bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolutionary history of phosphatidylinositol- 3-kinases: ancestral origin in eukaryotes and complex duplication patterns
Authors: Philippon Héloïse , Brochier-Armanet Céline , Perrière Guy 
Published: October 2015

AbstractBackgroundPhosphatidylinositol-3-kinases (PI3Ks) are a family of eukaryotic enzymes modifying phosphoinositides in phosphatidylinositols-3-phosphate. Located upstream of the AKT/mTOR signalling pathway, PI3Ks activate secondary messengers of extracellular signals. They are involved in many critical cellular processes such as cell survival, angiogenesis and autophagy. PI3K family is divided into three classes, including 14 human homologs. While class II enzymes are composed of a single catalytic subunit, class I and III also contain regulatory subunits. Here we present an in-depth phylogenetic analysis of all PI3K proteins.ResultsWe confirmed that PI3K catalytic subunits form a monophyletic group, whereas regulatory subunits form three distinct groups. The phylogeny of the catalytic subunits indicates that they underwent two major duplications during their evolutionary history: the most ancient arose in the Last Eukaryotic Common Ancestor (LECA) and led to the emergence of class III and class I/II, while the second – that led to the separation between class I and II – occurred later, in the ancestor of Unikonta (i.e., the clade grouping Amoebozoa, Fungi, and Metazoa). These two major events were followed by many lineage specific duplications in particular in vertebrates, but also in various protist lineages. Major loss events were also detected in Vidiriplantae and Fungi. For the regulatory subunits, we identified homologs of class III in all eukaryotic groups indicating that, for this class, both the catalytic and the regulatory subunits were presents in LECA. In contrast, homologs of the regulatory class I have a more recent origin.ConclusionsThe phylogenetic analysis of the PI3K shed a new light on the evolutionary history of these enzymes. We found that LECA already contained a PI3K class III composed of a catalytic and a regulatory subunit. Absence of class II regulatory subunits and the recent origin of class I regulatory subunits is puzzling given that the class I/II catalytic subunit was present in LECA and has been conserved in most present-day eukaryotic lineages. We also found surprising major loss and duplication events in various eukaryotic lineages. Given the functional specificity of PI3K proteins, this suggests dynamic adaptation during the diversification of eukaryotes.
Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads
Authors: Song Li , Florea Liliana 
Published: October 2015

Abstract

Background
Next-generation sequencing of cellular RNA (RNA-seq) is rapidly becoming the cornerstone of transcriptomic analysis. However, sequencing errors in the already short RNA-seq reads complicate bioinformatics analyses, in particular alignment and assembly. Error correction methods have been highly effective for whole-genome sequencing (WGS) reads, but are unsuitable for RNA-seq reads, owing to the variation in gene expression levels and alternative splicing.

Findings
We developed a k-mer based method, Rcorrector, to correct random sequencing errors in Illumina RNA-seq reads. Rcorrector uses a De Bruijn graph to compactly represent all trusted k-mers in the input reads. Unlike WGS read correctors, which use a global threshold to determine trusted k-mers, Rcorrector computes a local threshold at every position in a read.

Conclusions
Rcorrector has an accuracy higher than or comparable to existing methods, including the only other method (SEECER) designed for RNA-seq reads, and is more time and memory efficient. With a 5 GB memory footprint for 100 million reads, it can be run on virtually any desktop or server. The software is available free of charge under the GNU General Public License from https://github.com/mourisl/Rcorrector/.
Face and content validity of a virtual-reality simulator for myringotomy with tube placement
Authors: Huang Caiwen , Cheng Horace , Bureau Yves , Agrawal Sumit K. , Ladak Hanif M. 
Published: October 2015

