bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gene Regulation by H-NS as a Function of Growth Conditions Depends on Chromosomal Position in Escherichia coli
Authors: Brambilla Elisa , Sclavi Bianca 
Published: March 2015

Abstract
Cellular adaptation to changing environmental conditions requires the coordinated regulation of expression of large sets of genes by global regulatory factors such as nucleoid associated proteins. Although in eukaryotic cells genomic position is known to play an important role in regulation of gene expression, it remains to be established whether in bacterial cells there is an influence of chromosomal position on the efficiency of these global regulators. Here we show for the first time that genome position can affect transcription activity of a promoter regulated by the histone-like nucleoid-structuring protein (H-NS), a global regulator of bacterial transcription and genome organization. We have used as a local reporter of H-NS activity the level of expression of a fluorescent reporter protein under control of an H-NS−regulated promoter (Phns) at different sites along the genome. Our results show that the activity of the Phns promoter depends on whether it is placed within the AT-rich regions of the genome that are known to be bound preferentially by H-NS. This modulation of gene expression moreover depends on the growth phase and the growth rate of the cells, reflecting the changes taking place in the relative abundance of different nucleoid proteins and the inherent heterogeneous organization of the nucleoid. Genomic position can thus play a significant role in the adaptation of the cells to environmental changes, providing a fitness advantage that can explain the selection of a gene’s position during evolution.
A Survey of Imprinted Gene Expression in Mouse Trophoblast Stem Cells
Authors: Calabrese J Mauro , Starmer Joshua , Schertzer Megan D , Yee Della , Magnuson Terry 
Published: March 2015

AbstractSeveral hundred mammalian genes are expressed preferentially from one parental allele as the result of a process called genomic imprinting. Genomic imprinting is prevalent in extra-embryonic tissue, where it plays an essential role during development. Here, we profiled imprinted gene expression via RNA-Seq in a panel of six mouse trophoblast stem lines, which are ex vivo derivatives of a progenitor population that gives rise to the placental tissue of the mouse. We found evidence of imprinted expression for 48 genes, 31 of which had been described previously as imprinted and 17 of which we suggest as candidate imprinted genes. An equal number of maternally and paternally biased genes were detected. On average, candidate imprinted genes were more lowly expressed and had weaker parent-of-origin biases than known imprinted genes. Several known and candidate imprinted genes showed variability in parent-of-origin expression bias between the six trophoblast stem cell lines. Sixteen of the 48 known and candidate imprinted genes were previously or newly annotated noncoding RNAs and six encoded for a total of 60 annotated microRNAs. Pyrosequencing across our panel of trophoblast stem cell lines returned levels of imprinted expression that were concordant with RNA-Seq measurements for all eight genes examined. Our results solidify trophoblast stem cells as a cell culture-based experimental model to study genomic imprinting, and provide a quantitative foundation upon which to delineate mechanisms by which the process is maintained in the mouse.
Genetic Analysis of Substrain Divergence in Non-Obese Diabetic (NOD) Mice
Authors: Simecek Petr , Churchill Gary A , Yang Hyuna , Rowe Lucy B , Herberg Lieselotte , Serreze David V , Leiter Edward H 
Published: March 2015

Abstract
The non-obese diabetic (NOD) mouse is a polygenic model for type 1 diabetes that is characterized by insulitis, a leukocytic infiltration of the pancreatic islets. During ~35 years since the original inbred strain was developed in Japan, NOD substrains have been established at different laboratories around the world. Although environmental differences among NOD colonies capable of impacting diabetes incidence have been recognized, differences arising from genetic divergence have not been analyzed previously. We use both mouse diversity array and whole-exome capture sequencing platforms to identify genetic differences distinguishing five NOD substrains. We describe 64 single-nucleotide polymorphisms, and two short indels that differ in coding regions of the five NOD substrains. A 100-kb deletion on Chromosome 3 distinguishes NOD/ShiLtJ and NOD/ShiLtDvs from three other substrains, whereas a 111-kb deletion in the Icam2 gene on Chromosome 11 is unique to the NOD/ShiLtDvs genome. The extent of genetic divergence for NOD substrains is compared with similar studies for C57BL6 and BALB/c substrains. As mutations are fixed to homozygosity by continued inbreeding, significant differences in substrain phenotypes are to be expected. These results emphasize the importance of using embryo freezing methods to minimize genetic drift within substrains and of applying appropriate genetic nomenclature to permit substrain recognition when one is used.
Rock, Paper, Scissors: Harnessing Complementarity in Ortholog Detection Methods Improves Comparative Genomic Inference
Authors: Maher M Cyrus , Hernandez Ryan D 
Published: March 2015

