bluuebunny/crossref_metadata_2025_split huggingface dataset:
HPV16 E2 could act as down-regulator in cellular genes implicated in apoptosis, proliferation and cell differentiation
Authors: Ramírez-Salazar Eric , Centeno Federico , Nieto Karen , Valencia-Hernández Armando , Salcedo Mauricio , Garrido Efraín 
Published: May 2011

Abstract

Background
Human Papillomavirus (HPV) E2 plays several important roles in the viral cycle, including the transcriptional regulation of the oncogenes E6 and E7, the regulation of the viral genome replication by its association with E1 helicase and participates in the viral genome segregation during mitosis by its association with the cellular protein Brd4. It has been shown that E2 protein can regulate negative or positively the activity of several cellular promoters, although the precise mechanism of this regulation is uncertain. In this work we constructed a recombinant adenoviral vector to overexpress HPV16 E2 and evaluated the global pattern of biological processes regulated by E2 using microarrays expression analysis.

Results
The gene expression profile was strongly modified in cells expressing HPV16 E2, finding 1048 down-regulated genes, and 581 up-regulated. The main cellular pathway modified was WNT since we found 28 genes down-regulated and 15 up-regulated. Interestingly, this pathway is a convergence point for regulating the expression of genes involved in several cellular processes, including apoptosis, proliferation and cell differentiation; MYCN, JAG1 and MAPK13 genes were selected to validate by RT-qPCR the microarray data as these genes in an altered level of expression, modify very important cellular processes. Additionally, we found that a large number of genes from pathways such as PDGF, angiogenesis and cytokines and chemokines mediated inflammation, were also modified in their expression.

Conclusions
Our results demonstrate that HPV16 E2 has regulatory effects on cellular gene expression in HPV negative cells, independent of the other HPV proteins, and the gene profile observed indicates that these effects could be mediated by interactions with cellular proteins. The cellular processes affected suggest that E2 expression leads to the cells in to a convenient environment for a replicative cycle of the virus.
Positive end-expiratory pressure optimization with forced oscillation technique reduces ventilator induced lung injury: a controlled experimental study in pigs with saline lavage lung injury
Authors: Kostic Peter , Zannin Emanuela , Andersson Olerud Marie , Pompilio Pasquale P , Hedenstierna Göran , Pedotti Antonio , Larsson Anders , Frykholm Peter , Dellaca Raffaele L 
Published: May 2011

Abstract
Introduction
Protocols using high levels of positive end-expiratory pressure (PEEP) in combination with low tidal volumes have been shown to reduce mortality in patients with severe acute respiratory distress syndrome (ARDS). However, the optimal method for setting PEEP is yet to be defined. It has been shown that respiratory system reactance (Xrs), measured by the forced oscillation technique (FOT) at 5 Hz, may be used to identify the minimal PEEP level required to maintain lung recruitment. The aim of the present study was to evaluate if using Xrs for setting PEEP would improve lung mechanics and reduce lung injury compared to an oxygenation-based approach.

Methods
17 pigs, in which acute lung injury (ALI) was induced by saline lavage, were studied. Animals were randomized into two groups: in the first PEEP was titrated according to Xrs (FOT group), in the control group PEEP was set according to the ARDSNet protocol (ARDSNet group). The duration of the trial was 12 hours. In both groups recruitment maneuvers (RM) were performed every 2 hours, increasing PEEP to 20 cmH2O. In the FOT group PEEP was titrated by monitoring Xrs while PEEP was reduced from 20 cmH2O in steps of 2 cmH2O. PEEP was considered optimal at the step before which Xrs started to decrease. Ventilatory parameters, lung mechanics, blood gases and hemodynamic parameters were recorded hourly. Lung injury was evaluated by histopathological analysis.

Results
The PEEP levels set in the FOT group were significantly higher compared to those set in the ARDSNet group during the whole trial. These higher values of PEEP resulted in improved lung mechanics, reduced driving pressure, improved oxygenation, with a trend for higher PaCO2 and lower systemic and pulmonary pressure. After 12 hours of ventilation, histopathological analysis showed a significantly lower score of lung injury in the FOT group compared to the ARDSNet group.

