bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Study of Hydrocarbon Releases in the Gulf of Mexico, 1996 Thru 2010
Authors: Smith Louise Matilde , Smith John Rogers , Pattee Lauren , Langlinais Julius 
Published: August 2013

The events surrounding the Deepwater Horizon (Macondo) disaster have changed the face of deepwater operations. Safety and environmental systems (SEMS) plans and capping or containment capabilities are required to meet current Bureau of Safety and Environmental Enforcement (BSEE) permitting requirements for the Gulf of Mexico (GOM). More generally, industry must identify the operational risks associated with future deepwater operations and specify their plans for responding to those risks, in order to maximize the effectiveness of methods to prevent and respond to potential future releases of hazardous, polluting hydrocarbons. This paper describes a study of public BSEE (previously MMS and BOEMRE) data on incidents involving releases of formation fluids to the environment. The purpose of this study was to provide a factual basis for identifying the operational risk of hydrocarbon releases in offshore operations as a starting point for additional work on identifying opportunities to reduce the frequency, severity, and consequences of such releases, especially for deepwater operations.
Incidents reported over the past 15 years were reviewed and organized in a spreadsheet. A total of 90 non-pipeline incidents were identified as including enough description to be useful. Most of these incidents were spills greater than 50 barrels (bbls), but blowouts, fires, and explosions are important and included. To the extent possible, the review determined: the flow path taken from the formation to the point in the well or production system where the fluids were released, the release point, the barriers that were used to reestablish control, and what can these events tell us about potential future deepwater events.
It is notable that most of these releases occurred in shelf operations rather than deepwater (water depth ≥ 1,000 ft), which was expected due to the much larger number of wells on the GOM shelf. Nearly two-thirds of the releases happened during active drilling, completion, workover, or well-servicing operations. The remaining events occurred during other operations, particularly production, and include two spills after the wells were plugged and abandoned (P&A’d). The number of blowouts per year was relatively small, varying from 2 to 9 for the 15 year period. The number of blowouts has remained roughly constant despite the recent decrease in the rig activity level. Similarly, the size of most spills was relatively small, if the Macondo event is excluded. Nevertheless, the data gives a factual basis for identifying the kinds of events that could lead to future catastrophes if not prevented or identified and controlled successfully.
3D Simulation of Vortex Shedding Past Tapered Circular Cylinders in Subcritical Reynolds Numbers
Authors: Tamimi V. , Zeinoddini M. , Bakhtiari A. , Golestani M. 
Published: August 2013

In this paper results from simulating the vortex shedding phenomena behind a fixed tapered circular cylinder, at relatively high Reynolds numbers, are reported. Ansys-CFX computational fluid dynamics model, based on solving three-dimensional (3D) incompressible transient Navier Stokes equations, is employed for this purpose.
The geometries applied in the models resemble those used in wind tunnel experiments by other researchers. The taper slope along the cylinder span is uniform with a tangent of 24:1. The diameter at mid-span of the cylinder equals to 0.0389 m. The Reynolds number (based on the mid-span diameter) is around 29,000. The computational model has first been calibrated against experiments for uniform 3D cylinders as well as results from a Direct Numerical Simulation of turbulent wake with vortex shedding past a uniform circular cylinder, as obtained by other researchers.
The main flow characteristics for tapered cylinders such as vortex dislocations and splitting, cellular vortex shedding, oblique vortex shedding and the variation of the vorticity patterns along the tapered cylinder could be obtained from the simulations.
Characterization of Matrix Wettability and Mass Transfer From Matrix to Fractures in Carbonate Reservoirs
Authors: Gupta Anuj 
Published: August 2013

This paper presents results of an experimental investigation, supported by numerical analysis, to characterize oil recovery from fractured carbonate reservoirs. Imbibition recovery of oil is measured as a function of time for samples with varying wettability and shape factors. One of the objectives of this study is to verify the validity of exponential transfer function for matrix-fracture systems with varying wettability and flow-boundary conditions. Another objective is to establish the possibility of quantitatively determining the wettability of a sample based on history-matching of cumulative imbibition recovery and recovery rate data.
The productivity of most carbonate oil and gas reservoirs is closely tied to the natural or stimulated fracture system present in the reservoir. Further, the recovery from naturally fractured reservoirs, in presence of aquifer drive or waterflooding is closely tied to the wettability of the matrix. The approach presented in this paper offers means to evaluate how recovery factor in a fractured system can be affected by wettability. A detailed understanding of rock-fluid interactions and wettability alterations at the fracturing face should help design improved strategies for exploiting naturally fractured carbonate reservoirs.
Hydrodynamic Interaction Forces on Ship Hulls Equipped With Propulsors
Authors: Sutulo Serge , Guedes Soares C. 
Published: August 2013