Abstract
Ortholog detection (OD) is a lynchpin of most statistical methods in comparative genomics. This task involves accurately identifying genes across species that descend from a common ancestral sequence. OD methods comprise a wide variety of approaches, each with their own benefits and costs under a variety of evolutionary and practical scenarios. In this article, we examine the proteomes of ten mammals by using four methodologically distinct, rigorously filtered OD methods. In head-to-head comparisons, we find that these algorithms significantly outperform one another for 38–45% of the genes analyzed. We leverage this high complementarity through the development MOSAIC, or Multiple Orthologous Sequence Analysis and Integration by Cluster optimization, the first tool for integrating methodologically diverse OD methods. Relative to the four methods examined, MOSAIC more than quintuples the number of alignments for which all species are present while simultaneously maintaining or improving functional-, phylogenetic-, and sequence identity-based measures of ortholog quality. Further, this improvement in alignment quality yields more confidently aligned sites and higher levels of overall conservation, while simultaneously detecting of up to 180% more positively selected sites. We close by highlighting a MOSAIC-specific positively selected sites near the active site of TPSAB1, an enzyme linked to asthma, heart disease, and irritable bowel disease. MOSAIC alignments, source code, and full documentation are available at http://pythonhosted.org/bio-MOSAIC.
Gene-Expression Novelty in Allopolyploid Cotton: A Proteomic Perspective
Authors: Hu Guanjing , Koh Jin , Yoo Mi-Jeong , Chen Sixue , Wendel Jonathan F 
Published: March 2015

AbstractAllopolyploidization is accompanied by changes in gene expression that are thought to contribute to phenotypic diversification. Here we describe global changes in the single-celled cotton fiber proteome of two natural allopolyploid species (Gossypium hirsutum and G. barbadense) and living models of their diploid parents using two different proteomic approaches. In total, 1323 two-dimensional gel electrophoresis spots and 1652 identified proteins by isobaric tags for relative and absolute quantitation were quantitatively profiled during fiber elongation. Between allopolyploids and their diploid A- and D-genome progenitors, amounts of differential expression ranged from 4.4 to 12.8%. Over 80% of the allopolyploid proteome was additively expressed with respect to progenitor diploids. Interestingly, the fiber proteome of G. hirsutum resembles the parental A-genome more closely, where long, spinable fiber first evolved, than does the fiber proteome of G. barbadense. More protein expression patterns were A-dominant than D-dominant in G. hirsutum, but in G. barbadense, the direction of expression-level dominance switched from the D-genome to the A-genome during fiber development. Comparison of developmental changes between the two allopolyploid species revealed a high level of proteomic differentiation despite their shared ancestry, relatively recent evolutionary divergence, and similar gross morphology. These results suggest that the two allopolyploid species have achieved superficially similar modern fiber phenotypes through different evolutionary routes at the proteome level. We also detected homeolog-specific expression for 1001 proteins and present a novel approach to infer the relationship between homeolog-specific and duplicate expression patterns. Our study provides a proteomic perspective on understanding evolutionary consequences of allopolyploidization, showing how protein expression has been altered by polyploidization and subsequently has diversified among species.
Dicranocentrus heloisae Arlé &amp; Mendonça, 1982 (Collembola: Entomobryidae): first record of the genus in Espírito Santo state, Brazil
Authors: Xisto Thiago , Mendonça Maria Cleide , Abrantes Eduardo Assis 
Published: March 2015

