bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of a novel complex BRAF mutation in a follicular variant papillary thyroid carcinoma.
Authors: Barzon Luisa , Masi Giulia , Boschin Isabella Merante , Lavezzo Enrico , Pacenti Monia , Casal Ide Eric , Toniato Antonio , Toppo Stefano , Palù Giorgio , Pelizzo Maria Rosa 
Published: April 2008

IntroductionActivating mutations of the BRAF oncogene are frequently detected in papillary thyroid carcinoma (PTC) and have been associated with a worse prognosis. The amino acid substitution V600E accounts for 90% of all oncogenic BRAF mutations and is typically detected in classic PTCs, whereas other less frequent BRAF mutations seem to be associated with other PTC histotypes.CaseScreening for activating BRAF mutations in a series of 83 PTCs identified the most common V600E mutation in 39 cases (histologically, 38 classic PTCs and 1 sclerosing variant PTC) and a complex in-frame mutation involving amino acids V600–S605 in a stage III multicentric follicular variant PTC, occurring in a 50-year-old female patient, who was affected by hypothyroidism in autoimmune thyroiditis and had a family history of PTC and autoimmune thyroiditis. Since the identified BRAF mutation was novel in the literature, bioinformatic modeling was performed to predict its impact on BRAF activity. Although the mutation resulted in loss of a phosphorylation site in the activation loop of BRAF, it was predicted to increase BRAF kinase activity by mimicking an activating phosphorylation.ConclusionsThis study, which reports a new BRAF mutation, highlights the usefulness of bioinformatic modeling in the prediction of functional effects of new mutations and indicates that mutation-specific screening tests might miss some rare BRAF mutations. These facts should be taken into consideration in the molecular diagnosis of thyroid cancer and in the design of therapeutic protocols based on inhibitors of the BRAF pathway.
Semidominant Mutations in Reduced Epidermal Fluorescence 4 Reduce Phenylpropanoid Content in Arabidopsis
Authors: Stout Jake , Romero-Severson Ethan , Ruegger Max O , Chapple Clint 
Published: April 2008

Abstract
Plants synthesize an array of natural products that play diverse roles in growth, development, and defense. The plant-specific phenylpropanoid metabolic pathway produces as some of its major products flavonoids, monolignols, and hydroxycinnamic- acid conjugates. The reduced epidermal fluorescence 4 (ref4) mutant is partially dwarfed and accumulates reduced quantities of all phenylpropanoid-pathway end products. Further, plants heterozygous for ref4 exhibit intermediate growth and phenylpropanoid-related phenotypes, suggesting that these mutations are semidominant. The REF4 locus (At2g48110) was cloned by a combined map- and sequencing-based approach and was found to encode a large integral membrane protein that is unique to plants. The mutations in all ref4 alleles cause substitutions in conserved amino acids that are located adjacent to predicted transmembrane regions. Expression of the ref4-3 allele in wild-type and null REF4 plants caused reductions in sinapoylmalate content, lignin content, and growth, demonstrating that the mutant alleles are truly semidominant. Further, a suppressor mutant was isolated that abolishes a WW protein–protein interaction domain that may be important for REF4 function.
Interactions Between Stressful Environment and Gene Deletions Alleviate the Expected Average Loss of Fitness in Yeast
Authors: Jasnos Lukasz , Tomala Katarzyna , Paczesniak Dorota , Korona Ryszard 
Published: April 2008

Abstract
The conjecture that the deleterious effects of mutations are amplified by stress or interaction with one another remains unsatisfactorily tested. It is now possible to reapproach this problem systematically by using genomic collections of mutants and applying stress-inducing conditions with a well-recognized impact on metabolism. We measured the maximum growth rate of single- and double-gene deletion strains of yeast in several stress-inducing treatments, including poor nutrients, elevated temperature, high salinity, and the addition of caffeine. The negative impact of deletions on the maximum growth rate was relatively smaller in stressful than in favorable conditions. In both benign and harsh environments, double-deletion strains grew on average slightly faster than expected from a multiplicative model of interaction between single growth effects, indicating positive epistasis for the rate of growth. This translates to even higher positive epistasis for fitness defined as the number of progeny. We conclude that the negative impact of metabolic disturbances, regardless of whether they are of environmental or genetic origin, is absolutely and relatively highest when growth is fastest. The effect of further damages tends to be weaker. This results in an average alleviating effect of interactions between stressful environment and gene deletions and among gene deletions.
The Protease Activity of Yeast Separase (Esp1) Is Required for Anaphase Spindle Elongation Independently of Its Role In Cleavage of Cohesin
Authors: Baskerville Chris , Segal Marisa , Reed Steven I 
Published: April 2008