Typically, study of hydrodynamic interaction between vessels navigating in close proximity to each other is limited to hydrodynamics of bare hulls. Meanwhile, ship propulsors, especially heavily loaded, which may happen in accelerating motion, can alter substantially the flow and distribution of pressure on the hulls which can be viewed as generalization of the thrust deduction phenomenon.
The 3D doubled body potential interaction code based on the source panel method developed earlier by the authors has been enhanced to include the effect of a propeller on each of the interacting ships under the assumption that the propeller jets (slipstreams) are not involved into the interaction. Each propeller is simulated by a disk of sinks further approximated with a polygon composed of identical triangular panels with identical constant sink density linked to the thrust of the propulsor according to the actuator disk theory.
Comparative computations were carried out for two identical tanker vessels in the close-proximity overtaking manoeuvre at various values of the loading coefficient of each propeller. The loading coefficient is not supposed to be necessarily defined by the steady propulsion point. Numerical results demonstrate that a heavily loaded propeller substantially modifies the pressure distribution on both hulls resulting in alteration of the hydrodynamic interaction loads, especially of the surge force and yaw moment.
Drilling Vessels’ Hurricane Evasion in the Gulf of Mexico
Authors: Wishahy Momen A. , Weinzapfel Bob A. , Diaz Dante C. , Eyre Devin J. 
Published: August 2013

A study was carried out to determine the probability of avoiding severe weather conditions generated by historical hurricanes to improve the management of dynamically-positioned (DP) drilling vessels operating in the Gulf of Mexico during hurricane season. Rather than staying on location during an approaching hurricane, DP drilling vessels secure well operations, pull riser, and evade the hurricane.
The study considers several factors affecting the measure of success including inherent errors in forecasting hurricane strength, track and speed of advance; types and speeds of vessels; vessel sensitivity to wind and wave conditions; evasion time and direction of evasion; location of the drilling site relative to the hurricane track; and escape route water depth limitations.
The results provide a statistical basis for the required evasion time and would be part of the Hurricane Evacuation Plan that stakeholders agree upon to achieve acceptable risk. The simulations could also be used in a training program for captains and considered in the tactical decision-making process regarding when to leave the site and in which direction to go.
Development of a Six-Component Blade Load Measurement Test Setup for Propeller-Ice Impact
Authors: Hagesteijn G. , Brouwer J. , Bosman R. 
Published: August 2013

The impact of ice on a propeller is a complex process, which most likely results into a milling or crushing process, or a combination. The highly dynamic forces during an impact can change rapidly in amplitude as well as direction. Little information can be deducted from classic test setups with rigid propellers, especially forces on the individual blades are seldom successfully measured. The presented paper will outline the challenges which need to be overcome to measure these impacts more accurately and elaborate on a measurement setup which has proven to capture the impact loads of actual ice impacts in great detail.
Classic designs for propeller testing involve rigid propellers with force measurements located at the base of the propeller. From this type of setup, immediately two problems arise. First of all, when impacting relatively large ice blocks, it will be hard to derive which part of the measured forces contributes to one blade and which part to the other. Secondly, in practical test situations the natural frequency of the entire propeller mounted on a force transducer can be relatively low. Impacts are suspected to contain forces with high frequency components, causing the entire propeller assembly to vibrate and thereby obscuring a correct measurement of the impact loads.
A measurement setup has been designed to overcome both problems. Rather than measuring the forces on a complete propeller, only a single blade is mounted on a force transducer. This particular transducer is capable of measuring forces in x-, y- and z-directions as well as moments around the x-, y- and z-axis. The other propeller blades are mounted directly on the shaft drive. This measurement setup reduces the first problem, any impact visible in the measurements signals are solely due to forces on the instrumented ‘key-blade’.
Distribution-Based Clustering: Using Ecology To Refine the Operational Taxonomic Unit
Authors: Preheim Sarah P. , Perrotta Allison R. , Martin-Platero Antonio M. , Gupta Anika , Alm Eric J. 
Published: August 2013