Dicranocentrus heloisae is an easily recognized species by color pattern. It was described from the “Parque Nacional da Tijuca” and its distribution was previously restricted to Tijuca Forest, located in Rio de Janeiro State. Here we report the second record for the specie with distance about 320 km from its type locality and first record of the genus in the Espírito Santo state.
Control of the Length and Density of Carbon Nanotubes Grown on Carbon Fiber for Composites Reinforcement
Authors: Cardoso Lays D. R. , Trava-Airoldi Vladimir J. , Silva Fabio S. , Zanin Hudson G. , Antunes Erica F. , Corat Evaldo J. 
Published: March 2015

ABSTRACTAligned multi-walled carbon nanotubes were grown on carbon fiber surface in order to provide a way to tailor the thermal, electrical and mechanical properties of the fiber-resin interface of a polymer composite. As the deposition temperature of the nanotubes is very high, an elevated exposure time can lead to degradation of the carbon fiber. To overcome this obstacle we have developed a deposition technique where the fiber is exposed to an atmosphere of growth for just one minute, and different concentrations of precursor solution were used.
Sand Prediction: A Practical Finite-Element 3D Approach for Real Field Applications
Authors: Volonté G.. , Scarfato F.. , Brignoli M.. 
Published: March 2015

Summary
Sand production is a critical issue in the oil and gas industry. During the production of a well, sand production may have negative consequences, such as risk of well failure, erosion of pipelines and surface facilities, and the need for sand separation and disposal. Knowing the conditions for the onset of sand production allows optimizing sand free production and, eventually, avoiding or delaying the use of sand-control methods.
The aim of this work is to establish a reliable workflow for the estimation of the conditions for sand production in real field cases by means of finite-element modeling. The fundamental requirement is to set up a 3D coupled model that can be easily adjusted to the most complex conditions (e.g., stress anisotropy, deviated wells, and complex perforation patterns).
The most suitable geometries and associated meshing strategies to describe the wellbore, the perforation tunnels, and the surrounding formation are analyzed. Further improvements with respect to previous approaches include the fact that the drilling and completion phases were also simulated to compute the correct stress distribution before the production, and that fluid flow and rock deformation are simulated in a fully coupled way to investigate accurately the effect of drawdown.
Shear failure of reservoir rock, considered as an elastoplastic medium, is the main sand-production mechanisms analyzed, and the damage of the rock around the perforations is evaluated by analyzing the distribution of the equivalent plastic strain.
Two real field cases are simulated, and the results of the finite-element models are consistent with the ones obtained by means of an analytical models and with field observations. Moreover, this numerical approach allows quantifying the spatial distribution and the severity of the damage of the rock around the perforations, facts that are either oversimplified or not considered at all in analytical models.
For future applications, this model can be straightforwardly extended to more complex conditions and can also be improved to provide volumetric sand prediction.
Effect of Oil Saturation on the Flow of Emulsified Acids in Carbonate Rocks
Authors: Sayed Mohammed A. , Assem Ahmed I. , Nasr-El-Din Hisham A. 
Published: March 2015

