bluuebunny/crossref_metadata_2025_split huggingface dataset:
Central Role of Reverting Mutations in HLA Associations with Human Immunodeficiency Virus Set Point
Authors: Matthews Philippa C. , Prendergast Andrew , Leslie Alasdair , Crawford Hayley , Payne Rebecca , Rousseau Christine , Rolland Morgane , Honeyborne Isobella , Carlson Jonathan , Kadie Carl , Brander Christian , Bishop Karen , Mlotshwa Nonkululeko , Mullins James I. , Coovadia Hoosen , Ndung'u Thumbi , Walker Bruce D. , Heckerman David , Goulder Philip J. R. 
Published: July 2008

ABSTRACT

Much uncertainty still exists over what T-cell responses need to be induced by an effective human immunodeficiency virus (HIV) vaccine. Previous studies have hypothesized that the effective CD8
+
T-cell responses are those driving the selection of escape mutations that reduce viral fitness and therefore revert posttransmission. In this study, we adopted a novel approach to define better the role of reverting escape mutations in immune control of HIV infection. This analysis of sequences from 710 study subjects with chronic C-clade HIV type 1 infection demonstrates the importance of mutations that impose a fitness cost in the control of viremia. Consistent with previous studies, the viral set points associated with each HLA-B allele are strongly correlated with the number of Gag-specific polymorphisms associated with the relevant HLA-B allele (
r
= −0.56,
P
= 0.0034). The viral set points associated with each HLA-C allele were also strongly correlated with the number of Pol-specific polymorphisms associated with the relevant HLA-C allele (
r
= −0.67,
P
= 0.0047). However, critically, both these correlations were dependent solely on the polymorphisms identified as reverting. Therefore, despite the inevitable evolution of viral escape, viremia can be controlled through the selection of mutations that are detrimental to viral fitness. The significance of these results is in highlighting the rationale for an HIV vaccine that can induce these broad responses.
S Acylation of the Hemagglutinin of Influenza Viruses: Mass Spectrometry Reveals Site-Specific Attachment of Stearic Acid to a Transmembrane Cysteine
Authors: Kordyukova Larisa V. , Serebryakova Marina V. , Baratova Ludmila A. , Veit Michael 
Published: July 2008

ABSTRACT
S acylation of cysteines located in the transmembrane and/or cytoplasmic region of influenza virus hemagglutinins (HA) contributes to the membrane fusion and assembly of virions. Our results from using mass spectrometry (MS) show that influenza B virus HA possessing two cytoplasmic cysteines contains palmitate, whereas HA-esterase-fusion glycoprotein of influenza C virus having one transmembrane cysteine is stearoylated. HAs of influenza A virus having one transmembrane and two cytoplasmic cysteines contain both palmitate and stearate. MS analysis of recombinant viruses with deletions of individual cysteines, as well as tandem-MS sequencing, revealed the surprising result that stearate is exclusively attached to the cysteine positioned in the transmembrane region of HA.
The Broadly Neutralizing Anti-Human Immunodeficiency Virus Type 1 4E10 Monoclonal Antibody Is Better Adapted to Membrane-Bound Epitope Recognition and Blocking than 2F5
Authors: Huarte Nerea , Lorizate Maier , Maeso Rubén , Kunert Renate , Arranz Rocio , Valpuesta José M. , Nieva José L. 
Published: July 2008