Conclusions
In a lavage model of lung injury a PEEP optimization strategy based on maximizing Xrs attenuated the signs of ventilator induced lung injury. The respiratory system reactance measured by FOT could thus be an important component in a strategy for delivering protective ventilation to patients with ARDS/acute lung injury.
Variations of the aortic arch – a study on the most common branching patterns
Authors: Müller Marguerite , Schmitz Bernd L , Pauls Sandra , Schick Melanie , Röhrer Stefan , Kapapa Thomas , Schlötzer Wiebke 
Published: May 2011

Background Anatomical variants of the aortic arch and its branching patterns often appear as an incidental finding during routine computed tomography (CT) scanning. These variations can be of relevance when performing angiography or endovascular interventions and may cause symptoms such as dysphagia. Purpose To analyze common anatomical variations found within the arteries originating from the aortic arch in patients using contrast CT imaging techniques. Material and Methods A total of 2033 contrast CT scans were analyzed. To obtain a truly representative sample, cases were chosen from different hospital departments without previous knowledge of the patient history. Results The total percentage of variations within the analyzed patients was 13.3%. In 8.0% a truncus bicaroticus was found. 4.2% of the patients showed a left vertebral artery originating directly from the aortic arch, mostly proximal, and in 1 case distal to the left subclavian artery. In 1.0% we found an aberrant right subclavian artery. We also found a single case of a right descending aortic arch. Conclusion Variations of the aortic arch and its branching are frequently found, mostly as an incidental finding during routine diagnostic scanning. A contrast-enhanced CT scan is a good method with which to study the aortic arch and its associated branching pattern.
Cathepsins S, B and L with aminopeptidases display β-secretase activity associated with the pathogenesis of Alzheimer’s disease
Authors: Schechter Israel , Ziv Etty 
Published: May 2011

Abstractβ-site APP-cleaving enzyme (BACE1) cleaves the wild type (WT) β-site very slowly (kcat/Km: 46.6 m-1s-1). Therefore we searched for additional β-secretases and identified three cathepsins that split the WT β-site much faster. Human cathepsin S cleaves the WT β-site (kcat/Km: 54 700 m-1s-1) 1170-fold faster than BACE1 and cathepsins B and L are 440- and 74-fold faster than BACE1, respectively. These cathepsins split two bonds flanking the WT β-site (K-MD-A), where the K-M bond (85%) is cleaved more efficiently than the D-A bond (15%). Cleavage at the major K-M bond yields Aβ (amyloid β-peptide) extended by N-terminal Met that should be removed to generate Aβ initiated by Asp1. The activity of cytosol and microsomal aminopeptidases on relevant peptides revealed rapid removal of N-terminal Met but not N-terminal Asp. Brain aminopeptidases showed similar specificity. Thus, aminopeptidases would convert Aβ extended by Met into regular Aβ (Asp1) found in amyloid plaques. Earlier studies indicate that Aβ is likely produced in the endosome and lysosome system where cathepsins S, B and L are localized and cysteine cathepsin inhibitors reduce the level of Aβ in cells and animals. Taken together, cathepsins S, B and L deserve further evaluation as therapeutic targets to develop disease modifying drugs to treat Alzheimer’s disease.
Quantitative and qualitative approaches in the study of poverty and adolescent development: separation or integration?
Authors: Leung Janet T.Y. , Shek Daniel T.L. 
Published: May 2011

Abstract
This paper examines the use of quantitative and qualitative approaches to study the impact of economic disadvantage on family processes and adolescent development. Quantitative research has the merits of objectivity, good predictive and explanatory power, parsimony, precision and sophistication of analysis. Qualitative research, in contrast, provides a detailed, holistic, in-depth understanding of social reality and allows illumination of new insights. With the pragmatic considerations of methodological appropriateness, design flexibility, and situational responsiveness in responding to the research inquiry, a mixed methods approach could be a possibility of integrating quantitative and qualitative approaches and offers an alternative strategy to study the impact of economic disadvantage on family processes and adolescent development.
Assessment of Epidermal Growth Factor Receptor and K-Ras Mutation Status in Cytological Stained Smears of Non-Small Cell Lung Cancer Patients: Correlation with Clinical Outcomes
Authors: Lozano Maria D. , Zulueta Javier J. , Echeveste Jose I. , Gúrpide Alfonso , Seijo Luis M. , Martín-Algarra Salvador , Barrio Anabel , Pio Ruben , Idoate Miguel Angel , Labiano Tania , Perez-Gracia Jose Luis 
Published: May 2011

Abstract

Objective.
Epidermal growth factor receptor (EGFR) and K-ras mutations guide treatment selection in non-small cell lung cancer (NSCLC) patients. Although mutation status is routinely assessed in biopsies, cytological specimens are frequently the only samples available. We determined EGFR and K-ras mutations in cytological samples.