Summary
Matrix acid treatments in carbonate reservoirs target stimulation of the near-well region. Emulsified acid can be used in matrix acidizing and acid-fracturing treatments. The delayed nature of emulsified acid is useful in creating deep wormholes and etched fracture surfaces. Almost all previous coreflood work was performed on cores fully saturated with water. Therefore, the main objective of the present work is to study the effect of oil saturation in the formation on the flow of emulsified acids in carbonate cores and assess the performance of emulsified acid in stimulating carbonate formations.
A coreflood study was conducted using Indiana limestone cores that were 1.5 in. in diameter and 6 in. in length. The effect of the presence of crude oil on the volume of acid to breakthrough was studied. Also, the size, number, and distribution of the wormholes were determined with computed-tomography (CT) images. The effect of the acid injection rate on the performance of emulsified acid was investigated. Cores that were fully saturated with water, fully saturated with crude oil, and saturated with crude oil at irreducible water saturation were used. There was no optimum injection rate for emulsified acids when they were injected into Indiana limestone cores with permeabilities of 47 to 238 md. In such a range of permeability, emulsified acid enhanced the rock permeability when the acid was injected at both high (10.0 cm3/min) and low (0.5 cm3/min) rates. For cores fully saturated with crude oil, the volume of emulsified acid to achieve breakthrough was 2.2 times more than that required to achieve breakthrough in cores fully saturated with water. The increase in emulsified-acid volume refers to the increase in the volume of the continuous phase resulting from the mixture of the crude oil and diesel and the subsequent change in the acid/diesel volume fraction. As a result, more acid was consumed to create wormholes and achieve the breakthrough. The emulsified-acid system was effective in stimulating limestone cores, whether these cores were saturated with water, oil, or oil at irreducible water saturation.
Simulation of Fracturing-Induced Formation Damage and Gas Production From Fractured Wells in Tight Gas Reservoirs
Authors: Ding D.Y.. Y. , Langouët H.. , Jeannin L.. 
Published: March 2015

Summary
Fracturing fluid may jeopardize the production of hydraulically fractured tight gas formations. Because capillary forces act stronger in low-permeability formations, the invaded fracturing fluid is harder to remove. The increase of water saturation around the fractured well affects the mobility of the gas phase, particularly in tight formations where the gas relative permeability declines strongly when water saturation increases. This damage might greatly reduce the gas production in a very long cleanup period. This paper presents numerical simulation techniques to account for formation damage with both a near-well model and a full-field model for fractured wells in tight formations. For the full-field model, the skin determined from an inversion is suitable for long-term production simulations, and a sector model can be used to update the well skin through a coupled modeling so that the full-field model can be used correctly over the whole life of the project.
CFD Modeling and Experimental Observations of Changing Surface Profiles Caused by Solid-Particle Erosion
Authors: Wong Chong Y. , Solnordal Christopher B. , Wu Jie 
Published: March 2015

Summary
Traditional erosion modeling on oil and gas equipment frequently assumes a fixed erosion rate and unchanging surface profile throughout the erosion-exposure period. This approach does not account for the constantly changing surface and changes in the fluid flow, and therefore may lead to unquantified uncertainties in the prediction of equipment life. The literature presents limited experimental data of generic configurations in this topic. This paper addresses this gap by simultaneously investigating three generic configurations often encountered in oil and gas facilities. These configurations are a cylindrical rod, a hole in a flat plate, and a pipe cavity. Various eroded profiles of the physical configurations will be compared with traditional computational-fluid-dynamics (CFD) modeling with an unchanging model surface.
To validate this traditional assumption, the authors have used a modeling approach with multilayer paint modeling and geometry surface profiling of the aforementioned configurations exposed to a flow field with ambient air suspended with dilute solid particles.
Minimizing Environmental and Economic Risks With a Proppant-Sized Solid-Scale-Inhibitor Additive in the Bakken Formation
Authors: Szymczak Steve , Shen Dong , Higgins Rocky , Gupta D.V. Satya 
Published: March 2015

SummaryWithin the past decade, hydraulic fracturing has proved to enhance the efficiency and economics of recovering oil and natural gas from shale formations. In a previous paper (SPE-134414-MS, Gupta et al. 2010), a summary of treatment results from placing a solid scale inhibitor into formations by means of the fracturing process for more than 5 years and in more than 1,500 wells was discussed fully; however, the practice of hydraulic fracturing has come under scrutiny because of concerns about environmental impact, health, and safety. Therefore, a novel, biodegradable scale inhibitor with an outstanding ecotoxicity profile for fresh water incorporated into a solid matrix was recently developed and deployed in North Dakota. For one operator with 150 Bakken producing wells in this area, severe carbonate-mineral scaling in the pump and production tubing has been observed in 22 of these producing wells, which led to well failure (Cenegy et al. 2011), whereas the results from more than 290 Bakken wells now fractured with the new solid-inhibitor additives indicate no reported scale failures to date.This paper provides a detailed description of the first deployment of this environmentally preferred proppant-sized solid-scale-inhibitor additive under severe scaling conditions in the field. In addition, an analytical method developed to track the residual of this additive in the produced fluid containing polysaccharide contaminants is also discussed.
Experimental Investigation of Pressure-Drop/Flow-Rate Relationship for Small-Aperture Holes for High-Viscosity Fluids
Authors: Jain Rachna , Long Ted A. , Dickson Jasper , Brown Scott V. , Shtepani Edmond 
Published: March 2015