ABSTRACT
The broadly neutralizing 2F5 and 4E10 monoclonal antibodies (MAbs) recognize epitopes within the membrane-proximal external region (MPER) that connects the human immunodeficiency virus type 1 (HIV-1) envelope gp41 ectodomain with the transmembrane anchor. By adopting different conformations that stably insert into the virion external membrane interface, such as helical structures, a conserved aromatic-rich sequence within the MPER is thought to participate in HIV-1-cell fusion. Recent experimental evidence suggests that the neutralizing activity of 2F5 and 4E10 might correlate with the MAbs' capacity to recognize epitopes inserted into the viral membrane, thereby impairing MPER fusogenic activity. To gain new insights into the molecular mechanism underlying viral neutralization by these antibodies, we have compared the capacities of 2F5 and 4E10 to block the membrane-disorganizing activity of MPER peptides inserted into the surface bilayer of solution-diffusing unilamellar vesicles. Both MAbs inhibited leakage of vesicular aqueous contents (membrane permeabilization) and intervesicular lipid mixing (membrane fusion) promoted by MPER-derived peptides. Thus, our data support the idea that antibody binding to a membrane-inserted epitope may interfere with the function of the MPER during gp41-induced fusion. Antibody insertion into a cholesterol-containing, uncharged virion-like membrane is mediated by specific epitope recognition, and moreover, partitioning-coupled folding into a helix reduces the efficiency of 2F5 MAb binding to its epitope in the membrane. We conclude that the capacity to interfere with the membrane activity of conserved MPER sequences is best correlated with the broad neutralization of the 4E10 MAb.
Habitual Trust in Encountering Violence at Work
Authors: Virkki Tuija 
Published: July 2008

• Summary: This article analyses attitudes towards client-perpetrated violence among Finnish social workers and nurses. The research material consists of 25 theme interviews and 20 thematic writings which are examined by means of content analysis. • Findings: Although statistics show that among all the professional groups in Finland, people working in social welfare and health care are most likely to encounter violence, the risk of violence is underestimated by these professionals. In addition, violence that has taken place is not recognized as `real' violence, but as an excusable expression of clients' distress, or as a justified reaction to the employees' conduct. By using Niklas Luhmann's idea of trust as a way of ignoring risks in spite of being aware of them, the present study shows how trust is at the core of professional activity for caring professions such as those of social workers or nurses. Pierre Bourdieu's concept `habitus', in its part, explains the way in which trusting has became part of a professional orientation which works automatically and seems natural. The study shows that trust orientation is deeply embedded in professional practices, and therefore slow to change. • Applications : These findings have implications for the prevention of violence: the structural level of the social formation of the habitual trust orientation should be taken into account while the formal policies of prevention are planned.
Gynaecological morbidity among HIV positive pregnant women in Cameroon
Authors: Mbu Enow R , Kongnyuy Eugene J , Mbopi-Keou FX , Tonye Rebecca N , Nana Philip N , Leke Robert JI 
Published: July 2008

Abstract

Objective
To compare the prevalence of gynaecological conditions among HIV infected and non-infected pregnant women.

Methods
Two thousand and eight (2008) pregnant women were screened for HIV, lower genital tract infections and lower genital tract neoplasia at booking antenatal visit.

Results
About 10% (198/2008) were HIV positive. All lower genital tract infections except candidiasis were more prevalent among HIV positive compared to HIV negative women: vaginal candidiasis (36.9% vs 35.4%; p = 0.678), Trichomoniasis (21.2% vs 10.6%; p < 0.001), gonorrhoea (10.1% vs 2.5%; p < 0.001), bacterial vaginosis (21.2% vs 15.2%; p = 0.026), syphilis (35.9% vs 10.6%; p < 0.001), and Chlamydia trachomatis (38.4% vs 7.1%; p < 0.001). Similarly, HIV positive women more likely to have preinvasive cervical lesions: low-grade squamous intraepithelial lesion (SIL) (18.2% vs 4.4%; p < 0.001) and high-grade squamous intraepithelial lesion (12.1% vs 1.5%; p < 0.001).

Conclusion
We conclude that (i) sexually transmitted infections (STIs) are common in both HIV positive and HIV negative pregnant women in Cameroon, and (ii) STIs and preinvasive cervical lesions are more prevalent in HIV-infected pregnant women compared to their non-infected compatriots. We recommend routine screening and treatment of STIs during antenatal care in Cameroon and other countries with similar social profiles.
CSE1L/CAS, the cellular apoptosis susceptibility protein, enhances invasion and metastasis but not proliferation of cancer cells
Authors: Liao Ching-Fong , Luo Shue-Fen , Li Li-Tzu , Lin Chuang-Yu , Chen Ying-Chun , Jiang Ming-Chung 
Published: July 2008

Abstract

Background
The cellular apoptosis susceptibility (CAS) protein is regarded as a proliferation-associated protein that associates with tumour proliferation as it associates with microtubule and functions in the mitotic spindle checkpoint. However, there is no any actual experimental study showing CAS (or CSE1 and CSE1L) can increase the proliferation of cancer cells. Previous pathological study has reported that CAS was strongly positive stained in all of the metastasis melanoma that be examined. Thus, CAS may regulate the invasion and metastasis of cancers. CAS is highly expressed in cancers; if CAS is associated with cancer proliferation, then increased CAS expression should be able to increase the proliferation of cancer cells. We studied whether increased CAS expression can increase cancer cell proliferation and whether CAS regulates the invasion of cancer cells.