Background Myringotomy with tube insertion can be challenging for junior Otolaryngology residents as it is one of the first microscopic procedures they encounter. The Western myringotomy simulator was developed to allow trainees to practice microscope positioning, myringotomy, and tube placement. This virtual-reality simulator is viewed in stereoscopic 3D, and a haptic device is used to manipulate the digital ear model and surgical tools. Objective To assess the face and content validity of the Western myringotomy simulator. Methods The myringotomy simulator was integrated with new modules to allow speculum placement, manipulation of an operative microscope, and insertion of the ventilation tube through a deformable tympanic membrane. A questionnaire was developed in consultation with instructing surgeons. Fourteen face validity questions focused on the anatomy of the ear, simulation of the operative microscope, appearance and movement of the surgical instruments, deformation and cutting of the eardrum, and myringotomy tube insertion. Six content validity questions focused on training potential on surgical tasks such as speculum placement, microscope positioning, tool navigation, ear anatomy, myringotomy creation and tube insertion. A total of 12 participants from the Department of Otolaryngology—Head and Neck Surgery were recruited for the study. Prior to completing the questionnaire, participants were oriented to the simulator and given unlimited time to practice until they were comfortable with all of its aspects. Results Responses to 12 of the 14 questions on face validity were predominantly positive. One issue of concern was with contact modeling related to tube insertion into the eardrum, and the second was with the movement of the blade and forceps. The former could be resolved by using a higher resolution digital model for the eardrum to improve contact localization. The latter could be resolved by using a higher fidelity haptic device. With regard to content validity, 64 % of the responses were positive, 21 % were neutral, and 15 % were negative. Conclusions The Western myringotomy simulator appears to have sufficient face and content validity. Further development with automated metrics and skills transference testing is planned.
Steric Effects on the Cyclability of Benzoquinone-type Organic Cathode Active Materials for Rechargeable Batteries
Authors: Yokoji Takato , Kameyama Yuki , Sakaida Shun , Maruyama Norihiko , Satoh Masaharu , Matsubara Hiroshi 
Published: October 2015

Abstract
Benzoquinone derivatives, which undergo reversible two-electron redox reactions, should afford high capacity as positive electrode materials for rechargeable batteries. Although some benzoquinones have been reported as cathode active materials, their low cycle-life performance is a drawback. We prepared benzoquinones bearing alkyl groups with various degrees of bulkiness to investigate the relationship between the steric effects of the substituents on the benzoquinone skeleton and the battery performance. The introduction of bulky substituents, especially a tert-butyl group, on the skeleton significantly improved the cyclability.
Preparation of a PtPb/TiO2/Cup-stacked Carbon Nanotube Composite for Enhancement of the Electrocatalytic Reaction of the Oxygen Reduction Reaction
Authors: Ando Fuma , Gunji Takao , Fujima Hikaru , Takeda Tsuyoshi , Tanabe Toyokazu , Kaneko Shingo , Matsumoto Futoshi 
Published: October 2015

Abstract
PtPb ordered intermetallic nanoparticles (NPs) were deposited on titanium oxide (TiO2)/cup-stacked carbon nanotubes (CSCNT) to improve the activity of the electrochemical oxygen reduction reaction (ORR). The use of CSCNTs as a support material resulted in high loading of PtPb NPs/TiO2. The PtPb NPs/TiO2/CSCNTs were prepared by the step-by-step preparation method, viz. first annealing under an inert atmosphere with Ti-alkoxide to obtain TiO2, then Pt NP photodeposition, and finally microwave synthesis to prepare ordered intermetallic PtPb NPs on TiO2 via reaction of Pb2+ with Pt/TiO2. The new particles enhanced ORR electrocatalytic activity.
Sonication of seeds increase germination performance of sesame under low temperature stress
Authors: SHEKARI Fariborz , MUSTAFAVI Seyyed-Hamid , ABBASI Amin 
Published: October 2015