Summary
This paper studies the effect of viscosity and fines-particle loading on the pressure drop across a 4-mm orifice in a specific geometry built to mimic a representative well completion. It also provides experimental data in the range of operating conditions (high aspect ratio, low Reynolds number) that were not covered by any previous studies. The past experiments concentrated on studying the orifices with high aspect ratio (&gt;1) and high Reynolds number (&gt;1,000) or with a combination of low aspect ratio and low Reynolds number. In previous research conducted within the petroleum industry, most of these orifices were validated experimentally for viscosities up to 200 cp only for such completions. The current study focused on a wider viscosity variation (1 to 3,000 cp) with lower flow rates (0.5 to 30 m3/d). Even though fines are an integral part of the flow stream passing through the orifice for a sand reservoir, none of these studies further considered the effect of small particles on the orifice performance. The pressure drop was measured across the orifice and through the entire pipe assembly. The measured data were nondimensionalized by use of the Euler number and plotted against the Reynolds number for all rates and viscosities. The data were also compared and validated against commercially available computational-fluid-dynamics (CFD) software. The effect of sand-particle loading was also studied, and its effect on apparent viscosity increase was measured in the laboratory. The pressure-drop/flow-rate relationship and flow coefficient disclosed in this paper can be used to design effective completions for intermediate- to high-viscosity-oil applications and will be able to predict the completion pressure drop more accurately.
Full-Scale Testing Shows Advantages of a Quantitative Approach to Interpreting Inflow Tests
Authors: Rahmani R.. , Bourgoyne D.. , Smith J.R.. R. 
Published: March 2015

Summary
An inflow (commonly known as negative pressure) test is an important step in proving well integrity for some well operations. Although the concept is straightforward, there are no standard procedures for conducting and interpreting inflow tests. Recent industry experience has shown the potential for these tests to be misinterpreted, with disastrous results. This paper describes proper quantitative interpretation of both successful and unsuccessful tests demonstrated on two full-scale test wells.
Tests with and without leaks are simulated in two vertical wells with 2,971- and 5,884-ft depths. Test results are interpreted quantitatively to distinguish successes from failures. In addition, the impacts of leak rate and the differential pressure between the leak source and well are investigated. The impacts of gas as a leak fluid, different well volumes, different surface-piping arrangements, and measuring with different-sensitivity tanks are also shown.
The success of a test should be verified with both flow and pressure checks. For the flow check, the trend between bleed-off pressure and volume of bleedoff can be predicted on the basis of fluid compressibility, tubing expansion, and drainage from surface piping. Deviations from that trend will identify the onset of a leak. Early detection and control of a high-rate leak can reduce the formation-fluid volume entering the well and the consequent risks. Detecting a low-rate leak is difficult if the test duration is too short. Therefore, a 30-minute test duration was evaluated for detection of low-rate leaks.
The fundamental differences between a leak and no leak are demonstrated conclusively with quantitative results. Approaches for overcoming complications that interfere with conclusive test results are explained and demonstrated. The demonstration test results and the proposed interpretation methods are applicable to vertical wells. Drilling-fluid properties, multiple fluids, and thermal expansion can also influence results, but were not investigated in this study. Nevertheless, these results should provide a basis for improving field procedures and minimizing the risk of misinterpreting a leak as a successful test.