Methods.
DNA was extracted from 150 consecutive samples, including 120 Papanicolau smears (80%), 10 cell blocks (7%), nine fresh samples (6%), six ThinPrep® tests (4%), and five body cavity fluids (3.3%). Papanicolau smears were analyzed when they had &gt;50% malignant cells. Polymerase chain reaction and direct sequencing of exons 18–21 of EGFR and exon 2 of K-ras were performed. EGFR mutations were simultaneously determined in biopsies and cytological samples from 20 patients. Activity of EGFR tyrosine kinase inhibitors (TKIs) was assessed.

Results.
The cytological diagnosis was adenocarcinoma in 110 samples (73%) and nonadenocarcinoma in 40 (27%) samples. EGFR mutations were identified in 26 samples (17%) and K-ras mutations were identified in 18 (12%) samples. EGFR and K-ras mutations were mutually exclusive. In EGFR-mutated cases, DNA was obtained from stained smears in 24 cases (92%), pleural fluid in one case (4%), and cell block in one case (4%). The response rate to EGFR TKIs in patients harboring mutations was 75%. The mutation status was identical in patients who had both biopsies and cytological samples analyzed.

Conclusion.
Assessment of EGFR and K-ras mutations in cytological samples is feasible and comparable with biopsy results, making individualized treatment selection possible for NSCLC patients from whom tumor biopsies are not available.
Phase III Multicenter Clinical Trial of the Sialyl-TN (STn)-Keyhole Limpet Hemocyanin (KLH) Vaccine for Metastatic Breast Cancer
Authors: Miles David , Roché Henri , Martin Miguel , Perren Timothy J. , Cameron David A. , Glaspy John , Dodwell David , Parker Joanne , Mayordomo José , Tres Alejandro , Murray James Lee , Ibrahim Nuhad K. ,   the Theratope® Study Group
Published: May 2011

Abstract

Purpose.
This double-blind, randomized, phase III clinical trial evaluated time to progression (TTP) and overall survival in women with metastatic breast cancer (MBC) who received sialyl-TN (STn) keyhole limpet hemocyanin (KLH) vaccine. Secondary endpoints included vaccine safety and immune response.

Experimental design.
The study population consisted of 1,028 women with MBC across 126 centers who had previously received chemotherapy and had had either a complete or a partial response or no disease progression. All women received one-time i.v. cyclophosphamide (300 mg/m2) 3 days before s.c. injection of 100 μg STn-KLH plus adjuvant (treatment group) or 100 μg KLH plus adjuvant (control group) at weeks 0, 2, 5, and 9. Subsequently, STn-KLH without adjuvant or KLH without adjuvant was then administered monthly for 4 months, and then quarterly until disease progression, without cyclophosphamide.

Results.
STn-KLH vaccine was well tolerated; patients had mild to moderate injection-site reactions and reversible flu-like symptoms. Week-12 antibody testing revealed high specific IgG titers and a high rate of IgM-to-IgG seroconversion; the median IgG titers in STn-KLH recipients were 320 (anti-ovine submaxillary mucin) and 20,480 (anti-STn), with no detectable antimucin antibodies in the control group. The TTP was 3.4 months in the treatment group and 3.0 months in the control group. The median survival times were 23.1 months and 22.3 months, respectively.

Conclusions.
Although STn-KLH was well tolerated in this largest to date metastatic breast cancer vaccine trial, no overall benefit in TTP or survival was observed. Lessons were learned for future vaccine study designs.
Selective Application of Routine Preoperative Axillary Ultrasonography Reduces Costs for Invasive Breast Cancers
Authors: Turaga Kiran K. , Chau Alec , Eatrides Jennifer M. , Kiluk John V. , Khakpour Nazanin , Laronga Christine , Lee M. Catherine 
Published: May 2011

Abstract

Learning Objectives
After completing this course, the reader will be able to: Identify patients likely to benefit from preoperative axillary ultrasound.Define the clinical implications of a preoperative axillary ultrasound and FNA in patient care.
CME This article is available for continuing medical education credit at CME.TheOncologist.com

Purpose.
Preoperative axillary sonography with fine needle aspiration (FNA) in patients with invasive breast cancer identifies patients with nodal metastasis who can be spared further surgery. Indiscriminate use of the diagnostic modality can increase costs and yield inaccurate results. We evaluate the costs associated with the use of highly sensitive axillary ultrasonography in patients with stage ≥T2 tumors.

