an edge water drive from an extensive, fresh water aquifer.
The development of such a field must be planned properly to achieve a maximum efficiency in its exploitation.
This paper describes the reservoir and its geology, the production history, and the reservoir simulation study used as an aid to development planning.
Results show that the La Victoria field can be developed with eighteen producers. The ultimate recovery by natural depletion, at the end of 20 years, is predicted to be 84.5 MMSTB (13.4 × 106 m3 ) (38.2% STOIP). With the proposed development plan it may be possible to maintain the oil potential production above 30,000 B/D (4,769 m3/D) during the 1990-1992 period.
Geophysical Aspects of Horizontal Well Systems
Authors: Mari J. L. , Laurent J. 
Published: July 2008

ABSTRACTAmong possible characterization techniques used in horizontal wells, geophysical surveys seem to be very promising in giving a set of images of the reservoir and the surrounding layers at different scales. This paper demonstrates the usefulness of horizontal well geophysical surveys in different frequency bandwidths for reservoir studies. The paper shows several field examples. In the low frequency bandwidth, VSPs give a coarse image of the reservoir and of the layers situated below, with a vertical resolution of several 10's of m (first example). Full waveform acoustic data produce near-borehole structure images up to a distance of 15 m from the borehole with a vertical resolution of several 10's of cm (second example).The paper points out the necessity of having very high resolution seismics (intermediate between VSP data and acoustic data) to obtain structural images up to a distance of 100 m from the borehole. An example shows the results obtained in the 1-to-5 kHz bandwidth on a test site. The field records show reflected arrivals from boundaries up to a distance of 50 m from the horizontal borehole.
A Review of Formation Evaluation Practices in Horizontal Wells
Authors: Donahue Michael T. , Nice Sid B. , Lincecum Val J. 
Published: July 2008

ABSTRACT
The better return on investment that horizontal drilling techniques provide has prompted an increase of this activity worldwide. Initially, it was felt little or no data were required to evaluate the reservoirs produced through horizontal boreholes because early completion techniques consisted of simple openhole completions or placement of a slotted liner along the lateral borehole. However, because of productivity anomalies, a need for thorough evaluation techniques soon became apparent. This paper is a review of the latest techniques used to evaluate horizontal wells. Methods of instrument conveyance, formation evaluation techniques, and measurement-while-drilling applications are included.
The Fracture Intensity Log: A Proven Technique for Evaluating Fracturing in Low-Permeability Reservoirs
Authors: Sanders R. L. 
Published: July 2008

Abstract
The fracture intensity log provides a means for recognizing and evaluating naturally occurring fractures in the wellbore. An analysis of the fracture intensity presentation can then be used in "pipe-setting" decisions. The fracture intensity log is based upon the shear wave properties derived from acoustic full waveform logs.
Hydrocarbon Evaluation of the Delaware Sandstones Using the Shear Wave Travel Time and the Neutron Porosity
Authors: Sanders R. L. 
Published: July 2008

Abstract
A formation evaluation technique is being used to evaluate the Delaware sandstones of the Permian Basin for hydrocarbons. The technique consists of crossplotting the neutron porosity and the shear wave travel time. The sandstones reservoirs that are productive will exhibit a greater shear wave travel time than would be predicted from the neutron porosity. This technique is applicable to both open and cased hole conditions.
An adaptive nonlinear output feedback controller using dynamic bounding with an aircraft control application
Authors: Tang Xidong , Tao Gang 
Published: July 2008

AbstractAn adaptive output feedback control scheme is developed for a class of nonlinear systems with uncertain nonlinearities, which are bounded by both static and dynamic functions of the system output, and with actuator failures whose failure time instants, patterns and values are unknown, as motivated from an aircraft flight control application. An adaptive backstepping control law using dynamic bounding is constructed to deal with unknown actuator failures as well as system parameter and dynamics uncertainties to guarantee desired system performance. Complete stability and performance analysis and illustrative simulation results of an application to aircraft flight control are presented. Copyright © 2008 John Wiley & Sons, Ltd.
Longitudinal auto‐landing controller design via adaptive backstepping
Authors: Ju Hann‐Shing , Tsai Ching‐Chih 
Published: July 2008

AbstractThis paper presents an auto‐landing controller for glide‐slope tracking and the flare maneuver via adaptive backstepping design and describes a flight path command generator for indirect altitude control in order to provide precise altitude trajectories for auto‐landing of unmanned aerial vehicles (UAVs). Using the adaptive backstepping procedure to synthesize a glide‐slope tracking and flare maneuver control law is being used differently from designing the guidance and control loops separately in autopilot. An adaptive controller is proposed to control aircraft from glide‐slope to flare by following the flight path angle command for indirect altitude control via elevator and maintaining the constant airspeed control via throttle. Simulation results demonstrate that the adaptive auto‐landing controller is capable of effectively guiding the UAV along the flight path angle command under the presence of the wind turbulence. Copyright © 2008 John Wiley & Sons, Ltd.