Abstract
Separase is a caspase-family protease required for the metaphase–anaphase transition in eukaryotes. In budding yeast, the separase ortholog, Esp1, has been shown to cleave a subunit of cohesin, Mcd1 (Scc1), thereby releasing sister chromatids from cohesion and allowing anaphase. However, whether Esp1 has other substrates required for anaphase has been controversial. Whereas it has been reported that cleavage of Mcd1 is sufficient to trigger anaphase in the absence of Esp1 activation, another study using a temperature-sensitive esp1 mutant concluded that depletion of Mcd1 was not sufficient for anaphase in the absence of Esp1 function. Here we revisit the issue and demonstrate that neither depletion of Mcd1 nor ectopic cleavage of Mcd1 by Tev1 protease is sufficient to support anaphase in an esp1 temperature-sensitive mutant. Furthermore, we demonstrate that the catalytic activity of the Esp1 protease is required for this Mcd1-independent anaphase function. These data suggest that another protein, possibly a spindle-associated protein, is cleaved by Esp1 to allow anaphase. Such a function is consistent with the previous observation that Esp1 localizes to the mitotic spindle during anaphase.
Visual Mutations Reveal Opposing Effects of Illumination on Arousal in Drosophila
Authors: Cheng Yuzhong , Nash Howard A 
Published: April 2008

Abstract
The effect of illumination on alertness can be assessed by comparing the efficacy of an anesthetic under light vs. dark conditions. Results from such tests on wild-type flies and visual mutants demonstrate that, surprisingly, light has both positive and negative influences on arousal. These dual effects may explain aspects of the fly's daily activity and have potential clinical implications.
TheCaenorhabditis elegans rsd-2andrsd-6Genes Are Required for Chromosome Functions During Exposure to Unfavorable Environments
Authors: Han Wang , Sundaram Prema , Kenjale Himanshu , Grantham James , Timmons Lisa 
Published: April 2008

AbstractIn Caenorhabditis elegans, exogenous dsRNA can elicit systemic RNAi, a process that requires the function of many genes. Considering that the activities of many of these genes are also required for normal development, it is surprising that exposure to high concentrations of dsRNA does not elicit adverse consequences to animals. Here, we report inducible phenotypes in attenuated C. elegans strains reared in environments that include nonspecific dsRNA and elevated temperature. Under these conditions, chromosome integrity is compromised in RNAi-defective strains harboring mutations in rsd-2 or rsd-6. Specifically, rsd-2 mutants display defects in transposon silencing, while meiotic chromosome disjunction is affected in rsd-6 mutants. RSD-2 proteins localize to multiple cellular compartments, including the nucleolus and cytoplasmic compartments that, in part, are congruent with calreticulin and HAF-6. We considered that the RNAi defects in rsd-2 mutants might have relevance to membrane-associated functions; however, endomembrane compartmentalization and endocytosis/exocytosis markers in rsd-2 and rsd-6 mutants appear normal. The mutants also possess environmentally sensitive defects in cell-autonomous RNAi elicited from transgene-delivered dsRNAs. Thus, the ultimate functions of rsd-2 and rsd-6 in systemic RNAi are remarkably complex and environmentally responsive.
Functional Conservation of the Yeast and Arabidopsis RAD54-Like Genes
Authors: Klutstein Michael , Shaked Hezi , Sherman Amir , Avivi-Ragolsky Naomi , Shema Efrat , Zenvirth Drora , Levy Avraham A , Simchen Giora 
Published: April 2008