ABSTRACT
16S rRNA sequencing, commonly used to survey microbial communities, begins by grouping individual reads into operational taxonomic units (OTUs). There are two major challenges in calling OTUs: identifying bacterial population boundaries and differentiating true diversity from sequencing errors. Current approaches to identifying taxonomic groups or eliminating sequencing errors rely on sequence data alone, but both of these activities could be informed by the distribution of sequences across samples. Here, we show that using the distribution of sequences across samples can help identify population boundaries even in noisy sequence data. The logic underlying our approach is that bacteria in different populations will often be highly correlated in their abundance across different samples. Conversely, 16S rRNA sequences derived from the same population, whether slightly different copies in the same organism, variation of the 16S rRNA gene within a population, or sequences generated randomly in error, will have the same underlying distribution across sampled environments. We present a simple OTU-calling algorithm (distribution-based clustering) that uses both genetic distance and the distribution of sequences across samples and demonstrate that it is more accurate than other methods at grouping reads into OTUs in a mock community. Distribution-based clustering also performs well on environmental samples: it is sensitive enough to differentiate between OTUs that differ by a single base pair yet predicts fewer overall OTUs than most other methods. The program can decrease the total number of OTUs with redundant information and improve the power of many downstream analyses to describe biologically relevant trends.
Characterization of a Potential Listeria monocytogenes Virulence Factor Associated with Attachment to Fresh Produce
Authors: Bae Dongryeoul , Seo Keun Seok , Zhang Ting , Wang Chinling 
Published: August 2013

ABSTRACT

A study to determine the attachment of
L. monocytogenes
serotype 4b strain F2365 on vegetables and fruits was conducted. In an initial study, we screened 32 genes encoding surface proteins and lipases of the strain to find highly expressed genes on lettuce leaves. The results showed that transcription levels of LMOf2365_0413, LMOf2365_0498, LMOf2365_0859, LMOf2365_2052, and LMOf2365_2812 were significantly upregulated on lettuce leaves.
In silico
analysis showed that LMOf2365_0859 contains a putative cellulose binding domain. Thus, we hypothesized that this gene may be involved in an attachment to vegetables, and named it
lcp
(gene encoding
Listeria
cellulose binding protein [LCP]).
lcp
mutant (Δ
lcp
) and
lcp
complement (F2365::pMAD::
cat
::
lcp
) strains were generated by homologous recombination. The abilities of a wild-type (WT) strain, the Δ
lcp
strain, and the complemented strain to attach to lettuce leaves were evaluated, which indicated that the attachment of the Δ
lcp
strain to lettuce was significantly less than that of the WT and the complemented strains. Similar results were observed for baby spinach and cantaloupe. Fluorescence microscopy and field emission scanning microscopy analysis further supported these findings. The binding of
L. monocytogenes
to cellulose was determined using cellulose acetate-coated plates. The results showed that a binding ability of the Δ
lcp
strain was significantly lower than that of the wild type. Combined, these results strongly suggest that LCP plays an important role in an attachment to vegetables and fruits.
Design and Optimization of Short DNA Sequences That Can Be Used as 5′ Fusion Partners for High-Level Expression of Heterologous Genes in Escherichia coli
Authors: Kucharova Veronika , Skancke Jørgen , Brautaset Trygve , Valla Svein 
Published: August 2013

ABSTRACT

The 5′ terminal nucleotide sequence of a gene is often a bottleneck in recombinant protein production. The

ifn-α2b
S

gene is poorly expressed in
Escherichia coli
unless a translocation signal sequence (
pelB
) is fused to the 5′ end of the gene. A combined
in silico
and
in vivo
analysis reported here further indicates that the

ifn-α2b
S

5′ coding sequence is suboptimal for efficient gene expression.