Methods
We enhanced or reduced CAS expression by transfecting CAS or anti-CAS expression vectors into human MCF-7 breast cancer cells. The proliferations of cells were determined by trypan blue exclusion assay and flow cytometry analysis. Invasion of cancer cells were determined by matrigel-based invasion assay.

Results
Our studies showed that increased CAS expression was unable to enhance cancer cell proliferation. Immunofluorescence showed CAS was distributed in cytoplasm areas near cell membrane and cell protrusions. CAS was localized in cytoplasmic vesicle and immunogold electronmicroscopy showed CAS was located in vesicle membrane. CAS overexpression enhanced matrix metalloproteinase-2 (MMP-2) secretion and cancer cell invasion. Animal experiments showed CAS reduction inhibited the metastasis of B16-F10 melanoma cells by 56% in C57BL/6 mice.

Conclusion
Our results indicate that CAS increases the invasion but not the proliferation of cancer cells. Thus, CAS plus ECM-degradation proteinases may be used as the markers for predicting the advance of tumour metastasis.
Analytical Solution of Nonisothermal Buckley-Leverett Flow Including Tracers
Authors: Sumnu-Dindoruk Deniz , Dindoruk Birol 
Published: July 2008

Summary
Mass balances for two immiscible fluids and tracer and convective heat balance form a system of three equations (nonisothermal Buckley-Leverett Problem with tracers). Tracer component is considered to investigate the propagation of a tracer to track the flood (or to track a miscible inert contaminant introduced during drilling). We have solved the resulting nonisothermal two-phase convective flow equation in porous media analytically, including a tracer component (i.e., cold or hot waterflooding with and without tracer). Method of characteristics (MOC) is used as a solution technique after transforming the balance equations in a form that can be solved easily with two Welge tangents. Our solution technique is valid for both radial-and linear-flow models.
In practice, these solutions can be used
To investigate the convective flow behavior around the wells (i.e., sudden fluid losses, convective near-well tracer propagation, analyzing pressure transients). To interpret formation-testing-tool responses by detecting the location of the thermal front or to estimate the temperature-buildup time that is needed for Horner-type analysis (for the identification of the formation temperature). To calculate the location of the cold or hot water front (thermal water) while injecting cold-or hot-water. This will yield the limit of the maximum temperature disturbance around the well. To test/scale relative thermal effects of various systems against one another. To test the accuracy of simulators and provide benchmark solutions. To interpret relevant laboratory experiments quickly.
Such solutions helped us to understand the depth of influence of the temperature variations and their influence on the transport properties, in both radial and linear systems. Solutions analytically proved that the thermal front propagates much slower than the flood front. This explains why isothermal black-oil simulators still work although the injected-water temperature is not always equal to the reservoir temperature.
Furthermore, we have checked and verified our results against a commercial thermal simulator and investigated the impact of numerical diffusion on the thermal front as well as conductivity. This part of the work revealed that the temperature front is more prone to numerical diffusion.
The Application of Artificial Neural Networks With Small Data Sets: An Example for Analysis of Fracture Spacing in the Lisburne Formation, Northeastern Alaska
Authors: Kaviani D. , Bui T. D. , Jensen J. L. , Hanks C. L. 
Published: July 2008