Patients and Methods.
We constructed a decision analysis tree using TreeAge Pro 2009 software comparing direct hospital charges between patients with and without routine use of axillary ultrasound. Base case estimates were derived from our institutional data and compared with those derived from the literature. One- and two-way sensitivity analyses were performed to check the validity of our inferences.

Results.
We found that, for the base case estimate with 35% lymph node positivity in stage ≥T2 tumors and sensitivity of the axillary ultrasound set at 86% with a specificity of 40%, the strategy to perform preoperative axillary ultrasound yielded rollback costs of $15,215, compared with $15,940 for surgery plus sentinel lymph node biopsy (cost difference, $725 per patient favoring axillary ultrasound). On two-way sensitivity analysis, the cost benefit for axillary ultrasound was not seen in patients with a low risk for nodal metastasis.

Conclusion.
The adoption of routine preoperative axillary sonography with FNA is a lower-cost strategy than conventional strategies in patients with stage ≥T2 invasive breast cancer.
Hydrolysis and Precipitation of Polyacrylamides in Hard Brines at Elevated Temperatures
Authors: Moradi-Araghi Ahmad , Doe Peter H. 
Published: May 2011

Summary
Laboratory data are used to show that commercial polyacrylamides hydrolyze to an equilibrium degree that depends on the temperature of hydrolysis but is largely independent of the brine composition. At greater than 20 ppm hardness levels, polyaerylamide solutions pass through a sharp cloud point as their temperature is raised. This cloud-point temperature depends primarily on the hardness level of the brine and the degree of hydrolysis of the polymer, with lesser dependency on polymer molecular weight and polymer concentration. Indications are that these cloudy solutions cause plugging of porous media. Therefore, a polymer solution is potentially useful only below its cloud-point temperature. For application in a given reservoir, the temperature and frequently the hardness of the water are fixed. If a polyaerylamide hydrolyzes at reservoir conditions to where its cloud point in the field water falls below the reservoir temperature, it is not suitable for polymer flooding in that reservoir.
Cloud-point data, in conjunction with rate-of-hydrolysis data, indicate a "safe" limit of approximately 75°C [167°F] for brines containing 2,000 ppm hardness and above, increasing to around 88°C [190°F] at 500 ppm, 96°C [205°F] at 270 ppm, and at least 204°C [400°F] at 20 ppm and below. Most unsoftened injection waters will limit polyacrylamide use to below 93 °C [200°F]. Most produced waters will limit applicability to below 82°C [180°F].
Azimuth Preservation in Pre-Stack Time Migration using Offset Vector Tiles
Authors: Rowe R. Wilson , Al-Najjar Mohammed H. 
Published: May 2011

Abstract
Wide azimuth (WAZ) land 3D seismic recording geometry typically generates data that is spatially well sampled with a wide range of azimuths and a regular distribution of offsets at those azimuths. Unfortunately, the azimuth information is lost in the pre-stack time migration (PSTM) using traditional processing techniques. Preserving azimuth (the angle measured clockwise from north of a geometric ray that starts at the source point and passes through the receiver point) and offset (the distance between a trace's source and receiver points) information in image gathers is desirable so that the attributes can be used in the detection of horizontal transverse isotropy (HTI), which can provide insight into reservoir fracture orientation. This paper describes the Offset Vector Tile (OVT) processing approach, a new industry trend in seismic data processing to preserve shot-receiver azimuth on image gathers.
OVT, also commonly refered to as Common Offset Vector (COV) gathers, are minimal data sets that are linked to patch dimensions and repeat patterns observed in WAZ 3D recording geometry. The OVT method is used to produce single fold pre-stack data volumes that cover the full 3D survey area. All of the traces in a single OVT volume share similar offset and azimuth attributes. Additionally, they provide new opportunities for noise attenuation, trace interpolation, and data regularization. These signal enhancements lead to less migration noise and an overall image improvement. Migration is performed on all of the OVT volumes resulting in an equivalent number of pre-stack migrated data sets, each with their respective azimuth and offset preserved. Traces from each common image point of the numerous migrated OVT volumes are grouped to form image gathers, which can then be analyzed for azimuthal anisotriopy.
The OVT method is demonstrated as a case history on a WAZ land 3D survey in the Eastern Province of Saudi Arabia.
Workflow Automation of a 5-Stage Gate Upstream Technology Pilot Process
Authors: Alsayari Saleh M. , Lauritzen Jon E. , Alqurtas Abdulrahman M. 
Published: May 2011