ifn-α2b
S

therefore presents a suitable model gene for describing properties of 5′ fusions promoting expression. We show that short DNA sequences corresponding to the 5′ end of the highly expressed
celB
gene, whose protein product is cytosolic, can functionally replace
pelB
as a 5′ fusion partner for efficient

ifn-α2b
S

expression.
celB
fusions of various lengths (corresponding to a minimum of 8 codons) led to more than 7- and 60-fold stimulation of expression at the transcript and protein levels, respectively. Moreover, the presence of a
celB
-based fusion partner was found to moderately reduce the decay rate of the corresponding transcript. The 5′ fusions thus appear to act by enhancing translation, and bound ribosomes may accordingly contribute to increased mRNA stability and reduced mRNA decay. However, other effects, such as altered protein stability, cannot be excluded. We also developed an experimental protocol that enabled us to identify improved variants of the
celB
fusion, and one of these (
celB
D11
) could be used to additionally increase

ifn-α2b
S

expression more than 4-fold at the protein level. Interestingly,
celB
D11
also stimulated greater protein production of three other medically important human genes than the wild-type
celB
fragment.
Molecular and Phenotypic Characterization of Escherichia coli O26:H8 among Diarrheagenic E. coli O26 Strains Isolated in Brazil
Authors: Piazza Roxane M. F. , Delannoy Sabine , Fach Patrick , Saridakis Halha O. , Pedroso Margareth Z. , Rocha Letícia B. , Gomes Tânia A. T. , Vieira Mônica A. M. , Beutin Lothar , Guth Beatriz E. C. 
Published: August 2013

ABSTRACT

Escherichia coli
strains of serogroup O26 comprise two distinct groups of pathogens, characterized as enteropathogenic
E. coli
(EPEC) and enterohemorrhagic
E. coli
(EHEC). Among the several genes related to type III secretion system-secreted effector proteins,
espK
was found to be highly specific for EHEC O26:H11 and its
stx
-negative derivative strains isolated in European countries.
E. coli
O26 strains isolated in Brazil from infant diarrhea, foods, and the environment have consistently been shown to lack
stx
genes and are thus considered atypical EPEC. However, no further information related to their genetic background is known. Therefore, in this study, we aimed to discriminate and characterize these Brazilian O26
stx
-negative strains by phenotypic, genetic, and biochemical approaches. Among 44 isolates confirmed to be O26 isolates, most displayed flagellar antigen H11 or H32. Out of the 13 nonmotile isolates, 2 tested positive for
fliC
H11
, and 11 were
fliC
H8
positive. The identification of genetic markers showed that several O26:H11 and all O26:H8 strains tested positive for
espK
and could therefore be discriminated as EHEC derivatives. The presence of H8 among EHEC O26 and its
stx
-negative derivative isolates is described for the first time. The interaction of three isolates with polarized Caco-2 cells and with intestinal biopsy specimen fragments
ex vivo
confirmed the ability of the O26 strains analyzed to cause attaching-and-effacing (A/E) lesions. The O26:H32 strains, isolated mostly from meat, were considered nonvirulent. Knowledge of the virulence content of
stx
-negative O26 isolates within the same serotype helped to avoid misclassification of isolates, which certainly has important implications for public health surveillance.
Probing 3-Hydroxyflavone for
In Vitro
Glycorandomization of Flavonols by YjiC
Authors: Pandey Ramesh Prasad , Parajuli Prakash , Koirala Niranjan , Park Je Won , Sohng Jae Kyung 
Published: August 2013

ABSTRACT

The glycosylation of five different flavonols, fisetin, quercetin, myricetin, kaempferol, and 3-hydroxyflavone, was achieved by applying YjiC. 3-Hydroxyflavone was selected as a probe for
in vitro
glycorandomization of all flavonols using diverse nucleotide diphosphate-
d/l
-sugars. This study unlocked the possibilities of the glycodiversification of flavonols and the generation of novel compounds as future therapeutics.
Differential Gene Expression in Pycnoporus coccineus during Interspecific Mycelial Interactions with Different Competitors
Authors: Arfi Yonathan , Levasseur Anthony , Record Eric 
Published: August 2013