Abstract
The Saccharomyces cerevisiae RAD54 gene has critical roles in DNA double-strand break repair, homologous recombination, and gene targeting. Previous results show that the yeast gene enhances gene targeting when expressed in Arabidopsis thaliana. In this work we address the trans-species compatibility of Rad54 functions. We show that overexpression of yeast RAD54 in Arabidopsis enhances DNA damage resistance severalfold. Thus, the yeast gene is active in the Arabidopsis homologous-recombination repair system. Moreover, we have identified an A. thaliana ortholog of yeast RAD54, named AtRAD54. This gene, with close sequence similarity to RAD54, complements methylmethane sulfonate (MMS) sensitivity but not UV sensitivity or gene targeting defects of rad54Δ mutant yeast cells. Overexpression of AtRAD54 in Arabidopsis leads to enhanced resistance to DNA damage. This gene's assignment as a RAD54 ortholog is further supported by the interaction of AtRad54 with AtRad51 and the interactions between alien proteins (i.e., yeast Rad54 with AtRAD51 and yeast Rad51 with AtRad54) in a yeast two-hybrid experiment. These interactions hint at the molecular nature of this interkingdom complementation, although the stronger effect of the yeast Rad54 in plants than AtRad54 in yeast might be explained by an ability of the Rad54 protein to act alone, independently of its interaction with Rad51.
The extrapolation problem and how population modeling can help
Authors: Forbes Valery E , Calow Peter , Sibly Richard M 
Published: April 2008

AbstractWe argue that population modeling can add value to ecological risk assessment by reducing uncertainty when extrapolating from ecotoxicological observations to relevant ecological effects. We review other methods of extrapolation, ranging from application factors to species sensitivity distributions to suborganismal (biomarker and “-omics”) responses to quantitative structure–activity relationships and model ecosystems, drawing attention to the limitations of each. We suggest a simple classification of population models and critically examine each model in an extrapolation context. We conclude that population models have the potential for adding value to ecological risk assessment by incorporating better understanding of the links between individual responses and population size and structure and by incorporating greater levels of ecological complexity. A number of issues, however, need to be addressed before such models are likely to become more widely used. In a science context, these involve challenges in parameterization, questions about appropriate levels of complexity, issues concerning how specific or general the models need to be, and the extent to which interactions through competition and trophic relationships can be easily incorporated.
The Neogene Veracruz fault: evidences for left-lateral slip along the southern Mexico block
Authors: Andreani Louis , Rangin Claude , Martínez-Reyes Juventino , Le Roy Charlotte , Aranda-García Mario , Le Pichon Xavier , Peterson-Rodriguez Rolando 
Published: April 2008

AbstractStructural data combined with analysis of satellite images and seismic profiles show that a major left-lateral strike-slip fault affects the Veracruz basin and post-5 Ma volcanic rocks of the Los Tuxtlas volcanic field (LTVF). The main volcanic alignment of the LTVF is located along this fault. Additional structural data collected in the Trans-Mexican volcanic belt (areas of Xalapa, Teziutlán and Huauchinango) show that the shear zone affects Pliocene Trans-Mexican volcanic rocks. Low seismicity associated to faulted Quaternary markers such as alluvial fans, alluvial terraces and volcanoes argue for active faulting in this area. Plio-Quaternary strike-slip faulting in the Veracruz basin and in the eastern Trans-Mexican volcanic belt is important because it connects two important structural provinces: the left-lateral strike-slip faults province to the south and the left-lateral transtensive faulting that affects the central part of the Trans-Mexican volcanic belt. These three active deformation zones constitute the boundary between the southern Mexico block and the North American plate. It is generally assumed that strike-slip faulting along the Trans-Mexican and Central America volcanic arcs is the result of oblique subduction of the Cocos plate under the North American and Caribbean plates. However slip vectors along the Middle America trench are almost perpendicular to the trench. This Neogene sinistral strike-slip motion could be partially driven by the eastward motion of the Caribbean plate rather than by strain partitioning along the oblique Middle America trench subduction zone.
Development of an Ultra-Low Interfacial Tension Surfactant in a System with No-Alkali for Chemical Flooding
Authors: Wang D. M. , Liu C. D. , Wu W. X. , Wang G. 
Published: April 2008