Abstract
The introduction of new completion technologies in Saudi Aramco has historically undertaken a lengthy manual process for approval of use in Saudi Aramco wells. During this process, Petroleum Engineers develop and support production technologies based on analysis of lab and field studies. When the technology is deemed fit for purpose and beneficial to Saudi Aramco, the analysis is formalized and processed through management. Specialist engineers steward these assessment studies through multiple parties for their input. Because the process is manual and inconsistent, process and technology reliability — along with project time duration — cannot be easily estimated and quality assured. The solution is to automate, simplify and optimize the technology piloting process, by introducing a standardized 5-Stage Gate process, and implementing it through an electronic workflow system. The new solution will improve process transparency, tracking and monitoring. It also strengthens the organization's commitment in ensuring transparency and accountability; thus enabling a fair competitive market for technology introduction.
The Rock Physicochemical Basis for Time-Lapse Seismic Reservoir Monitoring of CO2 Injection
Authors: Vanorio Tiziana , Nur Amos , Diaz Elizabeth 
Published: May 2011

Abstract
This paper springs from a series of laboratory experiments and high-resolution imaging techniques assessing the changes in microstructure, transport, and seismic properties of brine-saturated sandstones and carbonates when injected with CO2. Results show that the injection of CO2 into a brine-rock system induces chemo-mechanical mechanisms, which permanently change the rock frame. The injection of CO2 into brine-saturated-sandstones induces salt precipitation primarily at grain contacts and/or within small pore throats. Salt precipitation decreases permeability and increases P- and S- wave velocities particularly in sandstones characterized by porosity lower than 10%. On the other hand, the injection of CO2-rich brine into carbonates induces dissolution of the microcrystalline matrix (i.e., micrite) leading to porosity enhancement. Dissolution counteracts and overwhelms a pressure-dependent, chemo-mechanical creeping of the rock leading to compaction. The overall result is the decrease of the elastic moduli of the dry rock frame. These findings demonstrate that monitoring the time-lapse seismic response of chemically stimulated systems is far from being a pure fluid-substitution problem.
Non-Linear Model for Evaluation of Elastomer Seals Subjected to Differential Pressure
Authors: Al-Kharusi M.S.M. , Qamar S.Z. , Pervez T. , Akhtar M. 
Published: May 2011

Abstract
The present paper discusses performance evaluation of swelling elastomer seals used in oil well applications under different field conditions. Swelling elastomers are a new type of advanced polymers, and have started to play an important role in improving existing wells, and in aiding oil recovery from difficult or abandoned fields. On the other hand, failure of these swell packers can lead to significant losses in terms of time and money. Performance evaluation of swelling-elastomer packers and other sealing elements prior to being put to use is therefore critically important. Theoretical investigation of the elastomer seal bonded between a metal tube and a rigid casing is carried out in the present paper. Numerical modeling and simulation for swelling-elastomer seals is also conducted using a Finite Element (FE) package such as ABAQUS. All Theoretical and numerical results of this study will help in predicting the seal behavior under different well conditions and the parameter that will affect on the sealing performance. Also, the study investigates both the effect of the material and geometrical properties of the elastomer on its sealing performance under different loading conditions. For the sealing environment, the study investigates the effect of radial strain (tubular expansion ratio) and the annular fluid pressure on the sealing performance under different seal geometries.
Introduction
Due to the continued forecast of increasing energy demand (oil and gas in particular), oil companies are stepping up their efforts in meeting the global demand. Drilling to increasing depths and producing from difficult reservoirs are already posing serious challenges to the petroleum development industry. Apart from this, there is a continued effort towards performance improvement, cost reduction and innovation for new tools and techniques to make the dream of a mono-bore diameter well a reality. Solid expandable tubular (SET) technology achieved quite a few milestones in this direction.