ABSTRACT

Fungi compete against each other for environmental resources. These interspecific combative interactions encompass a wide range of mechanisms. In this study, we highlight the ability of the white-rot fungus
Pycnoporus coccineus
to quickly overgrow or replace a wide range of competitor fungi, including the gray-mold fungus
Botrytis cinerea
and the brown-rot fungus
Coniophora puteana
. To gain a better understanding of the mechanisms deployed by
P. coccineus
to compete against other fungi and to assess whether common pathways are used to interact with different competitors, differential gene expression in
P. coccineus
during cocultivation was assessed by transcriptome sequencing and confirmed by quantitative reverse transcription-PCR analysis of a set of 15 representative genes. Compared with the pure culture, 1,343 transcripts were differentially expressed in the interaction with
C. puteana
and 4,253 were differentially expressed in the interaction with
B. cinerea
, but only 197 transcripts were overexpressed in both interactions. Overall, the results suggest that a broad array of functions is necessary for
P. coccineus
to replace its competitors and that different responses are elicited by the two competitors, although a portion of the mechanism is common to both. However, the functions elicited by the expression of specific transcripts appear to converge toward a limited set of roles, including detoxification of secondary metabolites.
Occurrence and Genetic Diversity of Arcobacter butzleri in an Artisanal Dairy Plant in Italy
Authors: Giacometti Federica , Lucchi Alex , Manfreda Gerardo , Florio Daniela , Zanoni Renato Giulio , Serraino Andrea 
Published: August 2013

ABSTRACT

The present study aimed to investigate the presence, distribution, and persistence of
Arcobacter
spp. in an artisanal dairy plant and to test the isolates to determine their different genotypes in the processing plant and in foods. Samples were collected in an artisanal cheese factory on four occasions between October and December 2012. Food samples (raw milk, ricotta cheese, mozzarella cheese, and conditioning liquid), water samples, and environmental samples were analyzed by the culture method; isolates were identified by multiplex PCR and genotyped by pulsed-field gel electrophoresis (PFGE) analysis.
Arcobacter butzleri
was isolated from 29 out of 59 samples (46.6%), 22 of which were from environmental samples and 7 of which were from food samples. Cluster analysis divided the strains into 47 PFGE patterns: 14 PFGE clusters and 33 unique types. Our findings indicate that the plant harbored numerous
A. butzleri
pulsotypes and that the manual cleaning and sanitation in the studied dairy plant do not effectively remove
Arcobacter
. The recurrent isolation of
A. butzleri
suggests that the environmental conditions in the dairy plant constitute a good ecological niche for the colonization of this microorganism. In some cases, the presence of indistinguishable strains isolated from the same facilities on different sampling days showed that these strains were persistent in the processing environment.
Mapping of Heavy Metal Ion Sorption to Cell-Extracellular Polymeric Substance-Mineral Aggregates by Using Metal-Selective Fluorescent Probes and Confocal Laser Scanning Microscopy
Authors: Hao Likai , Li Jianli , Kappler Andreas , Obst Martin 
Published: August 2013

ABSTRACT

Biofilms, organic matter, iron/aluminum oxides, and clay minerals bind toxic heavy metal ions and control their fate and bioavailability in the environment. The spatial relationship of metal ions to biomacromolecules such as extracellular polymeric substances (EPS) in biofilms with microbial cells and biogenic minerals is complex and occurs at the micro- and submicrometer scale. Here, we review the application of highly selective and sensitive metal fluorescent probes for confocal laser scanning microscopy (CLSM) that were originally developed for use in life sciences and propose their suitability as a powerful tool for mapping heavy metals in environmental biofilms and cell-EPS-mineral aggregates (CEMAs). The benefit of using metal fluorescent dyes in combination with CLSM imaging over other techniques such as electron microscopy is that environmental samples can be analyzed in their natural hydrated state, avoiding artifacts such as aggregation from drying that is necessary for analytical electron microscopy. In this minireview, we present data for a group of sensitive fluorescent probes highly specific for Fe
3+
, Cu
2+
, Zn
2+
, and Hg
2+
, illustrating the potential of their application in environmental science. We evaluate their application in combination with other fluorescent probes that label constituents of CEMAs such as DNA or polysaccharides and provide selection guidelines for potential combinations of fluorescent probes. Correlation analysis of spatially resolved heavy metal distributions with EPS and biogenic minerals in their natural, hydrated state will further our understanding of the behavior of metals in environmental systems since it allows for identifying bonding sites in complex, heterogeneous systems.