Abstract
The development and evaluation of a series of betaine amphoteric surfactants which have been synthesized recently is introduced in this paper.
This series of products were synthesized by adjusting the structure of the lipophilic group. A product of this series was comprehensively evaluated. The results show that interfacial tension (IFT) between this betaine amphoteric surfactant solutions and Daqing crude oil can reach an ultra–low value (10−3mN/m ~ 10−4mN/m) with no alkali or weak alkali (Na2CO3) and at ultra-low concentrations of surfactants of only 10 ~ 3000 ppm (wt). When the salinity of the make up water is 0 ~ 153,700 mg/L, concentration of divalent ions 0 ~ 1,500mg/L and concentration of polymer 0 ~ 2,000 mg/L, it hardly effects the IFT value, the IFT of the surfactant solutions with crude oil maintains an ultra-low value. Experiments in cores indicate that the displacement efficiency of the compound solution composed of polymers and surfactants (0.1% concentration) is higher than that of alkali/polymer/surfactant (ASP) solution (surfactant concentration 0.3%) used in the oil field now, the total recovery can reach 70 % OOIP or higher. It is shown that the IFT of the fluid gathered at the outlet of the cores, when flooding by 0.35 PV of this type of surfactant (0.2 % concentration), can still be in the range of 10−3mN/m ~ 10−4mN/m, this means that the entire volume of the core is flooded by ultra-low IFT fluid, which is seldom seen when using other types of surfactants. It is also shown that the surfactant can change the wettability and increase the recovery efficiency in micro-visual oil displacement experiments.
The above results show that this is a very promising surfactant for ultra-low IFT chemical flooding. It can be used in a wide range of reservoir conditions (both low and high salinities, divalent ion contents, temperatures, clay contents, different alkali etc.) to significantly increase the oil recovery. Since it only needs a very low concentration of surfactant to obtain an ultra-low IFT, the economics of chemical flooding using this type of surfactant should be better than that using conventional ones.
Study of Polymer Flooding in Class III Reservoir and Pilot Test
Authors: Pu Hui , Yin Daiyin 
Published: April 2008

Abstract
Daqing Oilfield is now at the stage of extra-high watercut after 48 years of development. Since 1996, the field scale polymer flooding has been targeting major reservoirs with thick pay zones and high permeability, and the commercial polymer in Class ІІ reservoirs (the effective thickness is 1~3m and the effective permeability is higher than 100×10−3 μm2) also started. In order to increase the recovery factor of Class ІІІ reservoir and to improve the development effect of mature oilfield, the study on polymer flooding in Class ІІІ reservoir (the effective permeability is less than 100×10−3 μm2, the effective thickness is smaller than 1m) and corresponding pilot test were performed. The objectives were to enhance oil recovery efficiency, increase recoverable reserves of Class ІІІ reservoir, and determine potential target layers for field scale polymer flooding. In this work, based on the detailed geological information, optimal polymer injection parameters were designed based on the coreflood tests and numerical simulation. The coreflood results indicated that the compatibility between the molecular size of polymer and pore structure of Class ІІІ reservoir is very important. Physical properties of reservoir, well log data, sealed coring data, the polymer injection parameters were also selected for the design. Six sets of polymer flood plans were calculated and compared. The results showed that the novel separate-layer injection with different molecular weights obtained higher oil recovery. The polymer injection in pilot test started in March 2007. The field application results of initial stage of polymer flooding are very promising.
A Pore Level Study of MIOR Displacement Mechanisms in Glass Micromodels Using Rhodococcus sp. 094
Authors: Crescente Christian , Rekdal Andreas , Abraiz Akram , Torsaeter Ole , Hultmann Lisbeth , Stroem Arne , Rasmussen Kjetil , Kowalewski Espen 
Published: April 2008

Abstract
Micromodel experiments have been executed in order to have better insight into the displacement mechanisms allowing Rhodococcus sp. 094 to increase oil recovery. Changes caused by the bacteria in the fluid interfaces and pore walls have been recorded and are presented. The previously suspected mechanisms are further confirmed by the results, but a much better insight into the details of how the process occurs has been obtained and a theory for this process is developed.
Mechanisms of Oil Recovery via Multi-Contact Miscible Gas Injection Process within Lensed Systems
Authors: Al-Wahaibi Yahya. M. , Al-Hadrami Abdullah. K. 
Published: April 2008