A laboratory experiment was conducted to determine the effect of ultrasound (US) exposure time on germination behavior of sesame seeds. All tests were carried out at 20 kHz in a water bath ultrasonic device varying two factors, treatment duration (10, 20 and 30 min) and germination temperature (15, 20 and 25 ºC). Parallel tests were run in which seeds were soaked in water without sonication in order to eliminate the effect of water from US test results. US treatments enhanced seeds water uptake. At mild exposure time it improved sesame seed germination performance and seedling growth at suboptimal temperatures as indicated by higher germination percentage and germination rate. US applying for 20 min had relatively high superoxide dismutase activity; however, had not significant differences with control and US duration for 10 min. The catalase activity was strongly increased by applying the US for a 10 and 20 min. Among the treatments, application of US vibration for 10 and 20 min reduced both of malondialdehyde and H2O2 contents, however high US duration (30 min) increased both of the traits. In general, ultrasonic priming technique can be useful for early planting the sesame seeds, and lead to higher yields.
Study of risk factors for atopic sensitization, asthma, and bronchial hyperresponsiveness in animal laboratory workers
Authors: Simoneti Christian Silva , Freitas Amanda Souza , Barbosa Michelle Christiane Rodrigues , Ferraz Erica , de Menezes Marcelo Bezerra , Bagatin Ericson , Arruda Luisa Karla , Vianna Elcio Oliveira 
Published: October 2015

Study of risk factors for atopic sensitization, asthma, and bronchial hyperresponsiveness in animal laboratory workers: Christian Silva Simoneti, et al. Department of Medicine, Medical School of Ribeirão Preto, University of São Paulo, BrazilObjectiveThe aim of this estudy was to investigate the influence of allergen exposure levels and other risk factors for allergic sensitization, asthma, and bronchial hyperresponsiveness (BHR) in workers exposed to laboratory animals.MethodsThis was a crosssectional study performed at two universities, 123 workplaces with 737 subjects. Dust samples were collected from laboratories and animal facilities housing rats, mice, guinea pigs, rabbits, or hamsters and analyzed by enzyme‐linked immunosorbent assay (ELISA) to measure allergen concentrations. We also sampled workplaces without animals. Asthma was defined by both symptoms and BHR to mannitol. The concentrations of allergens were tested for association with a skin prick test, respiratory symptoms, spirometry data, and BHR. This multivariate analysis was performed by using Poisson regression to estimate the relative risk (RR) for the exposed group.ResultsOur sample comprised students and workers, with 336 subjects in the nonexposed group and 401 subjects in the exposed group. Sixty‐nine subjects (17%) had positive results in the skin prick test for animal allergens in the exposed group; in the nonexposed group, 10 subjects had positive results (3%) (p<0.001). Exposure to laboratory animals over 2.8 years was associated with atopic sensitization (RR=1.85; 95% confidence interval: 1.09−3.15; p=0.02). Allergen concentration was not associated with sensitization, asthma, or BHR.ConclusionExposure to laboratory animals was associated with atopic sensitization. However, we did not find a cutoff allergen concentration that increased the risk for sensitization. Duration of exposure seems to be more relevant to sensitization than concentration of allergens in dust.
The determinants of presenteeism: a comprehensive investigation of stress‐related factors at work, health, and individual factors among the aging workforce
Authors: Yang Tianan , Zhu Mingjing , Xie Xiyao 
Published: October 2015

The determinants of presenteeism: a comprehensive investigation of stress‐related factors at work, health, and individual factors among the aging workforce: Tianan Yang, et al. Department of Organization and Human Resource Management, School of Management and Economics, Beijing Institute of Technology, P.R. ChinaObjectiveThe aim of this study was to identify the determinants of presenteeism, taking health and individual factors into account.MethodsA quantitative analysis applying structural equation modelling analysis was conducted on the basis of secondary data from the Health and Retirement Survey (2008 wave), which measured presenteeism and its determinants.ResultsStressrelated factors at work (β=−0.35, p<0.001), individual factors (β =−0.27, p<0.001), and health (β =0.24, p<0.001) were significantly related to presenteeism. Individual factors were found to be directly correlated with stress‐related factors at work (β=0.22, p<0.001). Significant indirect effects between stress‐related factors at work and presenteeism (Sobel z=−6.61; p<0.001) and between individual factors and presenteeism (Sobel z=−4.42; p<0.001), which were mediated by health, were also found. Overall, the final model accounted for 37% (R2=0.37) of the variance in presenteeism.ConclusionsOur study indicates some important and practical guidelines for employers to avoid the burdens of stress‐related presenteeism among their employees. These findings could help select target factors in the design and implementation of effective presenteeism interventions in the aging working population.
Structural complexity and component type increase intertidal biodiversity independently of area
Authors: Loke Lynette H. L. , Todd Peter A. 
Published: October 2015