SummaryArtificial neural networks (ANNs) have been used widely for prediction and classification problems. In particular, many methods for building ANNs have appeared in the last 2 decades. One of the continuing important limitations of using ANNs, however, is their poor ability to analyze small data sets because of overfitting. Several methods have been proposed in the literature to overcome this problem. On the basis of our study, we can conclude that ANNs that use radial basis functions (RBFs) can decrease the error of the prediction effectively when there is an underlying relationship between the variables. We have applied this and other methods to determine the factors controlling and related to fracture spacing in the Lisburne formation, northeastern Alaska.By comparing the RBF results with those from other ANN methods, we find that the former method gives a substantially smaller error than many of the alternative methods. For example, the errors in predicted fracture spacing for the Lisburne formation with conventional ANN methods are approximately 50 to 200% larger than those obtained with RBFs. With a method that predicts fracture spacing more accurately, we were able to identify more reliably the effects on the spacing of such factors as bed thickness, lithology, structural position, and degree of folding.By comparing performances of all the methods we tested, we observed that some methods that performed well in one test did not necessarily do as well in another test. This suggests that, while RBF can be expected to be among the best methods, there is no "best universal method" for all the cases, and testing different methods for each case is required. Nonetheless, through this study, we were able to identify several candidate methods and, thereby, narrow the work required to find a suitable ANN.In petroleum engineering and geosciences, the number of data is limited in many cases because of expense or logistical limitations (e.g., limited core, poor borehole conditions, or restricted logging suites). Thus, the methods used in this study should be attractive in many petroleum-engineering contexts in which complex, nonlinear relationships need to be modeled by use of small data sets.
Decline-Curve Analysis of Fractured Reservoirs With Fractal Geometry
Authors: Camacho Velázquez Rodolfo , Fuentes-Cruz Gorgonio , Vásquez-Cruz Mario 
Published: July 2008

Summary
Evaluation of reservoir parameters through well-test and decline-curve analysis is a current practice used to estimate formation parameters and to forecast production decline identifying different flow regimes, respectively. From practical experience, it has been observed that certain cases exhibit different wellbore pressure and production behavior from those presented in previous studies. The reason for this difference is not understood completely, but it can be found in the distribution of fractures within a naturally fractured reservoir (NFR). Currently, most of these reservoirs are studied by means of Euclidean models, which implicitly assume a uniform distribution of fractures and that all fractures are interconnected. However, evidence from outcrops, well logging, production-behavior studies, and the dynamic behavior observed in these systems, in general, indicate the above assumptions are not representative of these systems. Fractal theory considers a nonuniform distribution of fractures and the presence of fractures at different scales; thus, it can contribute to explain the behavior of many fractured reservoirs. The objective of this paper is to investigate the production-decline behavior in an NFR exhibiting single and double porosity with fractal networks of fractures. The diffusion equations used in this work are a fractal-continuity expressions presented in previous studies in the literature and a more recent generalization of these equations, which includes a temporal fractional derivative. The second objective is to present a combined analysis methodology, which uses transient-well-test and bound-ary-dominated-decline production data to characterize an NFR exhibiting fractures, depending on scale. Several analytical solutions for different diffusion equations in fractal systems are presented in Laplace space for both constant-wellbore-pressure and pressure-variable-rate inner-boundary conditions. Both single- and dual-porosity systems are considered. For the case of single-porosity reservoirs, analytical solutions for different diffusion equations in fractal systems are presented. For the dual-porosity case, an approximate analytical solution, which uses a pseudosteady-state matrix-to-fractal fracture-transfer function, is introduced. This solution is compared with a finite-difference solution, and good agreement is found for both rate and cumulative production. Short- and long-time approximations are used to obtain practical procedures in time for determining some fractal parameters. Thus, this paper demonstrates the importance of analyzing both transient and boundary-dominated flow-rate data for a single-well situation to fully characterize an NFR exhibiting fractal geometry.
Synthetic and field examples are presented to illustrate the methodology proposed in this work and to demonstrate that the fractal formulation consistently explains the peculiar behavior observed in some real production-decline curves.
Toward Field-Scale Wettability Modification—The Limitations of Diffusive Transport
Authors: Stoll W. M. , Hofman J. P. , Ligthelm D. J. , Faber M. J. , van den Hoek P. J. 
Published: July 2008