Abstract
The recovery of oil by injection of miscible gas has been a subject of interest and research in petroleum engineering over the past 40 years. In a first contact miscible displacement, the injected fluid forms only single-phase mixtures with oil in place, so in theory, 100% recovery can be achieved. Unfortunately, many phenomena conspire to limit the efficiency of the miscible flooding process including viscous fingering and permeability heterogeneity. One type of important heterogeneities that occur at the small scale is the lensed system. This is one of the most common sedimentary structures found in sandstone reservoirs and is almost universal.
This paper investigates the physics of gas-oil multi-contact miscible (MCM) displacements within lensed porous media using a combination of well-characterized laboratory experiments and detailed numerical simulation. The aims were to:
quantify the recovery efficiency of MCM displacements conducted at different flow conditions, provide a set of benchmark experimental data for MCM displacements performed within lensed porous media, and validate conventional compositional simulation of MCM displacements
The novel experimental studies were conducted in specially designed lens visual models packed with unconsolidated glass beads and used a two-phase three-component (IPA/water/cyclohexene) liquid system that exhibits an upper critical point at ambient conditions. First contact miscible (FCM), immiscible and MCM displacement experiments were performed. They were then simulated using a commercial compositional simulator with a single set of EOS parameters and without using history matching (all input data to the simulator were determined from independent experiments).
The produced oil and gas in the experiments were found not to be in compositional equilibrium. This was observed in both homogeneous (as reported previously by Al-Wahaibi et al, 20051) and lens models. This indicates that nonequilibrium occurs at even smaller scales than the lensed structure. As a result, the oil recoveries and gas cuts predicted by compositional simulation for MCM displacements differed significantly from the experimental results, although an excellent match was obtained for the FCM and immiscible displacements.
Further experiments investigating the effects of varying injection rates and gravity forces on the level of nonequilibrium observed in the produced fluids are described. Numerical simulation of these experiments provides additional insight into the physical mechanisms causing the nonequilibrium.
The experiments performed in this study are the first of their kind as they report the significance of nonequilibrium on MCM process prediction and the influence of lens heterogeneities on MCM injection. This study has important implications for the correct interpretation of core data, and for scale-up processes to reservoir scale, particularly for handling gas/oil nonequilibrium when modelling MCM displacements.
Mechanistic Modeling of Alkaline/Surfactant/Polymer Floods
Authors: Mohammadi Hourshad , Delshad Mojdeh , Pope Gary A. 
Published: April 2008

Abstract
Alkaline/surfactant/polymer (ASP) flooding is of increasing interest and importance due to high oil prices and the need to increase oil production. The benefits of combining alkali with surfactant are well established. The alkali has very important benefits such as lowering interfacial tension and reducing adsorption of anionic surfactants that decrease costs and make ASP a very attractive enhanced oil recovery method provided the consumption is not too large and the alkali can be propagated at the same rate as the synthetic surfactant and polymer. However, the process is complex so it is important that new candidates for ASP be selected taking into account the numerous chemical reactions that occur in the reservoir. The reaction of acid and alkali to generate soap and its subsequent effect on phase behavior is the most crucial for crude oils containing naphtenic acids. Mechanistic simulation of the ASP flood considering the chemical reactions, alkali consumption, and soap generation and the effect on the phase behavior is the key to success of future field operations. Using numerical models, the process can be designed and optimized to ensure the proper propagation of alkali and effective soap and surfactant concentrations to promote low interfacial tension and a favorable salinity gradient. In this paper, we describe the ASP module of UTCHEM simulator with particular attention to phase behavior and the effect of soap on optimum salinity and solubilization ratio. Phase behavior data are presented for sodium carbonate and a blend of surfactants with an acidic crude oil that followed the conventional Winsor phase transition with significant three-phase regions even at low surfactant concentrations. The solubilization data at different oil concentrations were successfully modeled using Hand's rule. Optimum salinity and solubilization ratio were correlated with soap mole fractions using mixing rules. ASP coreflood results were successfully modeled taking into account the aqueous reactions, alkali/rock interactions, and phase behavior of soap and surfactant. Mechanistic simulations give insights into the propagation of alkali, soap, and surfactant in the core and aid in future coreflood and field scale ASP designs.