AbstractComplexity is well accepted as one of the primary drivers of biodiversity, however, empirical support for such positive associations is often confounded with surface area and undermined by other potential explanatory factors, especially the type of structural component (e.g., pits, crevices, overhangs, etc.). In the present study, sample units (artificial substrates) of equal surface area (±0.2%) were used to simultaneously examine the independent effects of complexity and different structural component types on species richness (S), abundance (N), and community composition. We created simple and complex concrete substrates of four different geometric designs using novel software. The substrates (n = 8) were mounted onto granite seawalls (at two tidal heights) on two islands south of Singapore Island. After 13 months of colonization, all 384 tiles were collected and their assemblages compared. A total of 53 744 individuals of 70 species/morphospecies were collected and identified. Our results show that greater complexity can support greater species richness and different communities that are independent of surface area. Furthermore, the type of structure (e.g., “pits,” “grooves,” “towers”) can have an effect on richness and community composition that is independent of complexity.
Preformed-Particle-Gel Extrusion Through Open Conduits During Conformance-Control Treatments
Authors: Imqam Abdulmohsin , Bai Baojun , Ramadan Mustafa Al , Wei Mingzhen , Delshad Mojdeh , Sepehrnoori Kamy 
Published: October 2015

Summary
Millimeter-sized (10 μm–mm) preformed particle gels (PPGs) have been used successfully as conformance-control agents in more than 5,000 wells. They help to control both water and CO2 production through high-permeability streaks or conduits (large pore openings), which naturally exist or are aggravated either by mineral solution or by a high injection pressure during the flooding process. This paper explores several factors that can have an important impact on the injectivity and plugging efficiency of PPGs in these conduits. Extensive experiments were conducted to examine the effect of the conduit inner diameter and the PPG strength on the ratio of the particle size to the opening diameter, injectivity index, resistance factor, and plugging efficiency. Five-foot tubes with four internal diameters were designed to emulate the opening conduits. Three pressure taps were mounted along the tubes to monitor PPG transport and plugging performance. The results show that weak gel has less injection pressure at a large particle/opening ratio compared to strong gel. PPG strength affected injectivity more significantly than did particle/opening ratio. Resistance factor increased as the brine concentration and conduit inner diameter increased. PPGs can significantly reduce the permeability of a conduit, and their plugging efficiency depends highly on the particle strength and the conduit inner diameter. The particle size of PPGs was reduced during their transport through conduits. Experimental results confirm that the size reduction was caused by both dehydration and breakdown. On the basis of the laboratory data, two correlations were developed to quantitatively calculate the resistance factor and the stable injection pressure as a function of the particle strength, particle/opening ratio, and shear rate. This research provides significant insight into designing better millimeter-sized particle-gel treatments intended for use in large openings, including open fractures, caves, worm holes, and conduits.
Sixth SPE Comparative Solution Project: A Comparison of Dual-Porosity Simulators
Authors: Firoozabadi A. , Thomas L. K. 
Published: October 2015

ABSTRACT
Two problems for the comparison of fractured reservoir models are presented. The first problem is a simple single block example. The second problem is a more complicated cross-sectional example. The cross-sectional example has been developed to simulate depletion, gas injection and water injection cases.
In selecting the problems for the present Comparative Solution Project, various aspects of the physics of multiphase flow in fractured porous media have been considered. The question of fracture capillary pressure and its influence on reservoir performance has been addressed by including cases with zero and non-zero gas-oil capillary pressure in the fractures.
Ten organizations participated in the Sixth Comparative Solution Project. Most of the current techniques in dual-porosity simulation are represented in the results of the participants.
Submarine Channel Facies Control on Reservoir Performance
Authors: Cutler W. G. , Montoya G. L. , Ucok H. 
Published: October 2015