Summary
Densely-fractured oil-wet carbonate fields pose a true challenge for oil recovery that traditional primary and secondary processes fail to meet. The difficulty arises from the combination of two unfavorable characteristics: First, the dense fracturing frustrates an efficient waterflood; second, because of the oil-wetness, the water pressure exceeds the oil pressure inside the matrix blocks, thus inhibiting spontaneous imbibition of water. In the past decade, using a new class of surfactants, enhanced oil recovery (EOR) researchers have studied the options to chemically revert the wettability of carbonate rock without drastically decreasing the oil-water interfacial tension. These chemicals, termed "wettability modifiers" (WMs), effectively reverse the sign of capillary pressure at the prevalent saturation. With the oil pressure exceeding the water pressure, the capillary pressure becomes the driving force for oil expulsion from the matrix and into the fracture system.
Previous publications on chemical wettability modification focused on the performance of different chemical wettability modifiers for a chosen rock/oil/brine system. In some cases, they demonstrated an almost full oil recovery from core plugs. Little attention, however, has been given to the mechanism underlying the transport of the chemical into the matrix block and to the proper scaling of laboratory results to reservoir size. The present study aims to demonstrate that imbibition after wettability modification is diffusion-limited. To this end, the recovery profiles for spontaneous capillary imbibition, as well as for imbibition after wettability modification, are calculated. The results are then used to compare with the data of Amott cell imbibition experiments. It is confirmed that in both cases, the cumulative recovery is initially proportional to the square root of time. Imbibition after wettability modification, however, takes approximately 1,000 times longer than spontaneous capillary imbibition into a water-wet medium. The slow recovery observed in the case of imbibition after wettability modification is in excellent agreement with the assumption that, in the absence of significant spontaneous imbibition, the WM, to unfold its action, must first diffuse into the porous medium. In any diffusion process, the time scale is linked to the square of the length scale of the medium. Therefore, it would take up to 1,000 times longer (an equivalent of 200 years) before the same recovery is obtained from a meter-scale matrix block as is obtained from a centimeter-scale plug in a laboratory in 100 days.
Consequently, unless a significantly faster transport mechanism for the wettability modifier is identified, or unless viscous forces or buoyancy enable forced imbibition, the chemical wettability modification of fractured oil-wet carbonate rock does not provide an economically interesting opportunity.
Characterization of Crosslinked Gel Kinetics and Gel Strength by Use of NMR
Authors: Romero-Zerón L. , Manalo F. , Kantzas A. 
Published: July 2008

Summary
Highly crosslinked gels are used in high-permeability reservoirs to achieve appropriate fluid-loss control during well completion and workover operations. Crosslinked gels are also used to shut off unwanted gas and/or water influx into production wells and to improve the conformance of the near-wellbore injection profile in naturally fractured or high-permeability reservoirs. In all these applications, the appropriate design of the gel treatment is critical to ensure an efficient gel placement. Important variables of gel systems are gel rheology and gel strength during and after the gelation reaction is completed.
The rheology of gels and gelation rates is commonly determined by rheometry or, in a qualitative mode, through bottle testing with well-known gel-strength codes (i.e., Sydansk's code). Rheological measurements can be time-consuming, while bottle testing can lead to an inconsistent gel description as a result of the subjective nature of the gel-strength code. This paper evaluates the use of low-field nuclear magnetic resonance (NMR) as a nonin-trusive technique to monitor gelation rates and to characterize gel strength. Because of the nonintrusive nature of this technique, it could be considered to be a better alternative to conventional rhe-ological measurements and common qualitative methods, such as gel-strength codes. In addition, NMR could offer faster and more accurate gel-strength characterization and gelation monitoring compared to rheological methods. Furthermore, it can be used in porous media. NMR parameters are predicted and calibrated conducting concentration sweeps of polymer, crosslinker, and brine, as well as gelation-time sweeps. This then allows for a standardized method for gel characterization.
The findings of this work include a preliminary assessment of the use of different techniques, such as low-field NMR, rheometry, and bottle testing, for monitoring the gelation reaction and gel strength of partially hydrolyzed polyacrylamide chromium [(HPAm)/Cr(III)] acetate gel. The experimental results also include the initial identification of the gel point for different formulations of the gel system using low-field NMR.