ABSTRACT
A comprehensive geologic and engineering study of the A-10 North Pool of the Sansinena Oil Field has revealed the presence of two distinct reservoir facies, the Channel Core and the Channel Flank facies. The Channel Core sands are coarse-grained, locally pebbly and contain very little associated clay minerals. These sands have high permeability and good lateral continuity. The Channel Flank sands, however, are fine-grained, silty and contain abundant dispersed and laminar clay minerals. The Channel Flank sands have low permeability and poor lateral continuity.
A closer look at the internal arrangement of reservoir facies, coupled with historical production performance, explains the large differences in oil recovery from the Channel Core and Channel Flank sands, and provides a better understanding of the producing mechanisms within these different facies. In the Channel Core facies, considerations are focused on improving gravity drainage, which is the primary producing mechanism. In the Channel Flank facies, where fresh water clay-based drilling mud is believed to have caused significant formation damage, the main focus is on well stimulation and infill drilling.
The geologic and engineering study has also helped distinguish sands with good potential for enhanced oil recovery in the A-10 North Pool of the Sansinena Field.
A Fully Implicit Thermal Wellbore Model for Multi-Component Fluid Flows
Authors: Siu A. , Rozon B. , Li Y.-K. , Nghiem L. X. , Acteson W. H. , McCormack M. 
Published: October 2015

ABSTRACT
Steam injection processes have been used successfully in recovering heavy oil from hydrocarbon reservoirs. These methods have also been shown to increase oil recoveries from light oil reservoirs. The increased applications of thermal methods emphasize the importance of optimal thermal wellbore designs and efficient field operations for injectors and producers.
This paper describes a transient thermal wellbore model which simulates the flow hydraulics in the wellbore, and the heat transfer between the wellbore fluid and the overburden.
The equations of the thermal wellbore model consist of the transient differential equations for the multi-component three-phase fluid flow in the wellbore, and the transient heat conduction equation in the overburden. Phase behavior of the wellbore fluids is obtained from isenthalpic flash calculations which compute the phase splits and compositions at a specified pressure and enthalpy. The wellbore and overburden equations in the entire discretization domain are solved simultaneously with a fully implicit Newton's method.
The thermal wellbore model has been validated using steam injection and gas-condensate production field data. The calculated heat losses and pressure drops compared favorably with published models. The thermal wellbore model is also used to predict the critical production rate of methane above which hydrate will not form.
Sand Control in Horizontal Wells in Heavy Oil Reservoirs
Authors: Islam M. R. , George A. E. 
Published: October 2015

ABSTRACT
Horizontal wells are of great interest to most oil companies operating in heavy oil fields. Due to more extensive contact with the reservoir, horizontal wells allow fluid flow at lower fluid velocities yet providing total flows which are economic. While horizontal wells have the potential to make many more heavy oil reservoirs economic, one of the most pressing concerns has been to be able to complete the wells properly. Unfortunately, likely candidates of horizontal wells are mostly "quicksand" type formations and the critical velocities of sand in a wellbore is extremely low. Consequently, sand is very likely to enter the horizontal wellbore if not preventive measure is taken. Problems of sand production in a horizontal well is more complicated than in a vertical well due to difficulty in cleaning sands in horizontal wellbores.
The present study discusses the problems of sand production in a horizontal well and offers recommendation in controlling them. Physical simulation of the top part of the horizontal well showed that both gravitational and inertial forces help minimizing sand production. This will mean that increasing flow rates will decrease sand production. Experimental evidence showed that selection of liner diameter and wire spacing are important parameters in controlling sand productions. Permeability damage due to particle mixing in the annulus was quantified. It was shown that smaller annulus is of more importance in the case of smaller wire spacing, lower oil viscosity and thinner pay zone.
Audit Quality, Auditing Standards, and Legal Regimes: Implications for International Auditing Standards
Authors: Simunic Dan A. , Ye Minlei , Zhang Ping 
Published: October 2015

ABSTRACT
We summarize the analyses detailed in two papers on the relation between audit quality, auditing standards, and legal regimes. We show that optimal auditing standards for a country are a complex function of the legal system in that country. We then discuss the implications for the adoption of international auditing standards.